The bacterium proteins that are colored denote the protein is present at specific phage-related keywords (such as 'capsid', 'head', 'integrase', 'plate', 'tail', 'fiber', 'coat', 'transposase', 'portal', 'terminase', 'protease' or 'lysin' and 'tRNA')
TIGR03584, PseF, pseudaminic acid cytidylyltransferase. The sequences in this family include the pfam02348 (cytidyltransferase) domain and are homologous to the NeuA protein responsible for the transfer of CMP to neuraminic acid. According to, this gene is responsible for the transfer of CMP to the structurally related sugar, pseudaminic acid which is observed as a component of sugar modifications of flagellin in Campylobacter species. This gene is commonly observed in apparent operons with other genes responsible for the biosynthesis of pseudaminic acid and as a component of flagellar and exopolysaccharide biosynthesis loci.
cd05253, UDP_GE_SDE_e, UDP glucuronic acid epimerase, extended (e) SDRs. This subgroup contains UDP-D-glucuronic acid 4-epimerase, an extended SDR, which catalyzes the conversion of UDP-alpha-D-glucuronic acid to UDP-alpha-D-galacturonic acid. This group has the SDR's canonical catalytic tetrad and the TGxxGxxG NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
cd03808, GT4_CapM-like, capsular polysaccharide biosynthesis glycosyltransferase CapM and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. CapM in Staphylococcus aureus is required for the synthesis of type 1 capsular polysaccharides.
cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs. UDP-glucose 4 epimerase (aka UDP-galactose-4-epimerase), is a homodimeric extended SDR. It catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final step in Leloir galactose synthesis. This subgroup is comprised of bacterial proteins, and includes the Staphylococcus aureus capsular polysaccharide Cap5N, which may have a role in the synthesis of UDP-N-acetyl-d-fucosamine. This subgroup has the characteristic active site tetrad and NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
TIGR03589, PseB, UDP-N-acetylglucosamine 4,6-dehydratase (inverting). This enzyme catalyzes the first step in the biosynthesis of pseudaminic acid, the conversion of UDP-N-acetylglucosamine to UDP-4-keto-6-deoxy-N-acetylglucosamine. These sequences are members of the broader pfam01073 (3-beta hydroxysteroid dehydrogenase/isomerase family) family.
TIGR03590, PseG, UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase. This protein is found in association with enzymes involved in the biosynthesis of pseudaminic acid, a component of polysaccharide in certain Pseudomonas strains as well as a modification of flagellin in Campylobacter and Hellicobacter. The role of this protein is unclear, although it may participate in N-acetylation in conjunction with, or in the absence of PseH (TIGR03585) as it often scores above the trusted cutoff to pfam00583 representing a family of acetyltransferases.
pfam02397, 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.
cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase. Low molecular weight protein tyrosine phosphatases (LMW-PTP) are a family of small soluble single-domain enzymes that are characterized by a highly conserved active site motif (V/I)CXGNXCRS and share no sequence similarity with other types of protein tyrosine phosphatases (PTPs). LMW-PTPs play important roles in many biological processes and are widely distributed in prokaryotes and eukaryotes.
cd03807, GT4_WbnK-like, Shigella dysenteriae WbnK and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. WbnK in Shigella dysenteriae has been shown to be involved in the type 7 O-antigen biosynthesis.
TIGR03588, PseC, UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine transaminase. This family of enzymes are aminotransferases of the pfam01041 family involved in the biosynthesis of pseudaminic acid. They convert UDP-4-keto-6-deoxy-N-acetylglucosamine into UDP-4-amino-4,6-dideoxy-N-acetylgalactose. Pseudaminic acid has a role in surface polysaccharide in Pseudomonas as well as in the modification of flagellin in Campylobacter and Helicobacter species.
TIGR03586, PseI, pseudaminic acid synthase. Members of this family are included within the larger pfam03102 (NeuB) family. NeuB itself (TIGR03569) is involved in the biosynthesis of neuraminic acid by the condensation of phosphoenolpyruvate (PEP) with N-Acetyl-D-Mannosamine. In an analagous reaction, this enzyme, PseI, condenses PEP with 6-deoxy-beta-L-AltNAc4NAc to generate pseudaminic acid.
TIGR03025, EPS_sugtrans, exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase. Members of this family are generally found near other genes involved in the biosynthesis of a variety of exopolysaccharides. These proteins consist of two fused domains, an N-terminal hydrophobic domain of generally low conservation and a highly conserved C-terminal sugar transferase domain (pfam02397). Characterized and partially characterized members of this subfamily include Salmonella WbaP (originally RfbP), E. coli WcaJ, Methylobacillus EpsB, Xanthomonas GumD, Vibrio CpsA, Erwinia AmsG, Group B Streptococcus CpsE (originally CpsD), and Streptococcus suis Cps2E. Each of these is believed to act in transferring the sugar from, for instance, UDP-glucose or UDP-galactose, to a lipid carrier such as undecaprenyl phosphate as the first (priming) step in the synthesis of an oligosaccharide "block". This function is encoded in the C-terminal domain. The liposaccharide is believed to be subsequently transferred through a "flippase" function from the cytoplasmic to the periplasmic face of the inner membrane by the N-terminal domain. Certain closely related transferase enzymes, such as Sinorhizobium ExoY and Lactococcus EpsD, lack the N-terminal domain and are not found by this model.
TIGR02352, Glycine_oxidase, glycine oxidase ThiO. This family consists of the homotetrameric, FAD-dependent glycine oxidase ThiO, from species such as Bacillus subtilis that use glycine in thiamine biosynthesis. In general, members of this family will not be found in species such as E. coli that instead use tyrosine and the ThiH protein. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine].
cd00757, ThiF_MoeB_HesA_family, ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD and ThiS, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS. MoeB, as the MPT synthase (MoaE/MoaD complex) sulfurase, is involved in the biosynthesis of the molybdenum cofactor, a derivative of the tricyclic pterin, molybdopterin (MPT). ThiF catalyzes the adenylation of ThiS, as part of the biosynthesis pathway of thiamin pyrophosphate (vitamin B1). .
pfam04024, PspC, PspC domain. This family includes Phage shock protein C (PspC) that is thought to be a transcriptional regulator. The presumed domain is 60 amino acid residues in length.
TIGR02977, phage_shock_protein_A, phage shock protein A. Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects. [Cellular processes, Adaptations to atypical conditions].
cd00565, Ubl_ThiS, ubiquitin-like (Ubl) domain found in sulfur carrier protein ThiS. ThiS, also termed Thiamine biosynthesis protein (ThiaminS), is a sulfur carrier protein involved in thiamin biosynthesis in prokaryotes. It has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub), and is activated in an ATP-dependent manner by sulfurtransferases, similar to the activation mechanism of Ub-activating enzyme E1. ThiS has common evolutionary origin with Ub-related protein modifiers in eukaryotes, a beta-grasp fold as Ub, and is closely related to proteins MoaD and Urm1.
pfam03724, META, META domain. Small domain family found in proteins of of unknown function. Some are secreted and implicated in motility in bacteria. Also occurs in Leishmania spp. as an essential gene. Over-expression in L.amazonensis increases virulence. A pair of cysteine residues show correlated conservation, suggesting that they form a disulphide bond.
pfam04314, PCuAC, Copper chaperone PCu(A)C. PCu(A)C is a periplasmic copper chaperone. Its role may be to capture and transfer copper to two other copper chaperones, PrrC and Cox11, which in turn deliver Cu(I) to cytochrome c oxidase.
cd17906, CheX, chemotaxis phosphatase CheX. This family contains CheX CheY-P phosphatase which is very closely related to CheC chemotaxis phosphatase; both dephosphorylate CheY, although CheC requires binding of CheD to achieve the level of activity of CheX. CheX has been shown to be the most powerful CheY-P phosphatase of the CheC-FliY-CheX (CXY) family. Structural and functional data of CheX and its CheY3 substrate in Borrelia burgdorferi (the causative agent of Lyme disease) bound to the phosphoryl analog BeF3(-) and Mg2+ reveal a unique mode of binding, but a catalytic mechanism which is virtually identical to that used by the structurally unrelated CheZ, providing a striking example of convergent evolution. Thus, CheX is quite divergent from the rest of the CXY family; it forms a dimer and some may function outside chemotaxis. The data also suggest a possible CheX regulatory mechanism through dissociation of the CheX homodimer.
pfam10095, DUF2333, Uncharacterized protein conserved in bacteria (DUF2333). Members of this family of hypothetical bacterial proteins have no known function.
cd01169, HMPP_kinase, 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of the hydroxyl group of HMP to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate (HMP-P) and then the phophorylation of HMP-P to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine pyrophosphate (HMP-PP), which is the substrate for the thiamine synthase coupling reaction.
TIGR01730, COG0845:_Membrane-fusion_protein, RND family efflux transporter, MFP subunit. This model represents the MFP (membrane fusion protein) component of the RND family of transporters. RND refers to Resistance, Nodulation, and cell Division. It is, in part, a subfamily of pfam00529 (Pfam release 7.5) but hits substantial numbers of proteins missed by that model. The related HlyD secretion protein, for which pfam00529 is named, is outside the scope of this model. Attributed functions imply outward transport. These functions include nodulation, acriflavin resistance, heavy metal efflux, and multidrug resistance proteins. Most members of this family are found in Gram-negative bacteria. The proposed function of MFP proteins is to bring the inner and outer membranes together and enable transport to the outside of the outer membrane. Note, however, that a few members of this family are found in Gram-positive bacteria, where there is no outer membrane. [Transport and binding proteins, Unknown substrate].
