TIGR00507, Shikimate_dehydrogenase, shikimate dehydrogenase. This model finds proteins from prokaryotes and functionally equivalent domains from larger, multifunctional proteins of fungi and plants. Below the trusted cutoff of 180, but above the noise cutoff of 20, are the putative shikimate dehydrogenases of Thermotoga maritima and Mycobacterium tuberculosis, and uncharacterized paralogs of shikimate dehydrogenase from E. coli and H. influenzae. The related enzyme quinate 5-dehydrogenase scores below the noise cutoff. A neighbor-joining tree, constructed with quinate 5-dehydrogenases as the outgroup, shows the Clamydial homolog as clustering among the shikimate dehydrogenases, although the sequence is unusual in the degree of sequence divergence and the presence of an additional N-terminal domain. [Amino acid biosynthesis, Aromatic amino acid family].
cd08497, PBP2_NikA_DppA_OppA_like_14, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.
pfam18304, SabA_adhesion, SabA N-terminal extracellular adhesion domain. This is the N-terminal extracellular adhesion domain of Sialic acid binding adhesin (SabA) present in Helicobacter pylori. The N-terminal domain of SabA functions as a sugar-binding adhesion domain with conserved disulfide bonds. Notably, these amino acid residues are not only conserved among SabA orthologs but also between SabA and BabA.
pfam00892, EamA, EamA-like transporter family. This family includes many hypothetical membrane proteins of unknown function. Many of the proteins contain two copies of the aligned region. The family used to be known as DUF6. Members of this family usually carry 5+5 transmembrane domains, and this domain attempts to model five of these.
TIGR00749, Glucokinase_Glucose_kinase., glucokinase, proteobacterial type. This model represents glucokinase of E. coli and close homologs, mostly from other proteobacteria, presumed to have equivalent function. This glucokinase is more closely related to a number of uncharacterized paralogs than to the glucokinase glcK (fromerly yqgR) of Bacillus subtilis and its closest homologs, so the two sets are represented by separate models. [Energy metabolism, Glycolysis/gluconeogenesis].
TIGR01198, 6-phosphogluconolactonase_6PGL., 6-phosphogluconolactonase. This enzyme of the pentose phosphate pathway is often found as a part of a multifunctional protein with [Energy metabolism, Pentose phosphate pathway].
TIGR01182, KHG/KDPG_aldolase_., Entner-Doudoroff aldolase. 2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida [Amino acid biosynthesis, Glutamate family, Energy metabolism, Entner-Doudoroff].
cd05346, SDR_c5, classical (c) SDR, subgroup 5. These proteins are members of the classical SDR family, with a canonical active site tetrad and a typical Gly-rich NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes 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 (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) 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. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. 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. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction.
pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.
cd03376, TPP_PFOR_porB_like, Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea and some hyperthermophilic bacteria. PFOR catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria and eukaryotes that lack mitochondria (and therefore pyruvate dehydrogenase) use PFOR to oxidatively decarboxylate pyruvate, with ferredoxin or flavodoxin as the electron acceptor. The 36-kDa porB subunit contains the binding sites for the cofactors, TPP and a divalent metal cation, which are required for activity.
TIGR01196, Phosphogluconate_dehydratase, 6-phosphogluconate dehydratase. A close homolog, designated MocB (mannityl opine catabolism), is found in a mannopine catabolism region of a plasmid of Agrobacterium tumefaciens. However, it is not essential for mannopine catabolism, branches within the cluster of 6-phosphogluconate dehydratases (with a short branch length) in a tree rooted by the presence of other dehydyatases. It may represent an authentic 6-phosphogluconate dehydratase, redundant with the chromosomal copy shown to exist in plasmid-cured strains. This model includes mocB above the trusted cutoff, although the designation is somewhat tenuous. [Energy metabolism, Entner-Doudoroff].
pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.
cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family, reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in plant cells walls. CAD binds 2 zinc ions and is NADPH- dependent. CAD family members are also found in non-plant species, e.g. in yeast where they have an aldehyde reductase activity. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines.
TIGR00063, GTP_cyclohydrolase_1, GTP cyclohydrolase I. alternate names: Punch (Drosophila),GTP cyclohydrolase I (EC 3.5.4.16) catalyzes the biosynthesis of formic acid and dihydroneopterin triphosphate from GTP. This reaction is the first step in the biosynthesis of tetrahydrofolate in prokaryotes, of tetrahydrobiopterin in vertebrates, and of pteridine-containing pigments in insects. [Biosynthesis of cofactors, prosthetic groups, and carriers, Folic acid].
TIGR00013, Probable_tautomerase_K2, 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function. [Energy metabolism, Other].
TIGR00094, tRNA_pseudouridine_synthase_D, tRNA pseudouridine synthase, TruD family. an EGAD loading error caused one member to be called surE, but that's an adjacent gene. MJ11364 is a strong partial match from 50 to 230 aa. [Protein synthesis, tRNA and rRNA base modification].
pfam01300, Sua5_yciO_yrdC, Telomere recombination. This domain has been shown to bind preferentially to dsRNA. The domain is found in SUA5 as well as HypF and YrdC. It has also been shown to be required for telomere recombniation in yeast.
cd10432, BI-1-like_bacterial, Bacterial BAX inhibitor (BI)-1/YccA-like proteins. This family is comprised of bacterial relatives of the mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins, which have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. In plants, BI-1 like proteins play a role in pathogen resistance. A characterized prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes.
TIGR00615, Recombination_protein_RecR, recombination protein RecR. All proteins in this family for which functions are known are involved in the initiation of recombination and recombinational repair. RecF is also required. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair].
pfam02521, HP_OMP_2, Putative outer membrane protein. This family consists of putative outer membrane proteins from Helicobacter pylori (campylobacter pylori).
pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.
TIGR01786, hemoglobin-haptoglobin-binding_protein, TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein. This model represents a family of TonB-dependent outer membrane receptor/transporters acting on iron-containing proteins such as hemoglobin, transferrin and lactoferrin. Two subfamily models with a narrower scope are contained within this model, the heme/hemoglobin receptor family protein model (TIGR01785) and the transferrin/lactoferrin receptor family model (TIGR01776). Accessions which score above trusted to this model while not scoring above trusted to the more specific models are most likely to be hemoglobin transporters. Nearly all of the species containing trusted hits to this model have access to hemoglobin, transferrin or lactoferrin or related proteins in their biological niche. [Transport and binding proteins, Cations and iron carrying compounds, Transport and binding proteins, Porins].
pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.
TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I. This model represents glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the enzyme responsible for the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate, a central step in glycolysis and gluconeogenesis. Forms exist which utilize NAD (EC 1.2.1.12), NADP (EC 1.2.1.13) or either (1.2.1.59). In some species, NAD- and NADP- utilizing forms exist, generally being responsible for reactions in the anabolic and catabolic directions respectively. Two Pfam models cover the two functional domains of this protein; pfam00044 represents the N-terminal NAD(P)-binding domain and pfam02800 represents the C-terminal catalytic domain. An additional form of gap gene is found in gamma proteobacteria and is responsible for the conversion of erythrose-4-phosphate (E4P) to 4-phospho-erythronate in the biosynthesis of pyridoxine. This pathway of pyridoxine biosynthesis appears to be limited, however, to a relatively small number of bacterial species although it is prevalent among the gamma-proteobacteria. This enzyme is described by TIGR001532. These sequences generally score between trusted and noise to this GAPDH model due to the close evolutionary relationship. There exists the possiblity that some forms of GAPDH may be bifunctional and act on E4P in species which make pyridoxine and via hydroxythreonine and lack a separate E4PDH enzyme (for instance, the GAPDH from Bacillus stearothermophilus has been shown to posess a limited E4PD activity as well as a robust GAPDH activity). There are a great number of sequences in the databases which score between trusted and noise to this model, nearly all of them due to fragmentary sequences. It seems that study of this gene has been carried out in many species utilizing PCR probes which exclude the extreme ends of the consenses used to define this model. The noise level is set relative not to E4PD, but the next closest outliers, the class II GAPDH's (found in archaea, TIGR01546) and aspartate semialdehyde dehydrogenase (ASADH, TIGR01296) both of which have highest-scoring hits around -225 to the prior model. [Energy metabolism, Glycolysis/gluconeogenesis].
pfam01856, HP_OMP, Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.
TIGR03585, PseH, UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase. Sequences in this family are members of the pfam00583 (GNAT) superfamily of acetyltransferases and are proposed to perform a N-acetylation step in the process of pseudaminic acid biosynthesis 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. Significantly, many genomes containing other components of this pathway lack this gene, indicating that some other N-acetyl transferases may be incolved and/or the step is optional, resulting in a non-acetylated pseudaminic acid variant sugar.
TIGR00644, recJ, single-stranded-DNA-specific exonuclease RecJ. All proteins in this family are 5'-3' single-strand DNA exonucleases. These proteins are used in some aspects of mismatch repair, recombination, and recombinational repair. [DNA metabolism, DNA replication, recombination, and repair].
TIGR01215, Cell_division_topological_specificity_factor, cell division topological specificity factor MinE. This protein is involved in the process of cell division. This protein prevents the proteins MinC and MinD to inhibit cell division at internal sites, but allows inhibiton at polar sites. This allows for correct cell division at the proper sites. [Cellular processes, Cell division].
cd03392, PAP2_like_2, PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase.
sd00010, SLR, Sel1-like repeat. Sel1-like repeats (SLRs) share similar alpha-helical conformations with Tetratricopeptide repeats (TPRs), but with different consensus sequence lengths and superhelical topologies. SLRs contain 36 to 44 amino acids and are present in bacteria and eukaryotes but not in archaea. SLR proteins are involved in a variety of functions, and many serve as adaptor proteins for the assembly of macromolecular complexes. The SLR family was named after the Caenorhabditis elegans Sel1 protein which is predicted to fold into 11 SLRs, a transmembrane domain, and an N-terminal signal sequence. The human Sel1L protein contains an additional fibronectin type-II domain and an N-terminal PEST sequence. Its downregulation is associated with the development of breast and pancreatic carcinomas.
TIGR00207, Flagellar_motor_switch_protein_FliG, flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family. [Cellular processes, Chemotaxis and motility].
TIGR00206, Flagellar_M-ring_protein, flagellar basal-body M-ring protein/flagellar hook-basal body protein (fliF). Component of the M (cytoplasmic associated) ring, one of four rings (L,P,S,M) which make up the flagellar hook-basal body which is a major portion of the flagellar organelle. Although the basic structure of the flagella appears to be similar for all bacteria, additional rings and structures surrounding the basal body have been observed for some bacteria (eg Vibrio cholerae and Treponema pallidum). [Cellular processes, Chemotaxis and motility].
TIGR00732, Protein_smf, DNA protecting protein DprA. Disruption of this gene in both Haemophilus influenzae and Helicobacter pylori drastically reduces the efficiency of transformation with exogenous DNA, but with different levels of effect on chromosomal (linear) and plasmid (circular) DNA. This difference suggests the DprA is not active in recombination, and it has been shown not to affect DNA binding, leaving the intermediate step in natural transformation, DNA processing. In Strep. pneumoniae, inactivation of dprA had no effect on the uptake of DNA. All of these data indicated that DprA is required at a later stage in transformation. Subsequently DprA and RecA were both shown in S. pneumoniae to be required to protect incoming ssDNA from immediate degradation. Role of DprA in non-transformable species is not known. The gene symbol smf was assigned in E. coli, but without assignment of function. [Cellular processes, DNA transformation].
