0€0€ €Žpfam01912, eIF-6, eIF-6 family. This family includes eukaryotic translation initiation factor 6 as well as presumed archaebacterial homologs.¡€0€ª€0€ €CDD¡€ €²„¢€0€0€ €‚.pfam01913, FTR, Formylmethanofuran-tetrahydromethanopterin formyltransferase. This enzyme EC:2.3.1.101 is involved in archaebacteria in the formation of methane from carbon dioxide. N-terminal distal lobe of alpha+beta ferredoxin-like fold. SCOP reports fold duplication with C-terminal proximal lobe.¡€0€ª€0€ €CDD¡€ €²…¢€0€0€ €‚?pfam01914, MarC, MarC family integral membrane protein. Integral membrane protein family that includes the protein MarC. MarC was thought to be a multiple antibiotic resistance protein. Nevertheless, a study has shown that MarC is not involved in multiple antibiotic resistance. The function of this family is unclear.¡€0€ª€0€ €CDD¡€ €FU¢€0€0€ €Ìpfam01915, Glyco_hydro_3_C, Glycosyl hydrolase family 3 C-terminal domain. This domain is involved in catalysis and may be involved in binding beta-glucan. This domain is found associated with pfam00933.¡€0€ª€0€ €CDD¡€ €²†¢€0€0€ €‚pfam01916, DS, Deoxyhypusine synthase. Eukaryotic initiation factor 5A (eIF-5A) contains an unusual amino acid, hypusine [N epsilon-(4-aminobutyl-2-hydroxy)lysine]. The first step in the post-translational formation of hypusine is catalyzed by the enzyme deoxyhypusine synthase (DS) EC:1.1.1.249. The modified version of eIF-5A, and DS, are required for eukaryotic cell proliferation.¡€0€ª€0€ €CDD¡€ €²‡¢€0€0€ €ˆpfam01917, Arch_flagellin, Archaebacterial flagellin. Members of this family are the proteins that form the flagella in archaebacteria.¡€0€ª€0€ €CDD¡€ €²ˆ¢€0€0€ €jpfam01918, Alba, Alba. Alba is a novel chromosomal protein that coats archaeal DNA without compacting it.¡€0€ª€0€ €CDD¡€ €²‰¢€0€0€ €wpfam01920, Prefoldin_2, Prefoldin subunit. This family includes prefoldin subunits that are not detected by pfam02996.¡€0€ª€0€ €CDD¡€ €²Š¢€0€0€ €zpfam01921, tRNA-synt_1f, tRNA synthetases class I (K). This family includes only lysyl tRNA synthetases from prokaryotes.¡€0€ª€0€ €CDD¡€ €²‹¢€0€0€ €‚èpfam01922, SRP19, SRP19 protein. The signal recognition particle (SRP) binds to the signal peptide of proteins as they are being translated. The binding of the SRP halts translation and the complex is then transported to the endoplasmic reticulum's cytoplasmic surface. The SRP then aids translocation of the protein through the ER membrane. The SRP is a ribonucleoprotein that is composed of a small RNA and several proteins. One of these proteins is the SRP19 protein (Sec65 in yeast).¡€0€ª€0€ €CDD¡€ €²Œ¢€0€0€ €‚Êpfam01923, Cob_adeno_trans, Cobalamin adenosyltransferase. Cobalamin adenosyltransferase This family contains the gene products of PduO and EutT which are both cobalamin adenosyltransferases. PduO is a protein with ATP:cob(I)alamin adenosyltransferase activity. The main role of this protein is the conversion of inactive cobalamins to AdoCbl for 1,2-propanediol degradation.The EutT enzyme appears to be an adenosyl transferase, converting CNB12 to AdoB12.¡€0€ª€0€ €CDD¡€ €²¢€0€0€ €‚1pfam01924, HypD, Hydrogenase formation hypA family. HypD is involved in hydrogenase formation. It contains many possible metal binding residues, which may bind to nickel. Transposon Tn5 insertions into hypD resulted in R. leguminosarum mutants that lacked any hydrogenase activity in symbiosis with peas.¡€0€ª€0€ €CDD¡€ €²Ž¢€0€0€ €‚ppfam01925, TauE, Sulfite exporter TauE/SafE. This is a family of integral membrane proteins where the alignment appears to contain two duplicated modules of three transmembrane helices. The proteins are involved in the transport of anions across the cytoplasmic membrane during taurine metabolism as an exporter of sulfoacetate. This family used to be known as DUF81.¡€0€ª€0€ €CDD¡€ €²¢€0€0€ €‚ pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide.¡€0€ª€0€ €CDD¡€ €²¢€0€0€ €upfam01927, Mut7-C, Mut7-C RNAse domain. RNAse domain of the PIN fold with an inserted Zinc Ribbon at the C terminus.¡€0€ª€0€ €CDD¡€ €²‘¢€0€0€ €‚Ipfam01928, CYTH, CYTH domain. These sequences are functionally identified as members of the adenylate cyclase family, which catalyzes the conversion of ATP to 3',5'-cyclic AMP and pyrophosphate. Six distinct non-homologous classes of AC have been identified. The structure of three classes of adenylyl cyclases have been solved.¡€0€ª€0€ €CDD¡€ €²’¢€0€0€ €mpfam01929, Ribosomal_L14e, Ribosomal protein L14. This family includes the eukaryotic ribosomal protein L14.¡€0€ª€0€ €CDD¡€ €²“¢€0€0€ €›pfam01930, Cas_Cas4, Domain of unknown function DUF83. This domain has no known function. The domain contains three conserved cysteines at its C terminus.¡€0€ª€0€ €CDD¡€ €²”¢€0€0€ €‚Bpfam01931, NTPase_I-T, Protein of unknown function DUF84. NTPase_I-T is a family of NTPases with supreme activity against ITP and XTP. Active site analysis and structure comparison of YjjX strongly suggested that it is an NTP binding protein with nucleoside triphosphatase activity. YjjX exhibits a mixed alpha-beta fold.¡€0€ª€0€ €CDD¡€ €²•¢€0€0€ €=pfam01933, UPF0052, Uncharacterized protein family UPF0052. ¡€0€ª€0€ €CDD¡€ €²–¢€0€0€ €hpfam01934, DUF86, Protein of unknown function DUF86. The function of members of this family is unknown.¡€0€ª€0€ €CDD¡€ €²—¢€0€0€ €½pfam01935, DUF87, Domain of unknown function DUF87. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands.¡€0€ª€0€ €CDD¡€ €²˜¢€0€0€ €‚¬pfam01936, NYN, NYN domain. These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions. Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs.¡€0€ª€0€ €CDD¡€ €²™¢€0€0€ €Xpfam01937, DUF89, Protein of unknown function DUF89. This family has no known function.¡€0€ª€0€ €CDD¡€ €²š¢€0€0€ € pfam01938, TRAM, TRAM domain. This small domain has no known function. However it may perform a nucleic acid binding role (Bateman A. unpublished observation).¡€0€ª€0€ €CDD¡€ €Fk¢€0€0€ €jpfam01939, DUF91, Protein of unknown function DUF91. The function of this prokaryotic protein is unknown.¡€0€ª€0€ €CDD¡€ €Fl¢€0€0€ €¯pfam01940, DUF92, Integral membrane protein DUF92. Members of this family have several predicted transmembrane helices. The function of these prokaryotic proteins is unknown.¡€0€ª€0€ €CDD¡€ €²›¢€0€0€ €‚ópfam01941, AdoMet_Synthase, S-adenosylmethionine synthetase (AdoMet synthetase). This family consists of several archaebacterial S-adenosylmethionine synthetase C(AdoMet synthetase or MAT) (EC 2.5.1.6). S-Adenosylmethionine (AdoMet) occupies a central role in the metabolism of all cells. The biological roles of AdoMet include acting as the primary methyl group donor, as a precursor to the polyamines, and as a progenitor of a 5'-deoxyadenosyl radical. S-Adenosylmethionine synthetase catalyzes the only known route of AdoMet biosynthesis. The synthetic process occurs in a unique reaction in which the complete triphosphate chain is displaced from ATP and a sulfonium ion formed. MATs from various organisms contain ~400-amino acid polypeptide chains.¡€0€ª€0€ €CDD¡€ €²œ¢€0€0€ €‚gpfam01943, Polysacc_synt, Polysaccharide biosynthesis protein. Members of this family are integral membrane proteins. Many members of the family are implicated in production of polysaccharide. The family includes RfbX part of the O antigen biosynthesis operon. The family includes SpoVB from Bacillus subtilis, which is involved in spore cortex biosynthesis.¡€0€ª€0€ €CDD¡€ €Fo¢€0€0€ €‚Špfam01944, SpoIIM, Stage II sporulation protein M. SpoIIM is on e of four stage II sporulation proteins that is necessary for the forespore inside the mother-cell to be properly internalised through the breakdown of peptidoglycans trapped between the membranes of the septum separating the forespore and the mother-cell. The four proteins working in sequence are SpoIIB, pfam05036, SpoIIM, SpoIIP, pfam07454, and finally SpoIID, pfam08486. D, M and P are in a complex with each other and the complex assembles in a hierarchical manner such that M, which serves as a membrane anchor, recruits P to the septum and P, in turn, recruits D to the septum.¡€0€ª€0€ €CDD¡€ €²¢€0€0€ €\pfam01946, Thi4, Thi4 family. This family includes a putative thiamine biosynthetic enzyme.¡€0€ª€0€ €CDD¡€ €Fq¢€0€0€ €epfam01947, DUF98, Protein of unknown function (DUF98). This is a family of uncharacterized proteins.¡€0€ª€0€ €CDD¡€ €²ž¢€0€0€ €‚pfam01948, PyrI, Aspartate carbamoyltransferase regulatory chain, allosteric domain. The regulatory chain is involved in allosteric regulation of aspartate carbamoyltransferase. The N-terminal domain has ferredoxin-like fold, and provides the regulatory chain dimerisation interface.¡€0€ª€0€ €CDD¡€ €²Ÿ¢€0€0€ €upfam01949, DUF99, Protein of unknown function DUF99. The function of this archaebacterial protein family is unknown.¡€0€ª€0€ €CDD¡€ €² ¢€0€0€ €‚Apfam01950, FBPase_3, Fructose-1,6-bisphosphatase. This is a family of bacterial and archaeal fructose-1,6-bisphosphatases (FBPases). FBPase catalyzes the hydrolysis of D-fructose-1,6-bisphosphate (FBP) to D-fructose-6-phosphate (F6P) and orthophosphate and is an essential regulatory enzyme in the glyconeogenic pathway.¡€0€ª€0€ €CDD¡€ €²¡¢€0€0€ €õpfam01951, Archease, Archease protein family (MTH1598/TM1083). This archease family of proteins, has two SHS2 domains, with one inserted into another. It is predicted to be an enzyme. It is predicted to act as a chaperone in DNA/RNA metabolism.¡€0€ª€0€ €CDD¡€ €²¢¢€0€0€ €ïpfam01954, DUF104, Protein of unknown function DUF104. This family includes short archaebacterial proteins of unknown function. Archaeoglobus fulgidus has twelve copies of this protein, with several being clustered together in the genome.¡€0€ª€0€ €CDD¡€ €²£¢€0€0€ €ïpfam01955, CbiZ, Adenosylcobinamide amidohydrolase. This prokaryotic protein family includes CbiZ which converts adenosylcobinamide (AdoCbi) to adenosylcobyric acid (AdoCby), an intermediate of the de novo coenzyme B12 biosynthetic route.¡€0€ª€0€ €CDD¡€ €²¤¢€0€0€ €¨pfam01956, DUF106, Integral membrane protein DUF106. This archaebacterial protein family has no known function. Members are predicted to be integral membrane proteins.¡€0€ª€0€ €CDD¡€ €²¥¢€0€0€ €‚?pfam01957, NfeD, NfeD-like C-terminal, partner-binding. NfeD-like proteins are widely distributed throughout prokaryotes and are frequently associated with genes encoding stomatin-like proteins (slipins). There appear to be three major groups: an ancestral group with only an N-terminal serine protease domain and this C-terminal beta sheet-rich domain which is structurally very similar to the OB-fold domain, associated with its neighboring slipin cluster; a second major group with an additional middle, membrane-spanning domain, associated in some species with eoslipin and in others with yqfA; a final 'artificial' group which unites truncated forms lacking the protease region and associated with their ancestral gene partner, either yqfA or eoslipin. This NefD, C-terminal, domain appears to be the major one for relating to the associated protein. NfeD homologs are clearly reliant on their conserved gene neighbor which is assumed to be necessary for function, either through direct physical interaction or by functioning in the same pathway, possibly involve with lipid-rafts.¡€0€ª€0€ €CDD¡€ €Fz¢€0€0€ €Êpfam01958, DUF108, Domain of unknown function DUF108. This family has no known function. It is found to compose the complete protein in archaebacteria and a single domain in a large C. elegans protein.¡€0€ª€0€ €CDD¡€ €²¦¢€0€0€ €‚9pfam01959, DHQS, 3-dehydroquinate synthase (EC 4.6.1.3). 3-Dehydroquinate synthase is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyzes the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides.¡€0€ª€0€ €CDD¡€ €²§¢€0€0€ €pfam01960, ArgJ, ArgJ family. Members of the ArgJ family catalyze the first EC:2.3.1.1 and fifth steps EC:2.3.1.35 in arginine biosynthesis.¡€0€ª€0€ €CDD¡€ €²¨¢€0€0€ €‚+pfam01963, TraB, TraB family. pAD1 is a haemolysin/bacteriocin plasmid originally identified in Enterococcus faecalis DS16. It encodes a mating response to a peptide sex pheromone, cAD1, secreted by recipient bacteria. Once the plasmid pAD1 is acquired, production of the pheromone ceases--a trait related in part to a determinant designated traB. However a related protein is found in C. elegans, suggesting that members of the TraB family have some more general function. This family also includes the bacterial GumN protein. The family has a conserved GXXH motif close to the N-terminus, a conserved glutamate and a conserved arginine that may be catalytic. The family also includes a second conserved GXXH motif near the C-terminus. This family also contains the Tiki proteins that regulate Wnt signalling.¡€0€ª€0€ €CDD¡€ €²©¢€0€0€ €‚Zpfam01964, ThiC_Rad_SAM, Radical SAM ThiC family. ThiC is found within the thiamine biosynthesis operon. ThiC is involved in pyrimidine biosynthesis. ThiC participates in the formation of 4-Amino-5-hydroxymethyl-2-methylpyrimidine from AIR, an intermediate in the de novo pyrimidine biosynthesis. Thic is a member of the radical SAM superfamily.¡€0€ª€0€ €CDD¡€ €²ª¢€0€0€ €ˆpfam01965, DJ-1_PfpI, DJ-1/PfpI family. The family includes the protease PfpI. This domain is also found in transcriptional regulators.¡€0€ª€0€ €CDD¡€ €F€¢€0€0€ €Lpfam01966, HD, HD domain. HD domains are metal dependent phosphohydrolases.¡€0€ª€0€ €CDD¡€ €²«¢€0€0€ €–pfam01967, MoaC, MoaC family. Members of this family are involved in molybdenum cofactor biosynthesis. However their molecular function is not known.¡€0€ª€0€ €CDD¡€ €²¬¢€0€0€ €épfam01968, Hydantoinase_A, Hydantoinase/oxoprolinase. This family includes the enzymes hydantoinase and oxoprolinase EC:3.5.2.9. Both reactions involve the hydrolysis of 5-membered rings via hydrolysis of their internal imide bonds.¡€0€ª€0€ €CDD¡€ €²­¢€0€0€ €fpfam01969, DUF111, Protein of unknown function DUF111. This prokaryotic family has no known function.¡€0€ª€0€ €CDD¡€ €²®¢€0€0€ €‚pfam01970, TctA, Tripartite tricarboxylate transporter TctA family. This family, formerly known as DUF112, is a family of bacterial and archaeal tripartite tricarboxylate transporters of the extracytoplasmic solute binding receptor-dependent transporter group of families, distinct from the ABC and TRAP-T families. TctA is part of the tripartite TctABC system which, as characterized in S. typhimurium, is a secondary carrier that depends for activity on the extracytoplasmic tricarboxylate-binding receptor TctC as well as two integral membrane proteins, TctA and TctB. complete three-component systems are found only in bacteria. TctA is a large transmembrane protein with up to 12 predicted membrane spanning regions in bacteria and up to 11 such in archaea, with the N-terminal within the cytoplasm. TctA is thought to be a permease, and in most other bacteria functions without TctB and TctC molecules.¡€0€ª€0€ €CDD¡€ €²¯¢€0€0€ €‚Àpfam01972, SDH_sah, Serine dehydrogenase proteinase. This family of archaebacterial proteins, formerly known as DUF114, has been found to be a serine dehydrogenase proteinase distantly related to ClpP proteinases that belong to the serine proteinase superfamily. The family has a catalytic triad of Ser, Asp, His residues, which shows an altered residue ordering compared with the ClpP proteinases but similar to that of the carboxypeptidase clan.¡€0€ª€0€ €CDD¡€ €±L¢€0€0€ €zpfam01973, MAF_flag10, Protein of unknown function DUF115. This family of archaebacterial proteins has no known function.¡€0€ª€0€ €CDD¡€ €²°¢€0€0€ €¹pfam01974, tRNA_int_endo, tRNA intron endonuclease, catalytic C-terminal domain. Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.¡€0€ª€0€ €CDD¡€ €²±¢€0€0€ €‚tpfam01975, SurE, Survival protein SurE. E. coli cells with the surE gene disrupted are found to survive poorly in stationary phase. It is suggested that SurE may be involved in stress response. Yeast also contains a member of the family. Yarrowia lipolytica PHO2 can complement a mutation in acid phosphatase, suggesting that members of this family could be phosphatases.¡€0€ª€0€ €CDD¡€ €²²¢€0€0€ €Èpfam01976, DUF116, Protein of unknown function DUF116. This archaebacterial protein has no known function. The protein contains seven conserved cysteines and may also be an integral membrane protein.¡€0€ª€0€ €CDD¡€ €²³¢€0€0€ €‚"pfam01977, UbiD, 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. This family has been characterized as 3-octaprenyl-4- hydroxybenzoate carboxy-lyase enzymes. This enzyme catalyzes the third reaction in ubiquinone biosynthesis. For optimal activity the carboxy-lase was shown to require Mn2+.¡€0€ª€0€ €CDD¡€ €²´¢€0€0€ €åpfam01978, TrmB, Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.¡€0€ª€0€ €CDD¡€ €²µ¢€0€0€ €‚£pfam01979, Amidohydro_1, Amidohydrolase family. This family of enzymes are a a large metal dependent hydrolase superfamily. The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisation as a purine and also as a nitrogen source. This family also includes dihydroorotase and N-acetylglucosamine-6-phosphate deacetylases, EC:3.5.1.25 These enzymes catalyze the reaction N-acetyl-D-glucosamine 6-phosphate + H2O <=> D-glucosamine 6-phosphate + acetate. This family includes the catalytic domain of urease alpha subunit. Dihydroorotases (EC:3.5.2.3) are also included.¡€0€ª€0€ €CDD¡€ €²¶¢€0€0€ €=pfam01980, UPF0066, Uncharacterized protein family UPF0066. ¡€0€ª€0€ €CDD¡€ €²·¢€0€0€ €Žpfam01981, PTH2, Peptidyl-tRNA hydrolase PTH2. Peptidyl-tRNA hydrolases are enzymes that release tRNAs from peptidyl-tRNA during translation.¡€0€ª€0€ €CDD¡€ €²¸¢€0€0€ €‚[pfam01982, CTP-dep_RFKase, Domain of unknown function DUF120. This domain is a CTP-dependent riboflavin kinase (RFK), found in archaea, that catalyzes the phosphorylation of riboflavin to form flavin mononucleotide in riboflavin biosynthesis EC:2.7.1.26. Its structure resembles a RIFT barrel, structurally similar to but topologically distinct from bacterial and eukaryotic examples. The N-terminal is a winged helix-turn-helix DNA-binding domain, and the C-terminal half is most similar in sequence to a group of cradle-loop barrels. Archaeoglobus fulgidus RibK has this domain attached to pfam00325.¡€0€ª€0€ €CDD¡€ €²¹¢€0€0€ €‚ipfam01983, CofC, Guanylyl transferase CofC like. Coenzyme F420 is a hydride carrier cofactor that functions during methanogenesis. This family of proteins represents CofC, a nucleotidyl transferase that is involved in coenzyme F420 biosynthesis. CofC has been shown to catalyze the formation of lactyl-2-diphospho-5'-guanosine from 2-phospho-L-lactate and GTP.¡€0€ª€0€ €CDD¡€ €Ô†¢€0€0€ €ƒpfam01984, dsDNA_bind, Double-stranded DNA-binding domain. This domain is believed to bind double-stranded DNA of 20 bases length.¡€0€ª€0€ €CDD¡€ €²º¢€0€0€ €‚Þpfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.¡€0€ª€0€ €CDD¡€ €²»¢€0€0€ €‚tpfam01986, DUF123, Domain of unknown function DUF123. This archaebacterial domain has no known function. It is attached to an endonuclease domain in Methanocaldococcus jannaschii endonuclease III (nth). The domain contains several conserved cysteines and histidines. This suggests that the domain may be a zinc binding nucleic acid interaction domain (Bateman A unpubl.).¡€0€ª€0€ €CDD¡€ €²¼¢€0€0€ €žpfam01987, AIM24, Mitochondrial biogenesis AIM24. In eukaryotes, this domain is involved in mitochondrial biogenesis. Its function in prokaryotes in unknown.¡€0€ª€0€ €CDD¡€ €²½¢€0€0€ €Špfam01988, VIT1, VIT family. This family includes the vacuolar Fe2+/Mn2+ uptake transporter, Ccc1 and the vacuolar iron transporter VIT1.¡€0€ª€0€ €CDD¡€ €²¾¢€0€0€ €rpfam01989, DUF126, Protein of unknown function DUF126. This archaebacterial protein family has no known function.¡€0€ª€0€ €CDD¡€ €²¿¢€0€0€ €æpfam01990, ATP-synt_F, ATP synthase (F/14-kDa) subunit. This family includes 14-kDa subunit from vATPases, which is in the peripheral catalytic part of the complex. The family also includes archaebacterial ATP synthase subunit F.¡€0€ª€0€ €CDD¡€ €²À¢€0€0€ €ªpfam01991, vATP-synt_E, ATP synthase (E/31 kDa) subunit. This family includes the vacuolar ATP synthase E subunit, as well as the archaebacterial ATP synthase E subunit.¡€0€ª€0€ €CDD¡€ €F—¢€0€0€ €‚pfam01992, vATP-synt_AC39, ATP synthase (C/AC39) subunit. This family includes the AC39 subunit from vacuolar ATP synthase, and the C subunit from archaebacterial ATP synthase. The family also includes subunit C from the Sodium transporting ATP synthase from Enterococcus hirae.¡€0€ª€0€ €CDD¡€ €²Á¢€0€0€ €Äpfam01993, MTD, methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase. This enzyme family is involved in formation of methane from carbon dioxide EC:1.5.99.9. The enzyme requires coenzyme F420.¡€0€ª€0€ €CDD¡€ €²Â¢€0€0€ €‚Îpfam01994, Trm56, tRNA ribose 2'-O-methyltransferase, aTrm56. This family is an aTrm56 that catalyzes the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Biochemical assays showed that aTrm56 forms a dimer and prefers the L-shaped tRNA to the lambda form as its substrate. aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot for AdoMet binding, and a unique C-terminal beta-hairpin.¡€0€ª€0€ €CDD¡€ €²Ã¢€0€0€ €‚hpfam01995, DUF128, Domain of unknown function DUF128. This archaebacterial protein family has no known function. The domain is found duplicated in Methanothermobacter thermautotrophicus MTH_1569. Many of these are attached to an N-terminal winged helix domain suggesting these are transcriptional regulators and that this domain has a ligand binding function.¡€0€ª€0€ €CDD¡€ €²Ä¢€0€0€ €‚¶pfam01996, F420_ligase, F420-0:Gamma-glutamyl ligase. F420-0:Gamma-glutamyl ligase (EC:6.3.2.-) is an enzyme involved in F420 biosynthesis pathway. It catalyzes the GTP-dependent successive addition of multiple gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0). This reaction produces polyglutamated F420 derivatives. GTP + F420-0 + n L-glutamate -> GDP + phosphate + F420-n.¡€0€ª€0€ €CDD¡€ €²Å¢€0€0€ €øpfam01997, Translin, Translin family. Members of this family include Translin, which interacts with DNA and forms a ring around the DNA. This family also includes human TSNAX, which was found to interact with translin with yeast two-hybrid screen.¡€0€ª€0€ €CDD¡€ €²Æ¢€0€0€ €³pfam01998, DUF131, Protein of unknown function DUF131. This archaebacterial protein family has no known function. The proteins are predicted to contain two transmembrane helices.¡€0€ª€0€ €CDD¡€ €²Ç¢€0€0€ €opfam02001, DUF134, Protein of unknown function DUF134. This family of archaeal proteins has no known function.¡€0€ª€0€ €CDD¡€ €FŸ¢€0€0€ €‚pfam02002, TFIIE_alpha, TFIIE alpha subunit. The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha and TFIIE-beta and joins the pre-initiation complex after RNA polymerase II and TFIIF. This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits also Archaeoglobus fulgidus tfe.¡€0€ª€0€ €CDD¡€ €F ¢€0€0€ €‚Epfam02005, TRM, N2,N2-dimethylguanosine tRNA methyltransferase. This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA. The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs. The enzyme is found in both eukaryotes and archaebacteria.¡€0€ª€0€ €CDD¡€ €F¡¢€0€0€ €opfam02006, DUF137, Protein of unknown function DUF137. This family of archaeal proteins has no known function.¡€0€ª€0€ €CDD¡€ €²È¢€0€0€ €‚Ypfam02007, MtrH, Tetrahydromethanopterin S-methyltransferase MtrH subunit. The enzyme tetrahydromethanopterin S-methyltransferase EC:2.1.1.86 is composed of eight subunits. The enzyme is a membrane- associated enzyme complex which catalyzes an energy-conserving, sodium-ion-translocating step in methanogenesis from hydrogen and carbon dioxide.¡€0€ª€0€ €CDD¡€ €F£¢€0€0€ €‚_pfam02008, zf-CXXC, CXXC zinc finger domain. This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.¡€0€ª€0€ €CDD¡€ €Ô˜¢€0€0€ €‚pfam02009, Rifin_STEVOR, Rifin/stevor family. Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens.¡€0€ª€0€ €CDD¡€ €²É¢€0€0€ €‚ƒpfam02010, REJ, REJ domain. The REJ (Receptor for Egg Jelly) domain is found in PKD1 and the sperm receptor for egg jelly. The function of this domain is unknown. The domain is 600 amino acids long so is probably composed of multiple structural domains. There are six completely conserved cysteine residues that may form disulphide bridges. This region contains tandem PKD-like domains.¡€0€ª€0€ €CDD¡€ €²Ê¢€0€0€ €¾pfam02011, Glyco_hydro_48, Glycosyl hydrolase family 48. Members of this family are endoglucanase EC:3.2.1.4 and exoglucanase EC:3.2.1.91 enzymes that cleave cellulose or related substrate.¡€0€ª€0€ €CDD¡€ €²Ë¢€0€0€ €‚‡pfam02012, BNR, BNR/Asp-box repeat. Members of this family contain multiple BNR (bacterial neuraminidase repeat) repeats or Asp-boxes. The repeats are short, however the repeats are never found closer than 40 residues together suggesting that the repeat is structurally longer. These repeats are found in many glycosyl hydrolases as well as other extracellular proteins of unknown function.¡€0€ª€0€ €CDD¡€ €F§¢€0€0€ €‚æpfam02013, CBM_10, Cellulose or protein binding domain. This domain is found in two distinct sets of proteins with different functions. Those found in aerobic bacteria bind cellulose (or other carbohydrates); but in anaerobic fungi they are protein binding domains, referred to as dockerin domains or docking domains. They are believed to be responsible for the assembly of a multiprotein cellulase/hemicellulase complex, similar to the cellulosome found in certain anaerobic bacteria.¡€0€ª€0€ €CDD¡€ €Ôœ¢€0€0€ €#pfam02014, Reeler, Reeler domain. ¡€0€ª€0€ €CDD¡€ €²Ì¢€0€0€ €:pfam02015, Glyco_hydro_45, Glycosyl hydrolase family 45. ¡€0€ª€0€ €CDD¡€ €F©¢€0€0€ €‚µpfam02016, Peptidase_S66, LD-carboxypeptidase. Muramoyl-tetrapeptide carboxypeptidase hydrolyses a peptide bond between a di-basic amino acid and the C-terminal D-alanine in the tetrapeptide moiety in peptidoglycan. This cleaves the bond between an L- and a D-amino acid. The function of this activity is in murein recycling. This family also includes the microcin c7 self-immunity protein. This family corresponds to Merops family S66.¡€0€ª€0€ €CDD¡€ €²Í¢€0€0€ €Ÿpfam02017, CIDE-N, CIDE-N domain. This domain is found in CAD nuclease and ICAD, the inhibitor of CAD nuclease. The two proteins interact through this domain.¡€0€ª€0€ €CDD¡€ €²Î¢€0€0€ €lpfam02018, CBM_4_9, Carbohydrate binding domain. This family includes diverse carbohydrate binding domains.¡€0€ª€0€ €CDD¡€ €²Ï¢€0€0€ €‚³pfam02019, WIF, WIF domain. The WIF domain is found in the RYK tyrosine kinase receptors and WIF the Wnt-inhibitory-factor. The domain is extracellular and contains two conserved cysteines that may form a disulphide bridge. This domain is Wnt binding in WIF, and it has been suggested that RYK may also bind to Wnt. The WIF domain is a member of the immunoglobulin superfamily, and it comprises nine beta-strands and two alpha-helices, with two of the beta-strands (6 and 9) interrupted by four and six residues of irregular secondary structure, respectively. Considering that the activity of Wnts depends on the presence of a palmitoylated cysteine residue in their amino-terminal polypeptide segment, Wnt proteins are lipid-modified and can act as stem cell growth factors, it is likely that the WIF domain recognizes and binds to Wnts that have been activated by palmitoylation and that the recognition of palmitoylated Wnts by WIF-1 is effected by its WIF domain rather than by its EGF domains. A strong binding affinity for palmitoylated cysteine residues would further explain the remarkably high affinity of human WIF-1 not only for mammalian Wnts, but also for Wnts from Xenopus and Drosophila.¡€0€ª€0€ €CDD¡€ €²Ð¢€0€0€ €“pfam02020, W2, eIF4-gamma/eIF5/eIF2-epsilon. This domain of unknown function is found at the C-terminus of several translation initiation factors.¡€0€ª€0€ €CDD¡€ €²Ñ¢€0€0€ €dpfam02021, UPF0102, Uncharacterized protein family UPF0102. The function of this family is unknown.¡€0€ª€0€ €CDD¡€ €²Ò¢€0€0€ €‚opfam02022, Integrase_Zn, Integrase Zinc binding domain. Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.¡€0€ª€0€ €CDD¡€ €²Ó¢€0€0€ €àpfam02023, SCAN, SCAN domain. The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several pfam00096 proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerization.¡€0€ª€0€ €CDD¡€ €²Ô¢€0€0€ €pfam02024, Leptin, Leptin. ¡€0€ª€0€ €CDD¡€ €²Õ¢€0€0€ € pfam02025, IL5, Interleukin 5. ¡€0€ª€0€ €CDD¡€ €²Ö¢€0€0€ €´pfam02026, RyR, RyR domain. This domain is called RyR for Ryanodine receptor. The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown.¡€0€ª€0€ €CDD¡€ €²×¢€0€0€ €Ãpfam02027, RolB_RolC, RolB/RolC glucosidase family. This family of proteins includes RolB and RolC. RolC releases cytokinins from glucoside conjugates. Whereas RolB hydrolyses indole glucosides.¡€0€ª€0€ €CDD¡€ €²Ø¢€0€0€ €Fpfam02028, BCCT, BCCT, betaine/carnitine/choline family transporter. ¡€0€ª€0€ €CDD¡€ €²Ù¢€0€0€ €"pfam02029, Caldesmon, Caldesmon. ¡€0€ª€0€ €CDD¡€ €²Ú¢€0€0€ €‚pfam02030, Lipoprotein_8, Hypothetical lipoprotein (MG045 family). This family includes hypothetical lipoproteins, the amino terminal part of this protein is related to pfam01547, a family of solute binding proteins. This suggests this family also has a solute binding function.¡€0€ª€0€ €CDD¡€ €²Û¢€0€0€ €Upfam02031, Peptidase_M7, Streptomyces extracellular neutral proteinase (M7) family. ¡€0€ª€0€ €CDD¡€ €F¸¢€0€0€ €-pfam02033, RBFA, Ribosome-binding factor A. ¡€0€ª€0€ €CDD¡€ €²Ü¢€0€0€ € pfam02035, Coagulin, Coagulin. ¡€0€ª€0€ €CDD¡€ €²Ý¢€0€0€ €‚pfam02036, SCP2, SCP-2 sterol transfer family. This domain is involved in binding sterols. It is found in the SCP2 protein, as well as the C terminus of the enzyme estradiol 17 beta-dehydrogenase EC:1.1.1.62. The UNC-24 protein contains an SPFH domain pfam01145.¡€0€ª€0€ €CDD¡€ €²Þ¢€0€0€ €£pfam02037, SAP, SAP domain. The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.¡€0€ª€0€ €CDD¡€ €²ß¢€0€0€ €5pfam02038, ATP1G1_PLM_MAT8, ATP1G1/PLM/MAT8 family. ¡€0€ª€0€ €CDD¡€ €²à¢€0€0€ €3pfam02040, ArsB, Arsenical pump membrane protein. ¡€0€ª€0€ €CDD¡€ €²á¢€0€0€ €-pfam02041, Auxin_BP, Auxin binding protein. ¡€0€ª€0€ €CDD¡€ €F¾¢€0€0€ €ýpfam02042, RWP-RK, RWP-RK domain. This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development.¡€0€ª€0€ €CDD¡€ €²â¢€0€0€ €?pfam02043, Bac_chlorC, Bacteriochlorophyll C binding protein. ¡€0€ª€0€ €CDD¡€ €²ã¢€0€0€ €-pfam02044, Bombesin, Bombesin-like peptide. ¡€0€ª€0€ €CDD¡€ €FÁ¢€0€0€ €Spfam02045, CBFB_NFYA, CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B. ¡€0€ª€0€ €CDD¡€ €²ä¢€0€0€ €5pfam02046, COX6A, Cytochrome c oxidase subunit VIa. ¡€0€ª€0€ €CDD¡€ €²å¢€0€0€ €‚Ñpfam02048, Enterotoxin_ST, Heat-stable enterotoxin ST. This family consists of the heat stable enterotoxin ST from Escherichia coli. ST is a small peptide of 18 or 19 amino acid residues produced by enterotoxigenic E. coli and is one of the causes of acute diarrhoea in infants and travellers in developing countries. ST triggers a biological response by binding to a membrane-associated guanylyl cyclase C which is located on intestinal epithelial cell membranes.¡€0€ª€0€ €CDD¡€ €²æ¢€0€0€ €Bpfam02049, FliE, Flagellar hook-basal body complex protein FliE. ¡€0€ª€0€ €CDD¡€ €²ç¢€0€0€ €*pfam02050, FliJ, Flagellar FliJ protein. ¡€0€ª€0€ €CDD¡€ €²è¢€0€0€ €&pfam02052, Gallidermin, Gallidermin. ¡€0€ª€0€ €CDD¡€ €±”¢€0€0€ €+pfam02053, Gene66, Gene 66 (IR5) protein. ¡€0€ª€0€ €CDD¡€ €Ô´¢€0€0€ €Lpfam02055, Glyco_hydro_30, Glycosyl hydrolase family 30 TIM-barrel domain. ¡€0€ª€0€ €CDD¡€ €²é¢€0€0€ €8pfam02056, Glyco_hydro_4, Family 4 glycosyl hydrolase. ¡€0€ª€0€ €CDD¡€ €FÇ¢€0€0€ €:pfam02057, Glyco_hydro_59, Glycosyl hydrolase family 59. ¡€0€ª€0€ €CDD¡€ €²ê¢€0€0€ €*pfam02058, Guanylin, Guanylin precursor. ¡€0€ª€0€ €CDD¡€ €²ë¢€0€0€ € pfam02059, IL3, Interleukin-3. ¡€0€ª€0€ €CDD¡€ €²ì¢€0€0€ €?pfam02060, ISK_Channel, Slow voltage-gated potassium channel. ¡€0€ª€0€ €CDD¡€ €²í¢€0€0€ €}pfam02061, Lambda_CIII, Lambda Phage CIII. The CIII protein from bacteriophage lambda is an inhibitor of the FtsH peptidase.¡€0€ª€0€ €CDD¡€ €FÌ¢€0€0€ €#pfam02063, MARCKS, MARCKS family. ¡€0€ª€0€ €CDD¡€ €²î¢€0€0€ €2pfam02064, MAS20, MAS20 protein import receptor. ¡€0€ª€0€ €CDD¡€ €²ï¢€0€0€ €‚ pfam02065, Melibiase, Melibiase. Glycoside hydrolase families GH27, GH31 and GH36 form the glycoside hydrolase clan GH-D. Glycoside hydrolase family 36 can be split into 11 families, GH36A to GH36K. This family includes enzymes from GH36A-B and GH36D-K and from GH27.¡€0€ª€0€ €CDD¡€ €²ð¢€0€0€ €7pfam02066, Metallothio_11, Metallothionein family 11. ¡€0€ª€0€ €CDD¡€ €FТ€0€0€ €5pfam02067, Metallothio_5, Metallothionein family 5. ¡€0€ª€0€ €CDD¡€ €FÑ¢€0€0€ €?pfam02068, Metallothio_PEC, Plant PEC family metallothionein. ¡€0€ª€0€ €CDD¡€ €²ñ¢€0€0€ €:pfam02069, Metallothio_Pro, Prokaryotic metallothionein. ¡€0€ª€0€ €CDD¡€ €²ò¢€0€0€ €pfam02070, NMU, Neuromedin U. ¡€0€ª€0€ €CDD¡€ €²ó¢€0€0€ €¥pfam02071, NSF, Aromatic-di-Alanine (AdAR) repeat. This repeat is found in NSF attachment proteins. Its structure is similar to that found in TPR repeats pfam00515.¡€0€ª€0€ €CDD¡€ €²ô¢€0€0€ €#pfam02072, Orexin, Prepro-orexin. ¡€0€ª€0€ €CDD¡€ €²õ¢€0€0€ €?pfam02073, Peptidase_M29, Thermophilic metalloprotease (M29). ¡€0€ª€0€ €CDD¡€ €²ö¢€0€0€ €Hpfam02074, Peptidase_M32, Carboxypeptidase Taq (M32) metallopeptidase. ¡€0€ª€0€ €CDD¡€ €FØ¢€0€0€ €Apfam02075, RuvC, Crossover junction endodeoxyribonuclease RuvC. ¡€0€ª€0€ €CDD¡€ €FÙ¢€0€0€ €(pfam02076, STE3, Pheromone A receptor. ¡€0€ª€0€ €CDD¡€ €²÷¢€0€0€ €!pfam02077, SURF4, SURF4 family. ¡€0€ª€0€ €CDD¡€ €±«¢€0€0€ €rpfam02078, Synapsin, Synapsin, N-terminal domain. This family is structurally related to the PreATP-grasp domain.¡€0€ª€0€ €CDD¡€ €²ø¢€0€0€ €/pfam02079, TP1, Nuclear transition protein 1. ¡€0€ª€0€ €CDD¡€ €FÜ¢€0€0€ €‚pfam02080, TrkA_C, TrkA-C domain. This domain is often found next to the pfam02254 domain. The exact function of this domain is unknown. It has been suggested that it may bind an unidentified ligand. The domain is predicted to adopt an all beta structure.¡€0€ª€0€ €CDD¡€ €²ù¢€0€0€ €>pfam02081, TrpBP, Tryptophan RNA-binding attenuator protein. ¡€0€ª€0€ €CDD¡€ €²ú¢€0€0€ €–pfam02082, Rrf2, Transcriptional regulator. This family is related to pfam001022 and other transcription regulation families (personal obs: Yeats C).¡€0€ª€0€ €CDD¡€ €²û¢€0€0€ €(pfam02083, Urotensin_II, Urotensin II. ¡€0€ª€0€ €CDD¡€ €Fࢀ0€0€ €pfam02084, Bindin, Bindin. ¡€0€ª€0€ €CDD¡€ €ÔÆ¢€0€0€ €;pfam02085, Cytochrom_CIII, Class III cytochrome C family. ¡€0€ª€0€ €CDD¡€ €²ü¢€0€0€ €Rpfam02086, MethyltransfD12, D12 class N6 adenine-specific DNA methyltransferase. ¡€0€ª€0€ €CDD¡€ €²ý¢€0€0€ €&pfam02087, Nitrophorin, Nitrophorin. ¡€0€ª€0€ €CDD¡€ €±µ¢€0€0€ €pfam02088, Ornatin, Ornatin. ¡€0€ª€0€ €CDD¡€ €7¥¢€0€0€ €:pfam02089, Palm_thioest, Palmitoyl protein thioesterase. ¡€0€ª€0€ €CDD¡€ €²þ¢€0€0€ €Rpfam02090, SPAM, Salmonella surface presentation of antigen gene type M protein. ¡€0€ª€0€ €CDD¡€ €F䢀0€0€ €@pfam02091, tRNA-synt_2e, Glycyl-tRNA synthetase alpha subunit. ¡€0€ª€0€ €CDD¡€ €²ÿ¢€0€0€ €?pfam02092, tRNA_synt_2f, Glycyl-tRNA synthetase beta subunit. ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €¦pfam02093, Gag_p30, Gag P30 core shell protein. According to Swiss-Prot annotation this protein is the viral core shell protein. P30 is essential for viral assembly.¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €6pfam02095, Extensin_1, Extensin-like protein repeat. ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €3pfam02096, 60KD_IMP, 60Kd inner membrane protein. ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €)pfam02097, Filo_VP35, Filoviridae VP35. ¡€0€ª€0€ €CDD¡€ €Fꢀ0€0€ €9pfam02098, His_binding, Tick histamine binding protein. ¡€0€ª€0€ €CDD¡€ €ÔÌ¢€0€0€ € pfam02099, Josephin, Josephin. ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €‚vpfam02100, ODC_AZ, Ornithine decarboxylase antizyme. This family consists of ornithine decarboxylase antizyme proteins. The polyamine biosynthetic enzyme ornithine decarboxylase (ODC) is degraded by the 26 S proteasome via a ubiquitin-independent pathway. Its degradation is greatly accelerated by association with the polyamine-induced regulatory protein antizyme 1 (AZ1).¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €8pfam02101, Ocular_alb, Ocular albinism type 1 protein. ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €Fpfam02102, Peptidase_M35, Deuterolysin metalloprotease (M35) family. ¡€0€ª€0€ €CDD¡€ €ÔÏ¢€0€0€ €!pfam02104, SURF1, SURF1 family. ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €8pfam02106, Fanconi_C, Fanconi anaemia group C protein. ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €,pfam02107, FlgH, Flagellar L-ring protein. ¡€0€ª€0€ €CDD¡€ €³ ¢€0€0€ €3pfam02108, FliH, Flagellar assembly protein FliH. ¡€0€ª€0€ €CDD¡€ €³ ¢€0€0€ €‚bpfam02109, DAD, DAD family. Members of this family are thought to be integral membrane proteins. Some members of this family have been shown to cause apoptosis if mutated, these proteins are known as DAD for defender against death. The family also includes the epsilon subunit of the oligosaccharyltransferase that is involved in N-linked glycosylation.¡€0€ª€0€ €CDD¡€ €³ ¢€0€0€ €4pfam02110, HK, Hydroxyethylthiazole kinase family. ¡€0€ª€0€ €CDD¡€ €Fó¢€0€0€ €9pfam02112, PDEase_II, cAMP phosphodiesterases class-II. ¡€0€ª€0€ €CDD¡€ €Fô¢€0€0€ €Hpfam02113, Peptidase_S13, D-Ala-D-Ala carboxypeptidase 3 (S13) family. ¡€0€ª€0€ €CDD¡€ €³ ¢€0€0€ €"pfam02114, Phosducin, Phosducin. ¡€0€ª€0€ €CDD¡€ €ÔÖ¢€0€0€ €=pfam02115, Rho_GDI, RHO protein GDP dissociation inhibitor. ¡€0€ª€0€ €CDD¡€ €³ ¢€0€0€ €pfam02128, Peptidase_M36, Fungalysin metallopeptidase (M36). ¡€0€ª€0€ €CDD¡€ €G¢€0€0€ €Dpfam02129, Peptidase_S15, X-Pro dipeptidyl-peptidase (S15 family). ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €=pfam02130, UPF0054, Uncharacterized protein family UPF0054. ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ € pfam02132, RecR, RecR protein. ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €Xpfam02133, Transp_cyt_pur, Permease for cytosine/purines, uracil, thiamine, allantoin. ¡€0€ª€0€ €CDD¡€ €Ô墀0€0€ €‚pfam02135, zf-TAZ, TAZ zinc finger. The TAZ2 domain of CBP binds to other transcription factors such as the p53 tumor suppressor protein, E1A oncoprotein, MyoD, and GATA-1. The zinc coordinating motif that is necessary for binding to target DNA sequences consists of HCCC.¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €ˆpfam02136, NTF2, Nuclear transport factor 2 (NTF2) domain. This family includes the NTF2-like Delta-5-3-ketosteroid isomerase proteins.¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €‚ïpfam02137, A_deamin, Adenosine-deaminase (editase) domain. Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defense against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc.¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €'pfam02138, Beach, Beige/BEACH domain. ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €9pfam02140, Gal_Lectin, Galactose binding lectin domain. ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €æpfam02141, DENN, DENN (AEX-3) domain. DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €‚lpfam02142, MGS, MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site.¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €2pfam02144, Rad1, Repair protein Rad1/Rec1/Rad17. ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €"pfam02145, Rap_GAP, Rap/ran-GAP. ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €‚äpfam02146, SIR2, Sir2 family. This region is characteristic of Silent information regulator 2 (Sir2) proteins, or sirtuins. These are protein deacetylases that depend on nicotine adenine dinucleotide (NAD). They are found in many subcellular locations, including the nucleus, cytoplasm and mitochondria. Eukaryotic forms play in important role in the regulation of transcriptional repression. Moreover, they are involved in microtubule organisation and DNA damage repair processes.i.¡€0€ª€0€ €CDD¡€ €G ¢€0€0€ €Ipfam02148, zf-UBP, Zn-finger in ubiquitin-hydrolases and other protein. ¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €-pfam02149, KA1, Kinase associated domain 1. ¡€0€ª€0€ €CDD¡€ €³ ¢€0€0€ €=pfam02150, RNA_POL_M_15KD, RNA polymerases M/15 Kd subunit. ¡€0€ª€0€ €CDD¡€ €G¢€0€0€ €"pfam02151, UVR, UvrB/uvrC motif. ¡€0€ª€0€ €CDD¡€ €³!¢€0€0€ €Ëpfam02152, FolB, Dihydroneopterin aldolase. This enzyme EC:4.1.2.25 catalyzes the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin in the biosynthetic pathway of tetrahydrofolate.¡€0€ª€0€ €CDD¡€ €³"¢€0€0€ €Žpfam02153, PDH, Prephenate dehydrogenase. Members of this family are prephenate dehydrogenases EC:1.3.1.12 involved in tyrosine biosynthesis.¡€0€ª€0€ €CDD¡€ €G¢€0€0€ €7pfam02154, FliM, Flagellar motor switch protein FliM. ¡€0€ª€0€ €CDD¡€ €±î¢€0€0€ €*pfam02155, GCR, Glucocorticoid receptor. ¡€0€ª€0€ €CDD¡€ €³#¢€0€0€ €:pfam02156, Glyco_hydro_26, Glycosyl hydrolase family 26. ¡€0€ª€0€ €CDD¡€ €³$¢€0€0€ €™pfam02157, Man-6-P_recep, Mannose-6-phosphate receptor. This family includes both Cation-dependent and cation independent mannose-6-phosphate receptors.¡€0€ª€0€ €CDD¡€ €G¢€0€0€ €+pfam02158, Neuregulin, Neuregulin family. ¡€0€ª€0€ €CDD¡€ €³%¢€0€0€ €,pfam02159, Oest_recep, Oestrogen receptor. ¡€0€ª€0€ €CDD¡€ €³&¢€0€0€ €Cpfam02160, Peptidase_A3, Cauliflower mosaic virus peptidase (A3). ¡€0€ª€0€ €CDD¡€ €G¢€0€0€ €2pfam02161, Prog_receptor, Progesterone receptor. ¡€0€ª€0€ €CDD¡€ €³'¢€0€0€ €‚]pfam02162, XYPPX, XYPPX repeat (two copies). This repeat is found in a wide variety of proteins and generally consists of the motif XYPPX where X can be any amino acid. The family includes annexin VII and the carboxy tail of certain rhodopsins. This family also includes plaque matrix proteins, however this motif is embedded in a ten residue repeat in Mytilus edulis adhesive plaque matrix protein FP1. The molecular function of this repeat is unknown. It is also not clear is all the members of this family share a common evolutionary ancestor due to its short length and biased amino acid composition.¡€0€ª€0€ €CDD¡€ €7Ò¢€0€0€ €1pfam02163, Peptidase_M50, Peptidase family M50. ¡€0€ª€0€ €CDD¡€ €³(¢€0€0€ €'pfam02165, WT1, Wilm's tumor protein. ¡€0€ª€0€ €CDD¡€ €³)¢€0€0€ €/pfam02166, Androgen_recep, Androgen receptor. ¡€0€ª€0€ €CDD¡€ €³*¢€0€0€ €0pfam02167, Cytochrom_C1, Cytochrome C1 family. ¡€0€ª€0€ €CDD¡€ €³+¢€0€0€ €€pfam02169, LPP20, LPP20 lipoprotein. This family contains the LPP20 lipoprotein, which is a non-essential class of lipoprotein.¡€0€ª€0€ €CDD¡€ €³,¢€0€0€ €‚Òpfam02170, PAZ, PAZ domain. This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.¡€0€ª€0€ €CDD¡€ €³-¢€0€0€ €‚epfam02171, Piwi, Piwi domain. This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as Slicer, the enzyme that cleaves mRNA in the RNAi RISC complex. In addition, Mg+2 dependence and production of 3'-OH and 5' phosphate products are shared characteristics of RNaseH and RISC. The PIWI domain core has a tertiary structure belonging to the RNase H family of enzymes. RNase H fold proteins all have a five-stranded mixed beta-sheet surrounded by helices. By analogy to RNase H enzymes which cleave single-stranded RNA guided by the DNA strand in an RNA/DNA hybrid, the PIWI domain can be inferred to cleave single-stranded RNA, for example mRNA, guided by double stranded siRNA.¡€0€ª€0€ €CDD¡€ €³.¢€0€0€ €Ápfam02172, KIX, KIX domain. CBP and P300 bind to the CREB via a domain known as KIX. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.¡€0€ª€0€ €CDD¡€ €G"¢€0€0€ €upfam02173, pKID, pKID domain. CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB.¡€0€ª€0€ €CDD¡€ €³/¢€0€0€ €*pfam02174, IRS, PTB domain (IRS-1 type). ¡€0€ª€0€ €CDD¡€ €³0¢€0€0€ €‚¨pfam02175, 7TM_GPCR_Srb, Serpentine type 7TM GPCR chemoreceptor Srb. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srb is part of the Sra superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.¡€0€ª€0€ €CDD¡€ €²¢€0€0€ €,pfam02176, zf-TRAF, TRAF-type zinc finger. ¡€0€ª€0€ €CDD¡€ €G%¢€0€0€ €‚ pfam02177, APP_N, Amyloid A4 N-terminal heparin-binding. This N-terminal domain of APP, amyloid precursor protein, is the heparin-binding domain of the protein. this region is also responsible for stimulation of neurite outgrowth. The structure reveals both a highly charged basic surface that may interact with glycosaminoglycans in the brain and an abutting hydrophobic surface that is proposed to play an important functional role such as in dimerisation or ligand-binding. Structural similarities with cysteine-rich growth factors, taken together with its known growth-promoting properties, suggest the APP N-terminal domain could function as a growth factor in vivo.¡€0€ª€0€ €CDD¡€ €³1¢€0€0€ €kpfam02178, AT_hook, AT hook motif. At hooks are DNA binding motifs with a preference for A/T rich regions.¡€0€ª€0€ €CDD¡€ €³2¢€0€0€ €@pfam02179, BAG, BAG domain. Domain present in Hsp70 regulators.¡€0€ª€0€ €CDD¡€ €³3¢€0€0€ €*pfam02180, BH4, Bcl-2 homology region 4. ¡€0€ª€0€ €CDD¡€ €³4¢€0€0€ €+pfam02181, FH2, Formin Homology 2 Domain. ¡€0€ª€0€ €CDD¡€ €G*¢€0€0€ €‚Xpfam02182, SAD_SRA, SAD/SRA domain. The domain goes by several names including SAD, SRA and YDG. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria. Versions of this domain are known to bind hemi-methylated CpG dinucleotides and also other 5mC containing dinucleotides. The domain binds DNA by flipping out the methylated cytosine base from the DNA double helix.The conserved tyrosine and aspartate residues and a glycine rich patch are critical for recognition of the flipped out base. Mammalian UHRF1 that contains this domain plays an important role in maintenance of methylation at CpG dinucleotides by recruiting DNMT1 to hemimethylated sites associated with replication forks. The SAD/SRA domain has been combined with other domains involved in the ubiquitin pathway on multiple occasions and such proteins link recognition of DNA methylation to chromatin-protein ubiquitination. The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions. A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains. In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or hemi-methylated DNA.¡€0€ª€0€ €CDD¡€ €³5¢€0€0€ €6pfam02183, HALZ, Homeobox associated leucine zipper. ¡€0€ª€0€ €CDD¡€ €³6¢€0€0€ €rpfam02184, HAT, HAT (Half-A-TPR) repeat. The HAT (Half A TPR) repeat is found in several RNA processing proteins.¡€0€ª€0€ €CDD¡€ €² ¢€0€0€ €‚cpfam02185, HR1, Hr1 repeat. The HR1 repeat was first described as a three times repeated homology region of the N-terminal non-catalytic part of protein kinase PRK1(PKN). The first two of these repeats were later shown to bind the small G protein rho known to activate PKN in its GTP-bound form. Similar rho-binding domains also occur in a number of other protein kinases and in the rho-binding proteins rhophilin and rhotekin. Recently, the structure of the N-terminal HR1 repeat complexed with RhoA has been determined by X-ray crystallography. It forms an antiparallel coiled-coil fold termed an ACC finger.¡€0€ª€0€ €CDD¡€ €³7¢€0€0€ €‚pfam02186, TFIIE_beta, TFIIE beta subunit core domain. General transcription factor TFIIE consists of two subunits, TFIIE alpha pfam02002 and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The structure of the DNA binding core region has been solved and has a winged helix fold.¡€0€ª€0€ €CDD¡€ €³8¢€0€0€ €ápfam02187, GAS2, Growth-Arrest-Specific Protein 2 Domain. The GAR2 domain is common in plakin family members and Gas2 family members. The GAR domain comprises around 57 amino acids and has been shown to bind to microtubules.¡€0€ª€0€ €CDD¡€ €³9¢€0€0€ €"pfam02188, GoLoco, GoLoco motif. ¡€0€ª€0€ €CDD¡€ €³:¢€0€0€ €Bpfam02189, ITAM, Immunoreceptor tyrosine-based activation motif. ¡€0€ª€0€ €CDD¡€ €³;¢€0€0€ €‚Ïpfam02190, LON_substr_bdg, ATP-dependent protease La (LON) substrate-binding domain. This domain has been shown to be part of the PUA superfamily. This domain represents a general protein and polypeptide interaction domain for the ATP-dependent serine peptidase, LON, Peptidase_S16, pfam05362. ATP-dependent Lon proteases are conserved in all living organisms and catalyze rapid turnover of short-lived regulatory proteins and many damaged or denatured proteins.¡€0€ª€0€ €CDD¡€ €³<¢€0€0€ €+pfam02191, OLF, Olfactomedin-like domain. ¡€0€ª€0€ €CDD¡€ €³=¢€0€0€ €>pfam02192, PI3K_p85B, PI3-kinase family, p85-binding domain. ¡€0€ª€0€ €CDD¡€ €³>¢€0€0€ €Qpfam02194, PXA, PXA domain. This domain is associated with PX domains pfam00787.¡€0€ª€0€ €CDD¡€ €³?¢€0€0€ €.pfam02195, ParBc, ParB-like nuclease domain. ¡€0€ª€0€ €CDD¡€ €³@¢€0€0€ €.pfam02196, RBD, Raf-like Ras-binding domain. ¡€0€ª€0€ €CDD¡€ €³A¢€0€0€ €?pfam02197, RIIa, Regulatory subunit of type II PKA R-subunit. ¡€0€ª€0€ €CDD¡€ €G8¢€0€0€ €?pfam02198, SAM_PNT, Sterile alpha motif (SAM)/Pointed domain. ¡€0€ª€0€ €CDD¡€ €³B¢€0€0€ €)pfam02199, SapA, Saposin A-type domain. ¡€0€ª€0€ €CDD¡€ €³C¢€0€0€ €0pfam02200, STE, STE like transcription factor. ¡€0€ª€0€ €CDD¡€ €³D¢€0€0€ €‚Jpfam02201, SWIB, SWIB/MDM2 domain. This family includes the SWIB domain and the MDM2 domain. The p53-associated protein (MDM2) is an inhibitor of the p53 tumor suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2.¡€0€ª€0€ €CDD¡€ €³E¢€0€0€ €+pfam02202, Tachykinin, Tachykinin family. ¡€0€ª€0€ €CDD¡€ €G=¢€0€0€ €5pfam02203, TarH, Tar ligand binding domain homolog. ¡€0€ª€0€ €CDD¡€ €³F¢€0€0€ €Åpfam02204, VPS9, Vacuolar sorting protein 9 (VPS9) domain. This domain acts as a GDP-GTP exchange factor (GEF). It activates Rab GTPases by stimulating the release of GDP and allowing GTP to bind.¡€0€ª€0€ €CDD¡€ €³G¢€0€0€ €»pfam02205, WH2, WH2 motif. The WH2 motif (for Wiskott Aldrich syndrome homology region 2) has been shown in WASP and Scar1 (mammalian homolog) to be the region that interacts with actin.¡€0€ª€0€ €CDD¡€ €³H¢€0€0€ €-pfam02206, WSN, Domain of unknown function. ¡€0€ª€0€ €CDD¡€ €³I¢€0€0€ €Špfam02207, zf-UBR, Putative zinc finger in N-recognin (UBR box). This region is found in E3 ubiquitin ligases that recognize N-recognins.¡€0€ª€0€ €CDD¡€ €³J¢€0€0€ €,pfam02208, Sorb, Sorbin homologous domain. ¡€0€ª€0€ €CDD¡€ €³K¢€0€0€ €*pfam02209, VHP, Villin headpiece domain. ¡€0€ª€0€ €CDD¡€ €³L¢€0€0€ €pfam02210, Laminin_G_2, Laminin G domain. This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.¡€0€ª€0€ €CDD¡€ €³M¢€0€0€ €‚ëpfam02211, NHase_beta, Nitrile hydratase beta subunit. Nitrile hydratases EC:4.2.1.84 are unusual metalloenzymes that catalyze the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit.¡€0€ª€0€ €CDD¡€ €³N¢€0€0€ €1pfam02212, GED, Dynamin GTPase effector domain. ¡€0€ª€0€ €CDD¡€ €³O¢€0€0€ €¨pfam02213, GYF, GYF domain. The GYF domain is named because of the presence of Gly-Tyr-Phe residues. The GYF domain is a proline-binding domain in CD2-binding protein.¡€0€ª€0€ €CDD¡€ €³P¢€0€0€ €‚apfam02214, BTB_2, BTB/POZ domain. In voltage-gated K+ channels this domain is responsible for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. In KCTD1 this domain functions as a transcriptional repressor. It also mediates homomultimerisation of KCTD1 and interaction of KCTD1 with the transcription factor AP-2-alpha.¡€0€ª€0€ €CDD¡€ €³Q¢€0€0€ €—pfam02216, B, B domain. This family contains the B domain of Staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G.¡€0€ª€0€ €CDD¡€ €GJ¢€0€0€ €pfam02217, T_Ag_DNA_bind, Origin of replication binding protein. This domain of large T antigen binds to the SV40 origin of DNA replication.¡€0€ª€0€ €CDD¡€ €GK¢€0€0€ €ãpfam02218, HS1_rep, Repeat in HS1/Cortactin. The function of this repeat is unknown. Seven copies are found in cortactin and four copies are found in HS1. The repeats are always found amino terminal to an SH3 domain pfam00018.¡€0€ª€0€ €CDD¡€ €³R¢€0€0€ €‚pfam02219, MTHFR, Methylenetetrahydrofolate reductase. This family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from bacteria and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The structure for this domain is known to be a TIM barrel.¡€0€ª€0€ €CDD¡€ €GM¢€0€0€ €‚¯pfam02221, E1_DerP2_DerF2, ML domain. ML domain - MD-2-related lipid recognition domain. This family consists of proteins from plants, animals and fungi, including dust mite allergen Der P 2. It has been implicate in lipid recognition, particularly in the recognition of pathogen related products. A mutation in Npc2 causes a rare form of Niemann-Pick type C2 disease. This domain has a similar topology to immunoglobulin domains.¡€0€ª€0€ €CDD¡€ €³S¢€0€0€ €Õpfam02222, ATP-grasp, ATP-grasp domain. This family does not contain all known ATP-grasp domain members. This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.¡€0€ª€0€ €CDD¡€ €GO¢€0€0€ €1pfam02223, Thymidylate_kin, Thymidylate kinase. ¡€0€ª€0€ €CDD¡€ €GP¢€0€0€ €Ïpfam02224, Cytidylate_kin, Cytidylate kinase. Cytidylate kinase EC:2.7.4.14 catalyzes the phosphorylation of cytidine 5'-monophosphate (dCMP) to cytidine 5'-diphosphate (dCDP) in the presence of ATP or GTP.¡€0€ª€0€ €CDD¡€ €GQ¢€0€0€ €‚Špfam02225, PA, PA domain. The PA (Protease associated) domain is found as an insert domain in diverse proteases. The PA domain is also found in a plant vacuolar sorting receptor and members of the RZF family. It has been suggested that this domain forms a lid-like structure that covers the active site in active proteases, and is involved in protein recognition in vacuolar sorting receptors.¡€0€ª€0€ €CDD¡€ €³T¢€0€0€ €‚&pfam02226, Pico_P1A, Picornavirus coat protein (VP4). VP1, VP2, VP3 and VP4 for the basic unit that forms the icosahedral coat of picornaviruses. Five symmetry-related N termini of coat protein VP4 form a ten-stranded, antiparallel beta barrel around the base of the icosahedral fivefold axis.¡€0€ª€0€ €CDD¡€ €³U¢€0€0€ €upfam02228, Gag_p19, Major core protein p19. p19 is a component of the inner protein layer of the viral nucleocapsid.¡€0€ª€0€ €CDD¡€ €GT¢€0€0€ €‚epfam02229, PC4, Transcriptional Coactivator p15 (PC4). p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.¡€0€ª€0€ €CDD¡€ €³V¢€0€0€ €Þpfam02230, Abhydrolase_2, Phospholipase/Carboxylesterase. This family consists of both phospholipases and carboxylesterases with broad substrate specificity, and is structurally related to alpha/beta hydrolases pfam00561.¡€0€ª€0€ €CDD¡€ €GV¢€0€0€ €‚lpfam02232, Alpha_TIF, Alpha trans-inducing protein (Alpha-TIF). Alpha-TIF, a virion protein (VP16), is involved in transcriptional activation of viral immediate early (IE) promoters (alpha genes). Specificity of tegument protein VP16 for IE genes is conferred by the 400 residue N-terminal, the 80 residue C-terminal is responsible for transcriptional activation.¡€0€ª€0€ €CDD¡€ €GW¢€0€0€ €‚’pfam02233, PNTB, NAD(P) transhydrogenase beta subunit. This family corresponds to the beta subunit of NADP transhydrogenase in prokaryotes, and either the protein N- or C terminal in eukaryotes. The domain is often found in conjunction with pfam01262. Pyridine nucleotide transhydrogenase catalyzes the reduction of NAD+ to NADPH. A complete loss of activity occurs upon mutation of Gly314 in E. coli.¡€0€ª€0€ €CDD¡€ €³W¢€0€0€ €Êpfam02234, CDI, Cyclin-dependent kinase inhibitor. Cell cycle progression is negatively controlled by cyclin-dependent kinases inhibitors (CDIs). CDIs are involved in cell cycle arrest at the G1 phase.¡€0€ª€0€ €CDD¡€ €³X¢€0€0€ €Ûpfam02236, Viral_DNA_bi, Viral DNA-binding protein, all alpha domain. This family represents a domain of the viral DNA- binding protein, a multi functional protein involved in DNA replication and transcription control.¡€0€ª€0€ €CDD¡€ €GZ¢€0€0€ €Åpfam02237, BPL_C, Biotin protein ligase C terminal domain. The function of this structural domain is unknown. It is found to the C terminus of the biotin protein ligase catalytic domain pfam01317.¡€0€ª€0€ €CDD¡€ €G[¢€0€0€ €‚pfam02238, COX7a, Cytochrome c oxidase subunit VII. Cytochrome c oxidase, a 13 sub-unit complex, is the terminal oxidase in the mitochondrial electron transport chain. This family also contains both heart and liver isoforms of cytochrome c oxidase subunit VIIa.¡€0€ª€0€ €CDD¡€ €³Y¢€0€0€ €‚Fpfam02239, Cytochrom_D1, Cytochrome D1 heme domain. Cytochrome cd1 (nitrite reductase) catalyzes the conversion of nitrite to nitric oxide in the nitrogen cycle. This family represents the d1 heme binding domain of cytochrome cd1, in which His/Tyr side chains ligate the d1 heme iron of the active site in the oxidised state.¡€0€ª€0€ €CDD¡€ €³Z¢€0€0€ €‚ citrulline + NH3. Also found in this family is the Streptococcus anti tumor glycoprotein.¡€0€ª€0€ €CDD¡€ €³v¢€0€0€ €‚Ëpfam02275, CBAH, Linear amide C-N hydrolases, choloylglycine hydrolase family. This family includes several hydrolases which cleave carbon-nitrogen bonds, other than peptide bonds, in linear amides. These include choloylglycine hydrolase (conjugated bile acid hydrolase, CBAH) EC:3.5.1.24, penicillin acylase EC:3.5.1.11 and acid ceramidase EC:3.5.1.23. This domain forms the alpha-subunit for members from vertebral species, see family NAAA-beta, pfam15508.¡€0€ª€0€ €CDD¡€ €³w¢€0€0€ €‚Bpfam02276, CytoC_RC, Photosynthetic reaction centre cytochrome C subunit. Photosynthesis in purple bacteria is dependent on light-induced electron transfer in the reaction centre (RC), coupled to the uptake of protons from the cytoplasm. The RC contains a cytochrome molecule which re-reduces the oxidised electron donor.¡€0€ª€0€ €CDD¡€ €³x¢€0€0€ €‚(pfam02277, DBI_PRT, Phosphoribosyltransferase. This family of proteins represent the nicotinate-nucleotide- dimethylbenzimidazole phosphoribosyltransferase (NN:DBI PRT) enzymes involved in dimethylbenzimidazole synthesis. This function is essential to de novo cobalamin (vitamin B12) production in bacteria. Nicotinate mononucleotide (NaMN):5,6-dimethylbenzimidazole (DMB) phosphoribosyltransferase (CobT) from Salmonella enterica plays a central role in the synthesis of alpha-ribazole-5'-phosphate, an intermediate for the lower ligand of cobalamin.¡€0€ª€0€ €CDD¡€ €³y¢€0€0€ €‚-pfam02278, Lyase_8, Polysaccharide lyase family 8, super-sandwich domain. This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen.¡€0€ª€0€ €CDD¡€ €³z¢€0€0€ €‚pfam02281, Dimer_Tnp_Tn5, Transposase Tn5 dimerisation domain. Transposons are mobile DNA sequences capable of replication and insertion into the chromosome. Typically transposons code for the transposase enzyme, which catalyzes insertion, found between terminal inverted repeats. Tn5 has a unique method of self- regulation in which a truncated version of the transposase enzyme acts as an inhibitor. The catalytic domain of the Tn5 transposon is found in pfam01609. This domain mediates dimerisation in the known structure.¡€0€ª€0€ €CDD¡€ €G~¢€0€0€ €‚\pfam02282, Herpes_UL42, DNA polymerase processivity factor (UL42). The DNA polymerase processivity factor (UL42) of herpes simplex virus forms a heterodimer with UL30 to create the viral DNA polymerase complex. UL42 functions to increase the processivity of polymerization and makes little contribution to the catalytic activity of the polymerase.¡€0€ª€0€ €CDD¡€ €G¢€0€0€ €‚Ypfam02283, CobU, Cobinamide kinase / cobinamide phosphate guanyltransferase. This family is composed of a group of bifunctional cobalamin biosynthesis enzymes which display cobinamide kinase and cobinamide phosphate guanyltransferase activity. The crystal structure of the enzyme reveals the molecule to be a trimer with a propeller-like shape.¡€0€ª€0€ €CDD¡€ €³{¢€0€0€ €îpfam02284, COX5A, Cytochrome c oxidase subunit Va. Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit Va.¡€0€ª€0€ €CDD¡€ €³|¢€0€0€ €ñpfam02285, COX8, Cytochrome oxidase c subunit VIII. Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIII.¡€0€ª€0€ €CDD¡€ €³}¢€0€0€ €îpfam02286, Dehydratase_LU, Dehydratase large subunit. This family contains the large subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.¡€0€ª€0€ €CDD¡€ €³~¢€0€0€ €îpfam02287, Dehydratase_SU, Dehydratase small subunit. This family contains the small subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €ðpfam02288, Dehydratase_MU, Dehydratase medium subunit. This family contains the medium subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.¡€0€ª€0€ €CDD¡€ €³€¢€0€0€ €Ópfam02289, MCH, Cyclohydrolase (MCH). Methenyl tetrahydromethanopterin cyclohydrolase EC:3.5.4.27 is involved in methanogenesis in bacteria and archaea, producing methane from carbon monoxide or carbon dioxide.¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €‚ pfam02290, SRP14, Signal recognition particle 14kD protein. The signal recognition particle (SRP) is a multimeric protein involved in targeting secretory proteins to the rough endoplasmic reticulum membrane. SRP14 and SRP9 form a complex essential for SRP RNA binding.¡€0€ª€0€ €CDD¡€ €³‚¢€0€0€ €‚-pfam02291, TFIID-31kDa, Transcription initiation factor IID, 31kD subunit. This family represents the N-terminus of the 31kD subunit (42kD in drosophila) of transcription initiation factor IID (TAFII31). TAFII31 binds to p53, and is an essential requirement for p53 mediated transcription activation.¡€0€ª€0€ €CDD¡€ €³ƒ¢€0€0€ €”pfam02293, AmiS_UreI, AmiS/UreI family transporter. This family includes UreI and proton gated urea channel as well as putative amide transporters.¡€0€ª€0€ €CDD¡€ €³„¢€0€0€ €‚)pfam02294, 7kD_DNA_binding, 7kD DNA-binding domain. This family contains members of the hyper-thermophilic archaebacterium 7kD DNA-binding/endoribonuclease P2 family. There are five 7kD DNA-binding proteins, 7a-7e, found as monomers in the cell. Protein 7e shows the tightest DNA-binding ability.¡€0€ª€0€ €CDD¡€ €GŠ¢€0€0€ €‚Wpfam02295, z-alpha, Adenosine deaminase z-alpha domain. This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance.¡€0€ª€0€ €CDD¡€ €G‹¢€0€0€ €‚ pfam02296, Alpha_adaptin_C, Alpha adaptin AP2, C-terminal domain. Alpha adaptin is a hetero tetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site.¡€0€ª€0€ €CDD¡€ €³…¢€0€0€ €‚pfam02297, COX6B, Cytochrome oxidase c subunit VIb. Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of the potentially heme-binding subunit IVb of the oxidase.¡€0€ª€0€ €CDD¡€ €³†¢€0€0€ €òpfam02298, Cu_bind_like, Plastocyanin-like domain. This family represents a domain found in flowering plants related to the copper binding protein plastocyanin. Some members of this family may not bind copper due to the lack of key residues.¡€0€ª€0€ €CDD¡€ €GŽ¢€0€0€ €‚Gpfam02300, Fumarate_red_C, Fumarate reductase subunit C. Fumarate reductase is a membrane-bound flavoenzyme consisting of four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centers to the electron-transport chain. This family consists of the 15kD hydrophobic subunit C.¡€0€ª€0€ €CDD¡€ €³‡¢€0€0€ €‚”pfam02301, HORMA, HORMA domain. The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognize chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity.¡€0€ª€0€ €CDD¡€ €³ˆ¢€0€0€ €‚pfam02302, PTS_IIB, PTS system, Lactose/Cellobiose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases. This family also contains the fructose specific IIB subunit.¡€0€ª€0€ €CDD¡€ €³‰¢€0€0€ €Àpfam02303, Phage_DNA_bind, Helix-destabilizing protein. This family contains the bacteriophage helix-destabilizing protein, or single-stranded DNA binding protein, required for DNA synthesis.¡€0€ª€0€ €CDD¡€ €³Š¢€0€0€ €úpfam02304, Phage_B, Scaffold protein B. This is a family of proteins from single-stranded DNA bacteriophages. Scaffold proteins B and D are required for procapsid formation. Sixty copies of the internal scaffold protein B are found in the procapsid.¡€0€ª€0€ €CDD¡€ €G“¢€0€0€ €Îpfam02305, Phage_F, Capsid protein (F protein). This is a family of proteins from single-stranded DNA bacteriophages. Protein F is the major capsid component, sixty copies of which are found in the virion.¡€0€ª€0€ €CDD¡€ €³‹¢€0€0€ €Âpfam02306, Phage_G, Major spike protein (G protein). This is a family of proteins from single-stranded DNA bacteriophages. Five G proteins, each a tight beta barrel, from twelve surface spikes.¡€0€ª€0€ €CDD¡€ €G”¢€0€0€ €¡pfam02308, MgtC, MgtC family. The MgtC protein is found in an operon with the Mg2+ transporter protein MgtB. The function of MgtC and its homologs is not known.¡€0€ª€0€ €CDD¡€ €³Œ¢€0€0€ €ÿpfam02309, AUX_IAA, AUX/IAA family. Transcription of the AUX/IAA family of genes is rapidly induced by the plant hormone auxin. Some members of this family are longer and contain an N terminal DNA binding domain. The function of this region is uncertain.¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €‚pfam02310, B12-binding, B12 binding domain. This domain binds to B12 (adenosylcobamide), it is found in several enzymes, such as glutamate mutase, methionine synthase, and methylmalonyl-CoA mutase. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding.¡€0€ª€0€ €CDD¡€ €³Ž¢€0€0€ €‚Npfam02311, AraC_binding, AraC-like ligand binding domain. This family represents the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €‚Hpfam02312, CBF_beta, Core binding factor beta subunit. Core binding factor (CBF) is a heterodimeric transcription factor essential for genetic regulation of hematopoiesis and osteogenesis. The beta subunit enhances DNA-binding ability of the alpha subunit in vitro, and has been show to have a structure related to the OB fold.¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €‚Gpfam02313, Fumarate_red_D, Fumarate reductase subunit D. Fumarate reductase is a membrane-bound flavoenzyme consisting of four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centers to the electron-transport chain. This family consists of the 13kD hydrophobic subunit D.¡€0€ª€0€ €CDD¡€ €³‘¢€0€0€ €‚pfam02315, MDH, Methanol dehydrogenase beta subunit. Methanol dehydrogenase (MDH) is a bacterial periplasmic quinoprotein that oxidises methanol to formaldehyde. MDH is a tetramer of two alpha and two beta subunits. This family contains the small beta subunit.¡€0€ª€0€ €CDD¡€ €³’¢€0€0€ €‚pfam02316, HTH_Tnp_Mu_1, Mu DNA-binding domain. This family consists of MuA-transposase and repressor protein CI. These proteins contain homologous DNA-binding domains at their N-termini which compete for the same DNA site within the Mu bacteriophage genome.¡€0€ª€0€ €CDD¡€ €³“¢€0€0€ €‚pfam02317, Octopine_DH, NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain. This group of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The Pfam family consists mainly of octopine and nopaline dehydrogenases from Ti plasmids.¡€0€ª€0€ €CDD¡€ €³”¢€0€0€ €Ãpfam02318, FYVE_2, FYVE-type zinc finger. This FYVE-type zinc finger is found at the N-terminus of effector proteins including rabphilin-3A and regulating synaptic membrane exocytosis protein 2.¡€0€ª€0€ €CDD¡€ €³•¢€0€0€ €‚¾pfam02319, E2F_TDP, E2F/DP family winged-helix DNA-binding domain. This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins.¡€0€ª€0€ €CDD¡€ €³–¢€0€0€ €‚Fpfam02320, UCR_hinge, Ubiquinol-cytochrome C reductase hinge protein. The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This Pfam family represents the 'hinge' protein of the complex which is thought to mediate formation of the cytochrome c1 and cytochrome c complex.¡€0€ª€0€ €CDD¡€ €³—¢€0€0€ €‚“pfam02321, OEP, Outer membrane efflux protein. The OEP family (Outer membrane efflux protein) form trimeric channels that allow export of a variety of substrates in Gram negative bacteria. Each member of this family is composed of two repeats. The trimeric channel is composed of a 12 stranded all beta sheet barrel that spans the outer membrane, and a long all helical barrel that spans the periplasm.¡€0€ª€0€ €CDD¡€ €³˜¢€0€0€ €‚0pfam02322, Cyt_bd_oxida_II, Cytochrome bd terminal oxidase subunit II. This family consists of cytochrome bd type terminal oxidases that catalyze quinol-dependent, Na+-independent oxygen uptake. Members of this family are integral membrane proteins and contain a protohaem IX centre B558. One member of the family, Klebsiella pneumoniae CydB, is implicated in having an important role in micro-aerobic nitrogen fixation in the enteric bacterium Klebsiella pneumoniae. The family forms an integral functional unit with subunit I, family Bac_Ubq_Cox, pfam01654.¡€0€ª€0€ €CDD¡€ €³™¢€0€0€ €‚¡pfam02323, ELH, Egg-laying hormone precursor. This family consists of egg-laying hormone (ELH) precursor and atrial gland peptides form little and California sea hare. The family also includes ovulation prohormone precursor from great pond snail. This family thus represents a conserved gastropoda ovulation and egg production prohormone. Note that many of the proteins present are further cleaved to give individual peptides. Neuropeptidergic bag cells of the marine mollusk Aplysia californica synthesize an egg-laying hormone (ELH) precursor protein which is cleaved to generate several bioactive peptides including ELH, bag cell peptides (BCP) and acidic peptide (AP).¡€0€ª€0€ €CDD¡€ €87¢€0€0€ €‚þpfam02324, Glyco_hydro_70, Glycosyl hydrolase family 70. Members of this family belong to glycosyl hydrolase family 70 Glucosyltransferases or sucrose 6-glycosyl transferases (GTF-S) catalyze the transfer of D-glucopyramnosyl units from sucrose onto acceptor molecules, EC:2.4.1.5. This family roughly corresponds to the N-terminal catalytic domain of the enzyme. Members of this family also contain the Putative cell wall binding domain pfam01473, which corresponds with the C-terminal glucan-binding domain.¡€0€ª€0€ €CDD¡€ €G£¢€0€0€ €Åpfam02325, YGGT, YGGT family. This family consists of a repeat found in conserved hypothetical integral membrane proteins. The function of this region and the proteins which possess it is unknown.¡€0€ª€0€ €CDD¡€ €³š¢€0€0€ €¢pfam02326, YMF19, Plant ATP synthase F0. This family corresponds to subunit 8 (YMF19) of the F0 complex of plant and algae mitochondrial F-ATPases (EC:3.6.1.34).¡€0€ª€0€ €CDD¡€ €³›¢€0€0€ €‚pfam02327, BChl_A, Bacteriochlorophyll A protein. Bacteriochlorophyll A protein is involved in the energy transfer system of green photosynthetic bacteria. The protein forms a homotrimer, with each monomer unit containing seven molecules of bacteriochlorophyll A.¡€0€ª€0€ €CDD¡€ €³œ¢€0€0€ €ípfam02329, HDC, Histidine carboxylase PI chain. Histidine carboxylase catalyzes the formation of histamine from histidine. Cleavage of the proenzyme PI chain yields two subunits, alpha and beta, which arrange as a hexamer (alpha beta)6.¡€0€ª€0€ €CDD¡€ €G§¢€0€0€ €‚pfam02330, MAM33, Mitochondrial glycoprotein. This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q. It is thought to be involved in mitochondrial oxidative phosphorylation and in nucleus-mitochondrion interactions.¡€0€ª€0€ €CDD¡€ €³¢€0€0€ €üpfam02331, P35, Apoptosis preventing protein. This viral protein functions to block the host apoptotic response caused by infection by the virus. The apoptosis preventing protein (or early 35kD protein, P35) acts by blocking caspase protease activity.¡€0€ª€0€ €CDD¡€ €G©¢€0€0€ €‚Epfam02332, Phenol_Hydrox, Methane/Phenol/Toluene Hydroxylase. Bacterial phenol hydroxylase is a multicomponent enzyme that catabolises phenol and some of its methylated derivatives. This Pfam family contains both the P1 and P3 polypeptides of phenol hydroxylase and the alpha and beta chain of methane hydroxylase protein A.¡€0€ª€0€ €CDD¡€ €³ž¢€0€0€ €‚pfam02333, Phytase, Phytase. Phytase is a secreted enzyme which hydrolyses phytate to release inorganic phosphate. This family appears to represent a novel enzyme that shows phytase activity and has been shown to have a six- bladed propeller folding architecture.¡€0€ª€0€ €CDD¡€ €G«¢€0€0€ €‚ pfam02334, RTP, Replication terminator protein. The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site.¡€0€ª€0€ €CDD¡€ €G¬¢€0€0€ €‚(pfam02335, Cytochrom_C552, Cytochrome c552. Cytochrome c552 (cytochrome c nitrite reductase) is a crucial enzyme in the nitrogen cycle catalyzing the reduction of nitrite to ammonia. The crystal structure of cytochrome c552 reveals it to be a dimer, with with 10 close-packed type c haem groups.¡€0€ª€0€ €CDD¡€ €³Ÿ¢€0€0€ €Æpfam02336, Denso_VP4, Capsid protein VP4. Four different translation initiation sites of the densovirus capsid protein mRNA give rise to four viral proteins, VP1 to VP4. This family represents VP4.¡€0€ª€0€ €CDD¡€ €G®¢€0€0€ €‚ pfam02337, Gag_p10, Retroviral GAG p10 protein. This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10.¡€0€ª€0€ €CDD¡€ €³ ¢€0€0€ €‚pfam02338, OTU, OTU-like cysteine protease. This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian tumor (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases.¡€0€ª€0€ €CDD¡€ €G°¢€0€0€ €‚pfam02340, PRRSV_Env, PRRSV putative envelope protein. This family consists of a conserved probable envelope protein or ORF2 in porcine reproductive and respiratory syndrome virus (PRRSV) also in the family is a minor structural protein from lactate dehydrogenase-elevating virus.¡€0€ª€0€ €CDD¡€ €²“¢€0€0€ €‚pfam02341, RcbX, RbcX protein. The RBCX protein has been identified as having a possible chaperone-like function. The rbcX gene is juxtaposed to and cotranscribed with rbcL and rbcS encoding RuBisCO in Anabaena sp. CA. RbcX has been shown to possess a chaperone-like function assisting correct folding of RuBisCO in E. coli expression studies and is needed for RuBisCO to reach its maximal activity.¡€0€ª€0€ €CDD¡€ €G±¢€0€0€ €‚Èpfam02342, TerD, TerD domain. The TerD domain is found in TerD family proteins that include the paralogous TerD, TerA, TerE, TerF and TerZ proteins It is found in a stress response operon with TerB and TerC. TerD has a maximum of two calcium-binding sites depending on the conservation of aspartates. It has various fusions to nuclease domains, RNA binding domains, ubiquitin related domains, and metal binding domains. The ter gene products lie at the centre of membrane-linked metal recognition complexes with regulatory ramifications encompassing phosphorylation-dependent signal transduction, RNA-dependent regulation, biosynthesis of nucleoside-like metabolites and DNA processing linked to novel pathways.¡€0€ª€0€ €CDD¡€ €³¡¢€0€0€ €‚pfam02343, TRA-1_regulated, TRA-1 regulated protein R03H10.4. This family of proteins represents the protein product of the gene R03H10.4 which is located near a sequence that matches the TRA-1 binding consensus. TRA-1 is a transcription factor which controls sexual differentiation in C.elegans. R03H10.4 shows male-enriched reporter gene expression and acts as a direct target of TRA-1 regulation.¡€0€ª€0€ €CDD¡€ €³¢¢€0€0€ €‚Þpfam02344, Myc-LZ, Myc leucine zipper domain. This family consists of the leucine zipper dimerisation domain found in both cellular c-Myc proto-oncogenes and viral v-Myc oncogenes. Dimerisation via the leucine zipper motif with other basic helix-loop-helix-leucine zipper (b/HLH/lz) proteins such as Max is required for efficient DNA binding. The Myc-Max dimer is a transactivating complex activating expression of growth related genes promoting cell proliferation. The dimerisation is facilitated via interdigitating leucine residues every 7th position of the alpha helix. Like charge repulsion of adjacent residues in this region perturbs the formation of homodimers with heterodimers being promoted by opposing charge attractions.¡€0€ª€0€ €CDD¡€ €³£¢€0€0€ €‚[pfam02346, Vac_Fusion, Chordopoxvirus multifunctional envelope protein A27. This is a family of viral fusion proteins from the chordopoxviruses. The A27L gene product, a 14-kDa Vaccinia Virus protein, has been demonstrated to function as a viral fusion protein mediating cell fusion at endosmomal (low) pH. More recently it has been shown that A27 forms disulfide-linked protein complexes with A26 protein providing an anchor for A26 protein packaging into mature virions. A27 regulates virion-membrane fusion rather than inducing it and is critical for the successful egress of mature virus particles.¡€0€ª€0€ €CDD¡€ €Gµ¢€0€0€ €‚Þpfam02347, GDC-P, Glycine cleavage system P-protein. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1.2.10 (GDC) also annotated as glycine cleavage system or glycine synthase. GDC consists of four proteins P, H, L and T. The reaction catalyzed by this protein is:- Glycine + lipoylprotein <=> S-aminomethyldihydrolipoylprotein + CO2.¡€0€ª€0€ €CDD¡€ €G¶¢€0€0€ €‚`pfam02348, CTP_transf_3, Cytidylyltransferase. This family consists of two main Cytidylyltransferase activities: 1) 3-deoxy-manno-octulosonate cytidylyltransferase,, EC:2.7.7.38 catalyzing the reaction:- CTP + 3-deoxy-D-manno-octulosonate <=> diphosphate + CMP-3-deoxy-D-manno-octulosonate, 2) acylneuraminate cytidylyltransferase EC:2.7.7.43, catalyzing the reaction:- CTP + N-acylneuraminate <=> diphosphate + CMP-N-acylneuraminate. NeuAc cytydilyltransferase of Mannheimia haemolytica has been characterized describing kinetics and regulation by substrate charge, energetic charge and amino-sugar demand.¡€0€ª€0€ €CDD¡€ €³¤¢€0€0€ €‚pfam02349, MSG, Major surface glycoprotein. This is a novel repeat in Pneumocystis carinii Major surface glycoprotein (MSG) some members of the alignment have up to nine repeats of this family, the repeats containing several conserved cysteines. The MSG of P. carinii is an important protein in host-pathogen interactions. Surface glycoprotein A from Pneumocystis carinii is a main target for the host immune system, this protein is implicated in the attachment of Pneumocystis carinii to the host alveolar epithelial cells, alveolar macrophages, host surfactant and possibly accounts in part for the hypoxia seen in Pneumocystis carinii pneumonia (PCP).¡€0€ª€0€ €CDD¡€ €³¥¢€0€0€ €‚|pfam02350, Epimerase_2, UDP-N-acetylglucosamine 2-epimerase. This family consists of UDP-N-acetylglucosamine 2-epimerases EC:5.1.3.14 this enzyme catalyzes the production of UDP-ManNAc from UDP-GlcNAc. Note that some of the enzymes is this family are bifunctional, in these instances Pfam matches only the N-terminal half of the protein suggesting that the additional C-terminal part (when compared to mono-functional members of this family) is responsible for the UPD-N-acetylmannosamine kinase activity of these enzymes. This hypothesis is further supported by the assumption that the C-terminal part of rat Gne is the kinase domain.¡€0€ª€0€ €CDD¡€ €³¦¢€0€0€ €‚Úpfam02351, GDNF, GDNF/GAS1 domain. This cysteine rich domain is found in multiple copies in GNDF and GAS1 proteins. GDNF and neurturin (NTN) receptors are potent survival factors for sympathetic, sensory and central nervous system neurons. GDNF and neurturin promote neuronal survival by signaling through similar multicomponent receptors that consist of a common receptor tyrosine kinase and a member of a GPI-linked family of receptors that determines ligand specificity.¡€0€ª€0€ €CDD¡€ €³§¢€0€0€ €‚pfam02352, Decorin_bind, Decorin binding protein. This family consists of decorin binding proteins from Borrelia. The decorin binding protein of Borrelia burgdorferi the lyme disease spirochetes adheres to the proteoglycan decorin found on collagen fibres.¡€0€ª€0€ €CDD¡€ €G»¢€0€0€ €‚ S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid.¡€0€ª€0€ €CDD¡€ €G¼¢€0€0€ €‚¢pfam02354, Latrophilin, Latrophilin Cytoplasmic C-terminal region. This family consists of the cytoplasmic C-terminal region in latrophilin. Latrophilin is a synaptic Ca2+ independent alpha- latrotoxin (LTX) receptor and is a novel member of the secretin family of G-protein coupled receptors that are involved in secretion. Latrophilin mRNA is present only in neuronal tissue. Lactrophillin interacts with G-alpha O.¡€0€ª€0€ €CDD¡€ €³¨¢€0€0€ €‚Ipfam02355, SecD_SecF, Protein export membrane protein. This family consists of various prokaryotic SecD and SecF protein export membrane proteins. This SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC. SecD and SecF are required to maintain a proton motive force.¡€0€ª€0€ €CDD¡€ €G¾¢€0€0€ €9pfam02357, NusG, Transcription termination factor nusG. ¡€0€ª€0€ €CDD¡€ €³©¢€0€0€ €‚!pfam02358, Trehalose_PPase, Trehalose-phosphatase. This family consist of trehalose-phosphatases EC:3.1.3.12 these enzyme catalyze the de-phosphorylation of trehalose-6-phosphate to trehalose and orthophosphate. The aligned region is present in trehalose-phosphatases and comprises the entire length of the protein it is also found in the C-terminus of trehalose-6-phosphate synthase EC:2.4.1.15 adjacent to the trehalose-6-phosphate synthase domain - pfam00982. It would appear that the two equivalent genes in the E. coli otsBA operon otsA the trehalose-6-phosphate synthase and otsB trehalose-phosphatase (this family) have undergone gene fusion in most eukaryotes. Trehalose is a common disaccharide of bacteria, fungi and invertebrates that appears to play a major role in desiccation tolerance.¡€0€ª€0€ €CDD¡€ €GÀ¢€0€0€ €‚®pfam02359, CDC48_N, Cell division protein 48 (CDC48), N-terminal domain. This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases pfam00004 is a substrate 185-residue recognition domain.¡€0€ª€0€ €CDD¡€ €³ª¢€0€0€ €‚'pfam02361, CbiQ, Cobalt transport protein. This family consists of various cobalt transport proteins Most of which are found in Cobalamin (Vitamin B12) biosynthesis operons. In Salmonella the cbiN cbiQ (product CbiQ in this family) and cbiO are likely to form an active cobalt transport system.¡€0€ª€0€ €CDD¡€ €G¢€0€0€ €‚Jpfam02362, B3, B3 DNA binding domain. This is a family of plant transcription factors with various roles in development, the aligned region corresponds the B3 DNA binding domain as described in this domain is found in VP1/AB13 transcription factors. Some proteins also have a second AP2 DNA binding domain pfam00847 such as RAV1.¡€0€ª€0€ €CDD¡€ €³«¢€0€0€ €‚Dpfam02363, C_tripleX, Cysteine rich repeat. This Cysteine repeat C-X3-C-X3-C is repeated in sequences of this family, 34 times in an uncharacterized C. elegans protein. The function of these repeats is unknown as is the function of the proteins in which they occur. Most of the sequences in this family are from C. elegans.¡€0€ª€0€ €CDD¡€ €³¬¢€0€0€ €‚Çpfam02364, Glucan_synthase, 1,3-beta-glucan synthase component. This family consists of various 1,3-beta-glucan synthase components including Gls1, Gls2 and Gls3 from yeast. 1,3-beta-glucan synthase EC:2.4.1.34 also known as callose synthase catalyzes the formation of a beta-1,3-glucan polymer that is a major component of the fungal cell wall. The reaction catalyzed is:- UDP-glucose + {(1,3)-beta-D-glucosyl}(N) <=> UDP + {(1,3)-beta-D-glucosyl}(N+1).¡€0€ª€0€ €CDD¡€ €³­¢€0€0€ €‚4pfam02365, NAM, No apical meristem (NAM) protein. This is a family of no apical meristem (NAM) proteins these are plant development proteins. Mutations in NAM result in the failure to develop a shoot apical meristem in petunia embryos. NAM is indicated as having a role in determining positions of meristems and primordial. One member of this family NAP (NAC-like, activated by AP3/PI) is encoded by the target genes of the AP3/PI transcriptional activators and functions in the transition between growth by cell division and cell expansion in stamens and petals.¡€0€ª€0€ €CDD¡€ €³®¢€0€0€ €‚pfam02366, PMT, Dolichyl-phosphate-mannose-protein mannosyltransferase. This is a family of Dolichyl-phosphate-mannose-protein mannosyltransferase proteins EC:2.4.1.109. These proteins are responsible for O-linked glycosylation of proteins, they catalyze the reaction:- Dolichyl phosphate D-mannose + protein <=> dolichyl phosphate + O-D-mannosyl-protein. Also in this family is Drosophila rotated abdomen protein which is a putative mannosyltransferase. This family appears to be distantly related to pfam02516 (A Bateman pers. obs.).¡€0€ª€0€ €CDD¡€ €GÇ¢€0€0€ €¥pfam02367, TsaE, Threonylcarbamoyl adenosine biosynthesis protein TsaE. This family of proteins is involved in the synthesis of threonylcarbamoyl adenosine (t(6)A).¡€0€ª€0€ €CDD¡€ €³¯¢€0€0€ €Ñpfam02368, Big_2, Bacterial Ig-like domain (group 2). This family consists of bacterial domains with an Ig-like fold. Members of this family are found in bacterial and phage surface proteins such as intimins.¡€0€ª€0€ €CDD¡€ €³°¢€0€0€ €îpfam02369, Big_1, Bacterial Ig-like domain (group 1). This family consists of bacterial domains with an Ig-like fold. Members of this family are found in bacterial surface proteins such as intimins and invasins involved in pathogenicity.¡€0€ª€0€ €CDD¡€ €GÊ¢€0€0€ €‚Ypfam02370, M, M protein repeat. This short repeat is found in multiple copies in bacterial M proteins. The M proteins bind to IgA and are closely associated with virulence. The M protein has been postulated to be a major group A Streptococcal (GAS) virulence factor because of its contribution to the bacterial resistance to opsonophagocytosis.¡€0€ª€0€ €CDD¡€ €²¯¢€0€0€ €‚pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family. Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. This region is often found with pfam01548. The exact function of this region is uncertain. This family contains a HHH motif suggesting a DNA-binding function.¡€0€ª€0€ €CDD¡€ €³±¢€0€0€ €ýpfam02372, IL15, Interleukin 15. Interleukin-15 (IL-15) is a cytokine that possesses a variety of biological functions, including stimulation and maintenance of cellular immune responses. Structurally these proteins are short-chain 4-helical cytokines.¡€0€ª€0€ €CDD¡€ €³²¢€0€0€ €‚†pfam02373, JmjC, JmjC domain, hydroxylase. The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation.¡€0€ª€0€ €CDD¡€ €ð¢€0€0€ €üpfam02374, ArsA_ATPase, Anion-transporting ATPase. This Pfam family represents a conserved domain, which is sometimes repeated, in an anion-transporting ATPase. The ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell.¡€0€ª€0€ €CDD¡€ €GÍ¢€0€0€ €pfam02375, JmjN, jmjN domain. ¡€0€ª€0€ €CDD¡€ €³³¢€0€0€ €ípfam02376, CUT, CUT domain. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein.¡€0€ª€0€ €CDD¡€ €³´¢€0€0€ €‚pfam02377, Dishevelled, Dishevelled specific domain. This domain is specific to the signalling protein dishevelled. The domain is found adjacent to the PDZ domain pfam00595, often in conjunction with DEP (pfam00610) and DIX (pfam00778). Much of it is disordered and yet conserved.¡€0€ª€0€ €CDD¡€ €³µ¢€0€0€ €‚Ÿpfam02378, PTS_EIIC, Phosphotransferase system, EIIC. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific permease of the PTS consists of three domains (IIA, IIB and IIC). The IIC domain catalyzes the transfer of a phosphoryl group from IIB to the sugar substrate.¡€0€ª€0€ €CDD¡€ €³¶¢€0€0€ €ûpfam02380, Papo_T_antigen, T-antigen specific domain. This domain represents a conserved region in papovavirus small and middle T-antigens. It is found as the N-terminal domain in the small T-antigen, and is centrally located in the middle T-antigen.¡€0€ª€0€ €CDD¡€ €³·¢€0€0€ €‚hpfam02381, MraZ, MraZ protein, putative antitoxin-like. This small 70 amino acid domain is found duplicated in a family of bacterial proteins. These proteins may be DNA-binding transcription factors (Pers. comm. A Andreeva & A Murzin). It is likely, due to the similarity of fold, that this family acts as a bacterial antitoxin like the MazE antitoxin family.¡€0€ª€0€ €CDD¡€ €GÒ¢€0€0€ €‚pfam02382, RTX, RTX N-terminal domain. The RTX family of bacterial toxins are a group of cytolysins and cytotoxins. This Pfam family represents the N-terminal domain which is found in association with a glycine-rich repeat domain and hemolysinCabind pfam00353.¡€0€ª€0€ €CDD¡€ €³¸¢€0€0€ €øpfam02383, Syja_N, SacI homology domain. This Pfam family represents a protein domain which shows homology to the yeast protein SacI. The SacI homology domain is most notably found at the amino terminal of the inositol 5'-phosphatase synaptojanin.¡€0€ª€0€ €CDD¡€ €³¹¢€0€0€ €‚ pfam02384, N6_Mtase, N-6 DNA Methylase. Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The R-M system is a complex containing three polypeptides: M (this family), S (pfam01420), and R. This family consists of N-6 adenine-specific DNA methylase EC:2.1.1.72 from Type I and Type IC restriction systems. These methylases have the same sequence specificity as their corresponding restriction enzymes.¡€0€ª€0€ €CDD¡€ €GÕ¢€0€0€ €‚·pfam02386, TrkH, Cation transport protein. This family consists of various cation transport proteins (Trk) and V-type sodium ATP synthase subunit J or translocating ATPase J EC:3.6.1.34. These proteins are involved in active sodium up-take utilising ATP in the process. TrkH a member of the family from E. coli is a hydrophobic membrane protein and determines the specificity and kinetics of cation transport by the TrK system in E. coli.¡€0€ª€0€ €CDD¡€ €GÖ¢€0€0€ €‡pfam02387, IncFII_repA, IncFII RepA protein family. This protein is plasmid encoded and found to be essential for plasmid replication.¡€0€ª€0€ €CDD¡€ €G×¢€0€0€ €‚1pfam02388, FemAB, FemAB family. The femAB operon codes for two nearly identical approximately 50-kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan. These proteins are also considered as a factor influencing the level of methicillin resistance.¡€0€ª€0€ €CDD¡€ €³º¢€0€0€ €‚›pfam02389, Cornifin, Cornifin (SPRR) family. SPRR genes (formerly SPR) encode a novel class of polypeptides (small proline rich proteins) that are strongly induced during differentiation of human epidermal keratinocytes in vitro and in vivo. The most characteristic feature of the SPRR gene family resides in the structure of the central segments of the encoded polypeptides that are built up from tandemly repeated units of either eight (SPRR1 and SPRR3) or nine (SPRR2) amino acids with the general consensus XKXPEPXX where X is any amino acid. In order to avoid bacterial contamination due to the high polar-nature of the HMM the threshold has been set very high.¡€0€ª€0€ €CDD¡€ €GÙ¢€0€0€ €Öpfam02390, Methyltransf_4, Putative methyltransferase. This is a family of putative methyltransferases. The aligned region contains the GXGXG S-AdoMet binding site suggesting a putative methyltransferase activity.¡€0€ª€0€ €CDD¡€ €GÚ¢€0€0€ €‚špfam02391, MoaE, MoaE protein. This family contains the MoaE protein that is involved in biosynthesis of molybdopterin. Molybdopterin, the universal component of the pterin molybdenum cofactors, contains a dithiolene group serving to bind Mo. Addition of the dithiolene sulfurs to a molybdopterin precursor requires the activity of the converting factor. Converting factor contains the MoaE and MoaD proteins.¡€0€ª€0€ €CDD¡€ €³»¢€0€0€ €çpfam02392, Ycf4, Ycf4. This family consists of hypothetical Ycf4 proteins from various chloroplast genomes. It has been suggested that Ycf4 is involved in the assembly and/or stability of the photosystem I complex in chloroplasts.¡€0€ª€0€ €CDD¡€ €³¼¢€0€0€ €‚¼pfam02393, US22, US22 like. US22 proteins have been found across many animal DNA viruses and some vertebrates. The name sake of this family, US22, is an early nuclear protein that is secreted from cells. The US22 family may have a role in virus replication and pathogenesis. Domain analysis showed that US22 proteins usually contain two copies of conserved modules which is homologous to several other families like SMI1 and SYD (commonly called SUKH superfamily). Bacterial operon analysis revealed that all bacterial SUKH members function as immunity proteins against various toxins. Thus US22 family is predicted to counter diverse anti-viral responses by interacting with specific host proteins.¡€0€ª€0€ €CDD¡€ €³½¢€0€0€ €åpfam02394, IL1_propep, Interleukin-1 propeptide. The Interleukin-1 cytokines are translated as precursor proteins. The N terminal approx. 115 amino acids form a propeptide that is cleaved off to release the active interleukin-1.¡€0€ª€0€ €CDD¡€ €³¾¢€0€0€ €‚˜pfam02395, Peptidase_S6, Immunoglobulin A1 protease. This family consists of immunoglobulin A1 protease proteins. The immunoglobulin A1 protease cleaves immunoglobulin IgA and is found in pathogenic bacteria such as Neisseria gonorrhoeae. Not all of the members of this family are IgA proteases, EspP from E. coli O157:H7 cleaves human coagulation factor V and hbp is a hemoglobin protease from E. coli EB1.¡€0€ª€0€ €CDD¡€ €Gߢ€0€0€ €Çpfam02397, Bac_transf, Bacterial sugar transferase. This Pfam family represents a conserved region from a number of different bacterial sugar transferases, involved in diverse biosynthesis pathways.¡€0€ª€0€ €CDD¡€ €³¿¢€0€0€ €€pfam02398, Corona_7, Coronavirus protein 7. This is a family of proteins from coronavirus which may function in viral assembly.¡€0€ª€0€ €CDD¡€ €Gᢀ0€0€ €ºpfam02399, Herpes_ori_bp, Origin of replication binding protein. This Pfam family represents the herpesvirus origin of replication binding protein, probably involved in DNA replication.¡€0€ª€0€ €CDD¡€ €G⢀0€0€ €‚ pfam02401, LYTB, LytB protein. The mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis is essential in many eubacteria, plants, and the malaria parasite. The LytB gene is involved in the trunk line of the MEP pathway.¡€0€ª€0€ €CDD¡€ €³À¢€0€0€ €‚Ûpfam02402, Lysis_col, Lysis protein. These small bacterial proteins are required for colicin release and partial cell lysis. This family contains lysis proteins for several different forms of colicin. B. subtilis LytA has been included in this family, the similarity is not highly significant, however it is also a short protein, that is involved in secretion of other proteins (Bateman A pers. obs.). This family includes a signal peptide motif and a lipid attachment site.¡€0€ª€0€ €CDD¡€ €³Á¢€0€0€ €Ûpfam02403, Seryl_tRNA_N, Seryl-tRNA synthetase N-terminal domain. This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase.¡€0€ª€0€ €CDD¡€ €³Â¢€0€0€ €‚pfam02404, SCF, Stem cell factor. Stem cell factor (SCF) is a homodimer involved in hematopoiesis. SCF binds to and activates the SCF receptor (SCFR), a receptor tyrosine kinase. The crystal structure of human SCF has been resolved and a potential receptor-binding site identified.¡€0€ª€0€ €CDD¡€ €³Ã¢€0€0€ €‚Mpfam02405, MlaE, Permease MlaE. MlaE is a permease which in E. coli is a component of the Mla pathway, an ABC transport system that functions to maintain the asymmetry of the outer membrane. In NMB1965 it is involved in L-glutamate import into the cell. In Arabidopsis thaliana TGD1 it is involved in lipid transfer within the cell.¡€0€ª€0€ €CDD¡€ €³Ä¢€0€0€ €‚pfam02406, MmoB_DmpM, MmoB/DmpM family. This family consists of monooxygenase components such as MmoB methane monooxygenase (EC:1.14.13.25) regulatory protein B. When MmoB is present at low concentration it converts methane monooxygenase from an oxidase to a hydroxylase and stabilizes intermediates required for the activation of dioxygen. Also found in this family is DmpM or Phenol hydroxylase (EC:1.14.13.7) protein component P2, this protein lacks redox co-factors and is required for optimal turnover of Phenol hydroxylase.¡€0€ª€0€ €CDD¡€ €³Å¢€0€0€ €ùpfam02407, Viral_Rep, Putative viral replication protein. This is a family of viral ORFs from various plant and animal ssDNA circoviruses. Published evidence to support the annotated function "viral replication associated protein" has not be found.¡€0€ª€0€ €CDD¡€ €G颀0€0€ €âpfam02408, CUB_2, CUB-like domain. This is a family of hypothetical C. elegans proteins. The aligned region has no known function nor do any of the proteins which possess it. However, this domain is related to the CUB domain.¡€0€ª€0€ €CDD¡€ €Gꢀ0€0€ €‚épfam02410, RsfS, Ribosomal silencing factor during starvation. This family is expressed by almost all bacterial and eukaryotic genomes but not by archaea. Its function is to down-regulate protein synthesis under conditions of nutrient shortage, and it does this by binding to protein L14 of the large ribosomal subunit, thus acting as a ribosomal silencing factor (RsfS) by blocking the joining of the ribosomal subunits. This family is structurally homologous to nucleotidyltransferases.¡€0€ª€0€ €CDD¡€ €³Æ¢€0€0€ €ôpfam02411, MerT, MerT mercuric transport protein. MerT is an mercuric transport integral membrane protein and is responsible for transport of the Hg2+ iron from periplasmic MerP (also part of the transport system) to mercuric reductase (MerE).¡€0€ª€0€ €CDD¡€ €²Ö¢€0€0€ €‚pfam02412, TSP_3, Thrombospondin type 3 repeat. The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats. The repeat lacks defined secondary structure.¡€0€ª€0€ €CDD¡€ €³Ç¢€0€0€ €‚ pfam02413, Caudo_TAP, Caudovirales tail fibre assembly protein, lambda gpK. This family contains bacterial and phage tail fibre assembly proteins. E.coli contains several members of this family although the function of these proteins is uncertain. Using the lambda phage members as examples, there are both gptfa and gpK tail proteins here. GpK forms part of the TTC or tail-tip complex that is located at the distal end of the tail. TTCs form the platform on which the tail-tube proteins self-assemble and are also the attachment point for fibres or receptor-binding proteins that mediate phage-adsorption to the surface of the host cell. TTC assembly starts with gpJ, which is also known as the central tail fibre and is involved in host-cell adsorption. It is the C-terminus of gpJ that interacts with the lamB receptor on host cells. A number of intermediates including gpK then interact with gpJ during tail morphogenesis.¡€0€ª€0€ €CDD¡€ €Gí¢€0€0€ €ßpfam02414, Borrelia_orfA, Borrelia ORF-A. This protein is encoded by an open reading frame in plasmid borne DNA repeats of Borrelia species. This protein is known as ORF-A. The function of this putative protein is unknown.¡€0€ª€0€ €CDD¡€ €³È¢€0€0€ €‚pfam02415, Chlam_PMP, Chlamydia polymorphic membrane protein (Chlamydia_PMP) repeat. This family contains several Chlamydia polymorphic membrane proteins. Chlamydia pneumoniae is an obligate intracellular bacterium and a common human pathogen causing infection of the upper and lower respiratory tract. Common for the Pmps are the tetrapeptide GGA(I/V/L) motif repeated several times in the N-terminal part. The C-terminal half is characterized by conserved tryptophans and a carboxy-terminal phenylalanine. A signal peptide leader sequence is predicted in 20 C. pneumoniae Pmps, which indicates an outer membrane localization. Pmp10 and Pmp11 contain a signal peptidase II cleavage site suggesting lipid modification. The C. pneumoniae pmp genes represent 17.5% of the chlamydia-specific coding capacity and they are all transcribed during chlamydial growth but the function of Pmps remains unknown. This family shows some similarity to pfam05594 and hence is likely to also form a beta-helical structure (personal obs:C Yeats).¡€0€ª€0€ €CDD¡€ €³É¢€0€0€ €‚7pfam02416, MttA_Hcf106, mttA/Hcf106 family. Members of this protein family are involved in a sec independent translocation mechanism. This pathway has been called the DeltapH pathway in chloroplasts. Members of this family in E.coli are involved in export of redox proteins with a "twin arginine" leader motif.¡€0€ª€0€ €CDD¡€ €Gð¢€0€0€ €‚/pfam02417, Chromate_transp, Chromate transporter. Members of this family probably act as chromate transporters. Members of this family are found in both bacteria and archaebacteria. The proteins are composed of one or two copies of this region. The alignment contains two conserved motifs, FGG and PGP.¡€0€ª€0€ €CDD¡€ €³Ê¢€0€0€ €‚ CoA + N3'-acetyl-2-deoxystreptamine antibiotic. The enzyme can use a range of antibiotics with 2-deoxystreptamine rings as acceptor for its acetyltransferase activity, this inactivates and confers resistance to gentamicin, kanamycin, tobramycin, neomycin and apramycin amongst others.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚ pfam02524, KID, KID repeat. This is family contains the KID repeat as found in Borrelia spirochete RepA / Rep+ proteins. The function of these proteins is unknown. RepA and related Borrelia proteins have been suggested to play an important genus-wide role in the biology of the Borrelia.¡€0€ª€0€ €CDD¡€ €HP¢€0€0€ €‚"pfam02525, Flavodoxin_2, Flavodoxin-like fold. This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyze the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species. This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor <=> NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy. The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP. This family is related to pfam03358 and pfam00258.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚Epfam02526, GBP_repeat, Glycophorin-binding protein. This family contains glycophorin binding proteins from P. falciparum the malarial parasite. Glycophorin is a cell surface protein of erythrocytes. The Glycophorin binding protein contains a tandem 38 residue repeat. In Plasmodium falciparum GBP the repeat occurs 11 times.¡€0€ª€0€ €CDD¡€ €HR¢€0€0€ €‚þpfam02527, GidB, rRNA small subunit methyltransferase G. This is a family of bacterial glucose inhibited division proteins these are probably involved in the regulation of cell devision. GidB has been shown to be a methyltransferase G specific to the rRNA small subunit. Previously identified as a glucose-inhibited division protein B that appears to be present and in a single copy in all complete eubacterial genomes so far sequenced. GidB specifically methylates the N7 position of a guanosine in 16S rRNA.¡€0€ª€0€ €CDD¡€ €HS¢€0€0€ €‚pfam02529, PetG, Cytochrome B6-F complex subunit 5. This family consists of cytochrome B6-F complex subunit 5 (PetG). The cytochrome bf complex found in green plants, eukaryotic algae and cyanobacteria, connects photosystem I to photosystem II in the electron transport chain, functioning as a plastoquinol:plastocyanin/cytochrome c6 oxidoreductase. PetG or subunit 5 is associated with the bf complex and the absence of PetG affects either the assembly or stability of the cytochrome bf complex in Chlamydomonas reinhardtii.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚opfam02530, Porin_2, Porin subfamily. This family consists of porins from the alpha subdivision of Proteobacteria the members of this family are related to pfam00267. The porins form large aqueous channels in the cell membrane allowing the selective entry of hydrophilic compounds this so called 'molecular sieve' is found in the cell walls of gram negative bacteria.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚špfam02531, PsaD, PsaD. This family consists of PsaD from plants and cyanobacteria. PsaD is an extrinsic polypeptide of photosystem I (PSI) and is required for native assembly of PSI reaction clusters and is implicated in the electrostatic binding of ferredoxin within the reaction centre. PsaD forms a dimer in solution which is bound by PsaE however PsaD is monomeric in its native complexed PSI environment.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚Épfam02532, PsbI, Photosystem II reaction centre I protein (PSII 4.8 kDa protein). This family consists of various Photosystem II (PSII) reaction centre I proteins or PSII 4.8 kDa proteins, PsbI, from the chloroplast genome of many plants and Cyanobacteria. PsbI is a small, integral membrane component of PSII the role of which is not clear. Synechocystis mutants lacking PsbI have 20-30% loss of PSII activity however the PSII complex is not destabilized.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚ßpfam02533, PsbK, Photosystem II 4 kDa reaction centre component. This family consists of various photosystem II 4 kDa reaction centre components (PsbK) from plant and Cyanobacteria. The photosystem II reaction centre is responsible for catalyzing the core photosynthesis reaction the light-induced splitting of water and the consequential release of dioxygen. In C. reinhardtii the psbK product is required for the stable assembly and/or stability of the photosystem II complex.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚epfam02534, T4SS-DNA_transf, Type IV secretory system Conjugative DNA transfer. These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems. The C-terminus of this domain interacts with the relaxosome component TraM via the latter's tetramerisation domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore. The family contains a number of different DNA transfer proteins.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚êpfam02535, Zip, ZIP Zinc transporter. The ZIP family consists of zinc transport proteins and many putative metal transporters. The main contribution to this family is from the Arabidopsis thaliana ZIP protein family these proteins are responsible for zinc uptake in the plant. Also found within this family are C. elegans proteins of unknown function which are annotated as being similar to human growth arrest inducible gene product, although this protein in not found within this family.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚Õpfam02536, mTERF, mTERF. This family contains one sequence of known function Human mitochondrial transcription termination factor (mTERF) the rest of the family consists of hypothetical proteins none of which have any functional information. mTERF is a multizipper protein possessing three putative leucine zippers one of which is bipartite. The protein binds DNA as a monomer. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €Åpfam02537, CRCB, CrcB-like protein, Camphor Resistance (CrcB). CRCB is a family of bacterial integral membrane proteins with four TMs.. Over expression in E. coli also leads to camphor resistance.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚Jpfam02538, Hydantoinase_B, Hydantoinase B/oxoprolinase. This family includes N-methylhydaintoinase B which converts hydantoin to N-carbamyl-amino acids, and 5-oxoprolinase EC:3.5.2.9 which catalyzes the formation of L-glutamate from 5-oxo-L-proline. These enzymes are part of the oxoprolinase family and are related to pfam01968.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €¹pfam02540, NAD_synthase, NAD synthase. NAD synthase (EC:6.3.5.1) is involved in the de novo synthesis of NAD and is induced by stress factors such as heat shock and glucose limitation.¡€0€ª€0€ €CDD¡€ €H^¢€0€0€ €Ëpfam02541, Ppx-GppA, Ppx/GppA phosphatase family. This family consists of the N-terminal region of exopolyphosphatase (Ppx) EC:3.6.1.11 and guanosine pentaphosphate phospho-hydrolase (GppA) EC:3.6.1.40.¡€0€ª€0€ €CDD¡€ €H_¢€0€0€ €xpfam02542, YgbB, YgbB family. The ygbB protein is a putative enzyme of deoxy-xylulose pathway (terpenoid biosynthesis).¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚ÿpfam02543, Carbam_trans_N, Carbamoyltransferase N-terminus. This domain is found in NodU from Rhizobium, CmcH from Nocardia lactamdurans and the bifunctional carbamoyltransferase TobZ from Streptoalloteichus tenebrarius. NodU a Rhizobium nodulation protein involved in the synthesis of nodulation factors has 6-O-carbamoyltransferase-like activity. CmcH is involved in cephamycin (antibiotic) biosynthesis and has 3-hydroxymethylcephem carbamoyltransferase activity, EC:2.1.3.7 catalyzing the reaction: Carbamoyl phosphate + 3-hydroxymethylceph-3-EM-4-carboxylate <=> phosphate + 3-carbamoyloxymethylcephem. TobZ functions as an ATP carbamoyltransferase and tobramycin carbamoyltransferase. These proteins contain two domains, this is the larger, N-terminal, domain.¡€0€ª€0€ €CDD¡€ €Ha¢€0€0€ €‚3pfam02544, Steroid_dh, 3-oxo-5-alpha-steroid 4-dehydrogenase. This family consists of 3-oxo-5-alpha-steroid 4-dehydrogenases, EC:1.3.99.5 Also known as Steroid 5-alpha-reductase, the reaction catalyzed by this enzyme is: 3-oxo-5-alpha-steroid + acceptor <=> 3-oxo-delta(4)-steroid + reduced acceptor. The Steroid 5-alpha-reductase enzyme is responsible for the formation of dihydrotestosterone, this hormone promotes the differentiation of male external genitalia and the prostate during fetal development. In humans mutations in this enzyme can cause a form of male pseudohermaphorditism in which the external genitalia and prostate fail to develop normally. A related enzyme is also found in plants is DET2, a steroid reductase from Arabidopsis. Mutations in this enzyme cause defects in light-regulated development.¡€0€ª€0€ €CDD¡€ €Õ㢀0€0€ €xpfam02545, Maf, Maf-like protein. Maf is a putative inhibitor of septum formation in eukaryotes, bacteria, and archaea.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚pfam02547, Queuosine_synth, Queuosine biosynthesis protein. Queuosine (Q) biosynthesis protein, or S-adenosylmethionine:tRNA -ribosyltransferase-isomerase, is required for the synthesis of the queuosine precursor (oQ). It catalyzes the transfer and isomerisation of the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to form epoxyqueuosine (oQ-tRNA). Q is a hypermodified nucleoside usually found at the first position of the anticodon of asparagine, aspartate, histidine, and tyrosine tRNAs. In Streptococcus gordonii, QueA has been shown to play a role in the regulation of arginine deiminase genes.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €µpfam02548, Pantoate_transf, Ketopantoate hydroxymethyltransferase. Ketopantoate hydroxymethyltransferase (EC:2.1.2.11) is the first enzyme in the pantothenate biosynthesis pathway.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚pfam02550, AcetylCoA_hydro, Acetyl-CoA hydrolase/transferase N-terminal domain. This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase EC:3.1.2.1 catalyzes the formation of acetate from acetyl-CoA, CoA transferase (CAT1) EC:2.8.3.- produces succinyl-CoA, and acetate-CoA transferase EC:2.8.3.8 utilizes acyl-CoA and acetate to form acetyl-CoA.¡€0€ª€0€ €CDD¡€ €Õ碀0€0€ €¯pfam02551, Acyl_CoA_thio, Acyl-CoA thioesterase. This family represents the thioesterase II domain. Two copies of this domain are found in a number of acyl-CoA thioesterases.¡€0€ª€0€ €CDD¡€ €´ ¢€0€0€ €‚7pfam02552, CO_dh, CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit. This family consists of Carbon monoxide dehydrogenase I/II beta subunit EC:1.2.99.2 and acetyl-CoA synthase epsilon subunit. Carbon monoxide beta subunit catalyzes the reaction: CO + H2O + acceptor <=> CO2 + reduced acceptor.¡€0€ª€0€ €CDD¡€ €Õ颀0€0€ €‚Npfam02553, CbiN, Cobalt transport protein component CbiN. CbiN is part of the active cobalt transport system involved in uptake of cobalt in to the cell involved with cobalamin biosynthesis (vitamin B12). It has been suggested that CbiN may function as the periplasmic binding protein component of the active cobalt transport system.¡€0€ª€0€ €CDD¡€ €´!¢€0€0€ €Êpfam02554, CstA, Carbon starvation protein CstA. This family consists of Carbon starvation protein CstA a predicted membrane protein. It has been suggested that CstA is involved in peptide utilisation.¡€0€ª€0€ €CDD¡€ €´"¢€0€0€ €Êpfam02556, SecB, Preprotein translocase subunit SecB. This family consists of preprotein translocase subunit SecB. SecB is required for the normal export of envelope proteins out of the cell cytoplasm.¡€0€ª€0€ €CDD¡€ €´#¢€0€0€ €7pfam02557, VanY, D-alanyl-D-alanine carboxypeptidase. ¡€0€ª€0€ €CDD¡€ €´$¢€0€0€ €‚ pfam02558, ApbA, Ketopantoate reductase PanE/ApbA. This is a family of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, EC:1.1.1.169. The reaction catalyzed by this enzyme is: (R)-pantoate + NADP(+) <=> 2-dehydropantoate + NADPH. AbpA catalyzes the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway. ApbA and PanE are allelic. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway.¡€0€ª€0€ €CDD¡€ €´%¢€0€0€ €‚Žpfam02559, CarD_CdnL_TRCF, CarD-like/TRCF domain. CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain, CdnL. CarD interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF (transcription-repair-coupling factor) proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase. The family includes members otherwise referred to as CdnL, for CarD N-terminal like, whichdiffer functionally from CarD. The TRCF domain mentioned above is the RNA polymerase-interacting domain or RID.¡€0€ª€0€ €CDD¡€ €´&¢€0€0€ €‚qpfam02560, Cyanate_lyase, Cyanate lyase C-terminal domain. Cyanate lyase (also known as cyanase) EC:4.2.1.104 is responsible for the hydrolysis of cyanate, allowing organisms that possess the enzyme to overcome the toxicity of environmental cyanate. This enzyme is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain.¡€0€ª€0€ €CDD¡€ €´'¢€0€0€ €°pfam02561, FliS, Flagellar protein FliS. FliS is coded for by the FliD operon and is transcribed in conjunction with FliD and FliT, however this protein has no known function.¡€0€ª€0€ €CDD¡€ €´(¢€0€0€ €€pfam02562, PhoH, PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation.¡€0€ª€0€ €CDD¡€ €´)¢€0€0€ €¤pfam02563, Poly_export, Polysaccharide biosynthesis/export protein. This is a family of periplasmic proteins involved in polysaccharide biosynthesis and/or export.¡€0€ª€0€ €CDD¡€ €´*¢€0€0€ €•pfam02565, RecO_C, Recombination protein O C terminal. Recombination protein O (RecO) is involved in DNA repair and pfam00470 pathway recombination.¡€0€ª€0€ €CDD¡€ €´+¢€0€0€ €üpfam02566, OsmC, OsmC-like protein. Osmotically inducible protein C (OsmC) is a stress -induced protein found in E. Coli. This family also contains a organic hydroperoxide detoxification protein that has a novel pattern of oxidative stress regulation.¡€0€ª€0€ €CDD¡€ €´,¢€0€0€ €‚:pfam02567, PhzC-PhzF, Phenazine biosynthesis-like protein. PhzC/PhzF is involved in dimerisation of two 2,3-dihydro-3-oxo-anthranilic acid molecules to create PCA by P. fluorescens. This family also contains uncharacterized Mycobacterial proteins, though there is no significant sequence similarity to pfam00303 members. This family appears to be distantly related to pfam01678, including containing a weak internal duplication. However members of this family do not contain the conserved cysteines that are hypothesized to be active site residues (Bateman A pers obs).¡€0€ª€0€ €CDD¡€ €Hr¢€0€0€ €„pfam02568, ThiI, Thiamine biosynthesis protein (ThiI). ThiI is required for thiazole synthesis, required for thiamine biosynthesis.¡€0€ª€0€ €CDD¡€ €Hs¢€0€0€ €Ìpfam02569, Pantoate_ligase, Pantoate-beta-alanine ligase. Pantoate-beta-alanine ligase, also know as pantothenate synthase, (EC:6.3.2.1) catalyzes the formation of pantothenate from pantoate and alanine.¡€0€ª€0€ €CDD¡€ €´-¢€0€0€ €‚Hpfam02570, CbiC, Precorrin-8X methylmutase. This is a family Precorrin-8X methylmutases also known as Precorrin isomerase, CbiC/CobH, EC:5.4.1.2. This enzyme catalyzes the reaction: Precorrin-8X <=> hydrogenobyrinate. This enzyme is part of the Cobalamin (vitamin B12) biosynthetic pathway and catalyzes a methyl rearrangement.¡€0€ª€0€ €CDD¡€ €´.¢€0€0€ €‚"pfam02571, CbiJ, Precorrin-6x reductase CbiJ/CobK. This family consists of Precorrin-6x reductase EC:1.3.1.54. This enzyme catalyzes the reaction: precorrin-6Y + NADP(+) <=> precorrin-6X + NADPH. CbiJ and CobK both catalyze the reduction of macocycle in the colbalmin biosynthesis pathway.¡€0€ª€0€ €CDD¡€ €´/¢€0€0€ €‚rpfam02572, CobA_CobO_BtuR, ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin adenosyltransferase, EC:2.5.1.17, involved in cobalamin (vitamin B12) biosynthesis. These enzymes catalyze the adenosylation reaction: ATP + cob(I)alamin + H2O <=> phosphate + diphosphate + adenosylcobalamin.¡€0€ª€0€ €CDD¡€ €´0¢€0€0€ €‚[pfam02574, S-methyl_trans, Homocysteine S-methyltransferase. This is a family of related homocysteine S-methyltransferases enzymes: 5-methyltetrahydrofolate--homocysteine S-methyltransferases also known EC:2.1.1.13; Betaine--homocysteine S-methyltransferase (vitamin B12 dependent), EC:2.1.1.5; and Homocysteine S-methyltransferase, EC:2.1.1.10,.¡€0€ª€0€ €CDD¡€ €´1¢€0€0€ €‚Wpfam02575, YbaB_DNA_bd, YbaB/EbfC DNA-binding family. This is a family of DNA-binding proteins. Members of this family form homodimers which bind DNA via a tweezer-like structure. The conformation of the DNA is changed when bound to these proteins. In bacteria, these proteins may play a role in DNA replication-recovery following DNA damage.¡€0€ª€0€ €CDD¡€ €´2¢€0€0€ €>pfam02576, DUF150, Putative ribosome maturation factor RimP. ¡€0€ª€0€ €CDD¡€ €Hz¢€0€0€ €‚pfam02577, DNase-RNase, Bifunctional nuclease. This family is a bifunctional nuclease, with both DNase and RNase activity. It forms a wedge-shaped dimer, with each monomer being triangular in shape. A large groove at the thick end of the wedge contains a possible active site.¡€0€ª€0€ €CDD¡€ €´3¢€0€0€ €‚npfam02578, Cu-oxidase_4, Multi-copper polyphenol oxidoreductase laccase. Laccases are multi-copper oxidoreductases able to oxidise a wide variety of phenolic and non-phenolic compounds and are widely distributed among both prokaryotes and eukaryotes. There are two main active catalytic sites with conserved histidines that are capable of binding four copper atoms.¡€0€ª€0€ €CDD¡€ €´4¢€0€0€ €‚„pfam02579, Nitro_FeMo-Co, Dinitrogenase iron-molybdenum cofactor. This family contains several NIF (B, Y and X) proteins which are iron-molybdenum cofactors (FeMo-co) in the dinitrogenase enzyme which catalyzes the reduction of dinitrogen to ammonium. Dinitrogenase is a hetero-tetrameric (alpha(2)beta(2)) enzyme which contains the iron-molybdenum cofactor (FeMo-co) at its active site.¡€0€ª€0€ €CDD¡€ €´5¢€0€0€ €‚pfam02582, DUF155, Uncharacterized ACR, YagE family COG1723. ¡€0€ª€0€ €CDD¡€ €´7¢€0€0€ €‚Æpfam02583, Trns_repr_metal, Metal-sensitive transcriptional repressor. This is a family of metal-sensitive repressors, involved in resistance to metal ions. Members of this family bind copper, nickel or cobalt ions via conserved cysteine and histidine residues. In the absence of metal ions, these proteins bind to promoter regions and repress transcription. When bound to metal ions they are unable to bind DNA, leading to transcriptional derepression.¡€0€ª€0€ €CDD¡€ €´8¢€0€0€ €Õpfam02585, PIG-L, GlcNAc-PI de-N-acetylase. Members of this family are related to PIG-L an N-acetylglucosaminylphosphatidylinositol de-N-acetylase (EC:3.5.1.89) that catalyzes the second step in GPI biosynthesis.¡€0€ª€0€ €CDD¡€ €´9¢€0€0€ €‚õpfam02586, SRAP, SOS response associated peptidase (SRAP). The SRAP family functions as a DNA-associated autoproteolytic switch that recruits diverse repair enzymes onto DNA damage. We propose that the human protein Q96FZ2:UniProtKB, the eukaryotic member of the SRAP family, which has been recently shown to bind specifically to DNA with 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine, is a sensor for these oxidized bases generated by the TET (tetrahedral aminopeptidase of the M42 family) enzymes from methylcytosine. Hence, its autoproteolytic activity might help it act as a switch that recruits DNA repair enzymes to remove these oxidized methylcytosine species as part of the DNA demethylation pathway downstream of the TET enzymes.¡€0€ª€0€ €CDD¡€ €´:¢€0€0€ € pfam02588, YitT_membrane, Uncharacterized 5xTM membrane BCR, YitT family COG1284. This is probably a bacterial ABC transporter permease (personal obs:Yeats C).¡€0€ª€0€ €CDD¡€ €´;¢€0€0€ €‚apfam02589, LUD_dom, LUD domain. This entry represents a domain found in lactate utilization proteins B (LutB) and C (LutC), as well as several uncharacterized proteins. LutB and LutC are encoded by th conserved LutABC operon in bacteria. They are involved in lactate utilization and is implicated in the oxidative conversion of L-lactate into pyruvate.¡€0€ª€0€ €CDD¡€ €´<¢€0€0€ €pfam02590, SPOUT_MTase, Predicted SPOUT methyltransferase. This family of proteins are predicted to be SPOUT methyltransferases.¡€0€ª€0€ €CDD¡€ €´=¢€0€0€ €‚Äpfam02591, zf-RING_7, C4-type zinc ribbon domain. Zn-ribbon_9 is a Zn-ribbon domain rich in aromatic and positively charged amino acid residues. This C-terminal Zn-ribbon domain consists of two beta-strands acting as a scaffold for the two Zn knuckles. Both pairs of cysteines making up the two Zn knuckles are situated at highly conserved sharp beta-turns, an arrangement that facilitates the tetrahedral coordination of the divalent Zn ion. The two Zn-knuckle cysteine motifs are separated by 20 residues, 9 of which form an alpha-helix (helix 4).Structural modelling suggests this domain may bind nucleic acids. The domain appears to bind flaA-mRNA, thus contributing to flagellum formation and motility.¡€0€ª€0€ €CDD¡€ €´>¢€0€0€ €8pfam02592, Vut_1, Putative vitamin uptake transporter. ¡€0€ª€0€ €CDD¡€ €´?¢€0€0€ €‚|pfam02593, DUF166, Domain of unknown function. This family catalyzes the synthesis of thymidine monophosphate (dTMP) from deoxyuridine monophosphate (dUMP). The physiological co-substrate has not yet been identified. Previous designation of this famliy as being thymidylate synthase from one paper, PMID:10436953, has been shown to be erroneous. The proteins are uncharacterized.¡€0€ª€0€ €CDD¡€ €´@¢€0€0€ €>pfam02594, DUF167, Uncharacterized ACR, YggU family COG1872. ¡€0€ª€0€ €CDD¡€ €´A¢€0€0€ €Upfam02595, Gly_kinase, Glycerate kinase family. This is family of Glycerate kinases.¡€0€ª€0€ €CDD¡€ €´B¢€0€0€ €3pfam02596, DUF169, Uncharacterized ArCR, COG2043. ¡€0€ª€0€ €CDD¡€ €´C¢€0€0€ €‚"pfam02597, ThiS, ThiS family. ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in E. coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalyzed by IscS. MoaD, a protein involved sulphur transfer in molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.¡€0€ª€0€ €CDD¡€ €´D¢€0€0€ €‚@pfam02598, Methyltrn_RNA_3, Putative RNA methyltransferase. This family has a TIM barrel-like fold with a deep C-terminal trefoil knot. The arrangement of its hydrophilic and hydrophobic surfaces are opposite to that of the classic TIM barrel proteins. It is likely to bind RNA, and may function as a methyltransferase.¡€0€ª€0€ €CDD¡€ €´E¢€0€0€ €‚|pfam02599, CsrA, Global regulator protein family. This is a family of global regulator proteins. This protein is a RNA-binding protein and a global regulator of carbohydrate metabolism genes facilitating mRNA decay. In E. coli CsrA binds the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara RmsA has been shown to regulate the production of virulence determinants, such extracellular enzymes. RmsA binds to RmsB regulatory RNA.¡€0€ª€0€ €CDD¡€ €´F¢€0€0€ €‚âpfam02600, DsbB, Disulfide bond formation protein DsbB. This family consists of disulfide bond formation protein DsbB from bacteria. The DsbB protein oxidises the periplasmic protein DsbA which in turn oxidises cysteines in other periplasmic proteins in order to make disulfide bonds. DsbB acts as a redox potential transducer across the cytoplasmic membrane and is an integral membrane protein. DsbB posses six cysteines four of which are necessary for it proper function in vivo.¡€0€ª€0€ €CDD¡€ €´G¢€0€0€ €‚Apfam02601, Exonuc_VII_L, Exonuclease VII, large subunit. This family consist of exonuclease VII, large subunit EC:3.1.11.6 This enzyme catalyzes exonucleolytic cleavage in either 5'->3' or 3'->5' direction to yield 5'-phosphomononucleotides. This exonuclease VII enzyme is composed of one large subunit and 4 small ones.¡€0€ª€0€ €CDD¡€ €´H¢€0€0€ €‚5pfam02602, HEM4, Uroporphyrinogen-III synthase HemD. This family consists of uroporphyrinogen-III synthase HemD EC:4.2.1.75 also known as Hydroxymethylbilane hydrolyase (cyclizing) from eukaryotes, bacteria and archaea. This enzyme catalyzes the reaction: Hydroxymethylbilane <=> uroporphyrinogen-III + H(2)O. Some members of this family are multi-functional proteins possessing other enzyme activities related to porphyrin biosynthesis, such as HemD with pfam00590, however the aligned region corresponds with the uroporphyrinogen-III synthase EC:4.2.1.75 activity only. Uroporphyrinogen-III synthase is the fourth enzyme in the heme pathway. Mutant forms of the Uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria in humans a recessive inborn error of metabolism also known as Gunther disease.¡€0€ª€0€ €CDD¡€ €´I¢€0€0€ €‚2pfam02603, Hpr_kinase_N, HPr Serine kinase N terminus. This family represents the N-terminal region of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phospho-relay system in control of carbon catabolic repression in bacteria. This kinase in unusual in that it recognizes the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The blades are formed by two N-terminal domains each, and the compact central hub assembles the C-terminal kinase domains.¡€0€ª€0€ €CDD¡€ €´J¢€0€0€ €‚Épfam02604, PhdYeFM_antitox, Antitoxin Phd_YefM, type II toxin-antitoxin system. Members of this family act as antitoxins in type II toxin-antitoxin systems. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin. This domain complexes with Txe toxins containing pfam06769, Fic/DOC toxins containing pfam02661 and YafO toxins containing pfam13957.¡€0€ª€0€ €CDD¡€ €´K¢€0€0€ €‚!pfam02605, PsaL, Photosystem I reaction centre subunit XI. This family consists of the photosystem I reaction centre subunit XI, PsaL, from plants and bacteria. PsaL is one of the smaller subunits in photosystem I with only two transmembrane alpha helices and interacts closely with PsaI.¡€0€ª€0€ €CDD¡€ €´L¢€0€0€ €‚pfam02606, LpxK, Tetraacyldisaccharide-1-P 4'-kinase. This family consists of tetraacyldisaccharide-1-P 4'-kinase also known as Lipid-A 4'-kinase or Lipid A biosynthesis protein LpxK, EC:2.7.1.130. This enzyme catalyzes the reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-D -glucosaminyl-(beta-D-1,6)-2,3-bis(3-hydroxytetradecanoyl)-D-glu cosam inyl beta-phosphate <=> ADP + 2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D- glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate. This enzyme is involved in the synthesis of lipid A portion of the bacterial lipopolysaccharide layer (LPS). The family contains a P-loop motif at the N terminus.¡€0€ª€0€ €CDD¡€ €´M¢€0€0€ €‚ˆpfam02607, B12-binding_2, B12 binding domain. This B12 binding domain is found in methionine synthase EC:2.1.1.13, and other shorter proteins that bind to B12. This domain is always found to the N-terminus of pfam02310. The structure of this domain is known, it is a 4 helix bundle. Many of the conserved residues in this domain are involved in B12 binding, such as those in the MXXVG motif.¡€0€ª€0€ €CDD¡€ €´N¢€0€0€ €‚Ñpfam02608, Bmp, ABC transporter substrate-binding protein PnrA-like. Proteins containing this domain were originally annotated as basic membrane lipoproteins. However, several proteins containing this domain were later predicted as ABC transporter substrate-binding proteins, such as PnrA (also known as TmpC or TP0319) and RfuA (also known as Tpn38 or TP0298) from Treponema pallidum. RfuA transports purine nucleosides, while RfuA transports riboflavin. Proteins containing this domain also include Med from Bacillus subtilis. Med was annotated as a transcriptional activator protein that regulates comK. This domain can also found at the N terminus of glutamate receptor-like proteins from Dictyostelium (slime mold).¡€0€ª€0€ €CDD¡€ €H˜¢€0€0€ €‚@pfam02609, Exonuc_VII_S, Exonuclease VII small subunit. This family consist of exonuclease VII, small subunit EC:3.1.11.6 This enzyme catalyzes exonucleolytic cleavage in either 5'->3' or 3'->5' direction to yield 5'-phosphomononucleotides. This exonuclease VII enzyme is composed of one large subunit and 4 small ones.¡€0€ª€0€ €CDD¡€ €´O¢€0€0€ €‚vpfam02610, Arabinose_Isome, L-arabinose isomerase. This is a family of L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyze the reaction: L-arabinose <=> L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme.¡€0€ª€0€ €CDD¡€ €´P¢€0€0€ €Ïpfam02611, CDH, CDP-diacylglycerol pyrophosphatase. This is a family of CDP-diacylglycerol pyrophosphatases, EC:3.6.1.26. This enzyme catalyzes the reaction CDP-diacylglycerol + H2O <=> CMP + phosphatidate.¡€0€ª€0€ €CDD¡€ €´Q¢€0€0€ €‚àpfam02613, Nitrate_red_del, Nitrate reductase delta subunit. This family is the delta subunit of the nitrate reductase enzyme, The delta subunit is not part of the nitrate reductase enzyme but is most likely needed for assembly of the multi-subunit enzyme complex. In the absence of the delta subunit the core alpha beta enzyme complex is unstable. The delta subunit is essential for enzyme activity in vivo and in vitro. The nitrate reductase enzyme, EC:1.7.99.4 catalyze the conversion of nitrite to nitrate via the reduction of an acceptor. The nitrate reductase enzyme is composed of three subunits. Nitrate is the most widely used alternative electron acceptor after oxygen. This family also now contains the family TorD, a family of cytoplasmic chaperone proteins; like many prokaryotic molybdoenzymes, the TMAO reductase (TorA) of Escherichia coli requires the insertion of a bis(molybdopterin guanine dinucleotide) molybdenum (bis(MGD)Mo) cofactor in its catalytic site to be active and translocated to the periplasm. The TorD chaperone increases apoTorA activation up to four-fold, allowing maturation of most of the apoprotein. Therefore TorD is involved in the first step of TorA maturation to make it competent to receive the cofactor.¡€0€ª€0€ €CDD¡€ €´R¢€0€0€ €‚Çpfam02614, UxaC, Glucuronate isomerase. This is a family of Glucuronate isomerases also known as D-glucuronate isomerase, uronic isomerase, uronate isomerase, or uronic acid isomerase, EC:5.3.1.12. This enzyme catalyzes the reactions: D-glucuronate <=> D-fructuronate and D-galacturonate <=> D-tagaturonate. It is not however clear where the experimental evidence for this functional assignment came from and thus this family has no literature reference.¡€0€ª€0€ €CDD¡€ €´S¢€0€0€ €‚¡pfam02615, Ldh_2, Malate/L-lactate dehydrogenase. This family consists of bacterial and archaeal Malate/L-lactate dehydrogenase. L-lactate dehydrogenase, EC:1.1.1.27, catalyzes the reaction (S)-lactate + NAD(+) <=> pyruvate + NADH. Malate dehydrogenase, EC:1.1.1.37 and EC:1.1.1.82, catalyzes the reactions: (S)-malate + NAD(+) <=> oxaloacetate + NADH, and (S)-malate + NADP(+) <=> oxaloacetate + NADPH respectively.¡€0€ª€0€ €CDD¡€ €´T¢€0€0€ €‚Ãpfam02616, SMC_ScpA, Segregation and condensation protein ScpA. This is a family of proteins that from part of the condensin complex that regulates chromosome segregation. This is the A subunit, which binds to the ScpB subunit, pfam04079, and SMC, pfam02463, to participate in chromosomal partition during cell division. The condensin complex pulls DNA away from the mid-cell into both cell halves. These proteins are part of the Kleisin superfamily.¡€0€ª€0€ €CDD¡€ €HŸ¢€0€0€ €‚pfam02617, ClpS, ATP-dependent Clp protease adaptor protein ClpS. In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins.¡€0€ª€0€ €CDD¡€ €´U¢€0€0€ €‚7pfam02618, YceG, YceG-like family. This family of proteins is found in bacteria. Proteins in this family are typically between 332 and 389 amino acids in length. This family was previously incorrectly annotated and names as aminodeoxychorismate lyase. The structure of YceG was solved by X-ray crystallography.¡€0€ª€0€ €CDD¡€ €´V¢€0€0€ €2pfam02620, DUF177, Uncharacterized ACR, COG1399. ¡€0€ª€0€ €CDD¡€ €´W¢€0€0€ €‚%pfam02621, VitK2_biosynth, Menaquinone biosynthesis. This family includes two enzymes which are involved in menaquinone biosynthesis. One which catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate, and one which may be involved in the conversion of chorismate to futalosine. These enzymes comprise two domains with alpha/beta structures, a large domain and a small domain. A pocket between the two domains may form the active site, a conserved histidine located within this pocket could be the catalytic base.¡€0€ª€0€ €CDD¡€ €´X¢€0€0€ €2pfam02622, DUF179, Uncharacterized ACR, COG1678. ¡€0€ª€0€ €CDD¡€ €´Y¢€0€0€ €‚­pfam02623, FliW, FliW protein. The protein BSU35380 from Bacillus subtilis (renamed FliW) was characterized as being a flagellar assembly factor. Experimental characterization was also carried out in Treponema pallidum (TP0658). In Campylobacter jejuni, Cj1075 has been shown to be involved in motility and flagellin biosynthesis. The two paralogues in Helicobacter pylori (HP1154 and HP1377) were found to be able to bind to flagellin. FliW proteins are involved in flagellar assembly. FliW is part of a three-part feedback loop: in Bacillus subtilis FliW inhibits CsrA (an RNA-binding protein) which inhibits FliC translation; hence FliW is required for FliC (flagellin) production.¡€0€ª€0€ €CDD¡€ €´Z¢€0€0€ €‚epfam02624, YcaO, YcaO cyclodehydratase, ATP-ad Mg2+-binding. YcaO is an ATP- an Mg2+-binding protein involved in the peptidic biosynthesis of azoline. There three motifs involved in the binding are, in UniProtKB:P75838, 71-79: Sx3ExxER, 184-203: Sx6Ex3Qx3ExxER, and 286-290: RxxxE. Three slightly different functional families are represented in this family, proteins involved in TOMM (thiazole/oxazole-modified microcin) biogenesis, non-TOMM proteins such as UniProtKB:P75838, and TfuA-associated non-TOMM proteins involved in trifolitoxin biosynthesis. UniProtKB:P75838 hydrolyses ATP to AMP and pyrophosphate.¡€0€ª€0€ €CDD¡€ €´[¢€0€0€ €‚pfam02625, XdhC_CoxI, XdhC and CoxI family. This domain is often found in association with an NAD-binding region, related to TrkA-N (pfam02254; personal obs:C. Yeats). XdhC is believed to be involved in the attachment of molybdenum to Xanthine Dehydrogenase.¡€0€ª€0€ €CDD¡€ €´\¢€0€0€ €‚¼pfam02626, CT_A_B, Carboxyltransferase domain, subdomain A and B. Urea carboxylase (UC) catalyzes a two-step, ATP- and biotin-dependent carboxylation reaction of urea. It is composed of biotin carboxylase (BC), carboxyltransferase (CT), and biotin carboxyl carrier protein (BCCP) domains. The CT domain of UC consists of four subdomains, named A, B, C and D. This domain covers the A and B subdomains of the CT domain. This domain covers the whole length of KipA (kinase A) from Bacillus subtilis. It can also be found in S. cerevisiae urea amidolyase Dur1,2, which is a multifunctional biotin-dependent enzyme with domains for urea carboxylase and allophanate (urea carboxylate) hydrolase activity.¡€0€ª€0€ €CDD¡€ €´]¢€0€0€ €‚{pfam02627, CMD, Carboxymuconolactone decarboxylase family. Carboxymuconolactone decarboxylase (CMD) EC:4.1.1.44 is involved in protocatechuate catabolism. In some bacteria a gene fusion event leads to expression of CMD with a hydrolase involved in the same pathway. In these bifunctional proteins CMD represents the C-terminal domain, pfam00561 represents the N-terminal domain.¡€0€ª€0€ €CDD¡€ €´^¢€0€0€ €õpfam02628, COX15-CtaA, Cytochrome oxidase assembly protein. This is a family of integral membrane proteins. CtaA is required for cytochrome aa3 oxidase assembly in Bacillus subtilis. COX15 is required for cytochrome c oxidase assembly in yeast.¡€0€ª€0€ €CDD¡€ €´_¢€0€0€ €µpfam02629, CoA_binding, CoA binding domain. This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases.¡€0€ª€0€ €CDD¡€ €´`¢€0€0€ €‚‘pfam02630, SCO1-SenC, SCO1/SenC. This family is involved in biogenesis of respiratory and photosynthetic systems. SCO1 is required for a post-translational step in the accumulation of subunits COXI and COXII of cytochrome c oxidase. SenC is required for optimal cytochrome c oxidase activity and maximal induction of genes encoding the light-harvesting and reaction centre complexes of R. capsulatus.¡€0€ª€0€ €CDD¡€ €Ö)¢€0€0€ €µpfam02631, RecX, RecX family. RecX is a putative bacterial regulatory protein. The gene encoding RecX is found downstream of recA, and is thought to interact with the RecA protein.¡€0€ª€0€ €CDD¡€ €´a¢€0€0€ €Ôpfam02632, BioY, BioY family. A number of bacterial genes are involved in bioconversion of pimelate into dethiobiotin. BioY is a component of the BioMNY transport system involved in biotin uptake in prokaryotes.¡€0€ª€0€ €CDD¡€ €´b¢€0€0€ €¢pfam02633, Creatininase, Creatinine amidohydrolase. Creatinine amidohydrolase (EC:3.5.2.10), or creatininase, catalyzes the hydrolysis of creatinine to creatine.¡€0€ª€0€ €CDD¡€ €´c¢€0€0€ €‚†pfam02634, FdhD-NarQ, FdhD/NarQ family. A pan-bacterial lineage of proteins. Nitrate assimilation protein, NarQ, and FdhD are required for formate dehydrogenase activity. Structurally, they possess a deaminase fold with a characteristic binding pocket, suggesting that they might bind a nucleotide or related molecule allosterically to regulate the formate dehydrogenase catalytic subunit.¡€0€ª€0€ €CDD¡€ €´d¢€0€0€ €”pfam02635, DrsE, DsrE/DsrF-like family. DsrE is a small soluble protein involved in intracellular sulfur reduction. This family also includes DsrF.¡€0€ª€0€ €CDD¡€ €´e¢€0€0€ €òpfam02636, Methyltransf_28, Putative S-adenosyl-L-methionine-dependent methyltransferase. This family is a putative S-adenosyl-L-methionine (SAM)-dependent methyltransferase. In eukaryotes it plays a role in mitochondrial complex I activity.¡€0€ª€0€ €CDD¡€ €´f¢€0€0€ €Åpfam02637, GatB_Yqey, GatB domain. This domain is found in GatB. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB, which transamidates Glu-tRNA to Gln-tRNA.¡€0€ª€0€ €CDD¡€ €´g¢€0€0€ €žpfam02638, GHL10, Glycosyl hydrolase-like 10. This is family of bacterial glycosyl-hydrolase-like proteins falling into the family GHL10 as described above,.¡€0€ª€0€ €CDD¡€ €Ö1¢€0€0€ €Cpfam02639, DUF188, Uncharacterized BCR, YaiI/YqxD family COG1671. ¡€0€ª€0€ €CDD¡€ €´h¢€0€0€ €2pfam02641, DUF190, Uncharacterized ACR, COG1993. ¡€0€ª€0€ €CDD¡€ €´i¢€0€0€ €‚,pfam02643, DUF192, Uncharacterized ACR, COG1430. Two structures have been solved for members of this large (>500 members) family of bacterial proteins present mostly in environmental bacteria and metagenomes (distant homologs are also present in several Plasmodium species). TOPSAN analysis for Structure 3pjy shows that there is much similarity with the other solved structure, Structure 3m7a, solved for UniProt:Q2GA55 (Saro_0823), a homolog of Thermotoga maritima TM1668, UniProt:Q9X1Z6., The homolog in Caulobacter crescentus (CC1388), UniProt:Q9A8G6, is associated with CspD, a cold shock protein (CC1387), UniProt:Q9A8G7. However, the genomic context of UniProt:Q2GA55 is most conserved with a putative xylose isomerase, suggesting a possible role in extracellular sugar processing. Saro_0821, UniProt:Q2GA57, is annotated as an AMP-dependent synthetase and ligase. Structure 3m7a structure corresponds to the C-terminal (27-165) fragment of the YP_496102 (Saro_0823) protein and it is structurally unique, as the best hits from Dali have a Z-score of 3.8 (1nt0, 2j1t, 3kq4) and it is thus a likely candidate for a new fold. Interestingly, many of the top Dali hits are involved in sugar metabolism. There are no obvious active site-like cavities on the protein surface of 3m7a (http://www.topsan.org/Proteins/JCSG/).¡€0€ª€0€ €CDD¡€ €´j¢€0€0€ €‚^pfam02645, DegV, Uncharacterized protein, DegV family COG1307. The structure of this protein revealed a bound fatty-acid molecule in a pocket between the two protein domains. The structure indicates that this family has the molecular function of fatty-acid binding and may play a role in the cellular functions of fatty acid transport or metabolism.¡€0€ª€0€ €CDD¡€ €´k¢€0€0€ €‚Jpfam02646, RmuC, RmuC family. This family contains several bacterial RmuC DNA recombination proteins. The function of the RMUC protein is unknown but it is suspected that it is either a structural protein that protects DNA against nuclease action, or is itself involved in DNA cleavage at the regions of DNA secondary structures.¡€0€ª€0€ €CDD¡€ €´l¢€0€0€ €‚tpfam02649, GCHY-1, Type I GTP cyclohydrolase folE2. This is a family of prokaryotic proteins with type I GTP cyclohydrolase activity. GTP cyclohydrolase I is the first enzyme of the de novo tetrahydrofolate biosynthetic pathway present in bacteria, fungi, and plants, and encoded in Escherichia coli by the folE gene; it is also the first enzyme of the biopterin (BH4) pathway in Homo sapiens. The invariate, highly conserved glutamate residue at position 216 in Neisseria gonorrhoeae FolE2 is likely to be the substrate ligand and the metal ligand is likely to be the cysteine at position 147. The enzyme is Zinc 2+ dependent.¡€0€ª€0€ €CDD¡€ €´m¢€0€0€ €‚0pfam02650, HTH_WhiA, WhiA C-terminal HTH domain. This domain is found at the C-terminus of the sporulation regulator WhiA. It is predicted to form a DNA-binding helix-turn-helix structure. The WhiA protein also contains two N-terminal domains that are distant homologs of LAGLIDADG homing endonucleases.¡€0€ª€0€ €CDD¡€ €´n¢€0€0€ €Špfam02652, Lactate_perm, L-lactate permease. L-lactate permease is an integral membrane protein probably involved in L-lactate transport.¡€0€ª€0€ €CDD¡€ €Hº¢€0€0€ €‚Špfam02653, BPD_transp_2, Branched-chain amino acid transport system / permease component. This is a large family mainly comprising high-affinity branched-chain amino acid transporter proteins such as E. coli LivH and LivM, both of which are form the LIV-I transport system. Also found with in this family are proteins from the galactose transport system permease and a ribose transport system.¡€0€ª€0€ €CDD¡€ €H»¢€0€0€ €‚pfam02654, CobS, Cobalamin-5-phosphate synthase. This is family of Colbalmin-5-phosphate synthases, CobS, from bacteria. The CobS enzyme catalyzes the synthesis of AdoCbl-5'-p from AdoCbi-GDP and alpha-ribazole-5'-P. This enzyme is involved in the cobalamin (vitamin B12) biosynthesis pathway in particular the nucleotide loop assembly stage in conjunction with CobC, CobU and CobT.¡€0€ª€0€ €CDD¡€ €´o¢€0€0€ €Ìpfam02655, ATP-grasp_3, ATP-grasp domain. No functional information or experimental verification of function is known in this family. This family appears to be an ATP-grasp domain (Pers. obs. A Bateman).¡€0€ª€0€ €CDD¡€ €H½¢€0€0€ €‚ pfam02656, DUF202, Domain of unknown function (DUF202). This family consists of hypothetical proteins some of which are putative membrane proteins. No functional information or experimental verification of function is known. This domain is around 100 amino acids long.¡€0€ª€0€ €CDD¡€ €´p¢€0€0€ €¢pfam02657, SufE, Fe-S metabolism associated domain. This family consists of the SufE-related proteins. These have been implicated in Fe-S metabolism and export).¡€0€ª€0€ €CDD¡€ €´q¢€0€0€ €‚ìpfam02659, Mntp, Putative manganese efflux pump. MntP is a family of bacterial proteins with a signal peptide and four transmembrane domains. It is a putative manganese efflux pump, since deletion of the gene leads to profound manganese sensitivity and elevated intracellular manganese levels in bacteria. Manganese is a highly important trace nutrient for organisms from bacteria to humans, and acts as an important element in the defense against oxidative stress and as an enzyme cofactor.¡€0€ª€0€ €CDD¡€ €´r¢€0€0€ €Åpfam02660, G3P_acyltransf, Glycerol-3-phosphate acyltransferase. This family of enzymes catalyzes the transfer of an acyl group from acyl-ACP to glycerol-3-phosphate to form lysophosphatidic acid.¡€0€ª€0€ €CDD¡€ €´s¢€0€0€ €‚œpfam02661, Fic, Fic/DOC family. This family consists of the Fic (filamentation induced by cAMP) protein and doc (death on curing). The Fic protein is involved in cell division and is suggested to be involved in the synthesis of PAB or folate, indicating that the Fic protein and cAMP are involved in a regulatory mechanism of cell division via folate metabolism. This family contains a central conserved motif HPFXXGNG in most members. The exact molecular function of these proteins is uncertain. P1 lysogens of Escherichia coli carry the prophage as a stable low copy number plasmid. The frequency with which viable cells cured of prophage are produced is about 10(-5) per cell per generation. A significant part of this remarkable stability can be attributed to a plasmid-encoded mechanism that causes death of cells that have lost P1. In other words, the lysogenic cells appear to be addicted to the presence of the prophage. The plasmid withdrawal response depends on a gene named doc (death on curing) that is represented by this family. Doc induces a reversible growth arrest of E. coli cells by targetting the protein synthesis machinery. Doc hosts the C-terminal domain of its antitoxin partner Phd (prevents host death) through fold complementation, a domain that is intrinsically disordered in solution but that folds into an alpha-helix on binding to Doc.This domain forms complexes with Phd antitoxins containing pfam02604.¡€0€ª€0€ €CDD¡€ €´t¢€0€0€ €‚Èpfam02662, FlpD, Methyl-viologen-reducing hydrogenase, delta subunit. This family consist of methyl-viologen-reducing hydrogenase, delta subunit / heterodisulphide reductase. No specific functions have been assigned to this subunit. The aligned region corresponds to almost the entire delta chain sequence and contains 4 conserved cysteine residues. However, in two Archaeoglobus sequences this region corresponds to only the C-terminus of these proteins.¡€0€ª€0€ €CDD¡€ €´u¢€0€0€ €‚"pfam02663, FmdE, FmdE, Molybdenum formylmethanofuran dehydrogenase operon. This entry represents the FmdE protein that is encode by the molybdenum formylmethanofuran dehydrogenase operon. FmdE does not co-purify with the molybdenum isozyme that is formed by FmdC and FmdB. The domain is typically found as a single copy, but is repeated in some sequence two to three times. It is also common place to find this domain co-occurs with a zinc-beta ribbon domain, suggesting that is may bind nucleic acid and be involved in transcription regulation.¡€0€ª€0€ €CDD¡€ €´v¢€0€0€ €‚‰pfam02664, LuxS, S-Ribosylhomocysteinase (LuxS). This family consists of the LuxS protein involved in autoinducer AI2 synthesis and its hypothetical relatives. S-ribosylhomocysteinase (LuxS) catalyzes the cleavage of the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of type II bacterial quorum sensing molecule.¡€0€ª€0€ €CDD¡€ €´w¢€0€0€ €‚Zpfam02665, Nitrate_red_gam, Nitrate reductase gamma subunit. This family is the gamma subunit of the nitrate reductase enzyme, the gamma subunit is a b-type cytochrome that receives electrons from the quinone pool. It then transfers these via the iron-sulfur clusters of the beta subunit to the molybdenum cofactor found in the alpha subunit. The nitrate reductase enzyme, EC:1.7.99.4 catalyzes the conversion of nitrite to nitrate via the reduction of an acceptor. The nitrate reductase enzyme is composed of three subunits. Nitrate is the most widely used alternative electron acceptor after oxygen.¡€0€ª€0€ €CDD¡€ €´x¢€0€0€ €‚~pfam02666, PS_Dcarbxylase, Phosphatidylserine decarboxylase. This is a family of phosphatidylserine decarboxylases, EC:4.1.1.65. These enzymes catalyze the reaction: Phosphatidyl-L-serine <=> phosphatidylethanolamine + CO2. Phosphatidylserine decarboxylase plays a central role in the biosynthesis of aminophospholipids by converting phosphatidylserine to phosphatidylethanolamine.¡€0€ª€0€ €CDD¡€ €´y¢€0€0€ €öpfam02667, SCFA_trans, Short chain fatty acid transporter. This family consists of two sequences annotated as short chain fatty acid transporters, however, there are no references giving details of experimental characterization of this function.¡€0€ª€0€ €CDD¡€ €HÈ¢€0€0€ €‚%pfam02668, TauD, Taurine catabolism dioxygenase TauD, TfdA family. This family consists of taurine catabolism dioxygenases of the TauD, TfdA family. TauD from E. coli is a alpha-ketoglutarate-dependent taurine dioxygenase. This enzyme catalyzes the oxygenolytic release of sulfite from taurine. TfdA from Burkholderia sp. is a 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase. TfdA from Alcaligenes eutrophus JMP134 is a 2,4-dichlorophenoxyacetate monooxygenase. Also included are gamma-Butyrobetaine hydroxylase enzymes EC:1.14.11.1.¡€0€ª€0€ €CDD¡€ €´z¢€0€0€ €‚·pfam02669, KdpC, K+-transporting ATPase, c chain. This family consists of K+-transporting ATPase, c chain, KdpC. KdpC forms strong interactions with the KdpA subunit, serving to assemble and stabilize the Kdp complex. It has been suggested that KdpC could be one of the connecting links between the energy providing subunit KdpB and the K+-transporting subunit KdpA. The K+ transport system actively transports K+ ions via ATP hydrolysis.¡€0€ª€0€ €CDD¡€ €´{¢€0€0€ €‚Ypfam02670, DXP_reductoisom, 1-deoxy-D-xylulose 5-phosphate reductoisomerase. This is a family of 1-deoxy-D-xylulose 5-phosphate reductoisomerases. This enzyme catalyzes the formation of 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose-5-phosphate in the presence of NADPH. This reaction is part of the terpenoid biosynthesis pathway.¡€0€ª€0€ €CDD¡€ €´|¢€0€0€ €‚Kpfam02671, PAH, Paired amphipathic helix repeat. This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-loop-helix motif, which mediate protein-protein interactions.¡€0€ª€0€ €CDD¡€ €´}¢€0€0€ €‚pfam02672, CP12, CP12 domain. The function of this domain is unknown, it does contain three conserved cysteines and a histidine, that suggests this may be a zinc binding domain (Bateman A pers. observation). This domain is found associated with CBS domains in some proteins pfam00571.¡€0€ª€0€ €CDD¡€ €´~¢€0€0€ €‚{pfam02673, BacA, Bacitracin resistance protein BacA. Bacitracin resistance protein (BacA) is a putative undecaprenol kinase. BacA confers resistance to bacitracin, probably by phosphorylation of undecaprenol. More recent studies show that BacA has undecaprenyl pyrophosphate phosphatase activity. Undecaprenyl phosphate is a key lipid intermediate involved in the synthesis of various bacterial cell wall polymers. Bacitracin, a mixture of related cyclic polypeptide antibiotics, is used to treat surface tissue infections. Its primary mode of action is the inhibition of bacterial cell wall synthesis through sequestration of the essential carrier lipid undecaprenyl pyrophosphate, C55-PP, resulting in the loss of cell integrity and lysis. The characteristic phosphatase sequence-motif in this family is likely to be the PGxSRSGG, compared with the PSGH of the PAP family of phosphatases.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €Çpfam02674, Colicin_V, Colicin V production protein. Colicin V production protein is required in E. Coli for colicin V production from plasmid pColV-K30. This protein is coded for in the purF operon.¡€0€ª€0€ €CDD¡€ €´€¢€0€0€ €‚øpfam02675, AdoMet_dc, S-adenosylmethionine decarboxylase. This family contains several S-adenosylmethionine decarboxylase proteins from bacterial and archaebacterial species. S-adenosylmethionine decarboxylase (AdoMetDC), a key enzyme in the biosynthesis of spermidine and spermine, is first synthesized as a proenzyme, which is cleaved post translationally to form alpha and beta subunits. The alpha subunit contains a covalently bound pyruvoyl group derived from serine that is essential for activity.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚«pfam02676, TYW3, Methyltransferase TYW3. The methyltransferase TYW3 (tRNA-yW- synthesising protein 3) has been identified in yeast to be involved in wybutosine (yW) biosynthesis. yW is a complexly modified guanosine residue that contains a tricyclic base and is found at the 3' position adjacent the anticodon of phenylalanine tRNA. TYW3 is an N-4 methylase that methylates yW-86 to yield yW-72 in an Ado-Met-dependent manner.¡€0€ª€0€ €CDD¡€ €´‚¢€0€0€ €2pfam02677, DUF208, Uncharacterized BCR, COG1636. ¡€0€ª€0€ €CDD¡€ €´ƒ¢€0€0€ €‚ãpfam02678, Pirin, Pirin. This family consists of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localized within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures. A tomato homolog of human Pirin has been found to be induced during programmed cell death. Human Pirin interacts with Bcl-3 and NFI and hence is probably involved in the regulation of DNA transcription and replication. It appears to be an Fe(II)-containing member of the Cupin superfamily.¡€0€ª€0€ €CDD¡€ €HÓ¢€0€0€ €‚pfam02679, ComA, (2R)-phospho-3-sulfolactate synthase (ComA). In methanobacteria (2R)-phospho-3-sulfolactate synthase (ComA) catalyzes the first step of the biosynthesis of coenzyme M from phosphoenolpyruvate (P-enolpyruvate). This novel enzyme catalyzes the stereospecific Michael addition of sulfite to P-enolpyruvate, forming L-2-phospho-3-sulfolactate (PSL). It is suggested that the ComA-catalyzed reaction is analogous to those reactions catalyzed by beta-elimination enzymes that proceed through an enolate intermediate.¡€0€ª€0€ €CDD¡€ €´„¢€0€0€ €3pfam02680, DUF211, Uncharacterized ArCR, COG1888. ¡€0€ª€0€ €CDD¡€ €´…¢€0€0€ €rpfam02681, DUF212, Divergent PAP2 family. This family is related to the pfam01569 family (personal obs: C Yeats).¡€0€ª€0€ €CDD¡€ €´†¢€0€0€ €‚Æpfam02682, CT_C_D, Carboxyltransferase domain, subdomain C and D. Urea carboxylase (UC) catalyzes a two-step, ATP- and biotin-dependent carboxylation reaction of urea. It is composed of biotin carboxylase (BC), carboxyltransferase (CT), and biotin carboxyl carrier protein (BCCP) domains. The CT domain of UC consists of four subdomains, named A, B, C and D. This domain covers the C and D subdomains of the CT domain. This domain covers the whole length of kipI (kinase A inhibitor) from Bacillus subtilis. It can also be found in S. cerevisiae urea amidolyase Dur1,2, which is a multifunctional biotin-dependent enzyme with domains for urea carboxylase and allophanate (urea carboxylate) hydrolase activity.¡€0€ª€0€ €CDD¡€ €´‡¢€0€0€ €‚]pfam02683, DsbD, Cytochrome C biogenesis protein transmembrane region. This family consists of the transmembrane (i.e. non-catalytic) region of Cytochrome C biogenesis proteins also known as disulphide interchange proteins. These proteins posses a protein disulphide isomerase like domain that is not found within the aligned region of this family.¡€0€ª€0€ €CDD¡€ €HØ¢€0€0€ €‚ïpfam02684, LpxB, Lipid-A-disaccharide synthetase. This is a family of lipid-A-disaccharide synthetases, EC:2.4.2.128. These enzymes catalyze the reaction: UDP-2,3-bis(3-hydroxytetradecanoyl) glucosamine + 2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate <=> UDP + 2,3-bis(3-hydroxytetradecanoyl)-D-glucosaminyl-1,6 -beta-D-2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate. These enzymes catalyze the fist disaccharide step in the synthesis of lipid-A-disaccharide.¡€0€ª€0€ €CDD¡€ €HÙ¢€0€0€ €Ãpfam02685, Glucokinase, Glucokinase. This is a family of glucokinases or glucose kinases EC:2.7.1.2. These enzymes phosphorylate glucose using ATP as a donor to give glucose-6-phosphate and ADP.¡€0€ª€0€ €CDD¡€ €HÚ¢€0€0€ €‚épfam02686, Glu-tRNAGln, Glu-tRNAGln amidotransferase C subunit. This is a family of Glu-tRNAGln amidotransferase C subunits. The Glu-tRNA Gln amidotransferase enzyme itself is an important translational fidelity mechanism replacing incorrectly charged Glu-tRNAGln with the correct Gln-tRANGln via transmidation of the misacylated Glu-tRNAGln. This activity supplements the lack of glutaminyl-tRNA synthetase activity in gram-positive eubacterteria, cyanobacteria, Archaea, and organelles.¡€0€ª€0€ €CDD¡€ €´ˆ¢€0€0€ €‚ppfam02687, FtsX, FtsX-like permease family. This is a family of predicted permeases and hypothetical transmembrane proteins. Buchnera aphidicola LolC has been shown to transport lipids targeted to the outer membrane across the inner membrane. Both LolC and Streptococcus cristatus TptD have been shown to require ATP. This region contains three transmembrane helices.¡€0€ª€0€ €CDD¡€ €´‰¢€0€0€ €Þpfam02689, Herpes_Helicase, Helicase. This family consists of Helicases from the Herpes viruses. Helicases are responsible for the unwinding of DNA and are essential for replication and completion of the viral life cycle.¡€0€ª€0€ €CDD¡€ €HÝ¢€0€0€ €‚apfam02690, Na_Pi_cotrans, Na+/Pi-cotransporter. This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney the type II renal Na+/Pi-cotransporters protein allows re-absorption of filtered Pi in the proximal tubule.¡€0€ª€0€ €CDD¡€ €´Š¢€0€0€ €þpfam02691, VacA, Vacuolating cyotoxin. This family consists of Vacuolating cyotoxin proteins form Proteobacteria. These proteins are an important virulence determinate in H. pylori and induce cytoplasmic vacuolation in a variety of mammalian cell lines.¡€0€ª€0€ €CDD¡€ €³Ø¢€0€0€ €?pfam02694, UPF0060, Uncharacterized BCR, YnfA/UPF0060 family. ¡€0€ª€0€ €CDD¡€ €³Ù¢€0€0€ €?pfam02696, UPF0061, Uncharacterized ACR, YdiU/UPF0061 family. ¡€0€ª€0€ €CDD¡€ €´‹¢€0€0€ €spfam02697, DUF217, Uncharacterized ACR, COG1753. Structural modelling suggests this domain may bind nucleic acids.¡€0€ª€0€ €CDD¡€ €´Œ¢€0€0€ €‚1pfam02698, DUF218, DUF218 domain. This large family of proteins contains several highly conserved charged amino acids, suggesting this may be an enzymatic domain (Bateman A pers. obs). The family includes SanA, which is involved in Vancomycin resistance. This protein may be involved in murein synthesis.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €6pfam02699, YajC, Preprotein translocase subunit. See.¡€0€ª€0€ €CDD¡€ €´Ž¢€0€0€ €Žpfam02700, PurS, Phosphoribosylformylglycinamidine (FGAM) synthase. This family forms a component of the de novo purine biosynthesis pathway.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €pfam02701, zf-Dof, Dof domain, zinc finger. The Dof domain is a zinc finger DNA-binding domain, that shows resemblance to the Cys2 zinc finger.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €‚Spfam02702, KdpD, Osmosensitive K+ channel His kinase sensor domain. This is a family of KdpD sensor kinase proteins that regulate the kdpFABC operon responsible for potassium transport. The aligned region corresponds to the N-terminal cytoplasmic part of the protein which may be the sensor domain responsible for sensing turgor pressure.¡€0€ª€0€ €CDD¡€ €´‘¢€0€0€ €‚apfam02703, Adeno_E1A, Early E1A protein. This is a family of adenovirus early E1A proteins. The E1A protein is 32 kDa it can however be cleaved to yield the 28 kDa protein. The E1A protein is responsible for the transcriptional activation of the early genes with in the viral genome at the start of the infection process as well as some cellular genes.¡€0€ª€0€ €CDD¡€ €´’¢€0€0€ €‚ˆpfam02704, GASA, Gibberellin regulated protein. This is the GASA gibberellin regulated cysteine rich protein family. The expression of these proteins is up-regulated by the plant hormone gibberellin, most of these proteins have some role in plant development. There are 12 cysteine residues conserved within the alignment giving the potential for these proteins to posses 6 disulphide bonds.¡€0€ª€0€ €CDD¡€ €´“¢€0€0€ €Îpfam02705, K_trans, K+ potassium transporter. This is a family of K+ potassium transporters that are conserved across phyla, having both bacterial (KUP), yeast (HAK), and plant (AtKT) sequences as members.¡€0€ª€0€ €CDD¡€ €´”¢€0€0€ €‚upfam02706, Wzz, Chain length determinant protein. This family includes proteins involved in lipopolysaccharide (lps) biosynthesis. This family comprises the whole length of chain length determinant protein (or wzz protein) that confers a modal distribution of chain length on the O-antigen component of lps. This region is also found as part of bacterial tyrosine kinases.¡€0€ª€0€ €CDD¡€ €´•¢€0€0€ €‚pfam02707, MOSP_N, Major Outer Sheath Protein N-terminal region. This is a family of spirochete major outer sheath protein N-terminal regions. These proteins are present on the bacterial cell surface. In T. denticola the major outer sheath protein (Msp) binds immobilised laminin and fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola.¡€0€ª€0€ €CDD¡€ €Hꢀ0€0€ €‚tpfam02709, Glyco_transf_7C, N-terminal domain of galactosyltransferase. This is the N-terminal domain of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases. EC:2.4.1.90, N-acetyllactosamine synthase; EC:2.4.1.38, Beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase; and EC:2.4.1.22 Lactose synthase. Note that N-acetyllactosamine synthase is a component of Lactose synthase along with alpha-lactalbumin, in the absence of alpha-lactalbumin EC:2.4.1.90 is the catalyzed reaction.¡€0€ª€0€ €CDD¡€ €´–¢€0€0€ €\pfam02710, Hema_HEFG, Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein. ¡€0€ª€0€ €CDD¡€ €H좀0€0€ €ºpfam02711, Pap_E4, E4 protein. This is is a family of Papillomavirus proteins, E4, coded for by ORF4. A splice variant, E1--E4, exists but neither the function of E4 or E1--E4 is known.¡€0€ª€0€ €CDD¡€ €´—¢€0€0€ €êpfam02713, DUF220, Domain of unknown function DUF220. This is family consists of a region in several Arabidopsis thaliana hypothetical proteins none of which have any known function. The aligned region contains two cysteine residues.¡€0€ª€0€ €CDD¡€ €´˜¢€0€0€ €öpfam02714, RSN1_7TM, Calcium-dependent channel, 7TM region, putative phosphate. RSN1_7TM is the seven transmembrane domain region of putative phosphate transporter. The family is the 7TM region of osmosensitive calcium-permeable cation channels.¡€0€ª€0€ €CDD¡€ €´™¢€0€0€ €Õpfam02718, Herpes_UL31, Herpesvirus UL31-like protein. This is a family of Herpesvirus proteins including UL31, UL53, and the product of ORF 69 in some strains. The proteins in this family have no known function.¡€0€ª€0€ €CDD¡€ €´š¢€0€0€ €ùpfam02719, Polysacc_synt_2, Polysaccharide biosynthesis protein. This is a family of diverse bacterial polysaccharide biosynthesis proteins including the CapD protein, WalL protein, mannosyl-transferase, and several putative epimerases (e.g. WbiI).¡€0€ª€0€ €CDD¡€ €´›¢€0€0€ €ùpfam02720, DUF222, Domain of unknown function (DUF222). This family is often found associated to the N-terminus of the HNH endonuclease domain pfam01844. The function of this domain is uncertain. This family has been called the 13E12 repeat family.¡€0€ª€0€ €CDD¡€ €´œ¢€0€0€ €7pfam02721, DUF223, Domain of unknown function DUF223. ¡€0€ª€0€ €CDD¡€ €9:¢€0€0€ €‚pfam02722, MOSP_C, Major Outer Sheath Protein C-terminal region. This is a family of spirochete major outer sheath protein C-terminal regions. These proteins are present on the bacterial cell surface. In T. denticola the major outer sheath protein (Msp) binds immobilised laminin and fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola.¡€0€ª€0€ €CDD¡€ €Hó¢€0€0€ €ùpfam02723, NS3_envE, Non-structural protein NS3/Small envelope protein E. This is a family of small non-structural proteins, well conserved among Coronavirus strains. This protein is also found in murine hepatitis virus as small envelope protein E.¡€0€ª€0€ €CDD¡€ €Hô¢€0€0€ €÷pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. homologs of CDC45 have been identified in human, mouse and smut fungus, among others.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €”pfam02725, Paramyxo_NS_C, Non-structural protein C. This family consists of the polymerase accessory protein C from members of the paramyxoviridae.¡€0€ª€0€ €CDD¡€ €Hö¢€0€0€ €‚Õpfam02727, Cu_amine_oxidN2, Copper amine oxidase, N2 domain. This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ).¡€0€ª€0€ €CDD¡€ €´ž¢€0€0€ €‚Õpfam02728, Cu_amine_oxidN3, Copper amine oxidase, N3 domain. This domain is the second or third structural domain in copper amine oxidases, it is known as the N3 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ).¡€0€ª€0€ €CDD¡€ €´Ÿ¢€0€0€ €\pfam02729, OTCace_N, Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain. ¡€0€ª€0€ €CDD¡€ €´ ¢€0€0€ €‚@pfam02730, AFOR_N, Aldehyde ferredoxin oxidoreductase, N-terminal domain. Aldehyde ferredoxin oxidoreductase (AOR) catalyzes the reversible oxidation of aldehydes to their corresponding carboxylic acids with their accompanying reduction of the redox protein ferredoxin. This domain interacts with the tungsten cofactor.¡€0€ª€0€ €CDD¡€ €´¡¢€0€0€ €Rpfam02731, SKIP_SNW, SKIP/SNW domain. This domain is found in chromatin proteins.¡€0€ª€0€ €CDD¡€ €´¢¢€0€0€ €êpfam02732, ERCC4, ERCC4 domain. This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.¡€0€ª€0€ €CDD¡€ €´£¢€0€0€ €kpfam02733, Dak1, Dak1 domain. This is the kinase domain of the dihydroxyacetone kinase family EC:2.7.1.29.¡€0€ª€0€ €CDD¡€ €´¤¢€0€0€ €upfam02734, Dak2, DAK2 domain. This domain is the predicted phosphatase domain of the dihydroxyacetone kinase family.¡€0€ª€0€ €CDD¡€ €´¥¢€0€0€ €‚„pfam02735, Ku, Ku70/Ku80 beta-barrel domain. The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 and Ku80 proteins that form a DNA binding heterodimer.¡€0€ª€0€ €CDD¡€ €´¦¢€0€0€ €½pfam02736, Myosin_N, Myosin N-terminal SH3-like domain. This domain has an SH3-like fold. It is found at the N-terminus of many but not all myosins. The function of this domain is unknown.¡€0€ª€0€ €CDD¡€ €´§¢€0€0€ €vpfam02737, 3HCDH_N, 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain. This family also includes lambda crystallin.¡€0€ª€0€ €CDD¡€ €´¨¢€0€0€ €Spfam02738, Ald_Xan_dh_C2, Molybdopterin-binding domain of aldehyde dehydrogenase. ¡€0€ª€0€ €CDD¡€ €´©¢€0€0€ €Opfam02739, 5_3_exonuc_N, 5'-3' exonuclease, N-terminal resolvase-like domain. ¡€0€ª€0€ €CDD¡€ €´ª¢€0€0€ €}pfam02740, Colipase_C, Colipase, C-terminal domain. SCOP reports duplication of common fold with Colipase N-terminal domain.¡€0€ª€0€ €CDD¡€ €´«¢€0€0€ €‚Ipfam02741, FTR_C, FTR, proximal lobe. The FTR (Formylmethanofuran--tetrahydromethanopterin formyltransferase) enzyme EC:2.3.1.101 is involved in archaebacteria in the formation of methane from carbon dioxide. C-terminal proximal lobe of alpha+beta ferredoxin-like fold. SCOP reports fold duplication with N-terminal distal lobe.¡€0€ª€0€ €CDD¡€ €´¬¢€0€0€ €pfam02742, Fe_dep_repr_C, Iron dependent repressor, metal binding and dimerisation domain. This family includes the Diphtheria toxin repressor.¡€0€ª€0€ €CDD¡€ €´­¢€0€0€ €ípfam02743, dCache_1, Cache domain. Double cache domain 1 covers the last three strands from the membrane distal PAS-like domain, the first two strands of the membrane proximal domain, and the connecting elements between the two domains.¡€0€ª€0€ €CDD¡€ €´®¢€0€0€ €±pfam02744, GalP_UDP_tr_C, Galactose-1-phosphate uridyl transferase, C-terminal domain. SCOP reports fold duplication with N-terminal domain. Both involved in Zn and Fe binding.¡€0€ª€0€ €CDD¡€ €I¢€0€0€ €‚ƒpfam02745, MCR_alpha_N, Methyl-coenzyme M reductase alpha subunit, N-terminal domain. Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta (pfam02241), and 2 gamma (pfam02240) subunits with two identical nickel porphinoid active sites. The N-terminal domain has a ferredoxin-like fold.¡€0€ª€0€ €CDD¡€ €´¯¢€0€0€ €—pfam02746, MR_MLE_N, Mandelate racemase / muconate lactonizing enzyme, N-terminal domain. SCOP reports fold similarity with enolase N-terminal domain.¡€0€ª€0€ €CDD¡€ €´°¢€0€0€ €êpfam02747, PCNA_C, Proliferating cell nuclear antigen, C-terminal domain. N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.¡€0€ª€0€ €CDD¡€ €I ¢€0€0€ €‚+pfam02748, PyrI_C, Aspartate carbamoyltransferase regulatory chain, metal binding domain. The regulatory chain is involved in allosteric regulation of aspartate carbamoyltransferase. The C-terminal metal binding domain has a rubredoxin-like fold and provides the interface with the catalytic chain.¡€0€ª€0€ €CDD¡€ €´±¢€0€0€ €‚|pfam02749, QRPTase_N, Quinolinate phosphoribosyl transferase, N-terminal domain. Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase EC:2.4.2.19 is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyzes the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide. The QA substrate is bound between the C-terminal domain of one subunit, and the N-terminal domain of the other. The N-terminal domain has an alpha/beta hammerhead fold.¡€0€ª€0€ €CDD¡€ €´²¢€0€0€ €xpfam02750, Synapsin_C, Synapsin, ATP binding domain. Ca dependent ATP binding in this ATP grasp fold. Function unknown.¡€0€ª€0€ €CDD¡€ €´³¢€0€0€ €‚”pfam02751, TFIIA_gamma_C, Transcription initiation factor IIA, gamma subunit. Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The C-terminal domain of the gamma subunit is a 12 stranded beta-barrel.¡€0€ª€0€ €CDD¡€ €´´¢€0€0€ €pfam02752, Arrestin_C, Arrestin (or S-antigen), C-terminal domain. Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain.¡€0€ª€0€ €CDD¡€ €´µ¢€0€0€ €¿pfam02753, PapD_C, Pili assembly chaperone PapD, C-terminal domain. Ig-like beta-sandwich fold. This domain is the C-terminal part of the pilus and flagellar-assembly chaperone protein PapD.¡€0€ª€0€ €CDD¡€ €´¶¢€0€0€ €‚:pfam02754, CCG, Cysteine-rich domain. The key element of this family is the CX31-38CCX33-34CXXC sequence motif normally found at the C-terminus in archaeal and bacterial Hdr-like proteins. There may be one or two copies, and the motif is probably an iron-sulfur binding cluster. In some instances one of the cysteines is replaced by an aspartate, and aspartate can in principle also function as a ligand of an iron-sulfur cluster. The family includes a subunit from heterodisulphide reductase and a subunit from glycolate oxidase and glycerol-3-phosphate dehydrogenase.¡€0€ª€0€ €CDD¡€ €´·¢€0€0€ €„pfam02755, RPEL, RPEL repeat. The RPEL repeat is named after four conserved amino acids it contains. The RPEL motif binds to actin.¡€0€ª€0€ €CDD¡€ €´¸¢€0€0€ €äpfam02756, GYR, GYR motif. The GYR motif is found in several drosophila proteins. Its function is unknown, however the presence of completely conserved tyrosine residues may suggest it could be a substrate for tyrosine kinases.¡€0€ª€0€ €CDD¡€ €´¹¢€0€0€ €‚pfam02757, YLP, YLP motif. The YLP motif is found in several drosophila proteins. Its function is unknown, however the presence of completely conserved tyrosine residues and its presence in human ERBB4 may suggest it could be a substrate for tyrosine kinases.¡€0€ª€0€ €CDD¡€ €´º¢€0€0€ €Þpfam02758, PYRIN, PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain.¡€0€ª€0€ €CDD¡€ €´»¢€0€0€ €‚ pfam02759, RUN, RUN domain. This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.¡€0€ª€0€ €CDD¡€ €´¼¢€0€0€ €¶pfam02760, HIN, HIN-200/IF120x domain. This domain has no known function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain pfam02758.¡€0€ª€0€ €CDD¡€ €´½¢€0€0€ €‚Ãpfam02761, Cbl_N2, CBL proto-oncogene N-terminus, EF hand-like domain. Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conserved, and is known to bind to phosphorylated tyrosine residues. The so called N-terminal domain is actually 3 structural domains, of which this is the central EF hand domain.¡€0€ª€0€ €CDD¡€ €´¾¢€0€0€ €‚¾pfam02762, Cbl_N3, CBL proto-oncogene N-terminus, SH2-like domain. Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conserved, and is known to bind to phosphorylated tyrosine residues. The so called N-terminal domain is actually 3 structural domains, of which this is the C-terminal SH2 domain.¡€0€ª€0€ €CDD¡€ €´¿¢€0€0€ €µpfam02763, Diphtheria_C, Diphtheria toxin, C domain. N-terminal catalytic (C) domain - blocks protein synthesis by transfer of ADP-ribose from NAD to a diphthamide residue of EF-2.¡€0€ª€0€ €CDD¡€ €I¢€0€0€ €‚!pfam02764, Diphtheria_T, Diphtheria toxin, T domain. Central domain of diphtheria toxin is the translocation (T) domain. pH induced conformational change in this domain triggers insertion into the endosomal membrane and facilitates the transfer of the catalytic domain into the cytoplasm.¡€0€ª€0€ €CDD¡€ €I¢€0€0€ €‚opfam02765, POT1, Telomeric single stranded DNA binding POT1/CDC13. This domain binds single stranded telomeric DNA and adopts an OB fold. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping. POT1 is one component of the shelterin complex that protects telomere-ends from attack by DNA-repair mechanisms.¡€0€ª€0€ €CDD¡€ €´À¢€0€0€ €÷pfam02767, DNA_pol3_beta_2, DNA polymerase III beta subunit, central domain. A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.¡€0€ª€0€ €CDD¡€ €´Á¢€0€0€ €úpfam02768, DNA_pol3_beta_3, DNA polymerase III beta subunit, C-terminal domain. A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.¡€0€ª€0€ €CDD¡€ €I¢€0€0€ €‚zpfam02769, AIRS_C, AIR synthase related protein, C-terminal domain. This family includes Hydrogen expression/formation protein HypE, AIR synthases EC:6.3.3.1, FGAM synthase EC:6.3.5.3 and selenide, water dikinase EC:2.7.9.3. The function of the C-terminal domain of AIR synthase is unclear, but the cleft formed between N and C domains is postulated as a sulphate binding site.¡€0€ª€0€ €CDD¡€ €´Â¢€0€0€ €‚pfam02770, Acyl-CoA_dh_M, Acyl-CoA dehydrogenase, middle domain. Central domain of Acyl-CoA dehydrogenase has a beta-barrel fold.¡€0€ª€0€ €CDD¡€ €´Ã¢€0€0€ €pfam02771, Acyl-CoA_dh_N, Acyl-CoA dehydrogenase, N-terminal domain. The N-terminal domain of Acyl-CoA dehydrogenase is an all-alpha domain.¡€0€ª€0€ €CDD¡€ €´Ä¢€0€0€ €¡pfam02772, S-AdoMet_synt_M, S-adenosylmethionine synthetase, central domain. The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold.¡€0€ª€0€ €CDD¡€ €´Å¢€0€0€ €¤pfam02773, S-AdoMet_synt_C, S-adenosylmethionine synthetase, C-terminal domain. The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold.¡€0€ª€0€ €CDD¡€ €´Æ¢€0€0€ €Øpfam02774, Semialdhyde_dhC, Semialdehyde dehydrogenase, dimerisation domain. This Pfam entry contains the following members: N-acetyl-glutamine semialdehyde dehydrogenase (AgrC) Aspartate-semialdehyde dehydrogenase.¡€0€ª€0€ €CDD¡€ €´Ç¢€0€0€ €Xpfam02775, TPP_enzyme_C, Thiamine pyrophosphate enzyme, C-terminal TPP binding domain. ¡€0€ª€0€ €CDD¡€ €´È¢€0€0€ €Xpfam02776, TPP_enzyme_N, Thiamine pyrophosphate enzyme, N-terminal TPP binding domain. ¡€0€ª€0€ €CDD¡€ €´É¢€0€0€ €‚£pfam02777, Sod_Fe_C, Iron/manganese superoxide dismutases, C-terminal domain. superoxide dismutases (SODs) catalyze the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. C-terminal domain is a mixed alpha/beta fold.¡€0€ª€0€ €CDD¡€ €´Ê¢€0€0€ €±pfam02778, tRNA_int_endo_N, tRNA intron endonuclease, N-terminal domain. Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.¡€0€ª€0€ €CDD¡€ €´Ë¢€0€0€ €»pfam02779, Transket_pyr, Transketolase, pyrimidine binding domain. This family includes transketolase enzymes, pyruvate dehydrogenases, and branched chain alpha-keto acid decarboxylases.¡€0€ª€0€ €CDD¡€ €I*¢€0€0€ €žpfam02780, Transketolase_C, Transketolase, C-terminal domain. The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site.¡€0€ª€0€ €CDD¡€ €´Ì¢€0€0€ €Jpfam02781, G6PD_C, Glucose-6-phosphate dehydrogenase, C-terminal domain. ¡€0€ª€0€ €CDD¡€ €´Í¢€0€0€ €¯pfam02782, FGGY_C, FGGY family of carbohydrate kinases, C-terminal domain. This domain adopts a ribonuclease H-like fold and is structurally related to the N-terminal domain.¡€0€ª€0€ €CDD¡€ €´Î¢€0€0€ €‚pfam02783, MCR_beta_N, Methyl-coenzyme M reductase beta subunit, N-terminal domain. Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (pfam02249), 2 beta (this family), and 2 gamma (pfam02240) subunits with two identical nickel porphinoid active sites. The N-terminal domain has an alpha/beta ferredoxin-like fold.¡€0€ª€0€ €CDD¡€ €´Ï¢€0€0€ €àpfam02784, Orn_Arg_deC_N, Pyridoxal-dependent decarboxylase, pyridoxal binding domain. These pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates This domain has a TIM barrel fold.¡€0€ª€0€ €CDD¡€ €´Ð¢€0€0€ €‚Opfam02785, Biotin_carb_C, Biotin carboxylase C-terminal domain. Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyzes the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in this C-terminal domain.¡€0€ª€0€ €CDD¡€ €´Ñ¢€0€0€ €‚Ãpfam02786, CPSase_L_D2, Carbamoyl-phosphate synthase L chain, ATP binding domain. Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesize carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117. The ATP binding domain (this one) has an ATP-grasp fold.¡€0€ª€0€ €CDD¡€ €I1¢€0€0€ €‚Jpfam02787, CPSase_L_D3, Carbamoyl-phosphate synthetase large chain, oligomerization domain. Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain.¡€0€ª€0€ €CDD¡€ €´Ò¢€0€0€ €ªpfam02788, RuBisCO_large_N, Ribulose bisphosphate carboxylase large chain, N-terminal domain. The N-terminal domain of RuBisCO large chain adopts a ferredoxin-like fold.¡€0€ª€0€ €CDD¡€ €´Ó¢€0€0€ €Opfam02789, Peptidase_M17_N, Cytosol aminopeptidase family, N-terminal domain. ¡€0€ª€0€ €CDD¡€ €´Ô¢€0€0€ €£pfam02790, COX2_TM, Cytochrome C oxidase subunit II, transmembrane domain. The N-terminal domain of cytochrome C oxidase contains two transmembrane alpha-helices.¡€0€ª€0€ €CDD¡€ €I5¢€0€0€ €‚‚pfam02791, DDT, DDT domain. The DDT domain is named after (DNA binding homeobox and Different Transcription factors) and is approximately 60 residues in length. Along with the WHIM motifs, it comprises an entirely alpha helical module found in diverse eukaryotic chromatin proteins. Based on the structure of Ioc3, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. In particular, the DDT domain, in combination with the WHIM1 and WHIM2 motifs form the SLIDE domain binding pocket.¡€0€ª€0€ €CDD¡€ €´Õ¢€0€0€ €‚8pfam02792, Mago_nashi, Mago nashi protein. This family was originally identified in Drosophila and called mago nashi, it is a strict maternal effect, grandchildless-like, gene. The human homolog has been shown to interact with an RNA binding protein. An RNAi knockout of the C. elegans homolog causes masculinization of the germ line (Mog phenotype) hermaphrodites, suggesting it is involved in hermaphrodite germ-line sex determination. Mago nashi has been found to be part of the exon-exon junction complex that binds 20 nucleotides upstream of exon-exon junctions.¡€0€ª€0€ €CDD¡€ €´Ö¢€0€0€ €åpfam02793, HRM, Hormone receptor domain. This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.¡€0€ª€0€ €CDD¡€ €´×¢€0€0€ €‚pfam02794, HlyC, RTX toxin acyltransferase family. Members of this family are enzymes EC:2.3.1.-. involved in fatty acylation of the protoxins (HlyA) at lysine residues, thereby converting them to the active toxin. Acyl-acyl carrier protein (ACP) is the essential acyl donor. This family show a number of conserved residues that are possible candidates for participation in acyl transfer. Site-directed mutagenesis of the single conserved histidine residue in Escherichia coli HlyC resulted in complete inactivation of the enzyme.¡€0€ª€0€ €CDD¡€ €´Ø¢€0€0€ €9pfam02796, HTH_7, Helix-turn-helix domain of resolvase. ¡€0€ª€0€ €CDD¡€ €´Ù¢€0€0€ €‚"pfam02797, Chal_sti_synt_C, Chalcone and stilbene synthases, C-terminal domain. This domain of chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase. The differences in activity are accounted for by differences in the N-terminal domain.¡€0€ª€0€ €CDD¡€ €´Ú¢€0€0€ €‚Ùpfam02798, GST_N, Glutathione S-transferase, N-terminal domain. Function: conjugation of reduced glutathione to a variety of targets. Also included in the alignment, but not GSTs: S-crystallins from squid (similarity to GST previously noted); eukaryotic elongation factors 1-gamma (not known to have GST activity and similarity not previously recognized); HSP26 family of stress-related proteins including auxin-regulated proteins in plants and stringent starvation proteins in E. coli (not known to have GST activity and similarity not previously recognized). The glutathione molecule binds in a cleft between the N- and C-terminal domains - the catalytically important residues are proposed to reside in the N-terminal domain.¡€0€ª€0€ €CDD¡€ €´Û¢€0€0€ €Èpfam02799, NMT_C, Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain. The N and C-terminal domains of NMT are structurally similar, each adopting an acyl-CoA N-acyltransferase-like fold.¡€0€ª€0€ €CDD¡€ €´Ü¢€0€0€ €ápfam02800, Gp_dh_C, Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain. GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. C-terminal domain is a mixed alpha/antiparallel beta fold.¡€0€ª€0€ €CDD¡€ €´Ý¢€0€0€ €‚pfam02801, Ketoacyl-synt_C, Beta-ketoacyl synthase, C-terminal domain. The structure of beta-ketoacyl synthase is similar to that of the thiolase family (pfam00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains.¡€0€ª€0€ €CDD¡€ €´Þ¢€0€0€ €§pfam02803, Thiolase_C, Thiolase, C-terminal domain. Thiolase is reported to be structurally related to beta-ketoacyl synthase (pfam00109), and also chalcone synthase.¡€0€ª€0€ €CDD¡€ €I@¢€0€0€ €‚­pfam02805, Ada_Zn_binding, Metal binding domain of Ada. The Escherichia coli Ada protein repairs O6-methylguanine residues and methyl phosphotriesters in DNA by direct transfer of the methyl group to a cysteine residue. This domain contains four conserved cysteines that form a zinc binding site. One of these cysteines is a methyl group acceptor. The methylated domain can then specifically bind to the ada box on a DNA duplex.¡€0€ª€0€ €CDD¡€ €´ß¢€0€0€ €‚tpfam02806, Alpha-amylase_C, Alpha amylase, C-terminal all-beta domain. Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain.¡€0€ª€0€ €CDD¡€ €´à¢€0€0€ €|pfam02807, ATP-gua_PtransN, ATP:guanido phosphotransferase, N-terminal domain. The N-terminal domain has an all-alpha fold.¡€0€ª€0€ €CDD¡€ €´á¢€0€0€ €‚pfam02809, UIM, Ubiquitin interaction motif. This motif is called the ubiquitin interaction motif. One of the proteins containing this motif is a receptor for poly-ubiquitination chains for the proteasome. This motif has a pattern of conservation characteristic of an alpha helix.¡€0€ª€0€ €CDD¡€ €´â¢€0€0€ €‚^pfam02810, SEC-C, SEC-C motif. The SEC-C motif found in the C-terminus of the SecA protein, in the middle of some SWI2 ATPases and also solo in several proteins. The motif is predicted to chelate zinc with the CXC and C[HC] pairs that constitute the most conserved feature of the motif. It is predicted to be a potential nucleic acid binding domain.¡€0€ª€0€ €CDD¡€ €´ã¢€0€0€ €ypfam02811, PHP, PHP domain. The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain.¡€0€ª€0€ €CDD¡€ €´ä¢€0€0€ €Qpfam02812, ELFV_dehydrog_N, Glu/Leu/Phe/Val dehydrogenase, dimerisation domain. ¡€0€ª€0€ €CDD¡€ €´å¢€0€0€ €‚Õpfam02813, Retro_M, Retroviral M domain. Retroviruses contain a small protein, MA (matrix), which forms a protein lining immediately beneath the phospholipid membrane of the mature virus particle. MA is located in the N-terminal region of the Gag precursor polyprotein. The N-terminal segment of MA proteins directs the Gag protein to the plasma membrane where budding takes place, and has been called the M domain. This domain forms an alpha helical bundle structure.¡€0€ª€0€ €CDD¡€ €IH¢€0€0€ €ªpfam02814, UreE_N, UreE urease accessory protein, N-terminal domain. UreE is a urease accessory protein. Urease pfam00449 hydrolyses urea into ammonia and carbamic acid.¡€0€ª€0€ €CDD¡€ €´æ¢€0€0€ €pfam02815, MIR, MIR domain. The MIR (protein mannosyltransferase, IP3R and RyR) domain is a domain that may have a ligand transferase function.¡€0€ª€0€ €CDD¡€ €´ç¢€0€0€ €‚pfam02816, Alpha_kinase, Alpha-kinase family. This family is a novel family of eukaryotic protein kinase catalytic domains, which have no detectable similarity to conventional kinases. The family contains myosin heavy chain kinases and Elongation Factor-2 kinase and a bifunctional ion channel. This family is known as the alpha-kinase family. The structure of the kinase domain revealed unexpected similarity to eukaryotic protein kinases in the catalytic core as well as to metabolic enzymes with ATP-grasp domains.¡€0€ª€0€ €CDD¡€ €´è¢€0€0€ €®pfam02817, E3_binding, e3 binding domain. This family represents a small domain of the E2 subunit of 2-oxo-acid dehydrogenases responsible for the binding of the E3 subunit.¡€0€ª€0€ €CDD¡€ €´é¢€0€0€ €Qpfam02818, PPAK, PPAK motif. These motifs are found in the PEVK region of titin.¡€0€ª€0€ €CDD¡€ €´ê¢€0€0€ €vpfam02819, Toxin_9, Spider toxin. This family of spider neurotoxins are thought to be calcium ion channel inhibitors.¡€0€ª€0€ €CDD¡€ €´I¢€0€0€ €‚9pfam02820, MBT, mbt repeat. The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function.¡€0€ª€0€ €CDD¡€ €´ë¢€0€0€ €Apfam02821, Staphylokinase, Staphylokinase/Streptokinase family. ¡€0€ª€0€ €CDD¡€ €´ì¢€0€0€ €èpfam02822, Antistasin, Antistasin family. Members of this family are inhibitors of trypsin family proteases. This domain is highly disulphide bonded. The domain is also found in some large extracellular proteins in multiple copies.¡€0€ª€0€ €CDD¡€ €´í¢€0€0€ €‚kpfam02823, ATP-synt_DE_N, ATP synthase, Delta/Epsilon chain, beta-sandwich domain. Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. The subunit is called epsilon in bacteria and delta in mitochondria. In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP (pfam00213).¡€0€ª€0€ €CDD¡€ €´î¢€0€0€ €‚¯pfam02824, TGS, TGS domain. The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.¡€0€ª€0€ €CDD¡€ €´ï¢€0€0€ €Îpfam02825, WWE, WWE domain. The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.¡€0€ª€0€ €CDD¡€ €´ð¢€0€0€ €‚pfam02826, 2-Hacid_dh_C, D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain. This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family pfam00389.¡€0€ª€0€ €CDD¡€ €´ñ¢€0€0€ €‚&pfam02827, PKI, cAMP-dependent protein kinase inhibitor. Members of this family are extremely potent competitive inhibitors of camp-dependent protein kinase activity. These proteins interact with the catalytic subunit of the enzyme after the cAMP-induced dissociation of its regulatory chains.¡€0€ª€0€ €CDD¡€ €´ò¢€0€0€ €dpfam02828, L27, L27 domain. The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7.¡€0€ª€0€ €CDD¡€ €´ó¢€0€0€ €Èpfam02829, 3H, 3H domain. This domain is predicted to be a small molecule binding domain, based on its occurrence with other domains. The domain is named after its three conserved histidine residues.¡€0€ª€0€ €CDD¡€ €´ô¢€0€0€ €pfam02830, V4R, V4R domain. The V4R (vinyl 4 reductase) domain is a predicted small molecular binding domain, that may bind to hydrocarbons.¡€0€ª€0€ €CDD¡€ €´õ¢€0€0€ €‚ûpfam02831, gpW, gpW. gpW is a 68 residue protein known to be present in phage particles. Extracts of phage-infected cells lacking gpW contain DNA-filled heads, and active tails, but no infectious virions. gpW is required for the addition of gpFII to the head, which is, in turn, required for the attachment of tails. Since gpFII and tails are known to be attached at the connector, gpW is also likely to assemble at this site. The addition of gpW to filled heads increases the DNase resistance of the packaged DNA, suggesting that gpW either forms a plug at the connector to prevent ejection of the DNA, or binds directly to the DNA. The large number of positively charged residues in gpW (its calculated pI is 10.8) is consistent with a role in DNA interaction.¡€0€ª€0€ €CDD¡€ €IY¢€0€0€ €Qpfam02832, Flavi_glycop_C, Flavivirus glycoprotein, immunoglobulin-like domain. ¡€0€ª€0€ €CDD¡€ €IZ¢€0€0€ €‚%pfam02833, DHHA2, DHHA2 domain. This domain is often found adjacent to the DHH domain pfam01368 and is called DHHA2 for DHH associated domain. This domain is diagnostic of DHH subfamily 2 members. The domain is about 120 residues long and contains a conserved DXK motif at its amino terminus.¡€0€ª€0€ €CDD¡€ €´ö¢€0€0€ €‚Æpfam02834, LigT_PEase, LigT like Phosphoesterase. Members of this family are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known. They belong to the 2H phosphoesterase superfamily. They share a common active site, characterized by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.¡€0€ª€0€ €CDD¡€ €´÷¢€0€0€ €ªpfam02836, Glyco_hydro_2_C, Glycosyl hydrolases family 2, TIM barrel domain. This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities.¡€0€ª€0€ €CDD¡€ €I]¢€0€0€ €‚pfam02837, Glyco_hydro_2_N, Glycosyl hydrolases family 2, sugar binding domain. This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities and has a jelly-roll fold. The domain binds the sugar moiety during the sugar-hydrolysis reaction.¡€0€ª€0€ €CDD¡€ €´ø¢€0€0€ €hpfam02838, Glyco_hydro_20b, Glycosyl hydrolase family 20, domain 2. This domain has a zincin-like fold.¡€0€ª€0€ €CDD¡€ €´ù¢€0€0€ €ùpfam02839, CBM_5_12, Carbohydrate binding domain. This short domain is found in many different glycosyl hydrolase enzymes and is presumed to have a carbohydrate binding function. The domain has six aromatic groups that may be important for binding.¡€0€ª€0€ €CDD¡€ €I`¢€0€0€ €‚Zpfam02840, Prp18, Prp18 domain. The splicing factor Prp18 is required for the second step of pre-mRNA splicing. The structure of a large fragment of the Saccharomyces cerevisiae Prp18 is known. This fragment is fully active in yeast splicing in vitro and includes the sequences of Prp18 that have been evolutionarily conserved. The core structure consists of five alpha-helices that adopt a novel fold. The most highly conserved region of Prp18, a nearly invariant stretch of 19 aa, forms part of a loop between two alpha-helices and may interact with the U5 small nuclear ribonucleoprotein particles.¡€0€ª€0€ €CDD¡€ €´ú¢€0€0€ €‚pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain. Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP.¡€0€ª€0€ €CDD¡€ €´û¢€0€0€ €‚Æpfam02843, GARS_C, Phosphoribosylglycinamide synthetase, C domain. Phosphoribosylglycinamide synthetase catalyzes the second step in the de novo biosynthesis of purine. The reaction catalyzed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the C-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see pfam02787).¡€0€ª€0€ €CDD¡€ €´ü¢€0€0€ €‚pfam02844, GARS_N, Phosphoribosylglycinamide synthetase, N domain. Phosphoribosylglycinamide synthetase catalyzes the second step in the de novo biosynthesis of purine. The reaction catalyzed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see pfam00289). This domain is structurally related to the PreATP-grasp domain.¡€0€ª€0€ €CDD¡€ €´ý¢€0€0€ €‚'pfam02845, CUE, CUE domain. CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to pfam00627 and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2.¡€0€ª€0€ €CDD¡€ €´þ¢€0€0€ € pfam02847, MA3, MA3 domain. Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains.¡€0€ª€0€ €CDD¡€ €Ie¢€0€0€ €Åpfam02852, Pyr_redox_dim, Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases.¡€0€ª€0€ €CDD¡€ €´ÿ¢€0€0€ €‚pfam02854, MIF4G, MIF4G domain. MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.¡€0€ª€0€ €CDD¡€ €Ig¢€0€0€ €‚èpfam02861, Clp_N, Clp amino terminal domain, pathogenicity island component. This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site. In many bacterial species, including E.coli, this region represents the N-terminus of one of the key components of the pathogenicity island complex that injects toxin from one bacterium into another.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €‚Äpfam02862, DDHD, DDHD domain. The DDHD domain is 180 residues long and contains four conserved residues that may form a metal binding site. The domain is named after these four residues. This pattern of conservation of metal binding residues is often seen in phosphoesterase domains. This domain is found in retinal degeneration B proteins, as well as a family of probable phospholipases. It has been shown that this domain is found in a longer C terminal region that binds to PYK2 tyrosine kinase. These proteins have been called N-terminal domain-interacting receptor (Nir1, Nir2 and Nir3). This suggests that this region is involved in functionally important interactions in other members of this family.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €Dpfam02863, Arg_repressor_C, Arginine repressor, C-terminal domain. ¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €‚™pfam02864, STAT_bind, STAT protein, DNA binding domain. STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. This family represents the DNA binding domain of STAT, which has an ig-like fold. STAT proteins also include an SH2 domain pfam00017.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €‚Npfam02865, STAT_int, STAT protein, protein interaction domain. STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. STAT proteins also include an SH2 domain pfam00017.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €‚ûpfam02866, Ldh_1_C, lactate/malate dehydrogenase, alpha/beta C-terminal domain. L-lactate dehydrogenases are metabolic enzymes which catalyze the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyze the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes.¡€0€ª€0€ €CDD¡€ €Im¢€0€0€ €Fpfam02867, Ribonuc_red_lgC, Ribonucleotide reductase, barrel domain. ¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €Ppfam02868, Peptidase_M4_C, Thermolysin metallopeptidase, alpha-helical domain. ¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €`pfam02870, Methyltransf_1N, 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain. ¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €?pfam02872, 5_nucleotid_C, 5'-nucleotidase, C-terminal domain. ¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €òpfam02873, MurB_C, UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain. Members of this family are UDP-N-acetylenolpyruvoylglucosamine reductase enzymes EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan.¡€0€ª€0€ €CDD¡€ €µ ¢€0€0€ €·pfam02874, ATP-synt_ab_N, ATP synthase alpha/beta family, beta-barrel domain. This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella.¡€0€ª€0€ €CDD¡€ €µ ¢€0€0€ €‚~pfam02875, Mur_ligase_C, Mur ligase family, glutamate ligase domain. This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC, MurD, MurE, MurF, Mpl, and FolC. MurC, MurD, Mure and MurF catalyze consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesized by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate.¡€0€ª€0€ €CDD¡€ €µ ¢€0€0€ €Tpfam02876, Stap_Strp_tox_C, Staphylococcal/Streptococcal toxin, beta-grasp domain. ¡€0€ª€0€ €CDD¡€ €Iu¢€0€0€ €‚þpfam02877, PARP_reg, Poly(ADP-ribose) polymerase, regulatory domain. Poly(ADP-ribose) polymerase catalyzes the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active.¡€0€ª€0€ €CDD¡€ €µ ¢€0€0€ €Ypfam02878, PGM_PMM_I, Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I. ¡€0€ª€0€ €CDD¡€ €µ ¢€0€0€ €[pfam02879, PGM_PMM_II, Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II. ¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €]pfam02880, PGM_PMM_III, Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III. ¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €@pfam02881, SRP54_N, SRP54-type protein, helical bundle domain. ¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €apfam02882, THF_DHG_CYH_C, Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain. ¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €‚?pfam02883, Alpha_adaptinC2, Adaptin C-terminal domain. Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found in alpha, beta and gamma adaptins.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €‚9pfam02884, Lyase_8_C, Polysaccharide lyase family 8, C-terminal beta-sandwich domain. This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €ðpfam02885, Glycos_trans_3N, Glycosyl transferase family, helical bundle domain. This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €™pfam02886, LBP_BPI_CETP_C, LBP / BPI / CETP family, C-terminal domain. The N and C terminal domains of the LBP/BPI/CETP family are structurally similar.¡€0€ª€0€ €CDD¡€ €I¢€0€0€ €¦pfam02887, PK_C, Pyruvate kinase, alpha/beta domain. As well as being found in pyruvate kinase this family is found as an isolated domain in some bacterial proteins.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €‚pfam02888, CaMBD, Calmodulin binding domain. Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €™pfam02889, Sec63, Sec63 Brl domain. This domain (also known as the Brl domain) is required for assembly of functional endoplasmic reticulum translocons.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €¶pfam02890, DUF226, Borrelia family of unknown function DUF226. This family of proteins are found in Borrelia. The proteins are about 190 amino acids long and have no known function.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €¬pfam02891, zf-MIZ, MIZ/SP-RING zinc finger. This domain has SUMO (small ubiquitin-like modifier) ligase activity and is involved in DNA repair and chromosome organisation.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €%pfam02892, zf-BED, BED zinc finger. ¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €Ûpfam02893, GRAM, GRAM domain. The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins. Note the alignment is lacking the last two beta strands and alpha helix.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €¹pfam02894, GFO_IDH_MocA_C, Oxidoreductase family, C-terminal alpha/beta domain. This family of enzymes utilize NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot.¡€0€ª€0€ €CDD¡€ €I‡¢€0€0€ €»pfam02895, H-kinase_dim, Signal transducing histidine kinase, homodimeric domain. This helical bundle domain is the homodimer interface of the signal transducing histidine kinase family.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €Fpfam02896, PEP-utilizers_C, PEP-utilising enzyme, TIM barrel domain. ¡€0€ª€0€ €CDD¡€ €I‰¢€0€0€ €‚pfam02897, Peptidase_S9_N, Prolyl oligopeptidase, N-terminal beta-propeller domain. This unusual 7-stranded beta-propeller domain protects the catalytic triad of prolyl oligopeptidase (see pfam00326), excluding larger peptides and proteins from proteolysis in the cytosol.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €Bpfam02898, NO_synthase, Nitric oxide synthase, oxygenase domain. ¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €Jpfam02899, Phage_int_SAM_1, Phage integrase, N-terminal SAM-like domain. ¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €Opfam02900, LigB, Catalytic LigB subunit of aromatic ring-opening dioxygenase. ¡€0€ª€0€ €CDD¡€ €µ ¢€0€0€ €âpfam02901, PFL-like, Pyruvate formate lyase-like. This family of enzymes includes pyruvate formate lyase, choline trimethylamine lyase, glycerol dehydratase, 4-hydroxyphenylacetate decarboxylase, and benzylsuccinate synthase.¡€0€ª€0€ €CDD¡€ €µ!¢€0€0€ €ƒpfam02902, Peptidase_C48, Ulp1 protease family, C-terminal catalytic domain. This domain contains the catalytic triad Cys-His-Asn.¡€0€ª€0€ €CDD¡€ €µ"¢€0€0€ €Gpfam02903, Alpha-amylase_N, Alpha amylase, N-terminal ig-like domain. ¡€0€ª€0€ €CDD¡€ €µ#¢€0€0€ €vpfam02905, EBV-NA1, Epstein Barr virus nuclear antigen-1, DNA-binding domain. This domain has a ferredoxin-like fold.¡€0€ª€0€ €CDD¡€ €µ$¢€0€0€ €Qpfam02906, Fe_hyd_lg_C, Iron only hydrogenase large subunit, C-terminal domain. ¡€0€ª€0€ €CDD¡€ €µ%¢€0€0€ €‚Òpfam02907, Peptidase_S29, Hepatitis C virus NS3 protease. Hepatitis C virus NS3 protein is a serine protease which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. NS2-3 proteinase, a zinc-dependent enzyme, performs a single proteolytic cut to release the N-terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4A.¡€0€ª€0€ €CDD¡€ €´¢€0€0€ €Hpfam02909, TetR_C, Tetracyclin repressor, C-terminal all-alpha domain. ¡€0€ª€0€ €CDD¡€ €µ&¢€0€0€ € pfam02910, Succ_DH_flav_C, Fumarate reductase flavoprotein C-term. This family contains fumarate reductases, succinate dehydrogenases and L-aspartate oxidases.¡€0€ª€0€ €CDD¡€ €µ'¢€0€0€ €Cpfam02911, Formyl_trans_C, Formyl transferase, C-terminal domain. ¡€0€ª€0€ €CDD¡€ €µ(¢€0€0€ €Tpfam02912, Phe_tRNA-synt_N, Aminoacyl tRNA synthetase class II, N-terminal domain. ¡€0€ª€0€ €CDD¡€ €µ)¢€0€0€ €jpfam02913, FAD-oxidase_C, FAD linked oxidases, C-terminal domain. This domain has a ferredoxin-like fold.¡€0€ª€0€ €CDD¡€ €I—¢€0€0€ €1pfam02914, DDE_2, Bacteriophage Mu transposase. ¡€0€ª€0€ €CDD¡€ €Öࢀ0€0€ €Mpfam02915, Rubrerythrin, Rubrerythrin. This domain has a ferritin-like fold.¡€0€ª€0€ €CDD¡€ €µ*¢€0€0€ €9pfam02916, DNA_PPF, DNA polymerase processivity factor. ¡€0€ª€0€ €CDD¡€ €I™¢€0€0€ €6pfam02917, Pertussis_S1, Pertussis toxin, subunit 1. ¡€0€ª€0€ €CDD¡€ €´˜¢€0€0€ €Qpfam02918, Pertussis_S2S3, Pertussis toxin, subunit 2 and 3, C-terminal domain. ¡€0€ª€0€ €CDD¡€ €Iš¢€0€0€ €‚Xpfam02919, Topoisom_I_N, Eukaryotic DNA topoisomerase I, DNA binding fragment. Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. This family may be more than one structural domain.¡€0€ª€0€ €CDD¡€ €µ+¢€0€0€ €Bpfam02920, Integrase_DNA, DNA binding domain of tn916 integrase. ¡€0€ª€0€ €CDD¡€ €µ,¢€0€0€ €Ípfam02921, UCR_TM, Ubiquinol cytochrome reductase transmembrane region. Each subunit of the cytochrome bc1 complex provides a single helix (this family) to make up the transmembrane region of the complex.¡€0€ª€0€ €CDD¡€ €µ-¢€0€0€ €‚pfam02922, CBM_48, Carbohydrate-binding module 48 (Isoamylase N-terminal domain). This domain is found in a range of enzymes that act on branched substrates - isoamylase, pullulanase and branching enzyme. This family also contains the beta subunit of 5' AMP activated kinase.¡€0€ª€0€ €CDD¡€ €µ.¢€0€0€ €3pfam02923, BamHI, Restriction endonuclease BamHI. ¡€0€ª€0€ €CDD¡€ €IŸ¢€0€0€ €Bpfam02924, HDPD, Bacteriophage lambda head decoration protein D. ¡€0€ª€0€ €CDD¡€ €µ/¢€0€0€ €6pfam02925, gpD, Bacteriophage scaffolding protein D. ¡€0€ª€0€ €CDD¡€ €I¡¢€0€0€ €‚Èpfam02926, THUMP, THUMP domain. The THUMP domain is named after after thiouridine synthases, methylases and PSUSs. The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterized RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.¡€0€ª€0€ €CDD¡€ €µ0¢€0€0€ €9pfam02927, CelD_N, Cellulase N-terminal ig-like domain. ¡€0€ª€0€ €CDD¡€ €µ1¢€0€0€ €¿pfam02928, zf-C5HC2, C5HC2 zinc finger. Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function.¡€0€ª€0€ €CDD¡€ €µ2¢€0€0€ €Épfam02929, Bgal_small_N, Beta galactosidase small chain. This domain comprises the small chain of dimeric beta-galactosidases EC:3.2.1.23. This domain is also found in single chain beta-galactosidase.¡€0€ª€0€ €CDD¡€ €µ3¢€0€0€ €åpfam02931, Neur_chan_LBD, Neurotransmitter-gated ion-channel ligand binding domain. This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.¡€0€ª€0€ €CDD¡€ €µ4¢€0€0€ €£pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel transmembrane region. This family includes the four transmembrane helices that form the ion channel.¡€0€ª€0€ €CDD¡€ €µ5¢€0€0€ €‚¥pfam02933, CDC48_2, Cell division protein 48 (CDC48), domain 2. This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C-terminus. The VAT-N domain found in AAA ATPases pfam00004 is a substrate 185-residue recognition domain.¡€0€ª€0€ €CDD¡€ €µ6¢€0€0€ €cpfam02934, GatB_N, GatB/GatE catalytic domain. This domain is found in the GatB and GatE proteins.¡€0€ª€0€ €CDD¡€ €µ7¢€0€0€ €‚&pfam02935, COX7C, Cytochrome c oxidase subunit VIIc. Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIIc. The yeast member of this family is called COX VIII.¡€0€ª€0€ €CDD¡€ €µ8¢€0€0€ €‚fpfam02936, COX4, Cytochrome c oxidase subunit IV. Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit IV. The Dictyostelium member of this family is called COX VI. The yeast protein MTC3 appears to be the yeast COX IV subunit.¡€0€ª€0€ €CDD¡€ €µ9¢€0€0€ €ðpfam02937, COX6C, Cytochrome c oxidase subunit VIc. Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIc.¡€0€ª€0€ €CDD¡€ €µ:¢€0€0€ €lpfam02938, GAD, GAD domain. This domain is found in some members of the GatB and aspartyl tRNA synthetases.¡€0€ª€0€ €CDD¡€ €I­¢€0€0€ €Åpfam02939, UcrQ, UcrQ family. The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This family represents the 9.5 kDa subunit of the complex.¡€0€ª€0€ €CDD¡€ €µ;¢€0€0€ €ÿpfam02940, mRNA_triPase, mRNA capping enzyme, beta chain. The beta chain of mRNA capping enzyme has triphosphatase activity. The function of the capping enzyme also depends on the guanylyltransferase activity conferred by the alpha chain (see pfam01331).¡€0€ª€0€ €CDD¡€ €I¯¢€0€0€ €Npfam02941, FeThRed_A, Ferredoxin thioredoxin reductase variable alpha chain. ¡€0€ª€0€ €CDD¡€ €µ<¢€0€0€ €‚,pfam02942, Flu_B_NS1, Influenza B non-structural protein (NS1). A specific region of the influenza B virus NS1 protein, which includes part of its effector domain, blocks the covalent linkage of ISG15 to its target proteins both in vitro and in infected cells. Of the several hundred proteins induced by interferon (IFN) alpha/beta, the ubiquitin-like ISG15 protein is one of the most predominant. Influenza A virus employs a different strategy: its NS1 protein does not bind the ISG15 protein, but little or no ISG15 protein is produced during infection.¡€0€ª€0€ €CDD¡€ €I±¢€0€0€ €Npfam02943, FeThRed_B, Ferredoxin thioredoxin reductase catalytic beta chain. ¡€0€ª€0€ €CDD¡€ €µ=¢€0€0€ €‚™pfam02944, BESS, BESS motif. The BESS motif is named after the proteins in which it is found (BEAF, Suvar(3)7 and Stonewall). The motif is 40 amino acid residues long and is composed of two predicted alpha helices. Based on the protein in which it is found and the presence of conserved positively charged residues it is predicted to be a DNA binding domain. This domain appears to be specific to drosophila.¡€0€ª€0€ €CDD¡€ €µ>¢€0€0€ € NH3 + H2O). This activity is rather low. Hydroxylamine reductase activity was also found in CO-dehydrogenase in which the active site Ni was replaced by Fe. The CO dehydrogenase contains a Ni-3Fe-2S-3O centre.¡€0€ª€0€ €CDD¡€ €µ{¢€0€0€ €Žpfam03064, U79_P34, HSV U79 / HCMV P34. This family represents herpes virus protein U79 and cytomegalovirus early phosphoprotein P34 (UL112).¡€0€ª€0€ €CDD¡€ €J¢€0€0€ €«pfam03065, Glyco_hydro_57, Glycosyl hydrolase family 57. This family includes alpha-amylase (EC:3.2.1.1), 4--glucanotransferase (EC:2.4.1.-) and amylopullulanase enzymes.¡€0€ª€0€ €CDD¡€ €µ|¢€0€0€ €‚%pfam03066, Nucleoplasmin, Nucleoplasmin/nucleophosmin domain. Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays.¡€0€ª€0€ €CDD¡€ €µ}¢€0€0€ €‚¥pfam03067, LPMO_10, Lytic polysaccharide mono-oxygenase, cellulose-degrading. This domain is found associated with a wide variety of cellulose binding domains. This is a family of two very closely related proteins that together act as both a C1- and a C4-oxidising lytic polysaccharide mono-oxygenase, degrading cellulose. This domain is also found in baculoviral spheroidins and spindolins, protein of unknown function.¡€0€ª€0€ €CDD¡€ €µ~¢€0€0€ €‚pfam03068, PAD, Protein-arginine deiminase (PAD). Members of this family are found in mammals. In the presence of calcium ions, PAD enzymes EC:3.5.3.15 catalyze the post-translational modification reaction responsible for the formation of citrulline residues: Protein L-arginine + H2O <=> Protein L-citrulline + NH3. Several types are recognized (and included in the family) on the basis of molecular mass, substrate specificity, and tissue localization. The expression of type I PAD is known to be under the control of oestrogen.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €ëpfam03069, FmdA_AmdA, Acetamidase/Formamidase family. This family includes amidohydrolases of formamide EC:3.5.1.49 and acetamide. Methylophilus methylotrophus FmdA forms a homotrimer suggesting all the members of this family also do.¡€0€ª€0€ €CDD¡€ €µ€¢€0€0€ €‚pfam03070, TENA_THI-4, TENA/THI-4/PQQC family. Members of this family are found in all the three major phyla of life: archaebacteria, eubacteria, and eukaryotes. In Bacillus subtilis, TENA is one of a number of proteins that enhance the expression of extracellular enzymes, such as alkaline protease, neutral protease and levansucrase. The THI-4 protein, which is involved in thiamine biosynthesis, is also a member of this family. The C-terminal part of these proteins consistently show significant sequence similarity to TENA proteins. This similarity was first noted with the Neurospora crassa THI-4. This family includes bacterial coenzyme PQQ synthesis protein C or PQQC proteins. Pyrroloquinoline quinone (PQQ) is the prosthetic group of several bacterial enzymes,including methanol dehydrogenase of methylotrophs and the glucose dehydrogenase of a number of bacteria. PQQC has been found to be required in the synthesis of PQQ but its function is unclear. The exact molecular function of members of this family is uncertain.¡€0€ª€0€ €CDD¡€ €J¢€0€0€ €‚ðpfam03071, GNT-I, GNT-I family. Alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase (GNT-I, GLCNAC-T I) EC:2.4.1.101 transfers N-acetyl-D-glucosamine from UDP to high-mannose glycoprotein N-oligosaccharide. This is an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides. The enzyme is an integral membrane protein localized to the Golgi apparatus, and is probably distributed in all tissues. The catalytic domain is located at the C-terminus.¡€0€ª€0€ €CDD¡€ €J¢€0€0€ €‚Opfam03072, DUF237, MG032/MG096/MG288 family 1. This family consists entirely of mycoplasmal proteins. Their function is unknown. Another related family, pfam03086, also consists entirely of mycoplasmal proteins of the MG032/MG096/MG288 family. Some proteins are included in both families, but of course differ in the aligned residues.¡€0€ª€0€ €CDD¡€ €J¢€0€0€ €‚npfam03073, TspO_MBR, TspO/MBR family. Tryptophan-rich sensory protein (TspO) is an integral membrane protein that acts as a negative regulator of the expression of specific photosynthesis genes in response to oxygen/light. It is involved in the efflux of porphyrin intermediates from the cell. This reduces the activity of coproporphyrinogen III oxidase, which is thought to lead to the accumulation of a putative repressor molecule that inhibits the expression of specific photosynthesis genes. Several conserved aromatic residues are necessary for TspO function: they are thought to be involved in binding porphyrin intermediates. In, the rat mitochondrial peripheral benzodiazepine receptor (MBR) was shown to not only retain its structure within a bacterial outer membrane, but also to be able to functionally substitute for TspO in TspO- mutants, and to act in a similar manner to TspO in its in situ location: the outer mitochondrial membrane. The biological significance of MBR remains unclear, however. It is thought to be involved in a variety of cellular functions, including cholesterol transport in steroidogenic tissues.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €‚pfam03074, GCS, Glutamate-cysteine ligase. This family represents the catalytic subunit of glutamate-cysteine ligase (E.C. 6.3.2.2), also known as gamma-glutamylcysteine synthetase (GCS). This enzyme catalyzes the rate limiting step in the biosynthesis of glutathione. The eukaryotic enzyme is a dimer of a heavy chain and a light chain with all the catalytic activity exhibited by the heavy chain (this family).¡€0€ª€0€ €CDD¡€ €µ‚¢€0€0€ €€pfam03076, GP3, Equine arteritis virus GP3. This protein is encoded by ORF3 of equine arteritis virus. The function is unknown.¡€0€ª€0€ €CDD¡€ €J ¢€0€0€ €­pfam03077, VacA2, Putative vacuolating cytotoxin. This family contains a number of Helicobacter outer membrane proteins with multiple copies of this small conserved region.¡€0€ª€0€ €CDD¡€ €J!¢€0€0€ €‚wpfam03078, ATHILA, ATHILA ORF-1 family. ATHILA is a group of Arabidopsis thaliana retrotransposons belonging to the Ty3/gypsy family of the long terminal repeat (LTR) class of eukaryotic retrotransposons. The central region of ATHILA retrotransposons contains two or three open reading frames (ORFs). This family represents the ORF1 product. The function of ORF1 is unknown.¡€0€ª€0€ €CDD¡€ €×C¢€0€0€ €‚Úpfam03079, ARD, ARD/ARD' family. The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalyzed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels. This family also contains other members, whose functions are not well characterized.¡€0€ª€0€ €CDD¡€ €J"¢€0€0€ €¬pfam03080, DUF239, Domain of unknown function (DUF239). This is a family of plant and bacterial proteins, a small number of which are putative carboxy-terminal peptidases.¡€0€ª€0€ €CDD¡€ €µƒ¢€0€0€ €‚spfam03081, Exo70, Exo70 exocyst complex subunit. The Exo70 protein forms one subunit of the exocyst complex. First discovered in S. cerevisiae, Exo70 and other exocyst proteins have been observed in several other eukaryotes, including humans. In S. cerevisiae, the exocyst complex is involved in the late stages of exocytosis, and is localized at the tip of the bud, the major site of exocytosis in yeast. Exo70 interacts with the Rho3 GTPase. This interaction mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicles from the mother cell to the bud). In humans, the functions of Exo70 and the exocyst complex are less well characterized: Exo70 is expressed in several tissues and is thought to also be involved in exocytosis.¡€0€ª€0€ €CDD¡€ €µ„¢€0€0€ €‚Ýpfam03082, MAGSP, Male accessory gland secretory protein. The accessory gland of male insects is a genital tissue that secretes many components of the ejaculatory fluid, some of which affect the female's receptivity to courtship and her rate of oviposition. This protein is expressed exclusively in the male accessory glands of adult Drosophila melanogaster. The proteins are transferred to the female fly during copulation and are rapidly altered in the female genital tract.¡€0€ª€0€ €CDD¡€ €J%¢€0€0€ €‚Ápfam03083, MtN3_slv, Sugar efflux transporter for intercellular exchange. This family includes proteins such as drosophila saliva, MtN3 involved in root nodule development and a protein involved in activation and expression of recombination activation genes (RAGs). Although the molecular function of these proteins is unknown, they are almost certainly transmembrane proteins. This family contains a region of two transmembrane helices that is found in two copies in most members of the family. This family also contains specific sugar efflux transporters that are essential for the maintenance of animal blood glucose levels, plant nectar production, and plant seed and pollen development. In many organisims it meditaes gluose transport; in Arabidopsis it is necessary for pollen viability; and two of the rice homologs are specifically exploited by bacterial pathogens for virulence by means of direct binding of a bacterial effector to the SWEET promoter.¡€0€ª€0€ €CDD¡€ €J&¢€0€0€ €‚:pfam03084, Sigma_1_2, Reoviral Sigma1/Sigma2 family. Reoviruses are double-stranded RNA viruses. They lack a membrane envelope and their capsid is organised in two concentric icosahedral layers: an inner core and an outer capsid layer. The sigma1 protein is found in the outer capsid, and the sigma2 protein is found in the core. There are four other kinds of protein (besides sigma2) in the core, termed lambda 1-3, mu2. Interactions between sigma2 and lambda 1 and lambda 3 are thought to initiate core formation, followed by mu2 and lambda2. Sigma1 is a trimeric protein, and is positioned at the 12 vertices of the icosahedral outer capsid layer. Its N-terminal fibrous tail, arranged as a triple coiled coil, anchors it in the virion, and a C-terminal globular head interacts with the cellular receptor. These two parts form by separate trimerisation events. The N-terminal fibrous tail forms on the polysome, without the involvement of ATP or chaperones. The post- translational assembly of the C-terminal globular head involves the chaperone activity of Hsp90, which is associated with phosphorylation of Hsp90 during the process. Sigma1 protein acts as a cell attachment protein, and determines viral virulence, pathways of spread, and tropism. Junctional adhesion molecule has been identified as a receptor for sigma1. In type 3 reoviruses, a small region, predicted to form a beta sheet, in the N-terminal tail was found to bind target cell surface sialic acid (i.e. sialic acid acts as a co-receptor) and promote apoptosis. The sigma1 protein also binds to the lambda2 core protein.¡€0€ª€0€ €CDD¡€ €J'¢€0€0€ €‚^pfam03085, RAP-1, Rhoptry-associated protein 1 (RAP-1). Members of this family are found in Babesia species. Though not in this Pfam family, rhoptry-associated proteins are also found in Plasmodium falciparum. Indeed, animal infection with Babesia may produce a pattern similar to human malaria. Rhoptry organelles form part of the apical complex in apicomplexan parasites. Rhoptry-associated proteins are antigenic, and generate partially protective immune responses in infected mammals. Thus RAPs are among the targeted vaccine antigens for babesial (and malarial) parasites. However, RAP-1 proteins are encoded by by a multigene family; thus RAP-1 proteins are polymorphic, with B and T cell epitopes that are conserved among strains, but not across species. Antibodies to Babesia RAP-1 may also be helpful in the serological detection of Babesia infections.¡€0€ª€0€ €CDD¡€ €J(¢€0€0€ €‚Opfam03086, DUF240, MG032/MG096/MG288 family 2. This family consists entirely of mycoplasmal proteins. Their function is unknown. Another related family, pfam03072, also consists entirely of mycoplasmal proteins of the MG032/MG096/MG288 family. Some proteins are included in both families, but of course differ in the aligned residues.¡€0€ª€0€ €CDD¡€ €J)¢€0€0€ €’pfam03087, DUF241, Arabidopsis protein of unknown function. This family represents a number of Arabidopsis proteins. Their functions are unknown.¡€0€ª€0€ €CDD¡€ €µ…¢€0€0€ €Òpfam03088, Str_synth, Strictosidine synthase. Strictosidine synthase (E.C. 4.3.3.2) is a key enzyme in alkaloid biosynthesis. It catalyzes the condensation of tryptamine with secologanin to form strictosidine.¡€0€ª€0€ €CDD¡€ €J+¢€0€0€ €‚«pfam03089, RAG2, Recombination activating protein 2. V-D-J recombination is the combinatorial process by which the huge range of immunoglobulin and T cell binding specificity is generated from a limited amount of genetic material. This process is synergistically activated by RAG1 and RAG2 in developing lymphocytes. Defects in RAG2 in humans are a cause of severe combined immunodeficiency B cell negative and Omenn syndrome.¡€0€ª€0€ €CDD¡€ €µ†¢€0€0€ €‚Æpfam03090, Replicase, Replicase family. This is a family of bacterial plasmid DNA replication initiator proteins. Pfam: PF01051 is a similar family. These RepA proteins exist as monomers and dimers in equilibrium: monomers bind directly to repeated DNA sequences and thus activate replication; dimers repress repA transcription by binding an inversely repeated DNA operator. Dimer dissociation can occur spontaneously or be mediated by Hsp70 chaperones.¡€0€ª€0€ €CDD¡€ €µ‡¢€0€0€ €‚vpfam03091, CutA1, CutA1 divalent ion tolerance protein. Several gene loci with a possible involvement in cellular tolerance to copper have been identified. One such locus in eubacteria and archaebacteria, cutA, is thought to be involved in cellular tolerance to a wide variety of divalent cations other than copper. The cutA locus consists of two operons, of one and two genes. The CutA1 protein is a cytoplasmic protein, encoded by the single-gene operon and has been linked to divalent cation tolerance. It has no recognized structural motifs. This family also contains putative proteins from eukaryotes (human and Drosophila).¡€0€ª€0€ €CDD¡€ €µˆ¢€0€0€ €‚Êpfam03092, BT1, BT1 family. Members of this family are transmembrane proteins. Several are Leishmania putative proteins that are thought to be pteridine transporters. One such protein, previously termed (and still annotated as) ORFG, was shown to encode a biopterin transport protein using null mutants, thus being subsequently renamed BT1. The significant similarity of ORFG/BT1 to Trypanosoma brucei ESAG10 (a putative transmembrane protein and another member of this family) was previously noted. This family also contains five putative Arabidopsis thaliana proteins of unknown function. In addition, it also contains two predicted prokaryotic proteins (from the cyanobacteria Synechocystis and Synechococcus).¡€0€ª€0€ €CDD¡€ €µ‰¢€0€0€ €‚fpfam03094, Mlo, Mlo family. A family of plant integral membrane proteins, first discovered in barley. Mutants lacking wild-type Mlo proteins show broad spectrum resistance to the powdery mildew fungus, and dysregulated cell death control, with spontaneous cell death in response to developmental or abiotic stimuli. Thus wild-type Mlo proteins are thought to be inhibitors of cell death whose deficiency lowers the threshold required to trigger the cascade of events that result in plant cell death. Mlo proteins are localized in the plasma membrane and possess seven transmembrane regions; thus the Mlo family is the only major higher plant family to possess 7 transmembrane domains. It has been suggested that Mlo proteins function as G-protein coupled receptors in plants; however the molecular and biological functions of Mlo proteins remain to be fully determined.¡€0€ª€0€ €CDD¡€ €µŠ¢€0€0€ €‚‘pfam03095, PTPA, Phosphotyrosyl phosphate activator (PTPA) protein. Phosphotyrosyl phosphatase activator (PTPA) proteins stimulate the phosphotyrosyl phosphatase (PTPase) activity of the dimeric form of protein phosphatase 2A (PP2A). PTPase activity in PP2A (in vitro) is relatively low when compared to the better recognized phosphoserine/ threonine protein phosphorylase activity. The specific biological role of PTPA is unknown, Basal expression of PTPA depends on the activity of a ubiquitous transcription factor, Yin Yang 1 (YY1). The tumor suppressor protein p53 can inhibit PTPA expression through an unknown mechanism that negatively controls YY1.¡€0€ª€0€ €CDD¡€ €µ‹¢€0€0€ €‚·pfam03096, Ndr, Ndr family. This family consists of proteins from different gene families: Ndr1/RTP/Drg1, Ndr2, and Ndr3. Their similarity was previously noted. The precise molecular and cellular function of members of this family is still unknown. Yet, they are known to be involved in cellular differentiation events. The Ndr1 group was the first to be discovered. Their expression is repressed by the proto-oncogenes N-myc and c-myc, and in line with this observation, Ndr1 protein expression is down-regulated in neoplastic cells, and is reactivated when differentiation is induced by chemicals such as retinoic acid. Ndr2 and Ndr3 expression is not under the control of N-myc or c-myc. Ndr1 expression is also activated by several chemicals: tunicamycin and homocysteine induce Ndr1 in human umbilical endothelial cells; nickel induces Ndr1 in several cell types. Members of this family are found in wide variety of multicellular eukaryotes, including an Ndr1 type protein in Helianthus annuus (sunflower), known as Sf21. Interestingly, the highest scoring matches in the noise are all alpha/beta hydrolases pfam00561, suggesting that this family may have an enzymatic function (Bateman A pers. obs.).¡€0€ª€0€ €CDD¡€ €×N¢€0€0€ €‚Lpfam03097, BRO1, BRO1-like domain. This domain is found in a number proteins including Rhophilin and BRO1. It is known to have a role in endosomal targeting. ESCRT-III subunit Snf7 binds to a conserved hydrophobic patch in the BRO1 domain that is required for protein complex formation and for the protein-sorting function of BRO1.¡€0€ª€0€ €CDD¡€ €µŒ¢€0€0€ €3pfam03098, An_peroxidase, Animal haem peroxidase. ¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €‚ pfam03099, BPL_LplA_LipB, Biotin/lipoate A/B protein ligase family. This family includes biotin protein ligase, lipoate-protein ligase A and B. Biotin is covalently attached at the active site of certain enzymes that transfer carbon dioxide from bicarbonate to organic acids to form cellular metabolites. Biotin protein ligase (BPL) is the enzyme responsible for attaching biotin to a specific lysine at the active site of biotin enzymes. Each organism probably has only one BPL. Biotin attachment is a two step reaction that results in the formation of an amide linkage between the carboxyl group of biotin and the epsilon-amino group of the modified lysine. Lipoate-protein ligase A (LPLA) catalyzes the formation of an amide linkage between lipoic acid and a specific lysine residue in lipoate dependent enzymes. The unusual biosynthesis pathway of lipoic acid is mechanistically intertwined with attachment of the cofactor.¡€0€ª€0€ €CDD¡€ €µŽ¢€0€0€ €‚$pfam03100, CcmE, CcmE. CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €pfam03101, FAR1, FAR1 DNA-binding domain. This domain contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.¡€0€ª€0€ €CDD¡€ €J6¢€0€0€ €‚pfam03102, NeuB, NeuB family. NeuB is the prokaryotic N-acetylneuraminic acid (Neu5Ac) synthase. It catalyzes the direct formation of Neu5Ac (the most common sialic acid) by condensation of phosphoenolpyruvate (PEP) and N-acetylmannosamine (ManNAc). This reaction has only been observed in prokaryotes; eukaryotes synthesize the 9-phosphate form, Neu5Ac-9-P, and utilize ManNAc-6-P instead of ManNAc. Such eukaryotic enzymes are not present in this family. This family also contains SpsE spore coat polysaccharide biosynthesis proteins.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €Âpfam03103, DUF243, Domain of unknown function (DUF243). This family of uncharacterized proteins is only found in fly proteins. It is found associated with YLP motifs pfam02757 in some proteins.¡€0€ª€0€ €CDD¡€ €µ‘¢€0€0€ €pfam03104, DNA_pol_B_exo1, DNA polymerase family B, exonuclease domain. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold.¡€0€ª€0€ €CDD¡€ €µ’¢€0€0€ €‚Ñpfam03105, SPX, SPX domain. We have named this region the SPX domain after SYG1, Pho81 and XPR1. This 180 residue long domain is found at the amino terminus of a variety of proteins. In the yeast protein SYG1, the N-terminus directly binds to the G-protein beta subunit and inhibits transduction of the mating pheromone signal. Similarly, the N-terminus of the human XPR1 protein binds directly to the beta subunit of the G-protein heterotrimer leading to increased production of cAMP. These findings suggest that all the members of this family are involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors PHO81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, are also members of this family. The SPX domain of S. cerevisiae low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the physical interaction with Spl2 NUC-2 contains several ankyrin repeats pfam00023. Several members of this family are annotated as XPR1 proteins: the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with murine xenotropic and polytropic leukaemia viruses (MLV). Infection by these retroviruses can inhibit XPR1-mediated cAMP signalling and result in cell toxicity and death. The similarity between SYG1, phosphate regulators and XPR1 sequences has been previously noted, as has the additional similarity to several predicted proteins, of unknown function, from Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Schizosaccharomyces pombe, and Saccharomyces cerevisiae, and many other diverse organisms. In addition, given the similarities between XPR1 and SYG1 and phosphate regulatory proteins, it has been proposed that XPR1 might be involved in G-protein associated signal transduction and may itself function as a phosphate sensor.¡€0€ª€0€ €CDD¡€ €µ“¢€0€0€ €,pfam03106, WRKY, WRKY DNA -binding domain. ¡€0€ª€0€ €CDD¡€ €µ”¢€0€0€ €‚Äpfam03107, C1_2, C1 domain. This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in pfam00130, therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol (A Bateman pers. obs.). This family are found in plant proteins.¡€0€ª€0€ €CDD¡€ €µ•¢€0€0€ €úpfam03108, DBD_Tnp_Mut, MuDR family transposase. This region is found in plant proteins that are presumed to be the transposases for Mutator transposable elements. These transposons contain two ORFs. The molecular function of this region is unknown.¡€0€ª€0€ €CDD¡€ €µ–¢€0€0€ €‚2pfam03109, ABC1, ABC1 family. This family includes ABC1 from yeast and AarF from E. coli. These proteins have a nuclear or mitochondrial subcellular location in eukaryotes. The exact molecular functions of these proteins is not clear, however yeast ABC1 suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex and E. coli AarF is required for ubiquinone production. It has been suggested that members of the ABC1 family are novel chaperonins. These proteins are unrelated to the ABC transporter proteins.¡€0€ª€0€ €CDD¡€ €J>¢€0€0€ €‚npfam03110, SBP, SBP domain. SBP domains (for SQUAMOSA-pROMOTER BINDING PROTEIN) are found in plant proteins. It is a sequence specific DNA-binding domain. Members of family probably function as transcription factors involved in the control of early flower development. The domain contains 10 conserved cysteine and histidine residues that probably are zinc ligands.¡€0€ª€0€ €CDD¡€ €µ—¢€0€0€ €¤pfam03112, DUF244, Uncharacterized protein family (ORF7) DUF. Several members of this family are Borrelia burgdorferi plasmid proteins of uncharacterized function.¡€0€ª€0€ €CDD¡€ €J@¢€0€0€ €‚!pfam03113, RSV_NS2, Respiratory synctial virus non-structural protein NS2. The molecular structure and function of the NS2 protein is not known. However, mutants lacking the NS2 grow at slower rates when compared to the wild-type. Nevertheless, NS2 is not essential for viral replication.¡€0€ª€0€ €CDD¡€ €JA¢€0€0€ €‚ôpfam03114, BAR, BAR domain. BAR domains are dimerisation, lipid binding and curvature sensing modules found in many different protein families. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysin, endophilin, BRAP and Nadrin. BAR domains are also frequently found alongside domains that determine lipid specificity, like pfam00169 and pfam00787 domains in beta centaurins and sorting nexins respectively.¡€0€ª€0€ €CDD¡€ €JB¢€0€0€ €‚Wpfam03115, Astro_capsid_N, Astrovirus capsid protein precursor. This product is encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The 87kD precursor protein undergoes an intracellular cleavage to form a 79kD protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion.¡€0€ª€0€ €CDD¡€ €JC¢€0€0€ €‚pfam03116, NQR2_RnfD_RnfE, NQR2, RnfD, RnfE family. This family of bacterial proteins includes a sodium-translocating NADH-ubiquinone oxidoreductase (i.e. a respiration linked sodium pump). In Vibrio cholerae, it negatively regulates the expression of virulence factors through inhibiting (by an unknown mechanism) the transcription of the transcriptional activator ToxT. The family also includes proteins involved in nitrogen fixation, RnfD and RnfE. The similarity of these proteins to NADH-ubiquinone oxidoreductases was previously noted.¡€0€ª€0€ €CDD¡€ €µ˜¢€0€0€ €‚"pfam03117, Herpes_UL49_1, UL49 family. Members of this family, found in several herpesviruses, include EBV BFRF2 and other UL49 proteins (e.g. HCMVA UL49, HSV6 U33). There are eight conserved cysteine residues in this alignment, all lying towards the C-terminus. Their function is unknown.¡€0€ª€0€ €CDD¡€ €JE¢€0€0€ €‚rpfam03118, RNA_pol_A_CTD, Bacterial RNA polymerase, alpha chain C terminal domain. The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal.¡€0€ª€0€ €CDD¡€ €µ™¢€0€0€ €‚npfam03119, DNA_ligase_ZBD, NAD-dependent DNA ligase C4 zinc finger domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor. This family is a small zinc binding motif that is presumably DNA binding. IT is found only in NAD dependent DNA ligases.¡€0€ª€0€ €CDD¡€ €µš¢€0€0€ €‚’pfam03120, DNA_ligase_OB, NAD-dependent DNA ligase OB-fold domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor. This family is a small domain found after the adenylation domain pfam01653 in NAD dependent ligases. OB-fold domains generally are involved in nucleic acid binding.¡€0€ª€0€ €CDD¡€ €µ›¢€0€0€ €‚ópfam03121, Herpes_UL52, Herpesviridae UL52/UL70 DNA primase. Herpes simplex virus type 1 DNA replication in host cells is known to be mediated by seven viral-encoded proteins, three of which form a heterotrimeric DNA helicase-primase complex. This complex consists of UL5, UL8, and UL52 subunits. Heterodimers consisting of UL5 and UL52 have been shown to retain both helicase and primase activities. Nevertheless, UL8 is still essential for replication: though it lacks any DNA binding or catalytic activities, it is involved in the transport of UL5-UL52 and it also interacts with other replication proteins. The molecular mechanisms of the UL5-UL52 catalytic activities are not known. While UL5 is associated with DNA helicase activity and UL52 with DNA primase activity, the helicase activity requires the interaction of UL5 and UL52. It is not known if the primase activity can be maintained by UL52 alone. The region encompassed by residues 610-636 of HSV1 UL52 is thought to contain a divalent metal cation binding motif. Indeed, this region contains several aspartate and glutamate residues that might be involved in divalent cation binding. The biological significance of UL52-UL8 interaction is not known. Yeast two-hybrid analysis together with immunoprecipitation experiments have shown that the HSV1 UL52 region between residues 366-914 is essential for this interaction, while the first 349 N-terminal residues are dispensable. This family also includes protein UL70 from cytomegalovirus (CMV, a subgroup of the Herpesviridae) strains, which, by analogy with UL52, is thought to have DNA primase activity. Indeed, CMV strains also possess a DNA helicase-primase complex, the other subunits being protein UL105 (with known similarity to HSV1 UL5) and protein UL102.¡€0€ª€0€ €CDD¡€ €JI¢€0€0€ €‚>pfam03122, Herpes_MCP, Herpes virus major capsid protein. This family represents the major capsid protein (MCP) of herpes viruses. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces.¡€0€ª€0€ €CDD¡€ €JJ¢€0€0€ €‚!pfam03123, CAT_RBD, CAT RNA binding domain. This RNA binding domain is found at the amino terminus of transcriptional antitermination proteins such as BglG, SacY and LicT. These proteins control the expression of sugar metabolising operons in Gram+ and Gram- bacteria. This domain has been called the CAT (Co-AntiTerminator) domain. It binds as a dimer to short Ribonucleotidic Anti-Terminator (RAT) hairpin, each monomer interacting symmetrically with both strands of the RAT hairpin. In the full-length protein, CAT is followed by two phosphorylatable PTS regulation domains (pfam00874) that modulate the RNA binding activity of CAT. Upon activation, the dimeric proteins bind to RAT targets in the nascent mRNA, thereby preventing abortive dissociation of the RNA polymerase from the DNA template.¡€0€ª€0€ €CDD¡€ €µœ¢€0€0€ €‚Qpfam03124, EXS, EXS family. We have named this region the EXS family after (ERD1, XPR1, and SYG1). This family includes C-terminus portions from the SYG1 G-protein associated signal transduction protein from Saccharomyces cerevisiae, and sequences that are thought to be murine leukaemia virus (MLV) receptors (XPR1). N-terminus portions from these proteins are aligned in the SPX pfam03105 family. The previously noted similarity between SYG1 and MLV receptors over their whole sequences is thus borne out in pfam03105 and this family. While the N-termini aligned in pfam03105 are thought to be involved in signal transduction, the role of the C-terminus sequences aligned in this family is not known. This region of similarity contains several predicted transmembrane helices. This family also includes the ERD1 (ERD: ER retention defective) yeast proteins. ERD1 proteins are involved in the localization of endogenous endoplasmic reticulum (ER) proteins. erd1 null mutants secrete such proteins even though they possess the C-terminal HDEL ER lumen localization label sequence. In addition, null mutants also exhibit defects in the Golgi-dependent processing of several glycoproteins, which led to the suggestion that the sorting of luminal ER proteins actually occurs in the Golgi, with subsequent return of these proteins to the ER via `salvage' vesicles.¡€0€ª€0€ €CDD¡€ €µ¢€0€0€ €‚pfam03125, Sre, C. elegans Sre G protein-coupled chemoreceptor. Caenorhabditis elegans Sre proteins are candidate chemosensory receptors. There are four main recognized groups of such receptors: Odr-10, Sra, Sro, and Srg. Sre (this family), Sra pfam02117 and Srb pfam02175 comprise the Sra group. All of the above receptors are thought to be G protein-coupled seven transmembrane domain proteins. The existence of several different chemosensory receptors underlies the fact that in spite of having only 20-30 chemosensory neurones, C. elegans detects hundreds of different chemicals, with the ability to discern individual chemicals among combinations.¡€0€ª€0€ €CDD¡€ €×_¢€0€0€ €‚ pfam03126, Plus-3, Plus-3 domain. This domain is about 90 residues in length and is often found associated with the pfam02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor.¡€0€ª€0€ €CDD¡€ €µž¢€0€0€ €üpfam03127, GAT, GAT domain. The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 and ARF3. The GAT domain stabilizes membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins.¡€0€ª€0€ €CDD¡€ €µŸ¢€0€0€ €‚pfam03128, CXCXC, CXCXC repeat. This repeat contains the conserved pattern CXCXC where X can be any amino acid. The repeat is found in up to five copies in Vascular endothelial growth factor C. In the salivary glands of the dipteran Chironomus tentans, a specific messenger ribonucleoprotein (mRNP) particle, the Balbiani ring (BR) granule, can be visualised during its assembly on the gene and during its nucleocytoplasmic transport. This repeat is found over 70 copies in the balbiani ring protein 3. It is also found in some silk proteins.¡€0€ª€0€ €CDD¡€ €µ ¢€0€0€ €±pfam03129, HGTP_anticodon, Anticodon binding domain. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases it is probably the anticodon binding domain.¡€0€ª€0€ €CDD¡€ €JP¢€0€0€ €‚ûpfam03130, HEAT_PBS, PBS lyase HEAT-like repeat. This family contains a short bi-helical repeat that is related to pfam02985. Cyanobacteria and red algae harvest light energy using macromolecular complexes known as phycobilisomes (PBS), peripherally attached to the photosynthetic membrane. The major components of PBS are the phycobiliproteins. These heterodimeric proteins are covalently attached to phycobilins: open-chain tetrapyrrole chromophores, which function as the photosynthetic light-harvesting pigments. Phycobiliproteins differ in sequence and in the nature and number of attached phycobilins to each of their subunits. This family includes the lyase enzymes that specifically attach particular phycobilins to apophycobiliprotein subunits. The most comprehensively studied of these is the CpcE/F lyase, which attaches phycocyanobilin (PCB) to the alpha subunit of apophycocyanin. Similarly, MpeU/V attaches phycoerythrobilin to phycoerythrin II, while CpeY/Z is thought to be involved in phycoerythrobilin (PEB) attachment to phycoerythrin (PE) I (PEs I and II differ in sequence and in the number of attached molecules of PEB: PE I has five, PE II has six). All the reactions of the above lyases involve an apoprotein cysteine SH addition to a terminal delta 3,3'-double bond. Such a reaction is not possible in the case of phycoviolobilin (PVB), the phycobilin of alpha-phycoerythrocyanin (alpha-PEC). It is thought that in this case, PCB, not PVB, is first added to apo-alpha-PEC, and is then isomerised to PVB. The addition reaction has been shown to occur in the presence of either of the components of alpha-PEC-PVB lyase PecE or PecF (or both). The isomerisation reaction occurs only when both PecE and PecF components are present, i.e. the PecE/F phycobiliprotein lyase is also a phycobilin isomerase. Another member of this family is the NblB protein, whose similarity to the phycobiliprotein lyases was previously noted. This constitutively expressed protein is not known to have any lyase activity. It is thought to be involved in the coordination of PBS degradation with environmental nutrient limitation. It has been suggested that the similarity of NblB to the phycobiliprotein lyases is due to the ability to bind tetrapyrrole phycobilins via the common repeated motif.¡€0€ª€0€ €CDD¡€ €µ¡¢€0€0€ €‚–pfam03131, bZIP_Maf, bZIP Maf transcription factor. Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerisation and DNA binding property. Thus, this family is probably related to pfam00170. This family also includes the DNA_binding domain of Skn-1, this domain lacks the leucine zipper found in other bZip domains, and binds DNA is a monomer.¡€0€ª€0€ €CDD¡€ €µ¢¢€0€0€ €‚Fpfam03133, TTL, Tubulin-tyrosine ligase family. Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumor aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain.¡€0€ª€0€ €CDD¡€ €JS¢€0€0€ €‚Ípfam03134, TB2_DP1_HVA22, TB2/DP1, HVA22 family. This family includes members from a wide variety of eukaryotes. It includes the TB2/DP1 (deleted in polyposis) protein, which in humans is deleted in severe forms of familial adenomatous polyposis, an autosomal dominant oncological inherited disease. The family also includes the plant protein of known similarity to TB2/DP1, the HVA22 abscisic acid-induced protein, which is thought to be a regulatory protein.¡€0€ª€0€ €CDD¡€ €µ£¢€0€0€ €‚ˆpfam03135, CagE_TrbE_VirB, CagE, TrbE, VirB family, component of type IV transporter system. This family includes the Helicobacter pylori protein CagE, which together with other proteins from the cag pathogenicity island (PAI), encodes a type IV transporter secretion system. The precise role of CagE is not known, but studies in animal models have shown that it is essential for pathogenesis in Helicobacter pylori induced gastritis and peptic ulceration. Indeed, the expression of the cag PAI has been shown to be essential for stimulating human gastric epithelial cell apoptosis in vitro. Similar type IV transport systems are also found in other bacteria. This family includes the TrbE and VirB proteins from the respective trb and Vir conjugal transfer systems in Agrobacterium tumefaciens. homologs of VirB proteins from other species are also members of this family, e.g. VirB from Brucella suis.¡€0€ª€0€ €CDD¡€ €µ¤¢€0€0€ €‚Ùpfam03136, Pup_ligase, Pup-ligase protein. Pupylation is a novel protein modification system found in some bacteria. This family of proteins are the enzyme that can conjugate proteins of the Pup family to lysine residues in target proteins marking them for degradation. The archetypal protein in this family is PafA (proteasome accessory factor) from Mycobacterium tuberculosis. It has been suggested that these proteins are related to gamma-glutamyl-cysteine synthetases.¡€0€ª€0€ €CDD¡€ €µ¥¢€0€0€ €‚‹pfam03137, OATP, Organic Anion Transporter Polypeptide (OATP) family. This family consists of several eukaryotic Organic-Anion-Transporting Polypeptides (OATPs). Several have been identified mostly in human and rat. Different OATPs vary in tissue distribution and substrate specificity. Since the numbering of different OATPs in particular species was based originally on the order of discovery, similarly numbered OATPs in humans and rats did not necessarily correspond in function, tissue distribution and substrate specificity (in spite of the name, some OATPs also transport organic cations and neutral molecules). Thus, Tamai et al. initiated the current scheme of using digits for rat OATPs and letters for human ones. Prostaglandin transporter (PGT) proteins are also considered to be OATP family members. In addition, the methotrexate transporter OATK is closely related to OATPs. This family also includes several predicted proteins from Caenorhabditis elegans and Drosophila melanogaster. This similarity was not previously noted. Note: Members of this family are described (in the Swiss-Prot database) as belonging to the SLC21 family of transporters.¡€0€ª€0€ €CDD¡€ €µ¦¢€0€0€ €‚×pfam03139, AnfG_VnfG, Vanadium/alternative nitrogenase delta subunit. The nitrogenase complex EC:1.18.6.1 catalyzes the conversion of molecular nitrogen to ammonia (nitrogen fixation) as follows: 8 reduced ferredoxin + 8 H(+) + N(2) + 16 ATP <=> 8 oxidised ferredoxin + 2 NH(3) + 16 ADP + 16 phosphate. The complex is hexameric, consisting of 2 alpha, 2 beta, and 2 delta subunits. This family represents the delta subunit of a group of nitrogenases that do not utilize molybdenum (Mo) as a cofactor, but instead use either vanadium (V nitrogenases), or iron (alternative nitrogenases). V nitrogenases are encoded by vnf operons, and alternative nitrogenases by anf operons. The delta subunits are VnfG and AnfG, respectively.¡€0€ª€0€ €CDD¡€ €µ§¢€0€0€ €~pfam03140, DUF247, Plant protein of unknown function. The function of the plant proteins constituting this family is unknown.¡€0€ª€0€ €CDD¡€ €µ¨¢€0€0€ €¯pfam03141, Methyltransf_29, Putative S-adenosyl-L-methionine-dependent methyltransferase. This family is a putative S-adenosyl-L-methionine (SAM)-dependent methyltransferase.¡€0€ª€0€ €CDD¡€ €×k¢€0€0€ €‚pfam03142, Chitin_synth_2, Chitin synthase. Members of this family are fungal chitin synthase EC:2.4.1.16 enzymes. They catalyze chitin synthesis as follows: UDP-N-acetyl-D-glucosamine + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N) <=> UDP + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N+1).¡€0€ª€0€ €CDD¡€ €µ©¢€0€0€ €‚#pfam03143, GTP_EFTU_D3, Elongation factor Tu C-terminal domain. Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA and binding to EF-Ts pfam00889.¡€0€ª€0€ €CDD¡€ €µª¢€0€0€ €‚Ðpfam03144, GTP_EFTU_D2, Elongation factor Tu domain 2. Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to pfam03143, and in fact has weak sequence matches to this domain.¡€0€ª€0€ €CDD¡€ €µ«¢€0€0€ €‚pfam03145, Sina, Seven in absentia protein family. The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non- neuronal cell type. The Sina protein contains an N-terminal RING finger domain pfam00097. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that thus Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologs of Sina have also been identified. The human homolog Siah-1 also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is described in pfam00097, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologs, whose similarity was noted previously, this family also includes putative homologs from Caenorhabditis elegans, Arabidopsis thaliana.¡€0€ª€0€ €CDD¡€ €µ¬¢€0€0€ €‚†pfam03146, NtA, Agrin NtA domain. Agrin is a multidomain heparan sulphate proteoglycan, that is a key organiser for the induction of postsynaptic specialisations at the neuromuscular junction. Binding of agrin to basement membranes requires the amino terminal (NtA) domain. This region mediates high affinity interaction with the coiled-coil domain of laminins. The binding of agrin to laminins via the NtA domain is subject to tissue-specific regulation. The NtA domain-containing form of agrin is expressed in non-neuronal cells or in neurons that project to non-neuronal cell such as motor neurons. The structure of this domain is an OB-fold.¡€0€ª€0€ €CDD¡€ €µ­¢€0€0€ €²pfam03147, FDX-ACB, Ferredoxin-fold anticodon binding domain. This is the anticodon binding domain found in some phenylalanyl tRNA synthetases. The domain has a ferredoxin fold.¡€0€ª€0€ €CDD¡€ €µ®¢€0€0€ €‚ñpfam03148, Tektin, Tektin family. Tektins are cytoskeletal proteins. They have been demonstrated in such cellular sites as centrioles, basal bodies, and along ciliary and flagellar doublet microtubules. Tektins form unique protofilaments, organised as longitudinal polymers of tektin heterodimers with axial periodicity matching tubulin. Tektin polypeptides consist of several alpha-helical regions that are predicted to form coiled coils. Indeed, tektins share considerable structural similarities with intermediate filament proteins. Possible functional roles for tektins are: stabilisation of tubulin protofilaments; attachment of A and B-tubules in ciliary/flagellar microtubule doublets and C-tubules in centrioles; binding of axonemal components.¡€0€ª€0€ €CDD¡€ €µ¯¢€0€0€ €‚Çpfam03150, CCP_MauG, Di-haem cytochrome c peroxidase. This is a family of distinct cytochrome c peroxidases (CCPs) that contain two haem groups. Similar to other cytochrome c peroxidases, they reduce hydrogen peroxide to water using c-type haem as an oxidisable substrate. However, since they possess two, instead of one, haem prosthetic groups, bacterial CCPs reduce hydrogen peroxide without the need to generate semi-stable free radicals. The two haem groups have significantly different redox potentials. The high potential (+320 mV) haem feeds electrons from electron shuttle proteins to the low potential (-330 mV) haem, where peroxide is reduced (indeed, the low potential site is known as the peroxidatic site). The CCP protein itself is structured into two domains, each containing one c-type haem group, with a calcium-binding site at the domain interface. This family also includes MauG proteins, whose similarity to di-haem CCP was previously recognized.¡€0€ª€0€ €CDD¡€ €µ°¢€0€0€ €€pfam03151, TPT, Triose-phosphate Transporter family. This family includes transporters with a specificity for triose phosphate.¡€0€ª€0€ €CDD¡€ €µ±¢€0€0€ €‚spfam03152, UFD1, Ubiquitin fusion degradation protein UFD1. Post-translational ubiquitin-protein conjugates are recognized for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified. This family includes UFD1, a 40kD protein that is essential for vegetative cell viability. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterized by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation.¡€0€ª€0€ €CDD¡€ €µ²¢€0€0€ €‚ pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit. Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription.¡€0€ª€0€ €CDD¡€ €µ³¢€0€0€ €‚pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.¡€0€ª€0€ €CDD¡€ €µ´¢€0€0€ €‚>pfam03155, Alg6_Alg8, ALG6, ALG8 glycosyltransferase family. N-linked (asparagine-linked) glycosylation of proteins is mediated by a highly conserved pathway in eukaryotes, in which a lipid (dolichol phosphate)-linked oligosaccharide is assembled at the endoplasmic reticulum membrane prior to the transfer of the oligosaccharide moiety to the target asparagine residues. This oligosaccharide is composed of Glc(3)Man(9)GlcNAc(2). The addition of the three glucose residues is the final series of steps in the synthesis of the oligosaccharide precursor. Alg6 transfers the first glucose residue, and Alg8 transfers the second one. In the human alg6 gene, a C->T transition, which causes Ala333 to be replaced with Val, has been identified as the cause of a congenital disorder of glycosylation, designated as type Ic OMIM:603147.¡€0€ª€0€ €CDD¡€ €µµ¢€0€0€ €‚+pfam03157, Glutenin_hmw, High molecular weight glutenin subunit. Members of this family include high molecular weight subunits of glutenin. This group of gluten proteins is thought to be largely responsible for the elastic properties of gluten, and hence, doughs. Indeed, glutenin high molecular weight subunits are classified as elastomeric proteins, because the glutenin network can withstand significant deformations without breaking, and return to the original conformation when the stress is removed. Elastomeric proteins differ considerably in amino acid sequence, but they are all polymers whose subunits consist of elastomeric domains, composed of repeated motifs, and non-elastic domains that mediate cross-linking between the subunits. The elastomeric domain motifs are all rich in glycine residues in addition to other hydrophobic residues. High molecular weight glutenin subunits have an extensive central elastomeric domain, flanked by two terminal non-elastic domains that form disulphide cross-links. The central elastomeric domain is characterized by the following three repeated motifs: PGQGQQ, GYYPTS[P/L]QQ, GQQ. It possesses overlapping beta-turns within and between the repeated motifs, and assumes a regular helical secondary structure with a diameter of approx. 1.9 nm and a pitch of approx. 1.5 nm.¡€0€ª€0€ €CDD¡€ €Jg¢€0€0€ €Úpfam03158, DUF249, Multigene family 530 protein. Members of this family are multigene family 530 proteins from African swine fever viruses. These proteins may be involved in promoting survival of infected macrophages.¡€0€ª€0€ €CDD¡€ €Jh¢€0€0€ €‚Ïpfam03159, XRN_N, XRN 5'-3' exonuclease N-terminus. This family aligns residues towards the N-terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity EC:3.1.11.-. Thus, the aligned region may be necessary for 5' to 3' exonuclease function. The family also contains several Xrn1 and Xrn2 proteins. The 5'-3' exoribonucleases Xrn1p and Xrn2p/Rat1p function in the degradation and processing of several classes of RNA in Saccharomyces cerevisiae. Xrn1p is the main enzyme catalyzing cytoplasmic mRNA degradation in multiple decay pathways, whereas Xrn2p/Rat1p functions in the processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus.¡€0€ª€0€ €CDD¡€ €µ¶¢€0€0€ €)pfam03160, Calx-beta, Calx-beta domain. ¡€0€ª€0€ €CDD¡€ €µ·¢€0€0€ €âpfam03161, LAGLIDADG_2, LAGLIDADG DNA endonuclease family. This is a family of site-specific DNA endonucleases encoded by DNA mobile elements. Similar to pfam00961, the members of this family are also LAGLIDADG endonucleases.¡€0€ª€0€ €CDD¡€ €µ¸¢€0€0€ €€pfam03162, Y_phosphatase2, Tyrosine phosphatase family. This family is closely related to the pfam00102 and pfam00782 families.¡€0€ª€0€ €CDD¡€ €µ~¢€0€0€ €‚1pfam03164, Mon1, Trafficking protein Mon1. Members of this family have been called SAND proteins although these proteins do not contain a SAND domain. In Saccharomyces cerevisiae a protein complex of Mon1 and Ccz1 functions with the small GTPase Ypt7 to mediate vesicle trafficking to the vacuole. The Mon1/Ccz1 complex is conserved in eukaryotic evolution and members of this family (previously known as DUF254) are distant homologs to domains of known structure that assemble into cargo vesicle adapter (AP) complexes. describes orthologues in Fugu rubripes.¡€0€ª€0€ €CDD¡€ €µ¹¢€0€0€ €‚:pfam03165, MH1, MH1 domain. The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localization signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx.¡€0€ª€0€ €CDD¡€ €µº¢€0€0€ €‚pfam03166, MH2, MH2 domain. This is the MH2 (MAD homology 2) domain found at the carboxy terminus of MAD related proteins such as Smads. This domain is separated from the MH1 domain by a non-conserved linker region. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers. Unlike MH1, MH2 does not bind DNA. The well-studied MH2 domain of Smad4 is composed of five alpha helices and three loops enclosing a beta sandwich. Smads are involved in the propagation of TGF-beta signals by direct association with the TGF-beta receptor kinase which phosphorylates the last two Ser of a conserved 'SSXS' motif located at the C-terminus of MH2.¡€0€ª€0€ €CDD¡€ €µ»¢€0€0€ €5pfam03167, UDG, Uracil DNA glycosylase superfamily. ¡€0€ª€0€ €CDD¡€ €µ¼¢€0€0€ €‚«pfam03168, LEA_2, Late embryogenesis abundant protein. Different types of LEA proteins are expressed at different stages of late embryogenesis in higher plant seed embryos and under conditions of dehydration stress. The function of these proteins is unknown. This family represents a group of LEA proteins that appear to be distinct from those in pfam02987. The family DUF1511, pfam07427, has now been merged into this family.¡€0€ª€0€ €CDD¡€ €µ½¢€0€0€ €‚Ëpfam03169, OPT, OPT oligopeptide transporter protein. The OPT family of oligopeptide transporters is distinct from the ABC pfam00005 and PTR pfam00854 transporter families. OPT transporters were first recognized in fungi (Candida albicans and Schizosaccharomyces pombe), but this alignment also includes orthologues from Arabidopsis thaliana. OPT transporters are thought to have 12-14 transmembrane domains and contain the following motif: SPYxEVRxxVxxxDDP.¡€0€ª€0€ €CDD¡€ €µ¾¢€0€0€ €‚Ôpfam03170, BcsB, Bacterial cellulose synthase subunit. This family includes bacterial proteins involved in cellulose synthesis. Cellulose synthesis has been identified in several bacteria. In Agrobacterium tumefaciens, for instance, cellulose has a pathogenic role: it allows the bacteria to bind tightly to their host plant cells. While several enzymatic steps are involved in cellulose synthesis, potentially the only step unique to this pathway is that catalyzed by cellulose synthase. This enzyme is a multi subunit complex. This family encodes a subunit that is thought to bind the positive effector cyclic di-GMP. This subunit is found in several different bacterial cellulose synthase enzymes. The first recognized sequence for this subunit is BcsB. In the AcsII cellulose synthase, this subunit and the subunit corresponding to BcsA are found in the same protein. Indeed, this alignment only includes the C-terminal half of the AcsAII synthase, which corresponds to BcsB.¡€0€ª€0€ €CDD¡€ €µ¿¢€0€0€ €‚epfam03171, 2OG-FeII_Oxy, 2OG-Fe(II) oxygenase superfamily. This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalyzing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB.¡€0€ª€0€ €CDD¡€ €µÀ¢€0€0€ €‚6pfam03172, HSR, HSR domain. The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots (NDs). An ND-targeting region that coincides with a homodimerization domain was mapped in Sp100. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins and constitute a novel protein motif, termed HSR domain (for homogeneously-staining region). The HSR domain has also been named ASS (AIRE, Sp-100 and Sp140). This domain is usually found at the amino terminus of proteins that contain a SAND domain pfam01342.¡€0€ª€0€ €CDD¡€ €µÁ¢€0€0€ €‚hpfam03173, CHB_HEX, Putative carbohydrate binding domain. This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi. This suggests that this may be a carbohydrate binding domain.¡€0€ª€0€ €CDD¡€ €µÂ¢€0€0€ €‚pfam03174, CHB_HEX_C, Chitobiase/beta-hexosaminidase C-terminal domain. This short domain represents the C terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure. The function of this domain is unknown.¡€0€ª€0€ €CDD¡€ €µÃ¢€0€0€ €åpfam03175, DNA_pol_B_2, DNA polymerase type B, organellar and viral. Like pfam00136, members of this family are also DNA polymerase type B proteins. Those included here are found in plant and fungal mitochondria, and in viruses.¡€0€ª€0€ €CDD¡€ €Jv¢€0€0€ €‚Ypfam03176, MMPL, MMPL family. Members of this family are putative integral membrane proteins from bacteria. Several of the members are mycobacterial proteins. Many of the proteins contain two copies of this aligned region. The function of these proteins is not known, although it has been suggested that they may be involved in lipid transport.¡€0€ª€0€ €CDD¡€ €µÄ¢€0€0€ €‚dpfam03177, Nucleoporin_C, Non-repetitive/WGA-negative nucleoporin C-terminal. This is the C-termainl half of a family of nucleoporin proteins. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells, and mediate bidirectional nucleocytoplasmic transport, especially of mRNA and proteins. Two nucleoporin classes are known: one is characterized by the FG repeat pfam03093; the other is represented by this family, and lacks any repeats. RNA undergoing nuclear export first encounters the basket of the nuclear pore and many nucleoporins are accessible on the basket side of the pore.¡€0€ª€0€ €CDD¡€ €µÅ¢€0€0€ €‚Âpfam03178, CPSF_A, CPSF A subunit region. This family includes a region that lies towards the C-terminus of the cleavage and polyadenylation specificity factor (CPSF) A (160 kDa) subunit. CPSF is involved in mRNA polyadenylation and binds the AAUAAA conserved sequence in pre-mRNA. CPSF has also been found to be necessary for splicing of single-intron pre-mRNAs. The function of the aligned region is unknown but may be involved in RNA/DNA binding.¡€0€ª€0€ €CDD¡€ €µÆ¢€0€0€ €‚ƒpfam03179, V-ATPase_G, Vacuolar (H+)-ATPase G subunit. This family represents the eukaryotic vacuolar (H+)-ATPase (V-ATPase) G subunit. V-ATPases generate an acidic environment in several intracellular compartments. Correspondingly, they are found as membrane-attached proteins in several organelles. They are also found in the plasma membranes of some specialized cells. V-ATPases consist of peripheral (V1) and membrane integral (V0) heteromultimeric complexes. The G subunit is part of the V1 subunit, but is also thought to be strongly attached to the V0 complex. It may be involved in the coupling of ATP degradation to H+ translocation.¡€0€ª€0€ €CDD¡€ €µÇ¢€0€0€ €‚"pfam03180, Lipoprotein_9, NLPA lipoprotein. This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to pfam00497 which are solute binding proteins.¡€0€ª€0€ €CDD¡€ €J{¢€0€0€ €‚˜pfam03181, BURP, BURP domain. The BURP domain is found at the C-terminus of several different plant proteins. It was named after the proteins in which it was first identified: the BNM2 clone-derived protein from Brassica napus; USPs and USP-like proteins; RD22 from Arabidopsis thaliana; and PG1beta from Lycopersicon esculentum. This domain is around 230 amino acid residues long. It possesses the following conserved features: two phenylalanine residues at its N-terminus; two cysteine residues; and four repeated cysteine-histidine motifs, arranged as: CH-X(10)-CH-X(25-27)-CH-X(25-26)-CH, where X can be any amino acid. The function of this domain is unknown.¡€0€ª€0€ €CDD¡€ €µÈ¢€0€0€ €3pfam03183, Borrelia_rep, Borrelia repeat protein. ¡€0€ª€0€ €CDD¡€ €µ‘¢€0€0€ €‚ pfam03184, DDE_1, DDE superfamily endonuclease. This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere.¡€0€ª€0€ €CDD¡€ €µÉ¢€0€0€ €Epfam03185, CaKB, Calcium-activated potassium channel, beta subunit. ¡€0€ª€0€ €CDD¡€ €µÊ¢€0€0€ €‚upfam03186, CobD_Cbib, CobD/Cbib protein. This family includes CobD proteins from a number of bacteria, in Salmonella this protein is called Cbib. Salmonella CobD is a different protein. This protein is involved in cobalamin biosynthesis and is probably an enzyme responsible for the conversion of adenosylcobyric acid to adenosylcobinamide or adenosylcobinamide phosphate.¡€0€ª€0€ €CDD¡€ €µË¢€0€0€ €5pfam03187, Corona_I, Corona nucleocapsid I protein. ¡€0€ª€0€ €CDD¡€ €J€¢€0€0€ €‚Bpfam03188, Cytochrom_B561, Eukaryotic cytochrome b561. Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, that binds two heme groups non-covalently. This is a eukaryotic family. Members of the 'prokaryotic cytochrome b561' family can be found in Pfam: PF01292.¡€0€ª€0€ €CDD¡€ €µÌ¢€0€0€ €"pfam03189, Otopetrin, Otopetrin. ¡€0€ª€0€ €CDD¡€ €µÍ¢€0€0€ €Apfam03190, Thioredox_DsbH, Protein of unknown function, DUF255. ¡€0€ª€0€ €CDD¡€ €µÎ¢€0€0€ €Dpfam03192, DUF257, Pyrococcus protein of unknown function, DUF257. ¡€0€ª€0€ €CDD¡€ €µÏ¢€0€0€ €9pfam03193, DUF258, Protein of unknown function, DUF258. ¡€0€ª€0€ €CDD¡€ €J…¢€0€0€ €‚pfam03194, LUC7, LUC7 N_terminus. This family contains the N terminal region of several LUC7 protein homologs and only contains eukaryotic proteins. LUC7 has been shown to be a U1 snRNA associated protein with a role in splice site recognition. The family also contains human and mouse LUC7 like (LUC7L) proteins and human cisplatin resistance-associated overexpressed protein (CROP).¡€0€ª€0€ €CDD¡€ €µÐ¢€0€0€ €8pfam03195, DUF260, Protein of unknown function DUF260. ¡€0€ª€0€ €CDD¡€ €µÑ¢€0€0€ €9pfam03196, DUF261, Protein of unknown function, DUF261. ¡€0€ª€0€ €CDD¡€ €Jˆ¢€0€0€ €.pfam03197, FRD2, Bacteriophage FRD2 protein. ¡€0€ª€0€ €CDD¡€ €J‰¢€0€0€ €úpfam03198, Glyco_hydro_72, Glucanosyltransferase. This is a family of glycosylphosphatidylinositol-anchored beta(1-3)glucanosyltransferases. The active site residues in the Aspergillus fumigatus example are the two glutamate residues at 160 and 261.¡€0€ª€0€ €CDD¡€ €µÒ¢€0€0€ €;pfam03199, GSH_synthase, Eukaryotic glutathione synthase. ¡€0€ª€0€ €CDD¡€ €µÓ¢€0€0€ €‚¼pfam03200, Glyco_hydro_63, Glycosyl hydrolase family 63 C-terminal domain. This is a family of eukaryotic enzymes belonging to glycosyl hydrolase family 63. They catalyze the specific cleavage of the non-reducing terminal glucose residue from Glc(3)Man(9)GlcNAc(2). Mannosyl oligosaccharide glucosidase EC:3.2.1.106 is the first enzyme in the N-linked oligosaccharide processing pathway. This family represents the C-terminal catalytic domain.¡€0€ª€0€ €CDD¡€ €µÔ¢€0€0€ €Tpfam03201, HMD, H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase. ¡€0€ª€0€ €CDD¡€ €µÕ¢€0€0€ €Ppfam03202, Lipoprotein_10, Putative mycoplasma lipoprotein, C-terminal region. ¡€0€ª€0€ €CDD¡€ €µÖ¢€0€0€ €3pfam03203, MerC, MerC mercury resistance protein. ¡€0€ª€0€ €CDD¡€ €µ×¢€0€0€ €ipfam03205, MobB, Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop.¡€0€ª€0€ €CDD¡€ €µØ¢€0€0€ €‚Rpfam03206, NifW, Nitrogen fixation protein NifW. Nitrogenase is a complex metalloenzyme composed of two proteins designated the Fe-protein and the MoFe-protein. Apart from these two proteins, a number of accessory proteins are essential for the maturation and assembly of nitrogenase. Even though experimental evidence suggests that these accessory proteins are required for nitrogenase activity, the exact roles played by many of these proteins in the functions of nitrogenase are unclear. Using yeast two-hybrid screening it has been shown that NifW can interact with itself as well as NifZ.¡€0€ª€0€ €CDD¡€ €µÙ¢€0€0€ €;pfam03207, OspD, Borrelia outer surface protein D (OspD). ¡€0€ª€0€ €CDD¡€ €µÚ¢€0€0€ €‚pfam03208, PRA1, PRA1 family protein. This family includes the PRA1 (Prenylated rab acceptor) protein which is a Rab guanine dissociation inhibitor (GDI) displacement factor. This family also includes the glutamate transporter EAAC1 interacting protein GTRAP3-18.¡€0€ª€0€ €CDD¡€ €µÛ¢€0€0€ €hpfam03209, PUCC, PUCC protein. This protein is required for high-level transcription of the PUC operon.¡€0€ª€0€ €CDD¡€ €µÜ¢€0€0€ €‚-pfam03210, Paramyx_P_V_C, Paramyxovirus P/V phosphoprotein C-terminal. Paramyxoviridae P genes are able to generate more than one product, using alternative reading frames and RNA editing. The P gene encodes the structural phosphoprotein P. In addition, it encodes several non-structural proteins present in the infected cell but not in the virus particle. This family includes phosphoprotein P and the non-structural phosphoprotein V from different paramyxoviruses. Phosphoprotein P is essential for the activity of the RNA polymerase complex which it forms with another subunit, L pfam00946. Although all the catalytic activities of the polymerase are associated with the L subunit, its function requires specific interactions with phosphoprotein P. The P and V phosphoproteins are amino co-terminal, but diverge at their C-termini. This difference is generated by an RNA-editing mechanism in which one or two non-templated G residues are inserted into P-gene-derived mRNA. In measles virus and Sendai virus, one G residue is inserted and the edited transcript encodes the V protein. In mumps, simian virus type 5 and Newcastle disease virus, two G residues are inserted, and the edited transcript codes for the P protein. Being phosphoproteins, both P and V are rich in serine and threonine residues over their whole lengths. In addition, the V proteins are rich in cysteine residues at the C-termini. This C-terminal region of the P phosphoprotein is likely to be the nucleocapsid-binding domain, and is found to be intrinsically disordered and thus liable to induced folding.¡€0€ª€0€ €CDD¡€ €J•¢€0€0€ €*pfam03211, Pectate_lyase, Pectate lyase. ¡€0€ª€0€ €CDD¡€ €µÝ¢€0€0€ €"pfam03212, Pertactin, Pertactin. ¡€0€ª€0€ €CDD¡€ €µÞ¢€0€0€ €+pfam03213, Pox_P35, Poxvirus P35 protein. ¡€0€ª€0€ €CDD¡€ €J˜¢€0€0€ €6pfam03214, RGP, Reversibly glycosylated polypeptide. ¡€0€ª€0€ €CDD¡€ €µß¢€0€0€ €8pfam03215, Rad17, Rad17 cell cycle checkpoint protein. ¡€0€ª€0€ €CDD¡€ €×›¢€0€0€ €6pfam03216, Rhabdo_ncap_2, Rhabdovirus nucleoprotein. ¡€0€ª€0€ €CDD¡€ €Jš¢€0€0€ €3pfam03217, SLAP, Bacterial surface layer protein. ¡€0€ª€0€ €CDD¡€ €J›¢€0€0€ €*pfam03219, TLC, TLC ATP/ADP transporter. ¡€0€ª€0€ €CDD¡€ €µà¢€0€0€ €6pfam03220, Tombus_P19, Tombusvirus P19 core protein. ¡€0€ª€0€ €CDD¡€ €J¢€0€0€ €=pfam03221, HTH_Tnp_Tc5, Tc5 transposase DNA-binding domain. ¡€0€ª€0€ €CDD¡€ €µá¢€0€0€ €?pfam03222, Trp_Tyr_perm, Tryptophan/tyrosine permease family. ¡€0€ª€0€ €CDD¡€ €µâ¢€0€0€ €,pfam03223, V-ATPase_C, V-ATPase subunit C. ¡€0€ª€0€ €CDD¡€ €µã¢€0€0€ €‚þpfam03224, V-ATPase_H_N, V-ATPase subunit H. The yeast Saccharomyces cerevisiae vacuolar H+-ATPase (V-ATPase) is a multisubunit complex responsible for acidifying organelles. It functions as an ATP dependent proton pump that transports protons across a lipid bilayer. This domain corresponds to the N terminal domain of the H subunit of V-ATPase. The N-terminal domain is required for the activation of the complex whereas the C-terminal domain is required for coupling ATP hydrolysis to proton translocation.¡€0€ª€0€ €CDD¡€ €µä¢€0€0€ €Apfam03225, Viral_Hsp90, Viral heat shock protein Hsp90 homolog. ¡€0€ª€0€ €CDD¡€ €ס¢€0€0€ €‚3pfam03226, Yippee-Mis18, Yippee zinc-binding/DNA-binding /Mis18, centromere assembly. This family includes both Yippee-type proteins and Mis18 kinetochore proteins. Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of a small complex with Mis18-binding protein. Mis18-alpha is found to interact with DNA de-methylases through a Leu-rich region located at its carboxyl terminus. This entry also includes the CULT domain proteins such as Cereblon.¡€0€ª€0€ €CDD¡€ €µå¢€0€0€ €‚pfam03227, GILT, Gamma interferon inducible lysosomal thiol reductase (GILT). This family includes the two characterized human gamma-interferon-inducible lysosomal thiol reductase (GILT) sequences. It also contains several other eukaryotic putative proteins with similarity to GILT. The aligned region contains three conserved cysteine residues. In addition, the two GILT sequences possess a C-X(2)-C motif that is shared by some of the other sequences in the family. This motif is thought to be associated with disulphide bond reduction.¡€0€ª€0€ €CDD¡€ €µæ¢€0€0€ €‚Xpfam03228, Adeno_VII, Adenoviral core protein VII. The function of this protein is unknown. It has a conserved amino terminus of 50 residues followed by a positively charged tail, suggesting it may interact with nucleic acid. The major core protein of the adenovirus, protein VII, was found to be associated with viral DNA throughout infection. The precursor to protein VII were shown to be in vivo and in vitro acceptors of ADP-ribose. The ADP-ribosylated core proteins were assembled into mature virus particles. ADP-ribosylation of adenovirus core proteins may have a role in virus decapsidation.¡€0€ª€0€ €CDD¡€ €J¤¢€0€0€ €1pfam03229, Alpha_GJ, Alphavirus glycoprotein J. ¡€0€ª€0€ €CDD¡€ €×¥¢€0€0€ €ôpfam03230, Antirestrict, Antirestriction protein. This family includes various protein that are involved in antirestriction. The ArdB protein efficiently inhibits restriction by members of the three known families of type I systems of E. coli.¡€0€ª€0€ €CDD¡€ €µç¢€0€0€ €‚—pfam03231, Bunya_NS-S_2, Bunyavirus non-structural protein NS-S. This family represents the Bunyavirus NS-S family. Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase.¡€0€ª€0€ €CDD¡€ €ק¢€0€0€ €Ùpfam03232, COQ7, Ubiquinone biosynthesis protein COQ7. Members of this family contain two repeats of about 90 amino acids, that contains two conserved motifs. One of these DXEXXH may be part of an enzyme active site.¡€0€ª€0€ €CDD¡€ €µè¢€0€0€ €‚pfam03233, Cauli_AT, Aphid transmission protein. This protein is found in various caulimoviruses. It codes for an 18 kDa protein (PII), which is dispensable for infection but which is required for aphid transmission of the virus. This protein interacts with the PIII protein.¡€0€ª€0€ €CDD¡€ €ש¢€0€0€ €‚/pfam03234, CDC37_N, Cdc37 N terminal kinase binding. Cdc37 is a molecular chaperone required for the activity of numerous eukaryotic protein kinases. This domain corresponds to the N terminal domain which binds predominantly to protein kinases and is found N terminal to the Hsp (Heat shocked protein) 90-binding domain pfam08565. Expression of a construct consisting of only the N-terminal domain of Saccharomyces pombe Cdc37 results in cellular viability. This indicates that interactions with the cochaperone Hsp90 may not be essential for Cdc37 function.¡€0€ª€0€ €CDD¡€ €µé¢€0€0€ €8pfam03235, DUF262, Protein of unknown function DUF262. ¡€0€ª€0€ €CDD¡€ €µê¢€0€0€ €epfam03237, Terminase_6, Terminase-like family. This family represents a group of terminase proteins.¡€0€ª€0€ €CDD¡€ €µë¢€0€0€ €±pfam03238, ESAG1, ESAG protein. Expression-site-associated gene (ESAG) proteins are thought to be involved in VSG activation. This family includes ESAG 117A as well as ESAG IM.¡€0€ª€0€ €CDD¡€ €Jª¢€0€0€ €-pfam03239, FTR1, Iron permease FTR1 family. ¡€0€ª€0€ €CDD¡€ €×®¢€0€0€ €‚pfam03241, HpaB, 4-hydroxyphenylacetate 3-hydroxylase C terminal. HpaB encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli. HpaB is part of a heterodimeric enzyme that also requires HpaC. The enzyme is NADH-dependent and uses FAD as the redox chromophore. This family also includes PvcC may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis.¡€0€ª€0€ €CDD¡€ €µì¢€0€0€ €‚pfam03242, LEA_3, Late embryogenesis abundant protein. Members of this family are similar to late embryogenesis abundant proteins. Members of the family have been isolated in a number of different screens. However, the molecular function of these proteins remains obscure.¡€0€ª€0€ €CDD¡€ €µí¢€0€0€ €špfam03243, MerB, Alkylmercury lyase. Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate.¡€0€ª€0€ €CDD¡€ €µî¢€0€0€ €Ðpfam03244, PSI_PsaH, Photosystem I reaction centre subunit VI. Photosystem I (PSI) is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin.¡€0€ª€0€ €CDD¡€ €µï¢€0€0€ €‚¨pfam03245, Phage_lysis, Bacteriophage Rz lysis protein. This protein is involved in host lysis. This family is not considered to be a peptidase according to the MEROPs database. This family Rz and the Rz1 protein (pfam06085) represent a unique example of two genes located in different reading frames in the same nucleotide sequence, which encode different proteins that are both required in the same physiological pathway.¡€0€ª€0€ €CDD¡€ €J¯¢€0€0€ €;pfam03246, Pneumo_ncap, Pneumovirus nucleocapsid protein. ¡€0€ª€0€ €CDD¡€ €µð¢€0€0€ €ñpfam03247, Prothymosin, Prothymosin/parathymosin family. Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation.¡€0€ª€0€ €CDD¡€ €µñ¢€0€0€ €ïpfam03248, Rer1, Rer1 family. RER1 family protein are involved in involved in the retrieval of some endoplasmic reticulum membrane proteins from the early golgi compartment. The C terminus of yeast Rer1p interacts with a coatomer complex.¡€0€ª€0€ €CDD¡€ €µò¢€0€0€ €‚pfam03249, TSA, Type specific antigen. There are several antigenic variants in Rickettsia tsutsugamushi, and a type-specific antigen (TSA) of 56-kilodaltons located on the rickettsial surface is responsible for the variation. TSA proteins are probably integral membrane proteins.¡€0€ª€0€ €CDD¡€ €J³¢€0€0€ €‚apfam03250, Tropomodulin, Tropomodulin. Tropomodulin is a novel tropomyosin regulatory protein that binds to the end of erythrocyte tropomyosin and blocks head-to-tail association of tropomyosin along actin filaments. Limited proteolysis shows this protein is composed of two domains. The amino terminal domain contains the tropomyosin binding function.¡€0€ª€0€ €CDD¡€ €µó¢€0€0€ €‚‚pfam03251, Tymo_45kd_70kd, Tymovirus 45/70Kd protein. Tymoviruses are single stranded RNA viruses. This family includes a protein of unknown function that has been named based on its molecular weight. Tymoviruses such as the ononis yellow mosaic tymovirus encode only three proteins. Of these two are overlapping this protein overlaps a larger ORF that is thought to be the polymerase.¡€0€ª€0€ €CDD¡€ €Jµ¢€0€0€ €spfam03252, Herpes_UL21, Herpesvirus UL21. The UL21 protein appears to be a dispensable component in herpesviruses.¡€0€ª€0€ €CDD¡€ €J¶¢€0€0€ €‚pfam03253, UT, Urea transporter. Members of this family transport urea across membranes. The family includes a bacterial homolog.¡€0€ª€0€ €CDD¡€ €µô¢€0€0€ €‚wpfam03254, XG_FTase, Xyloglucan fucosyltransferase. Plant cell walls are crucial for development, signal transduction, and disease resistance in plants. Cell walls are made of cellulose, hemicelluloses, and pectins. Xyloglucan (XG), the principal load-bearing hemicellulose of dicotyledonous plants, has a terminal fucosyl residue. This fucosyltransferase adds this residue.¡€0€ª€0€ €CDD¡€ €µõ¢€0€0€ €°pfam03255, ACCA, Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit. Acetyl co-enzyme A carboxylase carboxyltransferase is composed of an alpha and beta subunit.¡€0€ª€0€ €CDD¡€ €µö¢€0€0€ €Epfam03256, ANAPC10, Anaphase-promoting complex, subunit 10 (APC10). ¡€0€ª€0€ €CDD¡€ €µ÷¢€0€0€ €ˆpfam03257, Adhesin_P1, Mycoplasma adhesin P1. This family corresponds to a short 100 residue region found in adhesins from Mycoplasmas.¡€0€ª€0€ €CDD¡€ €J»¢€0€0€ €ppfam03258, Baculo_FP, Baculovirus FP protein. The FP protein is missing in baculovirus (Few Polyhedra) mutants.¡€0€ª€0€ €CDD¡€ €J¼¢€0€0€ €‚£pfam03259, Robl_LC7, Roadblock/LC7 domain. This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions. This family also includes Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus, a protein involved in gliding motility. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.¡€0€ª€0€ €CDD¡€ €µø¢€0€0€ €Spfam03260, Lipoprotein_11, Lepidopteran low molecular weight (30 kD) lipoprotein. ¡€0€ª€0€ €CDD¡€ €µù¢€0€0€ €Ipfam03261, CDK5_activator, Cyclin-dependent kinase 5 activator protein. ¡€0€ª€0€ €CDD¡€ €µú¢€0€0€ €5pfam03262, Corona_6B_7B, Coronavirus 6B/7B protein. ¡€0€ª€0€ €CDD¡€ €JÀ¢€0€0€ €\pfam03263, Cucumo_2B, Cucumovirus protein 2B. This protein may be a viral movement protein.¡€0€ª€0€ €CDD¡€ €JÁ¢€0€0€ €‚Mpfam03264, Cytochrom_NNT, NapC/NirT cytochrome c family, N-terminal region. Within the NapC/NirT family of cytochrome c proteins, some members, such as NapC and NirT, bind four haem groups, while others, such as TorC, bind five haems. This family aligns the common N-terminal region that contains four haem-binding C-X(2)-CH motifs.¡€0€ª€0€ €CDD¡€ €µû¢€0€0€ €,pfam03265, DNase_II, Deoxyribonuclease II. ¡€0€ª€0€ €CDD¡€ €µü¢€0€0€ €‚6pfam03266, NTPase_1, NTPase. This domain is found across all species from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue.¡€0€ª€0€ €CDD¡€ €µý¢€0€0€ €Hpfam03268, DUF267, Caenorhabditis protein of unknown function, DUF267. ¡€0€ª€0€ €CDD¡€ €µþ¢€0€0€ €Hpfam03269, DUF268, Caenorhabditis protein of unknown function, DUF268. ¡€0€ª€0€ €CDD¡€ €µÿ¢€0€0€ €¬pfam03270, DUF269, Protein of unknown function, DUF269. Members of this family may be involved in nitrogen fixation, since they are found within nitrogen fixation operons.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €‚êpfam03271, EB1, EB1-like C-terminal motif. This motif is found at the C-terminus of proteins that are related to the EB1 protein. The EB1 proteins contain an N-terminal CH domain pfam00307. The human EB1 protein was originally discovered as a protein interacting with the C-terminus of the APC protein. This interaction is often disrupted in colon cancer, due to deletions affecting the APC C-terminus. Several EB1 orthologues are also included in this family. The interaction between EB1 and APC has been shown to have a potent synergistic effect on microtubule polymerization. Neither of EB1 or APC alone has this effect. It is thought that EB1 targets APC to the + ends of microtubules, where APC promotes microtubule polymerization. This process is regulated by APC phosphorylation by Cdc2, which disrupts APC-EB1 binding. Human EB1 protein can functionally substitute for the yeast EB1 homolog Mal3. In addition, Mal3 can substitute for human EB1 in promoting microtubule polymerization with APC.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €‚ pfam03272, Mucin_bdg, Putative mucin or carbohydrate-binding module. This family is the putative binding domain for the substrates of enhancin, and other similar metallopeptidases. This is not the enzymically active, peptidase, part of the proteins - see pfam13402.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €pfam03273, Baculo_gp64, Baculovirus gp64 envelope glycoprotein family. This family includes the gp64 glycoprotein from baculovirus as well as other viruses.¡€0€ª€0€ €CDD¡€ €JÊ¢€0€0€ €4pfam03274, Foamy_BEL, Foamy virus BEL 1/2 protein. ¡€0€ª€0€ €CDD¡€ €JË¢€0€0€ €-pfam03275, GLF, UDP-galactopyranose mutase. ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €/pfam03276, Gag_spuma, Spumavirus gag protein. ¡€0€ª€0€ €CDD¡€ €JÍ¢€0€0€ €0pfam03277, Herpes_UL4, Herpesvirus UL4 family. ¡€0€ª€0€ €CDD¡€ €J΢€0€0€ €‚$pfam03278, IpaB_EvcA, IpaB/EvcA family. This family includes IpaB, which is an invasion plasmid antigen from Shigella, as well as EvcA from E. coli. Members of this family seem to be involved in pathogenicity of some enterobacteria. However the exact function of this component is not clear.¡€0€ª€0€ €CDD¡€ €JÏ¢€0€0€ €Mpfam03279, Lip_A_acyltrans, Bacterial lipid A biosynthesis acyltransferase. ¡€0€ª€0€ €CDD¡€ €JТ€0€0€ €Cpfam03280, Lipase_chap, Proteobacterial lipase chaperone protein. ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €±pfam03281, Mab-21, Mab-21 protein. This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €'pfam03283, PAE, Pectinacetylesterase. ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €;pfam03284, PHZA_PHZB, Phenazine biosynthesis protein A/B. ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €$pfam03285, Paralemmin, Paralemmin. ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €6pfam03286, Pox_Ag35, Pox virus Ag35 surface protein. ¡€0€ª€0€ €CDD¡€ €JÖ¢€0€0€ €1pfam03287, Pox_C7_F8A, Poxvirus C7/F8A protein. ¡€0€ª€0€ €CDD¡€ €¶ ¢€0€0€ €‚-pfam03288, Pox_D5, Poxvirus D5 protein-like. This family includes D5 from Poxviruses which is necessary for viral DNA replication, and is a nucleic acid independent nucleoside triphosphatase. Members of this family are also found outside of poxviruses. This domain is a DNA-binding winged HTH domain.¡€0€ª€0€ €CDD¡€ €¶ ¢€0€0€ €)pfam03289, Pox_I1, Poxvirus protein I1. ¡€0€ª€0€ €CDD¡€ €JÙ¢€0€0€ €Cpfam03290, Peptidase_C57, Vaccinia virus I7 processing peptidase. ¡€0€ª€0€ €CDD¡€ €JÚ¢€0€0€ €[pfam03291, Pox_MCEL, mRNA capping enzyme. This family of enzymes are related to pfam03919.¡€0€ª€0€ €CDD¡€ €JÛ¢€0€0€ €6pfam03292, Pox_P4B, Poxvirus P4B major core protein. ¡€0€ª€0€ €CDD¡€ €JÜ¢€0€0€ €Npfam03293, Pox_RNA_pol, Poxvirus DNA-directed RNA polymerase, 18 kD subunit. ¡€0€ª€0€ €CDD¡€ €JÝ¢€0€0€ €Zpfam03294, Pox_Rap94, RNA polymerase-associated transcription specificity factor, Rap94. ¡€0€ª€0€ €CDD¡€ €JÞ¢€0€0€ €Fpfam03295, Pox_TAA1, Poxvirus trans-activator protein A1 C-terminal. ¡€0€ª€0€ €CDD¡€ €Jߢ€0€0€ €Vpfam03296, Pox_polyA_pol, Poxvirus poly(A) polymerase nucleotidyltransferase domain. ¡€0€ª€0€ €CDD¡€ €Jࢀ0€0€ €2pfam03297, Ribosomal_S25, S25 ribosomal protein. ¡€0€ª€0€ €CDD¡€ €¶ ¢€0€0€ €1pfam03298, Stanniocalcin, Stanniocalcin family. ¡€0€ª€0€ €CDD¡€ €¶ ¢€0€0€ €0pfam03299, TF_AP-2, Transcription factor AP-2. ¡€0€ª€0€ €CDD¡€ €¶ ¢€0€0€ €Hpfam03300, Tenui_NS4, Tenuivirus non-structural, movement protein NS4. ¡€0€ª€0€ €CDD¡€ €J䢀0€0€ €9pfam03301, Trp_dioxygenase, Tryptophan 2,3-dioxygenase. ¡€0€ª€0€ €CDD¡€ €J墀0€0€ €;pfam03302, VSP, Giardia variant-specific surface protein. ¡€0€ª€0€ €CDD¡€ €:º¢€0€0€ €}pfam03303, WTF, WTF protein. This is a family of hypothetical Schizosaccharomyces pombe proteins. Their function is unknown.¡€0€ª€0€ €CDD¡€ €J梀0€0€ €‚Žpfam03304, Mlp, Mlp lipoprotein family. The Mlp (for Multicopy Lipoprotein) family of lipoproteins is found in Borrelia species. This family were previously known as 2.9 lipoprotein genes. These surface expressed genes may represent new candidate vaccinogens for Lyme disease. Members of this family generally are downstream of four ORFs called A,B,C and D that are involved in hemolytic activity.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €špfam03305, Lipoprotein_X, Mycoplasma MG185/MG260 protein. Most of the aligned regions in this family are found towards the middle of the member proteins.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €=pfam03306, AAL_decarboxy, Alpha-acetolactate decarboxylase. ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €Cpfam03307, Adeno_E3_15_3, Adenovirus 15.3kD protein in E3 region. ¡€0€ª€0€ €CDD¡€ €Jꢀ0€0€ €Òpfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems.¡€0€ª€0€ €CDD¡€ €J뢀0€0€ €Äpfam03309, Pan_kinase, Type III pantothenate kinase. Type III pantothenate kinase catalyzes the phosphorylation of pantothenate (Pan), the first step in the universal pathway of CoA biosynthesis.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €>pfam03310, Cauli_DNA-bind, Caulimovirus DNA-binding protein. ¡€0€ª€0€ €CDD¡€ €××¢€0€0€ €*pfam03311, Cornichon, Cornichon protein. ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €‚pfam03312, DUF272, Protein of unknown function (DUF272). This family of proteins is restricted to C.elegans and has no known function. The protein contains a ubiquitin fold. The GO annotation for the protein indicates that it has a function in nematode larval development.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €‚9pfam03313, SDH_alpha, Serine dehydratase alpha chain. L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyzes the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €9pfam03314, DUF273, Protein of unknown function, DUF273. ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €‚7pfam03315, SDH_beta, Serine dehydratase beta chain. L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyzes the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €Zpfam03317, ELF, ELF protein. This is a family of hypothetical proteins from cereal crops.¡€0€ª€0€ €CDD¡€ €Jò¢€0€0€ €pfam03318, ETX_MTX2, Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2. This family appears to be distantly related to pfam01117.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €‚&pfam03319, EutN_CcmL, Ethanolamine utilisation protein EutN/carboxysome. The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (Structure 2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the center. this suggests that EutN forms a pore, with an opening of 26 Angstrom in diameter on one face and 14 Angstrom on the other face. EutN is involved in the cobalamin-dependent degradation of ethanolamine.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €Npfam03320, FBPase_glpX, Bacterial fructose-1,6-bisphosphatase, glpX-encoded. ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €0pfam03321, GH3, GH3 auxin-responsive promoter. ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €Gpfam03323, GerA, Bacillus/Clostridium GerA spore germination protein. ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €’pfam03324, Herpes_HEPA, Herpesvirus DNA helicase/primase complex associated protein. This family includes HSV UL8, EHV-1 54, VZV 52 AND HCMV 102.¡€0€ª€0€ €CDD¡€ €Jø¢€0€0€ €†pfam03325, Herpes_PAP, Herpesvirus polymerase accessory protein. The same proteins are also known as polymerase processivity factors.¡€0€ª€0€ €CDD¡€ €Jù¢€0€0€ €¬pfam03326, Herpes_TAF50, Herpesvirus transcription activation factor (transactivator). This family includes EBV BRLF1 and similar ORF 50 proteins from other herpesviruses.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €Bpfam03327, Herpes_VP19C, Herpesvirus capsid shell protein VP19C. ¡€0€ª€0€ €CDD¡€ €Jû¢€0€0€ €ªpfam03328, HpcH_HpaI, HpcH/HpaI aldolase/citrate lyase family. This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase and 4-hydroxy-2-oxovalerate aldolase.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €‚pfam03330, DPBB_1, Lytic transglycolase. Rare lipoprotein A (RlpA) contains a conserved region that has the double-psi beta-barrel (DPBB) fold. The function of RlpA is not well understood, but it has been shown to act as a prc mutant suppressor in Escherichia coli. The DPBB fold is often an enzymatic domain. The members of this family are quite diverse, and if catalytic this family may contain several different functions. Another example of this domain is found in the N terminus of pollen allergen. Recent studies show that the full-length RlpA protein from Pseudomonas Aeruginosa is an outer membrane protein that is a lytic transglycolase with specificity for peptidoglycan lacking stem peptides. Residue D157 in UniProtKB:Q9X6V6 is critical for lytic activity.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €œpfam03331, LpxC, UDP-3-O-acyl N-acetylglycosamine deacetylase. The enzymes in this family catalyze the second step in the biosynthetic pathway for lipid A.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €Ôpfam03332, PMM, Eukaryotic phosphomannomutase. This enzyme EC:5.4.2.8 is involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions.¡€0€ª€0€ €CDD¡€ €Jÿ¢€0€0€ €pfam03333, PapB, Adhesin biosynthesis transcription regulatory protein. This family includes PapB, DaaA, FanA, FanB, and AfaA.¡€0€ª€0€ €CDD¡€ €¶ ¢€0€0€ €§pfam03334, PhaG_MnhG_YufB, Na+/H+ antiporter subunit. This family includes PhaG from Rhizobium meliloti, MnhG from Staphylococcus aureus, YufB from Bacillus subtilis.¡€0€ª€0€ €CDD¡€ €¶!¢€0€0€ €2pfam03335, Phage_fiber, Phage tail fibre repeat. ¡€0€ª€0€ €CDD¡€ €K¢€0€0€ €1pfam03336, Pox_C4_C10, Poxvirus C4/C10 protein. ¡€0€ª€0€ €CDD¡€ €K¢€0€0€ €-pfam03337, Pox_F12L, Poxvirus F12L protein. ¡€0€ª€0€ €CDD¡€ €K¢€0€0€ €)pfam03338, Pox_J1, Poxvirus J1 protein. ¡€0€ª€0€ €CDD¡€ €K¢€0€0€ €1pfam03339, Pox_L3_FP4, Poxvirus L3/FP4 protein. ¡€0€ª€0€ €CDD¡€ €K¢€0€0€ €=pfam03340, Pox_Rif, Poxvirus rifampicin resistance protein. ¡€0€ª€0€ €CDD¡€ €K¢€0€0€ €‚Ãpfam03341, Pox_mRNA-cap, Poxvirus mRNA capping enzyme, small subunit. The small subunit of the poxvirus mRNA capping enzyme has been found to have a structure which suggests that it started life as an RNA cap 2-prime O-methyltransferase. It has subsequently evolved to a catalytically inactive form that has been retained in order to help stabilize the large subunit, D1, and to enhance its methyltransferase activity through an allosteric mechanism.¡€0€ª€0€ €CDD¡€ €K¢€0€0€ €Ypfam03342, Rhabdo_M1, Rhabdovirus M1 matrix protein (M1 polymerase-associated protein). ¡€0€ª€0€ €CDD¡€ €K ¢€0€0€ €‚>pfam03343, SART-1, SART-1 family. SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing. It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae. SART-1 is a known tumor antigen in a range of cancers recognized by T cells.¡€0€ª€0€ €CDD¡€ €¶"¢€0€0€ €‚1pfam03344, Daxx, Daxx N-terminal Rassf1C-interacting domain. The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis. Daxx forms a complex with Axin. Remodelling of the family to a short domain based on the Structure 2kzs structure gives a more representative family. DAXX is a scaffold protein shown to play diverse roles in transcription and cell cycle regulation. This N-terminal domain folds into a left-handed four-helix bundle (H1, H2, H4, H5) that binds to the N-terminal residues of the tumor-suppressor Rassf1C.¡€0€ª€0€ €CDD¡€ €¶#¢€0€0€ €‚Ûpfam03345, DDOST_48kD, Oligosaccharyltransferase 48 kDa subunit beta. Members of this family are involved in asparagine-linked protein glycosylation. In particular, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST), also known as oligosaccharyltransferase EC:2.4.1.119, transfers the high-mannose sugar GlcNAc(2)-Man(9)-Glc(3) from a dolichol-linked donor to an asparagine acceptor in a consensus Asn-X-Ser/Thr motif. In most eukaryotes, the DDOST complex is composed of three subunits, which in humans are described as a 48kD subunit, ribophorin I, and ribophorin II. However, the yeast DDOST appears to consist of six subunits (alpha, beta, gamma, delta, epsilon, zeta). The yeast beta subunit is a 45kD polypeptide, previously discovered as the Wbp1 protein, with known sequence similarity to the human 48kD subunit and the other orthologues. This family includes the 48kD-like subunits from several eukaryotes; it also includes the yeast DDOST beta subunit Wbp1.¡€0€ª€0€ €CDD¡€ €¶$¢€0€0€ €7pfam03347, TDH, Vibrio thermostable direct hemolysin. ¡€0€ª€0€ €CDD¡€ €K ¢€0€0€ €‚…pfam03348, Serinc, Serine incorporator (Serinc). This is a family of eukaryotic membrane proteins which incorporate serine into membranes and facilitate the synthesis of the serine-derived lipids phosphatidylserine and sphingolipid. Members of this family contain 11 transmembrane domains and form intracellular complexes with key enzymes involved in serine and sphingolipid biosynthesis.¡€0€ª€0€ €CDD¡€ €¶%¢€0€0€ €‚pfam03349, Toluene_X, Outer membrane protein transport protein (OMPP1/FadL/TodX). This family includes TodX from Pseudomonas putida F1 and TbuX from Ralstonia pickettii PKO1. These are membrane proteins of uncertain function that are involved in toluene catabolism. Related proteins involved in the degradation of similar aromatic hydrocarbons are also in this family, such as CymD. This family also includes FadL involved in translocation of long-chain fatty acids across the outer membrane. It is also a receptor for the bacteriophage T2.¡€0€ª€0€ €CDD¡€ €¶&¢€0€0€ €>pfam03350, UPF0114, Uncharacterized protein family, UPF0114. ¡€0€ª€0€ €CDD¡€ €¶'¢€0€0€ €‚pfam03351, DOMON, DOMON domain. The DOMON (named after dopamine beta-monooxygenase N-terminal) domain is 110-125 residues long. It is predicted to form an all beta fold with up to 11 strands and is secreted to the extracellular compartment. The beta-strand folding produces a hydrophobic pocket which appears to bind soluble haem. This is consistent with the predominant architectures where the protein is associated with cytochromes or enzymatic domains whose activity involves redox or electron transfer reactions potentially as a direct participant in the electron transfer process. The DOMON domain superfamily, of which this is just one member, shows (1) multiple hydrophobic residues that contribute to the hydrophobic core of the strands of the beta-sandwich, and small residues found at the boundaries of strands and loops, (2) a strongly conserved charged residue (usually arginine/lysine) at the end of strand 9, which possibly stabilizes the loop between 9 and 10, and (3) a polar residue (usually histidine, lysine or arginine), that interacts or coordinates with ligands. The suggested superfamily includes both haem- and sugar-binding members: the haem-binding families being the ethyl-Benzoate dehydrogenase family EB_dh, pfam09459, the cellobiose dehydrogenase family CBDH and this family, and the sugar-binding families being the xylanases, CBM_4_9, pfam02018. The common feature of the superfamily is the 11-beta-strand structure, although the first and eleventh strands are not well conserved either within families or between families.¡€0€ª€0€ €CDD¡€ €¶(¢€0€0€ €®pfam03352, Adenine_glyco, Methyladenine glycosylase. The DNA-3-methyladenine glycosylase I is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.¡€0€ª€0€ €CDD¡€ €¶)¢€0€0€ €‚Ópfam03353, Lin-8, Ras-mediated vulval-induction antagonist. LIN-8 is a nuclear protein, present at the sites of transcriptional repressor complexes, which interacts with LIN-35 Rb.Lin35 Rb is a product of the class B synMuv gene lin-35 which silences genes required for vulval specification through chromatin modification and remodelling. The biological role of the interaction has not yet been determined however predictions have been made. The interaction shows that class A synMuv genes control vulval induction through the transcriptional regulation of gene expression. LIN-8 normally functions as part of a protein complex however when the complex is absent, other family members can partially replace LIN-8 activity.¡€0€ª€0€ €CDD¡€ €K¢€0€0€ €øpfam03354, Terminase_1, Phage Terminase. The majority of the members of this family are bacteriophage proteins, several of which are thought to be terminase large subunit proteins. There are also a number of bacterial proteins of unknown function.¡€0€ª€0€ €CDD¡€ €K¢€0€0€ €upfam03355, Pox_TAP, Viral Trans-Activator Protein. These proteins function as a trans-activator of viral late genes.¡€0€ª€0€ €CDD¡€ €:ߢ€0€0€ €ýpfam03356, Pox_LP_H2, Viral late protein H2. All Members of this family show similarity to the vaccinia virus late protein H2. This protein is often referred to by its gene name of H2R. Members from this family all belong to the viral taxon Poxviridae.¡€0€ª€0€ €CDD¡€ €K¢€0€0€ €‚]pfam03357, Snf7, Snf7. This family of proteins are involved in protein sorting and transport from the endosome to the vacuole/lysosome in eukaryotic cells. Vacuoles/lysosomes play an important role in the degradation of both lipids and cellular proteins. In order to perform this degradative function, vacuoles/lysosomes contain numerous hydrolases which have been transported in the form of inactive precursors via the biosynthetic pathway and are proteolytically activated upon delivery to the vacuole/lysosome. The delivery of transmembrane proteins, such as activated cell surface receptors to the lumen of the vacuole/lysosome, either for degradation/downregulation, or in the case of hydrolases, for proper localization, requires the formation of multivesicular bodies (MVBs). These late endosomal structures are formed by invaginating and budding of the limiting membrane into the lumen of the compartment. During this process, a subset of the endosomal membrane proteins is sorted into the forming vesicles. Mature MVBs fuse with the vacuole/lysosome, thereby releasing cargo containing vesicles into its hydrolytic lumen for degradation. Endosomal proteins that are not sorted into the intralumenal MVB vesicles are either recycled back to the plasma membrane or Golgi complex, or remain in the limiting membrane of the MVB and are thereby transported to the limiting membrane of the vacuole/lysosome as a consequence of fusion. Therefore, the MVB sorting pathway plays a critical role in the decision between recycling and degradation of membrane proteins. A few archaeal sequences are also present within this family.¡€0€ª€0€ €CDD¡€ €¶*¢€0€0€ €4pfam03358, FMN_red, NADPH-dependent FMN reductase. ¡€0€ª€0€ €CDD¡€ €¶+¢€0€0€ €Fpfam03359, GKAP, Guanylate-kinase-associated protein (GKAP) protein. ¡€0€ª€0€ €CDD¡€ €¶,¢€0€0€ €¢€0€0€ €‚"pfam03391, Nepo_coat, Nepovirus coat protein, central domain. The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure.¡€0€ª€0€ €CDD¡€ €Ø¢€0€0€ €=pfam03392, OS-D, Insect pheromone-binding family, A10/OS-D. ¡€0€ª€0€ €CDD¡€ €¶?¢€0€0€ €7pfam03393, Pneumo_matrix, Pneumovirus matrix protein. ¡€0€ª€0€ €CDD¡€ €¶@¢€0€0€ €)pfam03394, Pox_E8, Poxvirus E8 protein. ¡€0€ª€0€ €CDD¡€ €K5¢€0€0€ €+pfam03395, Pox_P4A, Poxvirus P4A protein. ¡€0€ª€0€ €CDD¡€ €K6¢€0€0€ €Qpfam03396, Pox_RNA_pol_35, Poxvirus DNA-directed RNA polymerase, 35 kD subunit. ¡€0€ª€0€ €CDD¡€ €K7¢€0€0€ €7pfam03397, Rhabdo_matrix, Rhabdovirus matrix protein. ¡€0€ª€0€ €CDD¡€ €K8¢€0€0€ €‚ pfam03398, Ist1, Regulator of Vps4 activity in the MVB pathway. ESCRT-I, -II, and -III are endosomal sorting complexes required for transporting proteins and carry out cargo sorting and vesicle formation in the multivesicular bodies, MVBs, pathway. These complexes are transiently recruited from the cytoplasm to the endosomal membrane where they bind transmembrane proteins previously marked for degradation by mono-ubiquitination. Assembly of ESCRT-III, a complex composed of at least four subunits (Vps2, Vps24, Vps20, Snf7), is intimately linked with MVB vesicle formation, its disassembly being an essential step in the MVB vesicle formation, a reaction that is carried out by Vps4, an AAA-type ATPase. The family Ist1 is a regulator of Vps4 activity; by interacting with Did2 and Vps4, Ist1 appears to regulate the recruitment and oligomerization of Vps4. Together Ist1, Did2, and Vta1 form a network of interconnected regulatory proteins that modulate Vps4 activity, thereby regulating the flow of cargo through the MVB pathway.¡€0€ª€0€ €CDD¡€ €¶A¢€0€0€ €‚ pfam03399, SAC3_GANP, SAC3/GANP family. This family includes diverse proteins involved in large complexes. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3, and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localization of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle.¡€0€ª€0€ €CDD¡€ €¶B¢€0€0€ € pfam03400, DDE_Tnp_IS1, IS1 transposase. Transposase proteins are necessary for efficient DNA transposition. This family represents bacterial IS1 transposases.¡€0€ª€0€ €CDD¡€ €K;¢€0€0€ €‚Êpfam03401, TctC, Tripartite tricarboxylate transporter family receptor. These probable extra-cytoplasmic solute receptors are strongly overrepresented in several beta-proteobacteria. This family, formerly known as Bug - Bordetella uptake gene (bug) product - is a family of bacterial tripartite tricarboxylate receptors of the extracytoplasmic solute binding receptor-dependent transporter group of families, distinct from the ABC and TRAP-T families. The TctABC system has been characterized in S. typhimurium, and TctC is the extracytoplasmic tricarboxylate-binding receptor which binds the transporters TctA and TctB, two integral membrane proteins. Complete three-component systems are found only in bacteria.¡€0€ª€0€ €CDD¡€ €K<¢€0€0€ €Ÿpfam03402, V1R, Vomeronasal organ pheromone receptor family, V1R. This family represents one of two known vomeronasal organ receptor families, the V1R family.¡€0€ª€0€ €CDD¡€ €¶c¢€0€0€ €‚9pfam03403, PAF-AH_p_II, Platelet-activating factor acetylhydrolase, isoform II. Platelet-activating factor acetylhydrolase (PAF-AH) is a subfamily of phospholipases A2, responsible for inactivation of platelet-activating factor through cleavage of an acetyl group. Three known PAF-AHs are the brain heterotrimeric PAF-AH Ib, whose catalytic beta and gamma subunits are aligned in pfam02266, the extracellular, plasma PAF-AH (pPAF-AH), and the intracellular PAF-AH isoform II (PAF-AH II). This family aligns pPAF-AH and PAF-AH II, whose similarity was previously noted.¡€0€ª€0€ €CDD¡€ €Ø¢€0€0€ €Ëpfam03404, Mo-co_dimer, Mo-co oxidoreductase dimerisation domain. This domain is found in molybdopterin cofactor (Mo-co) oxidoreductases. It is involved in dimer formation, and has an Ig-fold structure.¡€0€ª€0€ €CDD¡€ €¶C¢€0€0€ €4pfam03405, FA_desaturase_2, Fatty acid desaturase. ¡€0€ª€0€ €CDD¡€ €¶D¢€0€0€ €¤pfam03406, Phage_fiber_2, Phage tail fibre repeat. This repeat is found in the tail fibres of phage. For example protein K. The repeats are about 40 residues long.¡€0€ª€0€ €CDD¡€ €¶E¢€0€0€ €¤pfam03407, Nucleotid_trans, Nucleotide-diphospho-sugar transferase. Proteins in this family have been been predicted to be nucleotide-diphospho-sugar transferases.¡€0€ª€0€ €CDD¡€ €¶F¢€0€0€ €Üpfam03408, Foamy_virus_ENV, Foamy virus envelope protein. Expression of the envelope (Env) glycoprotein is essential for viral particle egress. This feature is unique to the Spumavirinae, a subclass of the Retroviridae.¡€0€ª€0€ €CDD¡€ €KA¢€0€0€ €âpfam03409, Glycoprotein, Transmembrane glycoprotein. This family of proteins has some GO annotations for positive regulation of growth rate and nematode larval development. This is probably a family of membrane glycoproteins.¡€0€ª€0€ €CDD¡€ €¶G¢€0€0€ €‚pfam03410, Peptidase_M44, Metallopeptidase from vaccinia pox. This is a family of Poxviridae metalloendopeptidases. The members were often originally named as G1 proteins. The family carries three zinc-binding ligands and a catalytic glutamate. The first two zinc ligands are histidine residues, found together with the catalytic glutamate in a HXXEH motif, an inverse of the classical metallopeptidase motif, HEXXH. The third zinc ligand is a glutamate C-terminal to the HXXEH motif within a motif ELENEY (see MEROPS).¡€0€ª€0€ €CDD¡€ €KC¢€0€0€ €Hpfam03411, Peptidase_M74, Penicillin-insensitive murein endopeptidase. ¡€0€ª€0€ €CDD¡€ €¶H¢€0€0€ €‚®pfam03412, Peptidase_C39, Peptidase C39 family. Lantibiotic and non-lantibiotic bacteriocins are synthesized as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. Peptide bacteriocins are exported across the cytoplasmic membrane by a dedicated ATP-binding cassette (ABC) transporter. The ABC transporter is the maturation protease and its proteolytic domain resides in the N-terminal part of the protein. This peptidase domain is found in a wide range of ABC transporters, however the presumed catalytic cysteine and histidine are not conserved in all members of this family.¡€0€ª€0€ €CDD¡€ €¶I¢€0€0€ €‚9pfam03413, PepSY, Peptidase propeptide and YPEB domain. This region is likely to have an protease inhibitory function (personal obs:C Yeats). This model is likely to miss some members of this family as the separation from signal to noise is not clear. The name is derived from Peptidase & Bacillus subtilis YPEB.¡€0€ª€0€ €CDD¡€ €¶J¢€0€0€ €:pfam03414, Glyco_transf_6, Glycosyltransferase family 6. ¡€0€ª€0€ €CDD¡€ €¶K¢€0€0€ €/pfam03415, Peptidase_C11, Clostripain family. ¡€0€ª€0€ €CDD¡€ €KH¢€0€0€ €1pfam03416, Peptidase_C54, Peptidase family C54. ¡€0€ª€0€ €CDD¡€ €¶L¢€0€0€ €Lpfam03417, AAT, Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase. ¡€0€ª€0€ €CDD¡€ €KJ¢€0€0€ €1pfam03418, Peptidase_A25, Germination protease. ¡€0€ª€0€ €CDD¡€ €¶M¢€0€0€ €6pfam03419, Peptidase_U4, Sporulation factor SpoIIGA. ¡€0€ª€0€ €CDD¡€ €¶N¢€0€0€ €Apfam03420, Peptidase_S77, Prohead core protein serine protease. ¡€0€ª€0€ €CDD¡€ €KM¢€0€0€ €‚Gpfam03421, Acetyltransf_14, YopJ Serine/Threonine acetyltransferase. The Yersinia effector YopJ inhibits the innate immune response by blocking MAP kinase and NFkappaB signaling pathways. YopJ is a serine/threonine acetyltransferase which regulates signalling pathways by blocking phosphorylation. Specifically, YopJ has been shown to block phosphorylation of active site residues. It has also been shown that YopJ acetyltransferase is activated by eukaryotic host cell inositol hexakisphosphate. This family was previously incorrectly annotated in Pfam as being a peptidase family.¡€0€ª€0€ €CDD¡€ €¶O¢€0€0€ €;pfam03422, CBM_6, Carbohydrate binding module (family 6). ¡€0€ª€0€ €CDD¡€ €¶P¢€0€0€ €=pfam03423, CBM_25, Carbohydrate binding domain (family 25). ¡€0€ª€0€ €CDD¡€ €KP¢€0€0€ €Cpfam03424, CBM_17_28, Carbohydrate binding domain (family 17/28). ¡€0€ª€0€ €CDD¡€ €¶Q¢€0€0€ €=pfam03425, CBM_11, Carbohydrate binding domain (family 11). ¡€0€ª€0€ €CDD¡€ €¶R¢€0€0€ €=pfam03426, CBM_15, Carbohydrate binding domain (family 15). ¡€0€ª€0€ €CDD¡€ €KS¢€0€0€ €=pfam03427, CBM_19, Carbohydrate binding domain (family 19). ¡€0€ª€0€ €CDD¡€ €¶|¢€0€0€ €Špfam03428, RP-C, Replication protein C N-terminal domain. Replication protein C is involved in the early stages of viral DNA replication.¡€0€ª€0€ €CDD¡€ €¶S¢€0€0€ €‚pfam03429, MSP1b, Major surface protein 1B. The major surface protein (MSP1) of the cattle pathogen Anaplasma is a heterodimer comprised of MSP1a and MSP1b. This family is the MSP1b chain. There MSP1 proteins are putative adhesins for bovine erythrocytes.¡€0€ª€0€ €CDD¡€ €¶T¢€0€0€ €Õpfam03430, TATR, Trans-activating transcriptional regulator. This family of trans-activating transcriptional regulator (TATR), also known as intermediate early protein 1, are common to the Nucleopolyhedroviruses.¡€0€ª€0€ €CDD¡€ €KV¢€0€0€ €¢pfam03431, RNA_replicase_B, RNA replicase, beta-chain. This family is of Leviviridae RNA replicases. The replicase is also known as RNA dependent RNA polymerase.¡€0€ª€0€ €CDD¡€ €¶U¢€0€0€ €‚™pfam03432, Relaxase, Relaxase/Mobilisation nuclease domain. Relaxases/mobilisation proteins are required for the horizontal transfer of genetic information contained on plasmids that occurs during bacterial conjugation. The relaxase, in conjunction with several auxiliary proteins, forms the relaxation complex or relaxosome. Relaxases nick duplex DNA in a specific manner by catalyzing trans-esterification.¡€0€ª€0€ €CDD¡€ €¶V¢€0€0€ €‚²pfam03433, EspA, EspA-like secreted protein. EspA is the prototypical member of this family. EspA, together with EspB, EspD and Tir are exported by a type III secretion system. These proteins are essential for attaching and effacing lesion formation. EspA is a structural protein and a major component of a large, transiently expressed, filamentous surface organelle which forms a direct link between the bacterium and the host cell.¡€0€ª€0€ €CDD¡€ €¶W¢€0€0€ € pfam03434, DUF276, DUF276. This family is specific to Borrelia burgdorferi. The protein is encoded on extra-chromosomal DNA. This domain has no known function.¡€0€ª€0€ €CDD¡€ €¶X¢€0€0€ €‚Ppfam03435, Sacchrp_dh_NADP, Saccharopine dehydrogenase NADP binding domain. This family contains the NADP binding domain of saccharopine dehydrogenase. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase. The saccharopine dehydrogenase can also function as a saccharopine reductase.¡€0€ª€0€ €CDD¡€ €¶Y¢€0€0€ €¦pfam03436, DUF281, Domain of unknown function (DUF281). This family of worm domain has no known function. The boundaries of the presumed domain are rather uncertain.¡€0€ª€0€ €CDD¡€ €¶Z¢€0€0€ €¦pfam03437, BtpA, BtpA family. The BtpA protein is tightly associated with the thylakoid membranes, where it stabilizes the reaction centre proteins of photosystem I.¡€0€ª€0€ €CDD¡€ €K\¢€0€0€ €‚Öpfam03438, Pneumo_NS1, Pneumovirus NS1 protein. This non-structural protein is one of two found in pneumoviruses. The protein is about 140 amino acids in length. The NS1 protein appears to be important for efficient replication but not essential. The NS1 protein has been shown by yeast two-hybrid to interact with the viral P protein. This protein is also known as the 1C protein. It has also been shown that NS1 can potently inhibit transcription and RNA replication.¡€0€ª€0€ €CDD¡€ €K]¢€0€0€ €‚lpfam03439, Spt5-NGN, Early transcription elongation factor of RNA pol II, NGN section. Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit.¡€0€ª€0€ €CDD¡€ €¶[¢€0€0€ €©pfam03440, APT, Aerolysin/Pertussis toxin (APT) domain. This family represents the N-terminal domain of aerolysin and pertussis toxin and has a type-C lectin like fold.¡€0€ª€0€ €CDD¡€ €¶\¢€0€0€ €Apfam03441, FAD_binding_7, FAD binding domain of DNA photolyase. ¡€0€ª€0€ €CDD¡€ €¶]¢€0€0€ €‚œpfam03442, CBM_X2, Carbohydrate binding domain X2. This domain binds to cellulose and to bacterial cell walls. It is found in glycosyl hydrolases and in scaffolding proteins of cellulosomes (multiprotein glycosyl hydrolase complexes). In the cellulosome it may aid cellulose degradation by anchoring the cellulosome to the bacterial cell wall and by binding it to its substrate. This domain has an Ig-like fold.¡€0€ª€0€ €CDD¡€ €¶^¢€0€0€ €‚pfam03443, Glyco_hydro_61, Glycosyl hydrolase family 61. Although weak endoglucanase activity has been demonstrated in several members of this family, they lack the clustered conserved catalytic acidic amino acids present in most glycoside hydrolases. Many members of this family lack measurable cellulase activity on their own, but enhance the activity of other cellulolytic enzymes. They are therefore unlikely to be true glycoside hydrolases. The subsrate-binding surface of this family is a flat Ig-like fold.¡€0€ª€0€ €CDD¡€ €¶_¢€0€0€ €žpfam03444, HrcA_DNA-bdg, Winged helix-turn-helix transcription repressor, HrcA DNA-binding. This domain is always found with a pair of CBS domains pfam00571.¡€0€ª€0€ €CDD¡€ €Kc¢€0€0€ €‚>pfam03445, DUF294, Putative nucleotidyltransferase DUF294. This domain is found associated with pfam00571. This region is uncharacterized, however it seems to be similar to pfam01909, conserving the DXD motif. This strongly suggests that members of this family are also nucleotidyltransferases (Bateman A pers. obs.).¡€0€ª€0€ €CDD¡€ €¶`¢€0€0€ €¥pfam03446, NAD_binding_2, NAD binding domain of 6-phosphogluconate dehydrogenase. The NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold.¡€0€ª€0€ €CDD¡€ €¶a¢€0€0€ €‚ pfam03447, NAD_binding_3, Homoserine dehydrogenase, NAD binding domain. This domain adopts a Rossmann NAD binding fold. The C-terminal domain of homoserine dehydrogenase contributes a single helix to this structural domain, which is not included in the Pfam model.¡€0€ª€0€ €CDD¡€ €Kf¢€0€0€ €‚Äpfam03448, MgtE_N, MgtE intracellular N domain. This domain is found at the N-terminus of eubacterial magnesium transporters of the MgtE family pfam01769. This domain is an intracellular domain that has an alpha-helical structure. The crystal structure of the MgtE transporter shows two of 5 magnesium ions are in the interface between the N domain and the CBS domains. In the absence of magnesium there is a large shift between the N and CBS domains.¡€0€ª€0€ €CDD¡€ €¶b¢€0€0€ €xpfam03449, GreA_GreB_N, Transcription elongation factor, N-terminal. This domain adopts a long alpha-hairpin structure.¡€0€ª€0€ €CDD¡€ €¶c¢€0€0€ €Lpfam03450, CO_deh_flav_C, CO dehydrogenase flavoprotein C-terminal domain. ¡€0€ª€0€ €CDD¡€ €¶d¢€0€0€ €‚ïpfam03451, HELP, HELP motif. The founding member of the EMAP protein family is the 75 kDa Echinoderm Microtubule-Associated Protein, so-named for its abundance in sea urchin, sand dollar and starfish eggs. The Hydrophobic EMAP-Like Protein (HELP) motif was identified initially in the human EMAP-Like Protein 2 (EML2) and subsequently in the entire EMAP Protein family. The HELP motif is approximately 60-70 amino acids in length and is conserved amongst metazoans. Although the HELP motif is hydrophobic, there is no evidence that EMAP-Like Proteins are membrane-associated. All members of the EMAP-Like Protein family, identified to-date, are constructed with an amino terminal HELP motif followed by a WD domain. In C. elegans, EMAP-Like Protein-1 (ELP-1) is required for touch sensation indicating that ELP-1 may play a role in mechanosensation. The localization of ELP-1 to microtubules and adhesion sites implies that ELP-1 may transmit forces between the body surface and the touch receptor neurons.¡€0€ª€0€ €CDD¡€ €¶e¢€0€0€ €öpfam03452, Anp1, Anp1. The members of this family (Anp1, Van1 and Mnn9) are membrane proteins required for proper Golgi function. These proteins co-localize within the cis Golgi, and that they are physically associated in two distinct complexes.¡€0€ª€0€ €CDD¡€ €¶f¢€0€0€ €‚0pfam03453, MoeA_N, MoeA N-terminal region (domain I and II). This family contains two structural domains. One of these contains the conserved DGXA motif. This region is found in proteins involved in biosynthesis of molybdopterin cofactor however the exact molecular function of this region is uncertain.¡€0€ª€0€ €CDD¡€ €¶g¢€0€0€ €‚pfam03454, MoeA_C, MoeA C-terminal region (domain IV). This domain is found in proteins involved in biosynthesis of molybdopterin cofactor however the exact molecular function of this domain is uncertain. The structure of this domain is known and forms an incomplete beta barrel.¡€0€ª€0€ €CDD¡€ €¶h¢€0€0€ €‚þpfam03455, dDENN, dDENN domain. This region is always found associated with pfam02141. It is predicted to form a globular domain. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family. This N-terminal region of DENN folds into a longin module, consisting of a central antiparallel beta-sheet layered between helix H1 and helices H2 and H3 (strands S1-S5). Rab35 interacts with dDENN via residues in helix 1 and in the loop S3-S4.¡€0€ª€0€ €CDD¡€ €¶i¢€0€0€ €ƒpfam03456, uDENN, uDENN domain. This region is always found associated with pfam02141. It is predicted to form an all beta domain.¡€0€ª€0€ €CDD¡€ €¶j¢€0€0€ €æpfam03457, HA, Helicase associated domain. This short domain is found in multiple copies in bacterial helicase proteins. The domain is predicted to contain 3 alpha helices. The function of this domain may be to bind nucleic acid.¡€0€ª€0€ €CDD¡€ €¶k¢€0€0€ €ûpfam03458, UPF0126, UPF0126 domain. Domain always found as pair in bacterial membrane proteins of unknown function. This domain contains three transmembrane helices. The conserved glycines are suggestive of an ion channel (C. Yeats unpublished obs.).¡€0€ª€0€ €CDD¡€ €¶l¢€0€0€ €‚:pfam03459, TOBE, TOBE domain. The TOBE domain (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum and sulfate. Found in ABC transporters immediately after the ATPase domain.¡€0€ª€0€ €CDD¡€ €Kr¢€0€0€ €‚Ypfam03460, NIR_SIR_ferr, Nitrite/Sulfite reductase ferredoxin-like half domain. Sulfite and Nitrite reductases are key to both biosynthetic assimilation of sulfur and nitrogen and dissimilation of oxidised anions for energy transduction. Two copies of this repeat are found in Nitrite and Sulfite reductases and form a single structural domain.¡€0€ª€0€ €CDD¡€ €¶m¢€0€0€ €pfam03461, TRCF, TRCF domain. ¡€0€ª€0€ €CDD¡€ €¶n¢€0€0€ €Upfam03462, PCRF, PCRF domain. This domain is found in peptide chain release factors.¡€0€ª€0€ €CDD¡€ €¶o¢€0€0€ €‚pfam03463, eRF1_1, eRF1 domain 1. The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.¡€0€ª€0€ €CDD¡€ €¶p¢€0€0€ €‚pfam03464, eRF1_2, eRF1 domain 2. The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.¡€0€ª€0€ €CDD¡€ €¶q¢€0€0€ €‚pfam03465, eRF1_3, eRF1 domain 3. The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.¡€0€ª€0€ €CDD¡€ €¶r¢€0€0€ €”pfam03466, LysR_substrate, LysR substrate binding domain. The structure of this domain is known and is similar to the periplasmic binding proteins.¡€0€ª€0€ €CDD¡€ €¶s¢€0€0€ €Üpfam03467, Smg4_UPF3, Smg-4/UPF3 family. This family contains proteins that are involved in nonsense mediated mRNA decay. A process that is triggered by premature stop codons in mRNA. The family includes Smg-4 and UPF3.¡€0€ª€0€ €CDD¡€ €¶t¢€0€0€ €‚pfam03468, XS, XS domain. The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X and SGS3. SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain has recently been predicted to possess an RRM-like RNA-binding domain by fold recognition.¡€0€ª€0€ €CDD¡€ €¶u¢€0€0€ €‚epfam03469, XH, XH domain. The XH (rice gene X Homology) domain is found in a family of plant proteins including gene X. The molecular function of these proteins is unknown. However these proteins usually contain an XS domain that is also found in the PTGS protein SGS3. This domain contains a conserved glutamate residue that may be functionally important.¡€0€ª€0€ €CDD¡€ €¶v¢€0€0€ €–pfam03470, zf-XS, XS zinc finger domain. This domain is a putative nucleic acid binding zinc finger found in proteins that also contain an XS domain.¡€0€ª€0€ €CDD¡€ €ØM¢€0€0€ €‚Ôpfam03471, CorC_HlyC, Transporter associated domain. This small domain is found in a family of proteins with the pfam01595 domain and two CBS domains with this domain found at the C-terminus of the proteins, the domain is also found at the C terminus of some Na+/H+ antiporters. This domain is also found in CorC that is involved in Magnesium and cobalt efflux. The function of this domain is uncertain but might be involved in modulating transport of ion substrates.¡€0€ª€0€ €CDD¡€ €¶w¢€0€0€ €³pfam03472, Autoind_bind, Autoinducer binding domain. This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules.¡€0€ª€0€ €CDD¡€ €¶x¢€0€0€ €‚›pfam03473, MOSC, MOSC domain. The MOSC (MOCO sulfurase C-terminal) domain is a superfamily of beta-strand-rich domains identified in the molybdenum cofactor sulfurase and several other proteins from both prokaryotes and eukaryotes. These MOSC domains contain an absolutely conserved cysteine and occur either as stand-alone forms or fused to other domains such as NifS-like catalytic domain in Molybdenum cofactor sulfurase. The MOSC domain is predicted to be a sulfur-carrier domain that receives sulfur abstracted by the pyridoxal phosphate-dependent NifS-like enzymes, on its conserved cysteine, and delivers it for the formation of diverse sulfur-metal clusters.¡€0€ª€0€ €CDD¡€ €¶y¢€0€0€ €¾pfam03474, DMA, DMRTA motif. This region is found to the C-terminus of the pfam00751. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.¡€0€ª€0€ €CDD¡€ €¶z¢€0€0€ €êpfam03475, 3-alpha, 3-alpha domain. This small triple helical domain has been predicted to assume a topology similar to helix-turn-helix domains. These domains are found at the C-terminus of proteins related to Escherichia coli YiiM.¡€0€ª€0€ €CDD¡€ €¶{¢€0€0€ €Épfam03476, MOSC_N, MOSC N-terminal beta barrel domain. This domain is found to the N-terminus of pfam03473. The function of this domain is unknown, however it is predicted to adopt a beta barrel fold.¡€0€ª€0€ €CDD¡€ €K‚¢€0€0€ €'pfam03477, ATP-cone, ATP cone domain. ¡€0€ª€0€ €CDD¡€ €¶|¢€0€0€ €pfam03478, DUF295, Protein of unknown function (DUF295). This family of proteins are found in plants. The function of the proteins is unknown.¡€0€ª€0€ €CDD¡€ €¶}¢€0€0€ €‚Öpfam03479, DUF296, Domain of unknown function (DUF296). This putative domain is found in proteins that contain AT-hook motifs pfam02178, which strongly suggests a DNA-binding function for the proteins as a whole. There are three highly conserved histidine residues, eg at 117, 119 and 133 in Reut_B5223, which should be a structurally conserved metal-binding unit, based on structural comparison with known metal-binding structures. The proteins should work as trimers.¡€0€ª€0€ €CDD¡€ €¶~¢€0€0€ €‚Fpfam03480, DctP, Bacterial extracellular solute-binding protein, family 7. This family of proteins is involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes DctP, a C4-dicarboxylate-binding protein and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component.¡€0€ª€0€ €CDD¡€ €K†¢€0€0€ €‚pfam03481, SUA5, Putative GTP-binding controlling metal-binding. Structural investigation of this domain suggests that it might be a GTP-binding region that regulates metal binding and involves hydrolysis of ATP to AMP. It is found to the C-terminus of pfam01300.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €‚pfam03482, SIC, sic protein repeat. Serotype M1 group A Streptococcus strains cause epidemic waves of human infections. This 30 aa repeat occurs in the sic protein, an extracellular protein (streptococcal inhibitor of complement) that inhibits human complement.¡€0€ª€0€ €CDD¡€ €Kˆ¢€0€0€ €…pfam03483, B3_4, B3/4 domain. This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins.¡€0€ª€0€ €CDD¡€ €¶€¢€0€0€ €opfam03484, B5, tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €‚&pfam03485, Arg_tRNA_synt_N, Arginyl tRNA synthetase N terminal domain. This domain is found at the amino terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested that this domain will be involved in tRNA recognition.¡€0€ª€0€ €CDD¡€ €¶‚¢€0€0€ €.pfam03486, HI0933_like, HI0933-like protein. ¡€0€ª€0€ €CDD¡€ €KŒ¢€0€0€ €"pfam03487, IL13, Interleukin-13. ¡€0€ª€0€ €CDD¡€ €¶ƒ¢€0€0€ €Bpfam03488, Ins_beta, Nematode insulin-related peptide beta type. ¡€0€ª€0€ €CDD¡€ €¶¹¢€0€0€ €3pfam03489, SapB_2, Saposin-like type B, region 2. ¡€0€ª€0€ €CDD¡€ €¶„¢€0€0€ €Hpfam03490, Varsurf_PPLC, Variant-surface-glycoprotein phospholipase C. ¡€0€ª€0€ €CDD¡€ €K¢€0€0€ €Êpfam03491, 5HT_transport_N, Serotonin (5-HT) neurotransmitter transporter, N-terminus. This short domain lies at the very N-terminus of many serotonin and other transporter proteins, eg SNF, pfam00209.¡€0€ª€0€ €CDD¡€ €K¢€0€0€ €‚Òpfam03492, Methyltransf_7, SAM dependent carboxyl methyltransferase. This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesized through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N. The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyzes the second step to produce theobromine.¡€0€ª€0€ €CDD¡€ €¶…¢€0€0€ €Ppfam03493, BK_channel_a, Calcium-activated BK potassium channel alpha subunit. ¡€0€ª€0€ €CDD¡€ €¶†¢€0€0€ €7pfam03494, Beta-APP, Beta-amyloid peptide (beta-APP). ¡€0€ª€0€ €CDD¡€ €¶‡¢€0€0€ €£pfam03495, Binary_toxB, Clostridial binary toxin B/anthrax toxin PA. The N-terminal region of this family contains a calcium-binding motif that may be an EF-hand.¡€0€ª€0€ €CDD¡€ €K”¢€0€0€ €‚œpfam03496, ADPrib_exo_Tox, ADP-ribosyltransferase exoenzyme. This is a family of bacterial and viral bi-glutamic acid ADP-ribosyltransferases, where, in Aeromonas salmonicida AexT, E403 is the catalytic residue and E401 contributes to the transfer of ADP-ribose to the target protein. In clostridial species it is actin that is being ADP-ribosylated; this result is lethal and dermonecrotic in infected mammals.¡€0€ª€0€ €CDD¡€ €¶ˆ¢€0€0€ €4pfam03497, Anthrax_toxA, Anthrax toxin LF subunit. ¡€0€ª€0€ €CDD¡€ €K–¢€0€0€ €>pfam03498, CDtoxinA, Cytolethal distending toxin A/C domain. ¡€0€ª€0€ €CDD¡€ €¶‰¢€0€0€ €7pfam03500, Cellsynth_D, Cellulose synthase subunit D. ¡€0€ª€0€ €CDD¡€ €K˜¢€0€0€ €êpfam03501, S10_plectin, Plectin/S10 domain. This presumed domain is found at the N-terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.¡€0€ª€0€ €CDD¡€ €¶Š¢€0€0€ €Kpfam03502, Channel_Tsx, Nucleoside-specific channel-forming protein, Tsx. ¡€0€ª€0€ €CDD¡€ €¶‹¢€0€0€ €Jpfam03503, Chlam_OMP3, Chlamydia cysteine-rich outer membrane protein 3. ¡€0€ª€0€ €CDD¡€ €¶Œ¢€0€0€ €Jpfam03504, Chlam_OMP6, Chlamydia cysteine-rich outer membrane protein 6. ¡€0€ª€0€ €CDD¡€ €Kœ¢€0€0€ €2pfam03505, Clenterotox, Clostridium enterotoxin. ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €‚Kpfam03506, Flu_C_NS1, Influenza C non-structural protein (NS1). The influenza C virus genome consists of seven single-stranded RNA segments. The shortest RNA segment encodes a 286 amino acid non-structural protein NS1. This protein contains 6 conserved cysteines that may be functionally important, perhaps binding to a metal ion.¡€0€ª€0€ €CDD¡€ €K¢€0€0€ €!pfam03507, CagA, CagA exotoxin. ¡€0€ª€0€ €CDD¡€ €Kž¢€0€0€ €=pfam03508, Connexin43, Gap junction alpha-1 protein (Cx43). ¡€0€ª€0€ €CDD¡€ €¶Ž¢€0€0€ €=pfam03509, Connexin50, Gap junction alpha-8 protein (Cx50). ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €Lpfam03510, Peptidase_C24, 2C endopeptidase (C24) cysteine protease family. ¡€0€ª€0€ €CDD¡€ €K¡¢€0€0€ €8pfam03511, Fanconi_A, Fanconi anaemia group A protein. ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €:pfam03512, Glyco_hydro_52, Glycosyl hydrolase family 52. ¡€0€ª€0€ €CDD¡€ €¶‘¢€0€0€ €5pfam03513, Cloacin_immun, Cloacin immunity protein. ¡€0€ª€0€ €CDD¡€ €K¤¢€0€0€ €‚Ýpfam03514, GRAS, GRAS domain family. Proteins in the GRAS (GAI, RGA, SCR) family are known as major players in gibberellin (GA) signaling, which regulates various aspects of plant growth and development. Mutation of the SCARECROW (SCR) gene results in a radial pattern defect, loss of a ground tissue layer, in the root. The PAT1 protein is involved in phytochrome A signal transduction. A sequence, structure and evolutionary analysis showed that the GRAS family emerged in bacteria and belongs to the Rossmann-fold, AdoMET (SAM)-dependent methyltransferase superfamily. All bacterial, and a subset of plant GRAS proteins, are predicted to be active and function as small-molecule methylases. Several plant GRAS proteins lack one or more AdoMet (SAM)-binding residues while preserving their substrate-binding residues. Although GRAS proteins are implicated to function as transcriptional factors, the above analysis suggests that they instead might either modify or bind small molecules.¡€0€ª€0€ €CDD¡€ €Øe¢€0€0€ €‚pfam03515, Cloacin, Colicin-like bacteriocin tRNase domain. The C-terminal region of colicin-like bacteriocins is either a pore-forming or an endonuclease-like domain. Cloacin and Pyocins have similar structures and activities to the colicins from E coli and the klebicins from Klebsiella spp. Colicins E5 and D cleave the anticodon loops of distinct tRNAs of Escherichia coli both in vivo and in vitro. The full-length molecule has an N-terminal translocation domain and a middle, double alpha-helical region which is receptor-binding.¡€0€ª€0€ €CDD¡€ €¶’¢€0€0€ €"pfam03516, Filaggrin, Filaggrin. ¡€0€ª€0€ €CDD¡€ €¶“¢€0€0€ €‚Õpfam03517, Voldacs, Regulator of volume decrease after cellular swelling. ICln is a ubiquitously expressed multi-functional protein that plays a critical role in regulating volume decrease in cells after cellular swelling. In plants, ICln induces Cl- currents, thus regulating Cl- homoeostasis in eukaryotes. Structurally, the fold resembles a pleckstrin homology fold, on of whose roles is to recruit and tether their host protein to the cell membrane; and although the surface charges of the ICln fold are not equivalent to those of the PH domain, ICln can be phosphorylated in vitro and the PH-nature of the domain may be the part involving it in the transposition from cytosol to cell membrane during cytotonic swelling.¡€0€ª€0€ €CDD¡€ €¶”¢€0€0€ €3pfam03519, Invas_SpaK, Invasion protein B family. ¡€0€ª€0€ €CDD¡€ €¶•¢€0€0€ €‹pfam03520, KCNQ_channel, KCNQ voltage-gated potassium channel. This family matches to the C-terminal tail of KCNQ type potassium channels.¡€0€ª€0€ €CDD¡€ €¶–¢€0€0€ €6pfam03521, Kv2channel, Kv2 voltage-gated K+ channel. ¡€0€ª€0€ €CDD¡€ €¶—¢€0€0€ €-pfam03522, SLC12, Solute carrier family 12. ¡€0€ª€0€ €CDD¡€ €¶˜¢€0€0€ €8pfam03523, Macscav_rec, Macrophage scavenger receptor. ¡€0€ª€0€ €CDD¡€ €¶™¢€0€0€ €Ìpfam03524, CagX, Conjugal transfer protein. This family includes type IV secretion system CagX conjugation protein. Other members of this family are involved in conjugal transfer to plant cells of T-DNA.¡€0€ª€0€ €CDD¡€ €¶š¢€0€0€ €Bpfam03525, Meiotic_rec114, Meiotic recombination protein rec114. ¡€0€ª€0€ €CDD¡€ €K®¢€0€0€ €>pfam03526, Microcin, Colicin E1 (microcin) immunity protein. ¡€0€ª€0€ €CDD¡€ €¶Ý¢€0€0€ €pfam03527, RHS, RHS protein. ¡€0€ª€0€ €CDD¡€ €¶›¢€0€0€ € pfam03528, Rabaptin, Rabaptin. ¡€0€ª€0€ €CDD¡€ €¶œ¢€0€0€ €/pfam03529, TF_Otx, Otx1 transcription factor. ¡€0€ª€0€ €CDD¡€ €¶¢€0€0€ €@pfam03530, SK_channel, Calcium-activated SK potassium channel. ¡€0€ª€0€ €CDD¡€ €¶ž¢€0€0€ €ïpfam03531, SSrecog, Structure-specific recognition protein (SSRP1). SSRP1 has been implicated in transcriptional initiation and elongation and in DNA replication and repair. This domain belongs to the Pleckstrin homology fold superfamily.¡€0€ª€0€ €CDD¡€ €¶Ÿ¢€0€0€ €&pfam03532, OMS28_porin, OMS28 porin. ¡€0€ª€0€ €CDD¡€ €K´¢€0€0€ €'pfam03533, SPO11_like, SPO11 homolog. ¡€0€ª€0€ €CDD¡€ €¶ ¢€0€0€ €@pfam03534, SpvB, Salmonella virulence plasmid 65kDa B protein. ¡€0€ª€0€ €CDD¡€ €¶¡¢€0€0€ €‚pfam03535, Paxillin, Paxillin family. Paxillin is a multi-domain protein that localizes in cultured cells primarily to sites of cell adhesion to the extracellular matrix (ECM) called focal adhesions. The family here represents the N-terminal regions with the proline-rich part as well as the Paxillin part. Focal adhesions form a structural link between the ECM and the actin cytoskeleton and are also important sites of signal transduction; their components propagate signals arising from the activation of integrins following their engagement with ECM proteins, such as fibronectin, collagen and laminin. Importantly, focal adhesion proteins including paxillin also serve as a point of convergence for signals resulting from stimulation of various classes of growth factor receptor.¡€0€ª€0€ €CDD¡€ €¶¢¢€0€0€ €Apfam03536, VRP3, Salmonella virulence-associated 28kDa protein. ¡€0€ª€0€ €CDD¡€ €K¸¢€0€0€ €‚0pfam03537, Glyco_hydro_114, Glycoside-hydrolase family GH114. This family is recognized as a glycosyl-hydrolase family, number 114. It is endo-alpha-1,4-polygalactosaminidase, a rare enzyme. It is proposed to be TIM-barrel, the most common structure amongst the catalytic domains of glycosyl-hydrolases.¡€0€ª€0€ €CDD¡€ €¶£¢€0€0€ €Bpfam03538, VRP1, Salmonella virulence plasmid 28.1kDa A protein. ¡€0€ª€0€ €CDD¡€ €Kº¢€0€0€ €>pfam03539, Spuma_A9PTase, Spumavirus aspartic protease (A9). ¡€0€ª€0€ €CDD¡€ €¶ê¢€0€0€ €Qpfam03540, TFIID_30kDa, Transcription initiation factor TFIID 23-30kDa subunit. ¡€0€ª€0€ €CDD¡€ €¶¤¢€0€0€ €‚5pfam03542, Tuberin, Tuberin. Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterized by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation either TSC1 or TSC2 tumor suppressor gene. The TSC2 gene codes for tuberin and interacts with hamartin pfam04388, containing two coiled-coil regions, which have been shown to mediate binding to tuberin. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking.¡€0€ª€0€ €CDD¡€ €¶¥¢€0€0€ €Kpfam03543, Peptidase_C58, Yersinia/Haemophilus virulence surface antigen. ¡€0€ª€0€ €CDD¡€ €¶¦¢€0€0€ €‚‚pfam03544, TonB_C, Gram-negative bacterial TonB protein C-terminal. The TonB_C domain is the well-characterized C-terminal region of the TonB receptor molecule. This protein is bound to an inner membrane-bound protein ExbB via a globular domain and has a flexible middle region that is likely to help in positioning the C-terminal domain into the iron-transporter barrel in the outer membrane. TonB_C interacts with the N-terminal TonB box of the outer membrane transporter that binds the Fe3+-siderophore complex. The barrel of the transporter, consisting of 22 beta-sheets and an inside plug, binds the iron complex in the barrel entrance.¡€0€ª€0€ €CDD¡€ €K¾¢€0€0€ €9pfam03545, YopE, Yersinia virulence determinant (YopE). ¡€0€ª€0€ €CDD¡€ €K¿¢€0€0€ €@pfam03546, Treacle, Treacher Collins syndrome protein Treacle. ¡€0€ª€0€ €CDD¡€ €¶§¢€0€0€ €žpfam03547, Mem_trans, Membrane transport protein. This family includes auxin efflux carrier proteins and other transporter proteins from all domains of life.¡€0€ª€0€ €CDD¡€ €¶¨¢€0€0€ €Cpfam03548, LolA, Outer membrane lipoprotein carrier protein LolA. ¡€0€ª€0€ €CDD¡€ €¶©¢€0€0€ €‚ pfam03549, Tir_receptor_M, Translocated intimin receptor (Tir) intimin-binding domain. Intimin and its translocated intimin receptor (Tir) are bacterial proteins that mediate adhesion between mammalian cells and attaching and effacing (A/E) pathogens. A unique and essential feature of A/E bacterial pathogens is the formation of actin-rich pedestals beneath the intimately adherent bacteria and localized destruction of the intestinal brush border. The bacterial outer membrane adhesin, intimin, is necessary for the production of the A/E lesion and diarrhoea. The A/E bacteria translocate their own receptor for intimin, Tir, into the membrane of mammalian cells using the type III secretion system. The translocated Tir triggers additional host signalling events and actin nucleation, which are essential for lesion formation. This family represents the Tir intimin-binding domain (Tir IBD) which is needed to bind intimin and support the predicted topology for Tir, with both N- and C-terminal regions in the mammalian cell cytosol.¡€0€ª€0€ €CDD¡€ €¶ª¢€0€0€ €3pfam03550, LolB, Outer membrane lipoprotein LolB. ¡€0€ª€0€ €CDD¡€ €¶«¢€0€0€ €‚pfam03551, PadR, Transcriptional regulator PadR-like family. Members of this family are transcriptional regulators that appear to be related to the pfam01047 family. This family includes PadR, a protein that is involved in negative regulation of phenolic acid metabolism.¡€0€ª€0€ €CDD¡€ €¶¬¢€0€0€ €‚äpfam03552, Cellulose_synt, Cellulose synthase. Cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesized by plants, most algae, some bacteria and fungi, and even some animals. The genes that synthesize cellulose in higher plants differ greatly from the well-characterized genes found in Acetobacter and Agrobacterium sp. More correctly designated as 'cellulose synthase catalytic subunits', plant cellulose synthase (CesA) proteins are integral membrane proteins, approximately 1,000 amino acids in length. There are a number of highly conserved residues, including several motifs shown to be necessary for processive glycosyltransferase activity.¡€0€ª€0€ €CDD¡€ €KÅ¢€0€0€ €pfam03553, Na_H_antiporter, Na+/H+ antiporter family. This family includes integral membrane proteins, some of which are NA+/H+ antiporters.¡€0€ª€0€ €CDD¡€ €KÆ¢€0€0€ €‚{pfam03554, Herpes_UL73, UL73 viral envelope glycoprotein. This family groups together the viral proteins BLRF1, U46, 53, and UL73. The UL73-like envelope glycoproteins, which associates in a high molecular mass complex with its counterpart, gM, induce neutralising antibody responses in the host. These glycoprotein are highly polymorphic, particularly in the N-terminal region.¡€0€ª€0€ €CDD¡€ €KÇ¢€0€0€ €‚Ppfam03555, Flu_C_NS2, Influenza C non-structural protein (NS2). The influenza C virus genome consists of seven single-stranded RNA segments. The shortest RNA segment encodes a 286 amino acid non-structural protein NS1 pfam03506 as well as the NS2 protein. The NS2 protein is only about 60 amino acids in length and of unknown function.¡€0€ª€0€ €CDD¡€ €KÈ¢€0€0€ €‚ˆpfam03556, Cullin_binding, Cullin binding. This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ligase complex for neddylation. Neddylation is the process by which the C-terminal glycine of the ubiquitin-like protein Nedd8 is covalently linked to lysine residues in a protein through an isopeptide bond. The structure of this domain is composed entirely of alpha helices.¡€0€ª€0€ €CDD¡€ €¶­¢€0€0€ €‚¤pfam03557, Bunya_G1, Bunyavirus glycoprotein G1. Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This family contains the G1 glycoprotein which is the viral attachment protein.¡€0€ª€0€ €CDD¡€ €KÊ¢€0€0€ €Òpfam03558, TBSV_P22, TBSV core protein P21/P22. This protein is required for cell-to-cell movement in plants. Furthermore, the membrane-associated protein is dispensable for both replication and transcription.¡€0€ª€0€ €CDD¡€ €KË¢€0€0€ €‚¨pfam03559, Hexose_dehydrat, NDP-hexose 2,3-dehydratase. This family includes a range of proteins from antibiotic production pathways. The family includes gra-ORF27 product that probably functions at an early step, most likely as a dTDP-4-keto-6- deoxyglucose-2,3-dehydratase. Its homologs include dnmT from the daunorubicin biosynthetic gene cluster in S. peucetius, a similar gene from the daunomycin biosynthetic cluster in Streptomyces sp. strain C5, eryBVI from the erythromycin cluster in S. erythraea and snoH from the nogalamycin cluster in S. nogalater. The proteins in this family are composed of two copies of a 200 amino acid long unit that may be a structural domain.¡€0€ª€0€ €CDD¡€ €¶®¢€0€0€ €‚0pfam03561, Allantoicase, Allantoicase repeat. This family is found in pairs in Allantoicases, forming the majority of the protein. These proteins allow the use of purines as secondary nitrogen sources in nitrogen-limiting conditions through the reaction: allantoate + H(2)0 = (-)-ureidoglycolate + urea.¡€0€ª€0€ €CDD¡€ €¶¯¢€0€0€ €Æpfam03562, MltA, MltA specific insert domain. This beta barrel domain is found inserted in the MltA a murein degrading transglycosylase enzyme. This domain may be involved in peptidoglycan binding.¡€0€ª€0€ €CDD¡€ €¶°¢€0€0€ €‚±pfam03563, Bunya_G2, Bunyavirus glycoprotein G2. Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This family contains the G2 glycoprotein which interacts with the pfam03557 G1 glycoprotein.¡€0€ª€0€ €CDD¡€ €KÏ¢€0€0€ €—pfam03564, DUF1759, Protein of unknown function (DUF1759). This is a family of proteins of unknown function. Most of the members are gag-polyproteins.¡€0€ª€0€ €CDD¡€ €KТ€0€0€ €1pfam03566, Peptidase_A21, Peptidase family A21. ¡€0€ª€0€ €CDD¡€ €KÑ¢€0€0€ €‚›pfam03567, Sulfotransfer_2, Sulfotransferase family. This family includes a variety of sulfotransferase enzymes. Chondroitin 6-sulfotransferase catalyzes the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin. This family also includes Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan sulfate 6-sulfotransferase (HS6ST). Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development. Heparan sulphate 6- O -sulfotransferase (HS6ST) catalyzes the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate.¡€0€ª€0€ €CDD¡€ €¶±¢€0€0€ €1pfam03568, Peptidase_C50, Peptidase family C50. ¡€0€ª€0€ €CDD¡€ €¶²¢€0€0€ €/pfam03569, Peptidase_C8, Peptidase family C8. ¡€0€ª€0€ €CDD¡€ €KÔ¢€0€0€ €1pfam03571, Peptidase_M49, Peptidase family M49. ¡€0€ª€0€ €CDD¡€ €¶³¢€0€0€ €1pfam03572, Peptidase_S41, Peptidase family S41. ¡€0€ª€0€ €CDD¡€ €¶´¢€0€0€ €‚pfam03573, OprD, outer membrane porin, OprD family. This family includes outer membrane proteins related to OprD. OprD has been described as a serine type peptidase. However the proposed catalytic residues are not conserved suggesting that many of these proteins are not peptidases.¡€0€ª€0€ €CDD¡€ €¶µ¢€0€0€ €1pfam03574, Peptidase_S48, Peptidase family S48. ¡€0€ª€0€ €CDD¡€ €KØ¢€0€0€ €1pfam03575, Peptidase_S51, Peptidase family S51. ¡€0€ª€0€ €CDD¡€ €KÙ¢€0€0€ €1pfam03576, Peptidase_S58, Peptidase family S58. ¡€0€ª€0€ €CDD¡€ €¶¶¢€0€0€ €1pfam03577, Peptidase_C69, Peptidase family C69. ¡€0€ª€0€ €CDD¡€ €KÛ¢€0€0€ €Èpfam03578, HGWP, HGWP repeat. This short (30 amino acids) repeat is found in a number of plant proteins. It contains a conserved HGWP motif, hence its name. The function of these proteins is unknown.¡€0€ª€0€ €CDD¡€ €KÜ¢€0€0€ €Þpfam03579, SHP, Small hydrophobic protein. The small hydrophobic integral membrane protein, SH (previously designated 1A) is found to have a variety of glycosylated forms. This protein is a component of the mature virion.¡€0€ª€0€ €CDD¡€ €KÝ¢€0€0€ €‚dpfam03580, Herpes_UL14, Herpesvirus UL14-like protein. This is a family of Herpesvirus proteins including UL14. UL14 protein is a minor component of the virion tegument and is expressed late in infection. UL14 protein can influence the intracellular localization patterns of a number of proteins belonging to the capsid or the DNA encapsidation machinery.¡€0€ª€0€ €CDD¡€ €KÞ¢€0€0€ €ºpfam03581, Herpes_UL33, Herpesvirus UL33-like protein. This is a family of Herpesvirus proteins including UL33 and UL51. The proteins in this family are involved in packaging viral DNA.¡€0€ª€0€ €CDD¡€ €Kߢ€0€0€ €‚Bpfam03583, LIP, Secretory lipase. These lipases are expressed and secreted during the infection cycle of these pathogens. In particular, C. albicans has a large number of different lipases, possibly reflecting broad lipolytic activity, which may contribute to the persistence and virulence of C. albicans in human tissue.¡€0€ª€0€ €CDD¡€ €Kࢀ0€0€ €‚‚pfam03584, Herpes_ICP4_N, Herpesvirus ICP4-like protein N-terminal region. The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection. ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer. ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the N-terminal region that contains sites for DNA binding and homodimerisation.¡€0€ª€0€ €CDD¡€ €Kᢀ0€0€ €‚…pfam03585, Herpes_ICP4_C, Herpesvirus ICP4-like protein C-terminal region. The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection. ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer. ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the C-terminal region that probably acts as an enhancer for the N-terminal region.¡€0€ª€0€ €CDD¡€ €K⢀0€0€ €‚Úpfam03586, Herpes_UL36, Herpesvirus UL36 tegument protein. The UL36 open reading frame (ORF) encodes the largest herpes simplex virus type 1 (HSV-1) protein, a 270-kDa polypeptide designated VP1/2, which is also a component of the virion tegument. A null mutation in the UL36 gene of herpes simplex virus type 1 results in accumulation of unenveloped DNA-filled capsids in the cytoplasm of infected cells. This family only covers a small central part of this large protein.¡€0€ª€0€ €CDD¡€ €K㢀0€0€ €ípfam03587, EMG1, EMG1/NEP1 methyltransferase. Members of this family are essential for 40S ribosomal biogenesis. The structure of EMG1 has revealed that it is a novel member of the superfamily of alpha/beta knot fold methyltransferases.¡€0€ª€0€ €CDD¡€ €¶·¢€0€0€ €Ipfam03588, Leu_Phe_trans, Leucyl/phenylalanyl-tRNA protein transferase. ¡€0€ª€0€ €CDD¡€ €¶¸¢€0€0€ €/pfam03589, Antiterm, Antitermination protein. ¡€0€ª€0€ €CDD¡€ €¶¹¢€0€0€ €,pfam03590, AsnA, Aspartate-ammonia ligase. ¡€0€ª€0€ €CDD¡€ €¶º¢€0€0€ € pfam03591, AzlC, AzlC protein. ¡€0€ª€0€ €CDD¡€ €¶»¢€0€0€ €‚+pfam03592, Terminase_2, Terminase small subunit. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site.¡€0€ª€0€ €CDD¡€ €¶¼¢€0€0€ €7pfam03594, BenE, Benzoate membrane transport protein. ¡€0€ª€0€ €CDD¡€ €Kꢀ0€0€ €‚qpfam03595, SLAC1, Voltage-dependent anion channel. This family of transporters has ten alpha helical transmembrane segments. The structure of a bacterial homolog of SLAC1 shows it to have a trimeric arrangement. The pore is composed of five helices with a conserved Phe residue involved in gating. One homolog, Mae1 from the yeast Schizosaccharomyces pombe, functions as a malate uptake transporter; another, Ssu1 from Saccharomyces cerevisiae and other fungi including Aspergillus fumigatus, is characterized as a sulfite efflux pump; and TehA from Escherichia coli is identified as a tellurite resistance protein by virtue of its association in the tehA/tehB operon. In plants, this family is found in the stomatal guard cells functioning as an anion-transporting pore. Many homologs are incorrectly annotated as tellurite resistance or dicarboxylate transporter (TDT) proteins.¡€0€ª€0€ €CDD¡€ €¶½¢€0€0€ €1pfam03596, Cad, Cadmium resistance transporter. ¡€0€ª€0€ €CDD¡€ €K좀0€0€ €Cpfam03597, FixS, Cytochrome oxidase maturation protein cbb3-type. ¡€0€ª€0€ €CDD¡€ €¶¾¢€0€0€ €Mpfam03598, CdhC, CO dehydrogenase/acetyl-CoA synthase complex beta subunit. ¡€0€ª€0€ €CDD¡€ €¶¿¢€0€0€ €Fpfam03599, CdhD, CO dehydrogenase/acetyl-CoA synthase delta subunit. ¡€0€ª€0€ €CDD¡€ €Ø¢€0€0€ €)pfam03600, CitMHS, Citrate transporter. ¡€0€ª€0€ €CDD¡€ €¶À¢€0€0€ €@pfam03601, Cons_hypoth698, Conserved hypothetical protein 698. ¡€0€ª€0€ €CDD¡€ €Kð¢€0€0€ €>pfam03602, Cons_hypoth95, Conserved hypothetical protein 95. ¡€0€ª€0€ €CDD¡€ €Kñ¢€0€0€ €9pfam03603, DNA_III_psi, DNA polymerase III psi subunit. ¡€0€ª€0€ €CDD¡€ €¶Á¢€0€0€ €Hpfam03604, DNA_RNApol_7kD, DNA directed RNA polymerase, 7 kDa subunit. ¡€0€ª€0€ €CDD¡€ €Kó¢€0€0€ €Hpfam03605, DcuA_DcuB, Anaerobic c4-dicarboxylate membrane transporter. ¡€0€ª€0€ €CDD¡€ €¶Â¢€0€0€ €6pfam03606, DcuC, C4-dicarboxylate anaerobic carrier. ¡€0€ª€0€ €CDD¡€ €Kõ¢€0€0€ €pfam03607, DCX, Doublecortin. ¡€0€ª€0€ €CDD¡€ €¶Ã¢€0€0€ €Dpfam03608, EII-GUT, PTS system enzyme II sorbitol-specific factor. ¡€0€ª€0€ €CDD¡€ €¶Ä¢€0€0€ €@pfam03609, EII-Sor, PTS system sorbose-specific iic component. ¡€0€ª€0€ €CDD¡€ €¶Å¢€0€0€ €9pfam03610, EIIA-man, PTS system fructose IIA component. ¡€0€ª€0€ €CDD¡€ €¶Æ¢€0€0€ €‚ùpfam03611, EIIC-GAT, PTS system sugar-specific permease component. This family includes bacterial transmembrane proteins with a putative sugar-specific permease function, including and analogous to the IIC component of the PTS system. It has been suggested that this permease may form part of an L-ascorbate utilisation pathway, with proposed specificity for 3-keto-L-gulonate (formed by hydrolysis of L-ascorbate). This family includes the IIC component of the galactitol specific GAT family PTS system.¡€0€ª€0€ €CDD¡€ €¶Ç¢€0€0€ €Kpfam03612, EIIBC-GUT_N, Sorbitol phosphotransferase enzyme II N-terminus. ¡€0€ª€0€ €CDD¡€ €¶È¢€0€0€ €Ppfam03613, EIID-AGA, PTS system mannose/fructose/sorbose family IID component. ¡€0€ª€0€ €CDD¡€ €¶É¢€0€0€ €;pfam03614, Flag1_repress, Repressor of phase-1 flagellin. ¡€0€ª€0€ €CDD¡€ €Ký¢€0€0€ €$pfam03615, GCM, GCM motif protein. ¡€0€ª€0€ €CDD¡€ €Kþ¢€0€0€ €7pfam03616, Glt_symporter, Sodium/glutamate symporter. ¡€0€ª€0€ €CDD¡€ €¶Ê¢€0€0€ €Ÿpfam03617, IBV_3A, IBV 3A protein. The gene product of gene 3 from Avian infectious bronchitis virus. Currently, the function of this protein remains unknown.¡€0€ª€0€ €CDD¡€ €L¢€0€0€ €®pfam03618, Kinase-PPPase, Kinase/pyrophosphorylase. This family of regulatory proteins has ADP-dependent kinase and inorganic phosphate-dependent pyrophosphorylase activity.¡€0€ª€0€ €CDD¡€ €¶Ë¢€0€0€ €‚@pfam03619, Solute_trans_a, Organic solute transporter Ostalpha. This family is a transmembrane organic solute transport protein. In vertebrates these proteins form a complex with Ostbeta, and function as bile transporters. In plants they may transport brassinosteroid-like compounds and act as regulators of cell death.¡€0€ª€0€ €CDD¡€ €¶Ì¢€0€0€ €œpfam03620, IBV_3C, IBV 3C protein. Product of ORF 3C from Avian infectious bronchitis virus (IBV). Currently, the function of this protein remains unknown.¡€0€ª€0€ €CDD¡€ €L¢€0€0€ €‚›pfam03621, MbtH, MbtH-like protein. This domain is found in the MbtH protein as well as at the N terminus of the antibiotic synthesis protein NIKP1. MbtH and its homologs were first noted in gene clusters involved in non-ribosomal peptides and other secondary metabolites by Quadri et al. This domain is about 70 amino acids long and contains 3 fully conserved tryptophan residues. The structure of the PA2412 protein shows it adopts a beta-beta-beta-alpha-alpha topology with the short C-terminal helix forming the tip of an overall arrowhead shape. MbtH proteins have been shown to be required for the synthesis of antibiotics, siderophores and glycopeptidolipids.¡€0€ª€0€ €CDD¡€ €¶Í¢€0€0€ €œpfam03622, IBV_3B, IBV 3B protein. Product of ORF 3B from Avian infectious bronchitis virus (IBV). Currently, the function of this protein remains unknown.¡€0€ª€0€ €CDD¡€ €L¢€0€0€ €‚Âpfam03623, Focal_AT, Focal adhesion targeting region. Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signaling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal 'focal adhesion targeting' (FAT) region is necessary and sufficient for localising FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin. The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not.¡€0€ª€0€ €CDD¡€ €¶Î¢€0€0€ €‚4pfam03625, DUF302, Domain of unknown function DUF302. Domain is found in an undescribed set of proteins. Normally occurs uniquely within a sequence, but is found as a tandem repeat. Shows interesting phylogenetic distribution with majority of examples in bacteria and archaea, but also in in D.melanogaster.¡€0€ª€0€ €CDD¡€ €¶Ï¢€0€0€ €‚Apfam03626, COX4_pro, Prokaryotic Cytochrome C oxidase subunit IV. Cytochrome c oxidase (COX) is a multi-subunit enzyme complex that catalyzes the final step of electron transfer through the respiratory chain on the mitochondrial inner membrane. This family is composed of cytochrome c oxidase subunit 4 from prokaryotes.¡€0€ª€0€ €CDD¡€ €¶Ð¢€0€0€ €‚tpfam03627, PapG_N, PapG carbohydrate binding domain. PapG, the adhesin of the P-pili, is situated at the tip and is only a minor component of the whole pilus structure. A two-domain structure has been postulated for PapG; a carbohydrate binding N-terminus (this domain) and chaperone binding C-terminus. The carbohydrate-binding domain interacts with the receptor glycan.¡€0€ª€0€ €CDD¡€ €·<¢€0€0€ €‚Êpfam03628, PapG_C, PapG chaperone-binding domain. PapG, the adhesin of the P-pili, is situated at the tip and is only a minor component of the whole pilus structure. A two-domain structure has been postulated for PapG; a carbohydrate binding N-terminus and chaperone binding C-terminus (this domain). The chaperone-binding domain is highly conserved, and is essential for the correct assembly of the pili structure when aided by the chaperone molecule PapD.¡€0€ª€0€ €CDD¡€ €è梀0€0€ €»pfam03629, SASA, Carbohydrate esterase, sialic acid-specific acetylesterase. The catalytic triad of this esterase enzyme comprises residues Ser127, His403 and Asp391 in UniProtKB:P70665.¡€0€ª€0€ €CDD¡€ €¶Ñ¢€0€0€ €‚¸pfam03630, Fumble, Fumble. Fumble is required for cell division in Drosophila. Mutants lacking fumble exhibit abnormalities in bipolar spindle organisation, chromosome segregation, and contractile ring formation. Analyses have demonstrated that encodes three protein isoforms, all of which contain a domain with high similarity to the pantothenate kinases of A. nidulans and mouse. A role of fumble in membrane synthesis has been proposed.¡€0€ª€0€ €CDD¡€ €¶Ò¢€0€0€ €‚4pfam03631, Virul_fac_BrkB, Virulence factor BrkB. This family acts as a virulence factor. In Bordetella pertussis, BrkB is essential for resistance to complement-dependent killing by serum. This family was originally predicted to be ribonuclease BN, but this prediction has since been shown to be incorrect.¡€0€ª€0€ €CDD¡€ €¶Ó¢€0€0€ €‚‰pfam03632, Glyco_hydro_65m, Glycosyl hydrolase family 65 central catalytic domain. This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The central domain is the catalytic domain, which binds a phosphate ion that is proximal the the highly conserved Glu. The arrangement of the phosphate and the glutamate is thought to cause nucleophilic attack on the anomeric carbon atom. The catalytic domain also forms the majority of the dimerisation interface.¡€0€ª€0€ €CDD¡€ €L ¢€0€0€ €‚çpfam03633, Glyco_hydro_65C, Glycosyl hydrolase family 65, C-terminal domain. This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The C-terminal domain forms a two layered jelly roll motif. This domain is situated at the base of the catalytic domain, however its function remains unknown.¡€0€ª€0€ €CDD¡€ €¶Ô¢€0€0€ €‚Fpfam03634, TCP, TCP family transcription factor. This is a family of TCP plant transcription factors. TCP proteins were named after the first characterized members (TB1, CYC and PCFs) and they are involved in multiple developmental control pathways. This region contains a DNA binding basic-Helix-Loop-Helix (bHLP) structure.¡€0€ª€0€ €CDD¡€ €¶Õ¢€0€0€ €‚§pfam03635, Vps35, Vacuolar protein sorting-associated protein 35. Vacuolar protein sorting-associated protein (Vps) 35 is one of around 50 proteins involved in protein trafficking. In particular, Vps35 assembles into a retromer complex with at least four other proteins Vps5, Vps17, Vps26 and Vps29. Vps35 contains a central region of weaker sequence similarity, thought to indicate the presence of at least three domains.¡€0€ª€0€ €CDD¡€ €¶Ö¢€0€0€ €‚¶pfam03636, Glyco_hydro_65N, Glycosyl hydrolase family 65, N-terminal domain. This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. This domain is believed to be essential for catalytic activity although its precise function remains unknown.¡€0€ª€0€ €CDD¡€ €¶×¢€0€0€ €‚¯pfam03637, Mob1_phocein, Mob1/phocein family. Mob1 is an essential Saccharomyces cerevisiae protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known structural motifs; however MOB1 is a member of a conserved gene family and shares sequence similarity with a nonessential yeast gene, MOB2. Mob1 is a phosphoprotein in vivo and a substrate for the Mps1p kinase in vitro. Conditional alleles of MOB1 cause a late nuclear division arrest at restrictive temperature. This family also includes phocein, a rat protein that by yeast two hybrid interacts with striatin.¡€0€ª€0€ €CDD¡€ €¶Ø¢€0€0€ €‚pfam03638, TCR, Tesmin/TSO1-like CXC domain, cysteine-rich domain. This family includes proteins that have two copies of a cysteine rich motif as follows: C-X-C-X4-C-X3-YC-X-C-X6-C-X3-C-X-C-X2-C. The family includes Tesmin and TSO1. This family is called a CXC domain in.¡€0€ª€0€ €CDD¡€ €¶Ù¢€0€0€ €‚—pfam03639, Glyco_hydro_81, Glycosyl hydrolase family 81. Family of eukaryotic beta-1,3-glucanases. Within the Aspergillus fumigatus protein ENGL1, two perfectly conserved Glu residues (E550 or E554) have been proposed as putative nucleophiles of the active site of the Engl1 endoglucanase, while the proton donor would be D475. The endo-beta-1,3-glucanase activity is essential for efficient spore release.¡€0€ª€0€ €CDD¡€ €¶Ú¢€0€0€ €¦pfam03640, Lipoprotein_15, Secreted repeat of unknown function. This family occurs as tandem repeats in a set of lipoproteins. The alignment contains a Y-X4-D motif.¡€0€ª€0€ €CDD¡€ €¶Û¢€0€0€ €‚pfam03641, Lysine_decarbox, Possible lysine decarboxylase. The members of this family share a highly conserved motif PGGXGTXXE that is probably functionally important. This family includes proteins annotated as lysine decarboxylases, although the evidence for this is not clear.¡€0€ª€0€ €CDD¡€ €L¢€0€0€ €Ùpfam03642, MAP, MAP domain. This presumed 110 amino acid residue domain is found in multiple copies in MAP (MHC class II analogue protein). The protein has been found in a wide range of extracellular matrix proteins.¡€0€ª€0€ €CDD¡€ €L¢€0€0€ €‚ipfam03643, Vps26, Vacuolar protein sorting-associated protein 26. Vacuolar protein sorting-associated protein (Vps) 26 is one of around 50 proteins involved in protein trafficking. In particular, Vps26 assembles into a retromer complex with at least four other proteins Vps5, Vps17, Vps29 and Vps35. This family also contains Down syndrome critical region 3/A.¡€0€ª€0€ €CDD¡€ €; ¢€0€0€ €pfam03644, Glyco_hydro_85, Glycosyl hydrolase family 85. Family of endo-beta-N-acetylglucosaminidases. These enzymes work on a broad spectrum of substrates.¡€0€ª€0€ €CDD¡€ €¶Ü¢€0€0€ €ñpfam03645, Tctex-1, Tctex-1 family. Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.¡€0€ª€0€ €CDD¡€ €¶Ý¢€0€0€ €npfam03646, FlaG, FlaG protein. Although important for flagella the exact function of this protein is unknown.¡€0€ª€0€ €CDD¡€ €¶Þ¢€0€0€ €tpfam03647, Tmemb_14, Transmembrane proteins 14C. This family of short membrane proteins are as yet uncharacterized.¡€0€ª€0€ €CDD¡€ €¶ß¢€0€0€ €‚ pfam03648, Glyco_hydro_67N, Glycosyl hydrolase family 67 N-terminus. Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the N-terminal region of alpha-glucuronidase. The N-terminal domain forms a two-layer sandwich, each layer being formed by a beta sheet of five strands. A further two helices form part of the interface with the central, catalytic, module (pfam07488).¡€0€ª€0€ €CDD¡€ €L¢€0€0€ €?pfam03649, UPF0014, Uncharacterized protein family (UPF0014). ¡€0€ª€0€ €CDD¡€ €¶à¢€0€0€ €;pfam03650, MPC, Uncharacterized protein family (UPF0041). ¡€0€ª€0€ €CDD¡€ €¶á¢€0€0€ €Žpfam03652, RuvX, Holliday junction resolvase. This family of nucleases resolves the Holliday junction intermediates in genetic recombination.¡€0€ª€0€ €CDD¡€ €¶â¢€0€0€ €?pfam03653, UPF0093, Uncharacterized protein family (UPF0093). ¡€0€ª€0€ €CDD¡€ €¶ã¢€0€0€ €‚´pfam03656, Pam16, Pam16. The Pam16 protein is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM). In Saccharomyces cerevisiae, Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane. Pam16 has a degenerate J domain. J-domain proteins play important regulatory roles as co-chaperones, recruiting Hsp70 partners and accelerating the ATP-hydrolysis step of the chaperone cycle. Pam16's J-like domain strongly interacts with Pam18's J domain, leading to a productive interaction of Pam18 with mtHsp70 at the mitochondria import channel. Pam18 stimulates the ATPase activity of mtHsp70.¡€0€ª€0€ €CDD¡€ €ظ¢€0€0€ €?pfam03657, UPF0113, Uncharacterized protein family (UPF0113). ¡€0€ª€0€ €CDD¡€ €L ¢€0€0€ €‚pfam03658, Ub-RnfH, RnfH family Ubiquitin. A member of the RnfH family of the ubiquitin superfamily. Members of this family strongly co-occur in two distinct gene neighborhood contexts. In one it is associated with a START domain protein, a membrane protein SmpA and the transfer mRNA binding protein SmpB. This association suggests a possible role in the SmpB-tmRNA-based tagging and degadation system of bacteria, which is interesting given that other members of the ubiquitin system are analogously involved in protein-tagging and degradation across eukaryotes and various prokaryotes. The second context in which the RnfH genes are present is in a membrane associated complex involved in transporting electrons for various reductive reactions such as nitrogen fixation.¡€0€ª€0€ €CDD¡€ €¶ä¢€0€0€ €Ypfam03659, Glyco_hydro_71, Glycosyl hydrolase family 71. Family of alpha-1,3-glucanases.¡€0€ª€0€ €CDD¡€ €¶å¢€0€0€ €‚Vpfam03660, PHF5, PHF5-like protein. This family of proteins the superfamily of PHD-finger proteins. At least one example, from mouse, may act as a chromatin-associated protein. The S. pombe ini1 gene is essential, required for splicing. It is localized in the nucleus, but not detected in the nucleolus and can be complemented by human ini1.¡€0€ª€0€ €CDD¡€ €¶æ¢€0€0€ €ppfam03661, UPF0121, Uncharacterized protein family (UPF0121). Uncharacterized integral membrane protein family.¡€0€ª€0€ €CDD¡€ €¶ç¢€0€0€ €‚Ùpfam03662, Glyco_hydro_79n, Glycosyl hydrolase family 79, N-terminal domain. Family of endo-beta-N-glucuronidase, or heparanase. Heparan sulfate proteoglycans (HSPGs) play a key role in the self- assembly, insolubility and barrier properties of basement membranes and extracellular matrices. Hence, cleavage of heparan sulfate (HS) affects the integrity and functional state of tissues and thereby fundamental normal and pathological phenomena involving cell migration and response to changes in the extracellular micro-environment. Heparanase degrades HS at specific intra-chain sites. The enzyme is synthesized as a latent approximately 65 kDa protein that is processed at the N-terminus into a highly active approximately 50 kDa form. Experimental evidence suggests that heparanase may facilitate both tumor cell invasion and neovascularization, both critical steps in cancer progression. The enzyme is also involved in cell migration associated with inflammation and autoimmunity.¡€0€ª€0€ €CDD¡€ €¶è¢€0€0€ €Ypfam03663, Glyco_hydro_76, Glycosyl hydrolase family 76. Family of alpha-1,6-mannanases.¡€0€ª€0€ €CDD¡€ €¶é¢€0€0€ €épfam03664, Glyco_hydro_62, Glycosyl hydrolase family 62. Family of alpha -L-arabinofuranosidase (EC 3.2.1.55). This enzyme hydrolysed aryl alpha-L-arabinofuranosides and cleaves arabinosyl side chains from arabinoxylan and arabinan.¡€0€ª€0€ €CDD¡€ €L'¢€0€0€ €‚4pfam03665, UPF0172, Uncharacterized protein family (UPF0172). In Chlamydomonas reinhardtii the protein TLA1 (truncated light-harvesting chlorophyll antenna size) apparently regulates genes that define the chlorophyll-a antenna size in the photosynthetic apparatus. This family was formerly known as UPF0172.¡€0€ª€0€ €CDD¡€ €¶ê¢€0€0€ €‚tpfam03666, NPR3, Nitrogen Permease regulator of amino acid transport activity 3. This family, also known in yeasts as Rmd11, complexes with NPR2, pfam06218. This complex heterodimer is responsible for inactivating TORC1. an evolutionarily conserved protein complex that controls cell size via nutritional input signals, specifically, in response to amino acid starvation.¡€0€ª€0€ €CDD¡€ €¶ë¢€0€0€ €pfam03668, ATP_bind_2, P-loop ATPase protein family. This family contains an ATP-binding site and could be an ATPase (personal obs:C Yeats).¡€0€ª€0€ €CDD¡€ €·c¢€0€0€ €?pfam03669, UPF0139, Uncharacterized protein family (UPF0139). ¡€0€ª€0€ €CDD¡€ €¶ì¢€0€0€ €?pfam03670, UPF0184, Uncharacterized protein family (UPF0184). ¡€0€ª€0€ €CDD¡€ €·e¢€0€0€ €‚pfam03671, Ufm1, Ubiquitin fold modifier 1 protein. This is a family of short ubiquitin-like proteins, that is like neither type-1 or type-2. It is a ubiquitin-fold modifier 1 (Ufm1) that is synthesized in a precursor form of 85 amino-acid residues. In humans the enzyme for Ufm1 is Uba5 and the conjugating enzyme is Ufc1. Prior to activation by Uba5 the extra two amino acids at the C-terminal region of the human pro-Ufm1 protein are removed to expose Gly whose residue is necessary for conjugation to target molecule(s). The mature Ufm1 is conjugated to yet unidentified endogenous proteins. While Ubiquitin and many Ubls possess the conserved C-terminal di-glycine that is adenylated by each specific E1 or E1-like enzyme, respectively, in an ATP-dependent manner, Ufm1(1-83) possesses a single glycine at its C-terminus, which is followed by a Ser-Cys dipeptide in the precursor form of Ufm1. The C-terminally processed Ufm1(1-83) is specifically activated by Uba5, an E1-like enzyme, and then transferred to its cognate Ufc1, an E2-like enzyme.¡€0€ª€0€ €CDD¡€ €¶í¢€0€0€ €Špfam03672, UPF0154, Uncharacterized protein family (UPF0154). This family contains a set of short bacterial proteins of unknown function.¡€0€ª€0€ €CDD¡€ €¶î¢€0€0€ €§pfam03673, UPF0128, Uncharacterized protein family (UPF0128). The members of this family are about 240 amino acids in length. The proteins are as yet uncharacterized.¡€0€ª€0€ €CDD¡€ €¶ï¢€0€0€ €wpfam03676, UPF0183, Uncharacterized protein family (UPF0183). This family of proteins includes Lin-10 from C. elegans.¡€0€ª€0€ €CDD¡€ €¶ð¢€0€0€ €~pfam03677, UPF0137, Uncharacterized protein family (UPF0137). This family includes GP6-D a virulence plasmid encoded protein.¡€0€ª€0€ €CDD¡€ €L/¢€0€0€ €‚Kpfam03678, Adeno_hexon_C, Hexon, adenovirus major coat protein, C-terminal domain. Hexon is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer. The 240 copies of the hexon trimer are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices. The N and C-terminal domains adopt the same PNGase F-like fold although they are significantly different in length.¡€0€ª€0€ €CDD¡€ €¶ñ¢€0€0€ €?pfam03682, UPF0158, Uncharacterized protein family (UPF0158). ¡€0€ª€0€ €CDD¡€ €¶ò¢€0€0€ €wpfam03683, UPF0175, Uncharacterized protein family (UPF0175). This family contains small proteins of unknown function.¡€0€ª€0€ €CDD¡€ €¶ó¢€0€0€ €Ápfam03684, UPF0179, Uncharacterized protein family (UPF0179). The function of this family is unknown, however the proteins contain two cysteine clusters that may be iron sulphur redox centers.¡€0€ª€0€ €CDD¡€ €¶ô¢€0€0€ €tpfam03685, UPF0147, Uncharacterized protein family (UPF0147). This family of small proteins have no known function.¡€0€ª€0€ €CDD¡€ €¶õ¢€0€0€ €rpfam03686, UPF0146, Uncharacterized protein family (UPF0146). The function of this family of proteins is unknown.¡€0€ª€0€ €CDD¡€ €L5¢€0€0€ €Ðpfam03687, UPF0164, Uncharacterized protein family (UPF0164). This family of uncharacterized proteins are only found in Treponema pallidum. They contain a putative signal peptide so may be secreted proteins.¡€0€ª€0€ €CDD¡€ €L6¢€0€0€ €‚'pfam03688, Nepo_coat_C, Nepovirus coat protein, C-terminal domain. The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure.¡€0€ª€0€ €CDD¡€ €;¼¢€0€0€ €‚'pfam03689, Nepo_coat_N, Nepovirus coat protein, N-terminal domain. The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure.¡€0€ª€0€ €CDD¡€ €¶ö¢€0€0€ €‚ pfam03690, UPF0160, Uncharacterized protein family (UPF0160). This family of proteins contains a large number of metal binding residues. The patterns are suggestive of a phosphoesterase function. The conserved DHH motif may mean this family is related to pfam01368.¡€0€ª€0€ €CDD¡€ €¶÷¢€0€0€ €™pfam03691, UPF0167, Uncharacterized protein family (UPF0167). The proteins in this family are about 200 amino acids long and each contain 3 CXXC motifs.¡€0€ª€0€ €CDD¡€ €¶ø¢€0€0€ €‚™pfam03692, CxxCxxCC, Putative zinc- or iron-chelating domain. This family of proteins contains 8 conserved cysteines. It has in the past been annotated as being one of the complex of proteins of the flagellar Fli complex. However this was due to a mis-annotation of the original Salmonella LT2 Genbank entry of 'fliB'. With all its conserved cysteines it is possibly a domain that chelates iron or zinc ions.¡€0€ª€0€ €CDD¡€ €¶ù¢€0€0€ €‚†pfam03693, ParD_antitoxin, Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH. ParD is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is ParE in, pfam05016. The family contains several related antitoxins from Cyanobacteria, Proteobacteria and Actinobacteria. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerizes with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all type II antitoxins.¡€0€ª€0€ €CDD¡€ €L:¢€0€0€ €‚ëpfam03694, Erg28, Erg28 like protein. This is a family of integral membrane proteins, which may contain four transmembrane helices. Members of this family are thought to be involved in sterol C-4 demethylation. In S. cerevisiae they may tether Erg26p (sterol dehydrogenase/decarboxylase) and Erg27p (3-ketoreductase) to the endoplasmic reticulum or may facilitate interaction between these proteins. The family contains a conserved arginine and histidine that may be functionally important.¡€0€ª€0€ €CDD¡€ €¶ú¢€0€0€ €¤pfam03695, UPF0149, Uncharacterized protein family (UPF0149). The protein in this family are about 190 amino acids long. The function of these proteins is unknown.¡€0€ª€0€ €CDD¡€ €¶û¢€0€0€ €}pfam03698, UPF0180, Uncharacterized protein family (UPF0180). The members of this family are small uncharacterized proteins.¡€0€ª€0€ €CDD¡€ €¶ü¢€0€0€ €pfam03699, UPF0182, Uncharacterized protein family (UPF0182). This family contains uncharacterized integral membrane proteins.¡€0€ª€0€ €CDD¡€ €¶ý¢€0€0€ €‚pfam03700, Sorting_nexin, Sorting nexin, N-terminal domain. These proteins bins to the cytoplasmic domain of plasma membrane receptors. and are involved in endocytic protein trafficking. The N-terminal domain appears to be specific to sorting nexins 1 and 2.¡€0€ª€0€ €CDD¡€ €¶þ¢€0€0€ €©pfam03701, UPF0181, Uncharacterized protein family (UPF0181). This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH.¡€0€ª€0€ €CDD¡€ €¶ÿ¢€0€0€ €‚¶pfam03702, AnmK, Anhydro-N-acetylmuramic acid kinase. Anhydro-N-acetylmuramic acid kinase catalyzes the specific phosphorylation of 1,6-anhydro-N-acetylmuramic acid (anhMurNAc) with the simultaneous cleavage of the 1,6-anhydro ring, generating MurNAc-6-P. It is also required for the utilization of anhMurNAc, either imported from the medium, or derived from its own cell wall murein, and in so doing plays a role in cell wall recycling.¡€0€ª€0€ €CDD¡€ €LA¢€0€0€ €ïpfam03703, bPH_2, Bacterial PH domain. Domain found in uncharacterized family of membrane proteins. 1-3 copies found in each protein, with each copy flanked by transmembrane helices. Members of this family have a PH domain like structure.¡€0€ª€0€ €CDD¡€ €·¢€0€0€ €‚pfam03704, BTAD, Bacterial transcriptional activator domain. Found in the DNRI/REDD/AFSR family of regulators. This region of AFSR, along with the C terminal region, is capable of independently directing actinorhodin production. This family contains TPR repeats.¡€0€ª€0€ €CDD¡€ €LC¢€0€0€ €‚ pfam03705, CheR_N, CheR methyltransferase, all-alpha domain. CheR proteins are part of the chemotaxis signaling mechanism in bacteria. CheR methylates the chemotaxis receptor at specific glutamate residues. CheR is an S-adenosylmethionine- dependent methyltransferase.¡€0€ª€0€ €CDD¡€ €·¢€0€0€ €‚epfam03706, LPG_synthase_TM, Lysylphosphatidylglycerol synthase TM region. LPG_synthase_TM is the N-terminal region of this family of bacterial phosphatidylglycerol lysyltransferases. The function of the family is to add lysyl groups to membrane lipids, and this region is the transmembrane domain of 7xTMs. In order to counteract attack by membrane-damaging external cationic antimicrobial molecules - from host immune systems, bacteriocins, defencins, etc - bacteria modify their anionic membrane phosphatidylglycerol with positively-charged L-lysine; this results in repulsion of the foreign cationic peptides.¡€0€ª€0€ €CDD¡€ €·¢€0€0€ €‚#pfam03707, MHYT, Bacterial signalling protein N terminal repeat. Found as an N terminal triplet tandem repeat in bacterial signalling proteins. Family includes CoxC and CoxH from P.carboxydovorans. Each repeat contains two transmembrane helices. Domain is also described as the MHYT domain.¡€0€ª€0€ €CDD¡€ €·¢€0€0€ €‚Bpfam03708, Avian_gp85, Avian retrovirus envelope protein, gp85. Family of a vain specific viral glycoproteins that forms a receptor-binding gp85 polypeptide that is linked through disulfide to a membrane-spanning gp37 spike. Gp85 confers a high degree of subgroup specificity for interaction with distinct cell receptors.¡€0€ª€0€ €CDD¡€ €LG¢€0€0€ €Âpfam03709, OKR_DC_1_N, Orn/Lys/Arg decarboxylase, N-terminal domain. This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure.¡€0€ª€0€ €CDD¡€ €·¢€0€0€ €‚Tpfam03710, GlnE, Glutamate-ammonia ligase adenylyltransferase. Conserved repeated domain found in GlnE proteins. These proteins adenylate and deadenylate glutamine synthases: ATP + {L-Glutamate:ammonia ligase (ADP-forming)} = Diphosphate + Adenylyl-{L-Glutamate:Ammonia ligase (ADP-forming)}. The family is related to the pfam01909 domain.¡€0€ª€0€ €CDD¡€ €LI¢€0€0€ €Fpfam03711, OKR_DC_1_C, Orn/Lys/Arg decarboxylase, C-terminal domain. ¡€0€ª€0€ €CDD¡€ €·¢€0€0€ €¸pfam03712, Cu2_monoox_C, Copper type II ascorbate-dependent monooxygenase, C-terminal domain. The N and C-terminal domains of members of this family adopt the same PNGase F-like fold.¡€0€ª€0€ €CDD¡€ €·¢€0€0€ €‚Èpfam03713, DUF305, Domain of unknown function (DUF305). Domain found in small family of bacterial secreted proteins with no known function. Also found in Paramecium bursaria chlorella virus 1. This domain is short and found in one or two copies. The domain has a conserved HH motif that may be functionally important. This domain belongs to the ferritin superfamily. It contains two sequence similar repeats each of which is composed of two alpha helices.¡€0€ª€0€ €CDD¡€ €·¢€0€0€ €‚Epfam03714, PUD, Bacterial pullanase-associated domain. Domain is found in pullanase - carbohydrate de-branching - proteins. It is found both to the N or the C terminii of of the alpha-amylase active site region. This domain contains several conserved aromatic residues that are suggestive of a carbohydrate binding function.¡€0€ª€0€ €CDD¡€ €·¢€0€0€ €‚&pfam03715, Noc2, Noc2p family. At least one member, Noc2p from yeast, is required for a late step in 60S subunit export from the nucleus. It has also been shown to co-precipitate with Nug1p, a nuclear GTPase also required for ribosome nucleus export. This family was formerly known as UPF0120.¡€0€ª€0€ €CDD¡€ €· ¢€0€0€ €špfam03716, WCCH, WCCH motif. The WCCH motif is found in a retrotransposons and Gemini viruses. A specific function has not been associated to this motif.¡€0€ª€0€ €CDD¡€ €ñ¢€0€0€ €‚Ipfam03717, PBP_dimer, Penicillin-binding Protein dimerisation domain. This domain is found at the N terminus of Class B High Molecular Weight Penicillin-Binding Proteins. Its function has not been precisely defined, but is strongly implicated in PBP polymerization. The domain forms a largely disordered 'sugar tongs' structure.¡€0€ª€0€ €CDD¡€ €· ¢€0€0€ €Äpfam03718, Glyco_hydro_49, Glycosyl hydrolase family 49. Family of dextranase (EC 3.2.1.11) and isopullulanase (EC 3.2.1.57). Dextranase hydrolyses alpha-1,6-glycosidic bonds in dextran polymers.¡€0€ª€0€ €CDD¡€ €LP¢€0€0€ €Epfam03719, Ribosomal_S5_C, Ribosomal protein S5, C-terminal domain. ¡€0€ª€0€ €CDD¡€ €· ¢€0€0€ €‚25000 per cell. A second Asp23-family protein, AmaP, which is encoded within the asp23-operon, is required to localize Asp23 to the cell membrane. The overall function for the family is thus a cell envelope-related one in Gram-positive bacteria.¡€0€ª€0€ €CDD¡€ €·=¢€0€0€ €‚"pfam03781, FGE-sulfatase, Sulfatase-modifying factor enzyme 1. This domain is found in eukaryotic proteins required for post-translational sulfatase modification (SUMF1). These proteins are associated with the rare disorder multiple sulfatase deficiency (MSD). The protein product of the SUMF1 gene is FGE, formylglycine (FGly),-generating enzyme, which is a sulfatase. Sulfatases are enzymes essential for degradation and remodelling of sulfate esters, and formylglycine (FGly), the key catalytic in the active site, is unique to sulfatases. FGE is localized to the endoplasmic reticulum (ER) and interacts with and modifies the unfolded form of newly synthesized sulfatases. FGE is a single-domain monomer with a surprising paucity of secondary structure that adopts a unique fold which is stabilized by two Ca2+ ions. The effect of all mutations found in MSD patients is explained by the FGE structure, providing a molecular basis for MSD. A redox-active disulfide bond is present in the active site of FGE. An oxidised cysteine residue, possibly cysteine sulfenic acid, has been detected that may allow formulation of a structure-based mechanism for FGly formation from cysteine residues in all sulfatases. In Mycobacteria and Treponema denticola this enzyme functions as an iron(II)-dependent oxidoreductase.¡€0€ª€0€ €CDD¡€ €·>¢€0€0€ €‚ pfam03782, AMOP, AMOP domain. This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges.¡€0€ª€0€ €CDD¡€ €·?¢€0€0€ €‚pfam03783, CsgG, Curli production assembly/transport component CsgG. CsgG is an outer membrane-located lipoprotein that is highly resistant to protease digestion. During curli assembly, an adhesive surface fibre, CsgG is required to maintain the stability of CsgA and CsgB.¡€0€ª€0€ €CDD¡€ €·@¢€0€0€ €‚mpfam03784, Cyclotide, Cyclotide family. This family contains a set of cyclic peptides with a variety of activities. The structure consists of a distorted triple-stranded beta-sheet and a cysteine-knot arrangement of the disulfide bonds. Cyclotides can be separated into two subfamilies, namely bracelet and moebius. The bracelet cyclotide subfamily tends to contain a larger number of positively charged residues and has a bracelet-like circularisation of the backbone. The moebius cyclotide subfamily contains a backbone twist due to a cis-Pro peptide bond and may conceptually be regarded as a molecular Moebius strip.¡€0€ª€0€ €CDD¡€ €¢€0€0€ €Npfam03785, Peptidase_C25_C, Peptidase family C25, C terminal ig-like domain. ¡€0€ª€0€ €CDD¡€ €L‹¢€0€0€ €vpfam03786, UxuA, D-mannonate dehydratase (UxuA). UxuA (this family) and UxuB are required for hexuronate degradation.¡€0€ª€0€ €CDD¡€ €LŒ¢€0€0€ €‚Jpfam03787, RAMPs, RAMP superfamily. The molecular function of these proteins is not yet known. However, they have been identified and called the RAMP (Repair Associated Mysterious Proteins) superfamily. The members of this family have no known function they are around 300 amino acids in length and have several conserved motifs.¡€0€ª€0€ €CDD¡€ €·A¢€0€0€ €“pfam03788, LrgA, LrgA family. This family is uncharacterized. It contains the protein LrgA that has been hypothesized to export murein hydrolases.¡€0€ª€0€ €CDD¡€ €·B¢€0€0€ €Òpfam03789, ELK, ELK domain. This domain is required for the nuclear localization of these proteins. All of these proteins are members of the Tale/Knox homeodomain family, a subfamily within homeobox pfam00046.¡€0€ª€0€ €CDD¡€ €·C¢€0€0€ €ëpfam03790, KNOX1, KNOX1 domain. The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerisation.¡€0€ª€0€ €CDD¡€ €·D¢€0€0€ €ëpfam03791, KNOX2, KNOX2 domain. The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerisation.¡€0€ª€0€ €CDD¡€ €·E¢€0€0€ €‰pfam03792, PBC, PBC domain. The PBC domain is a member of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins.¡€0€ª€0€ €CDD¡€ €·F¢€0€0€ €‚¨pfam03793, PASTA, PASTA domain. This domain is found at the C termini of several Penicillin-binding proteins and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain.¡€0€ª€0€ €CDD¡€ €·G¢€0€0€ €‚Xpfam03795, YCII, YCII-related domain. The majority of proteins in this family consist of a single copy of this domain, though it is also found as a repeat. A strongly conserved histidine and a aspartate suggest that the domain has an enzymatic function. This family also now includes the family formerly known as the DGPF domain (COG3795). Although its function is unknown it is found fused to a sigma-70 factor family domain in CC_1329. Suggesting that this domain plays a role in transcription initiation (Bateman A per. obs.). This domain is named after the most conserved motif in the alignment.¡€0€ª€0€ €CDD¡€ €·H¢€0€0€ €‚,pfam03796, DnaB_C, DnaB-like helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.¡€0€ª€0€ €CDD¡€ €·I¢€0€0€ €‚^pfam03797, Autotransporter, Autotransporter beta-domain. Secretion of protein products occurs by a number of different pathways in bacteria. One of these pathways known as the type V pathway was first described for the IgA1 protease. The protein component that mediates secretion through the outer membrane is contained within the secreted protein itself, hence the proteins secreted in this way are called autotransporters. This family corresponds to the presumed integral membrane beta-barrel domain that transports the protein. This domain is found at the C terminus of the proteins it occurs in. The N terminus contains the variable passenger domain that is translocated across the membrane. Once the passenger domain is exported it is cleaved auto-catalytically in some proteins, in others a different protease is used and in some cases no cleavage occurs.¡€0€ª€0€ €CDD¡€ €·J¢€0€0€ €(pfam03798, TRAM_LAG1_CLN8, TLC domain. ¡€0€ª€0€ €CDD¡€ €·K¢€0€0€ €ºpfam03799, FtsQ, Cell division protein FtsQ. FtsQ is one of several cell division proteins. FtsQ interacts with other Fts proteins, reviewed in. The precise function of FtsQ is unknown.¡€0€ª€0€ €CDD¡€ €·L¢€0€0€ €‚ópfam03800, Nuf2, Nuf2 family. Members of this family are components of the mitotic spindle. It has been shown that Nuf2 from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle. An arabidopsis protein has been included in this family that has previously not been identified as a member of this family. The match is not strong, but in common with other members of this family contains coiled-coil to the C terminus of this region.¡€0€ª€0€ €CDD¡€ €·M¢€0€0€ €‚pfam03801, Ndc80_HEC, HEC/Ndc80p family. Members of this family are components of the mitotic spindle. It has been shown that Ndc80/HEC from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle.¡€0€ª€0€ €CDD¡€ €·N¢€0€0€ €Npfam03802, CitX, Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase. ¡€0€ª€0€ €CDD¡€ €·O¢€0€0€ €‚_pfam03803, Scramblase, Scramblase. Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury.¡€0€ª€0€ €CDD¡€ €Ù¢€0€0€ €6pfam03804, DUF325, Viral domain of unknown function. ¡€0€ª€0€ €CDD¡€ €Lœ¢€0€0€ €‚Üpfam03805, CLAG, Cytoadherence-linked asexual protein. Clag (cytoadherence linked asexual gene) is a malaria surface protein which has been shown to be involved in the binding of Plasmodium falciparum infected erythrocytes to host endothelial cells, a process termed cytoadherence. The cytoadherence phenomenon is associated with the sequestration of infected erythrocytes in the blood vessels of the brain, cerebral malaria. Clag is a multi-gene family in Plasmodium falciparum with at least 9 members identified to date. Orthologous proteins in the rodent malaria species Plasmodium chabaudi (Lawson D Unpubl. obs.) suggest that the gene family is found in other malaria species and may play a more generic role in cytoadherence.¡€0€ª€0€ €CDD¡€ €·P¢€0€0€ €=pfam03806, ABG_transport, AbgT putative transporter family. ¡€0€ª€0€ €CDD¡€ €Lž¢€0€0€ €Hpfam03807, F420_oxidored, NADP oxidoreductase coenzyme F420-dependent. ¡€0€ª€0€ €CDD¡€ €LŸ¢€0€0€ €Ipfam03808, Glyco_tran_WecB, Glycosyl transferase WecB/TagA/CpsF family. ¡€0€ª€0€ €CDD¡€ €·Q¢€0€0€ €4pfam03810, IBN_N, Importin-beta N-terminal domain. ¡€0€ª€0€ €CDD¡€ €·R¢€