SII-SWORD/CoKE huggingface dataset:
Thiamine transporter ThiT (Thia_Transptr_ThiT)
Type: Family

Members of this protein family have been assigned as thiamine transporters by a phylogenomic analysis of families of genes regulated by the THI element, a broadly conserved RNA secondary structure element through which thiamine pyrophosphate (TPP) levels can regulate transcription of many genes related to thiamine transport, salvage, and de novo biosynthesis. Species with this protein always lack the ThiBPQ ABC transporter. In some species (e.g. Streptococcus mutans and Streptococcus pyogenes), YuaJ is the only THI-regulated gene.

The thiamine transporter YuaJ, also known as ThiT, is a member of the energy coupling factor (ECF) transporters, a new class of transport proteins that shares some resemblance with ABC transporters .
Energy coupling factor transporter S component ThiW (ThiW)
Type: Family

Levels of thiamine pyrophosphate (TPP) or thiamine regulate transcription or translation of a number of thiamine biosynthesis, salvage, or transport genes in a wide range of prokaryotes. The mechanism involves direct binding, with no protein involved, to a structural element called THI found in the untranslated upstream region of thiamine metabolism gene operons. This element is called a riboswitch and is seen also for other metabolites such as FMN and glycine. This protein family consists of proteins identified in operons controlled by the THI riboswitch and designated ThiW. The hydrophobic nature of this protein and reconstructed metabolic background suggests that this protein acts in transport of a thiazole precursor of thiamine .
Dimethylamine methyltransferase MtbB (Dimeth_MeTrfase_MtbB)
Type: Family

This family consists of dimethylamine methyltransferase MtbB, mainly from the genus Methanosarcina. It is found in three nearly identical copies in each of Methanosarcina acetivorans, Methanosarcina barkeri, and Methanosarcina mazei. It is one of a suite of three non-homologous enzymes with a critical UAG-encoded pyrrolysine residue in these species (along with trimethylamine methyltransferase and monomethylamine methyltransferase) . MtbB demethylates dimethylamine, leaving monomethylamine, and methylates the prosthetic group of the small corrinoid protein MtbC . The methyl group is then transferred by methylcorrinoid:coenzyme M methyltransferase to coenzyme M. Note that the pyrrolysine residue is variously translated as K or X, or as a stop codon that truncates the sequence.
Conserved hypothetical protein CHP02391 (CHP02391)
Type: Domain

This entry consists of a relatively rare prokaryotic protein family (about 8 occurrences per 200 genomes). Genes for members of this family appear to be associated variously with phage and plasmid regions, restriction system loci, transposons, and housekeeping genes. Their function is unknown.
Uncharacterised protein YrzI (YrzI)
Type: Family

Members of this family are very small proteins, about 47 residues each. An EIxxE motif present in most members of this family resembles cleavage sites by the germination protease GPR in a number of small acid-soluble spore proteins (SASP). A role in sporulation is possible.
Conserved hypothetical protein CHP02421, QEGLA (CHP02421_QEGLA)
Type: Family

Members of this family include a possible metal-binding motif HEXXXH and, nearby, a perfectly conserved motif QEGLA. All members belong to the proteobacteria, including Agrobacterium tumefaciens and several species of Vibrio and Pseudomonas, and are found in only one copy per chromosome (Vibrio vulnificus, with two chromosomes, has two). The function is unknown.
23S rRNA-intervening sequence protein (23S_rRNA-intervening_sequence)
Type: Family

This family consists of bacterial proteins encoded within an intervening sequence present within some 23S rRNA genes . It folds into an anti-parallel four-helix bundle and forms homopentamers .
Uncharacterized protein YheV (YheV)
Type: Family

Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminal and a probable metal-binding motif CPXCX(18)CXXC, including the uncharacterised protein YheV from E. coli. Members are found in various proteobacteria.
Conserved hypothetical protein CHP02444 (CHP02444)
Type: Family

Members of this family are bacterial hypothetical proteins, about 160 amino acids in length, found in various proteobacteria, including members of the genera Pseudomonas and Vibrio. The C-terminal region is poorly conserved and is not included in the model.
Thioesterase, putative (YiiD_C)
Type: Domain

This entry consists of a broadly distributed uncharacterised domain found often as a standalone protein. The member from is described from crystallography work as a putative thioesterase. About half of the members of this family are fused to an N-terminal acetyltransferase domain (

). The function of these proteins are unknown.
Conserved hypothetical protein CHP02448 (CHP02448)
Type: Family

This family consists of small hypothetical proteins, about 100 amino acids in length. The family includes five members (three in tandem) in Pseudomonas aeruginosa PAO1, and also in Pseudomonas putida (strain KT2440), four in Pseudomonas syringae pv. tomato str. DC3000, and single members in several other Proteobacteria. The function is unknown.
Conserved hypothetical protein CHP02449 (CHP02449)
Type: Family

Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Conserved hypothetical protein CHP02450, tryptophan-rich (CHP02450_Tryp)
Type: Family

Members of this family are small hypothetical proteins of 60 to 100 residues from Cyanobacteria and some Proteobacteria. Prochlorococcus marinus strains have two members, other species one only. Interestingly, of the eight most conserved residues, four are aromatic and three are invariant tryptophans. It appears all species that encode this protein can synthesize tryptophan de novo.
Conserved hypothetical protein CHP02452 (CHP02452)
Type: Family

Members of this uncharacterised protein family are found in Streptomyces, Anabaena sp. (strain PCC 7120), Clostridium acetobutylicum, Lactobacillus johnsonii NCC 533, Deinococcus radiodurans, and Pirellula sp. for a broad but sparse phylogenetic distribution that at least suggests lateral gene transfer.
Trehalose synthase (Trehalose_synth)
Type: Family

Trehalose synthase catalyzes a one-step conversion of maltose to trehalose . This is an alternative to the OtsAB and TreYZ pathways. This family includes a characterised example from Pseudomonas stutzeri and other very closely related sequences from other Pseudomonads. Not all functionally equivalent sequences may be included in this family.
Cobalt transporter subunit CbtA, putative (CbtA_put)
Type: Family

This entry represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems . Evidence for this assignment includes 1) prediction of five transmembrane segments, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream proximity of B12 transcriptional regulatory sites, 4) the absence of other known cobalt import systems and 5) the obligate co-localization with a small protein (CbtB) having a single additional transmembrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site.
Cobalt transporter subunit CbtB, putative (CbtB_put)
Type: Family

This entry represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems . Evidence for this assignment includes 1) prediction of a single transmembrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream proximity of B12 transcriptional regulatory sites, 4) the absence of other known cobalt import systems and 5) the obligate co-localization with a protein (CbtA) predicted to have five additional transmembrane segments.
Conserved hypothetical protein CHP02466 (CHP02466)
Type: Family

This family consists of uncharacterised proteins in:

Caulobacter crescentus CB15,

Bdellovibrio bacteriovorus HD100,

Synechococcus sp. (strain WH8102),

Silicibacter pomeroyi DSS-3, and

Hyphomonas neptunium (strain ATCC 15444).

The context of nearby genes differs substantially between members and does not point to any specific biological role.
Pectic acid lyase (Pectate_lyase)
Type: Family

Members of this family are isozymes of pectate lyase (

), also called polygalacturonic transeliminase and alpha-1,4-D-endopolygalacturonic acid lyase.
Type III secretion system, YscI/HrpB (T3SS_YscI/HrpB)
Type: Family

This entry consists of bacterial type III secretion system proteins which share a conserved C-terminal domain. These proteins are designated YscI (Yop proteins translocation protein I) in Yersinia and HrpB (hypersensitivity response and pathogenicity protein B) in plant pathogens such as Pseudomonas syringae. This entry also includes PscI from Pseudomonas aeruginosa. PscI is a type III secretion needle anchoring protein that polymerizes into flexible and regularly twisted fibrils and plays an essential role in needle assembly .
Type III export protein PscE/YscE (T3SS_PscE/YscE)
Type: Family

Members of this family are found exclusively in type III secretion apparatus gene clusters in bacteria. Those bacteria with a protein from this family tend to target animal cells, as does Yersinia pestis . This is a small protein (about 70 amino acids) known as YscE in Y. pestis, SsaE of Salmonella spp., PscE of P. aeruginosa, AscE of A. hydrophila and EscE in Edwardsiella piscicida. They are described as the chaperones of the type III secretion (T3S) injectisome that translocates effector toxins into host cells, facilitating the establishment and dissemination of infection. EscE forms a complex with EsaH which interacts with EsaG, stabilizing it and therefore, controlling T3SS protein secretion as EsaG secretion itself leads to the secretion of the middle and late T3SS substrates . PscE prevents premature polymerization of PscF, along with PscG, within the cytoplasm , it is required for type III secretion needle assembly and also for cytotoxicity by influencing PscF levels.
Type III secretion system YscX (T3SS_YscX)
Type: Family

Members of this family are encoded within bacterial type III secretion gene clusters. Among all species with type III secretion, those with this protein are found among those that target animal rather than plant cells. The member of this family in Yersinia was shown by mutation to be required for type III secretion of Yops effector proteins and therefore is believed to be part of the secretion machinery .
Type III secretion system chaperone SycN (T3SS_SynN)
Type: Family

Members of this protein family are part of the machinery of bacterial type III secretion in a number of bacteria that target animal cells. In the well-studied system from Yersinia, a complex of this protein (SycN) and YscB acts as a chaperone for the export of YopN . YopN then acts to control effector protein secretion, in response to calcium levels, so that secretion occurs only after contact with the targeted eukaryotic cell.
Calycin (Calycin)
Type: Homologous_superfamily

Calycins form a large protein superfamily that share similar β-barrel structures. Calycins can be divided into families that include lipocalins, fatty acid binding proteins, triabin, and thrombin inhibitor . Of these families, the lipocalin family (

) is the largest and functionally the most diverse. Lipocalins are extracellular proteins that share several common recognition properties such as ligand binding, receptor binding and the formation of complexes with other macromolecules. Lipocalins include the retinol binding protein, lipocalin allergen, aphrodisin (a sex hormone), alpha-2U-globulin, prostaglandin D synthase, beta-lactoglobulin, bilin-binding protein, and the nitrophorins . Bacterial hypothetical proteins YodA from Escherichia coli and YwiB from Bacillus subtilis share a similar calycin β-barrel structure. Part of the YodA hypothetical protein has a calycin-like structure .
Beta-grasp domain superfamily (Beta-grasp_dom_sf)
Type: Homologous_superfamily

This superfamily represents a domain with a β-grasp fold and a core structure consisting of β(2)-α-β(2), which is similar to that found in ubiquitin . Domains with this type of structure are found in the 2Fe-2S ferredoxin family (including putidaredoxin and adrenodoxin) , the 2Fe-2S ferredoxin-related family (including aldehyde reductase, and xanthine dehydrogenase) , the TGS family (including threonyl-tRNA synthetase) and the MoaD/ThiS family (including molybdopterin, and thiamine biosynthesis sulphur carrier protein) .
TGS-like (TGS-like)
Type: Homologous_superfamily

The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine 3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) . The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi).
Nucleotide-binding alpha-beta plait domain superfamily (Nucleotide-bd_a/b_plait_sf)
Type: Homologous_superfamily

This superfamily represents nucleotide-binding domains with an α-β plait structure, which consists of either a ferredoxin-like (β-α-β)2 fold, such as that found in RNA-binding domains of various ribonucleoproteins or in viral DNA-binding domains ; or a β-(α)-β-α-β(2) fold, such as that found in the ribosomal protein L23 .
Ribosomal protein uL23/eL15/eS24 core domain superfamily (Ribosomal_uL23/eL15/eS24_sf)
Type: Homologous_superfamily

Ribosomal proteins uL23, eL15 and eS24 share a common core domain consisting of a β-(α)-β-α-β(2) structure folded into three layers, α/β/α, where the β-sheets are antiparallel.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Nucleobase cation symporter-1, NCS1 (NCS1)
Type: Family

The Nucleobase Cation Symporter-1 (NCS1) family are H+/Na+ symporters specific for the uptake of purines, pyrimidines and related metabolites (http://www.tcdb.org/search/result.php?tc=2.A.39). This entry consists of bacterial and yeast transporters of the NCS1 family. Members of this family possess twelve putative transmembrane α-helical spanners (TMSs).
Conserved hypothetical protein CHP02302, transmembrane (CHP02302_TM)
Type: Family

Members of this family are found predominantly in the alphaproteobacteria and bacteroidetes. Each has 2-3 predicted transmembrane helices near the N terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted to be outside the membrane. Bradyrhizobium japonicum contains two tandem copies that are, together, homologous to the single members found in other species.
4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit (HPA_isomer/decarb_C)
Type: Domain

This entry represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation . In Escherichia coli and some other species, this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (

). In other species such as Pasteurella multocida, these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
Conserved hypothetical protein CHP02304, F390 synthetase-related (CHP02304_F390_synth-rel)
Type: Family

Members of this family form a distinct clade within a larger family of proteins that also includes coenzyme F390 synthetase, an enzyme known in Methanobacterium thermoautotrophicum and a few other methanogenic archaea. The enzyme adenylates coenzyme F420 to F390, a reversible process, during oxygen stress. Other informative homologies include domains of the non-ribosomal peptide synthetases involved in activation by adenylation. This family is likely to be an adenylate-forming enzyme related to but distinct from coenzyme F390 synthetase.
4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, N-terminal subunit (HPA_isomer/decarb_N)
Type: Domain

This entry represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation . In Escherichia coli and some other species this enzyme is encoded by a single polypeptide containing both this domain and the closely related C-terminal domain (

). In other species such as Pasteurella multocida these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
4-HPA 3-monooxygenase large component, Deinococcus-type (HpaB_Deino-type)
Type: Family

This entry represents the monooxygenase found within apparent operons for the degradation of 4-hydroxyphenylacetic acid in Deinococcus, Thermus and Oceanobacillus. Phylogenetic trees support inclusion of the Bacillus halodurans sequence, although the complete 4-hydroxyphenylacetic acid degradation pathway may not exist in that organism. Generally, this enzyme acts with the assistance of a small flavin reductase domain protein, HpaC. This family of sequences is a member of a larger family of monooxygenases HpaB.
4-hydroxyphenylacetate 3-monooxygenase oxygenase component, gammaproteobacteria (HpaB_gammaproteobact)
Type: Family

4-hydroxyphenylacetate (4HPA) 3-monooxygenase consists of two components, a large component, HpaB, which is an oxygenase, and a small component, HpaC, which is a reductase. 4-HPA 3-monooxygenase is NADH-dependent and uses FAD as the redox chromophore. HpaB utilises FADH2 supplied by HpaC to catalyse the hydroxylation of 4-hydroxyphenylacetic acid, leading to the production of 3,4-dihydroxyphenylacetic acid (DHPA) .

This entry represents the HpaB from Escherichia coli and similar proteins found in Gammaproteobacteria.
2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (HpaI)
Type: Family

This entry represents the aldolase which performs the final step unique to the 4-hydroxyphenylacetic acid catabolism pathway in which 2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into pyruvate and succinate-semialdehyde . The gene for this enzyme is generally found adjacent to other genes for this pathway .
2-oxo-hept-4-ene-1,7-dioic acid hydratase (HpcG)
Type: Family

This entry represents the enzyme which hydrates the double bond of 2-oxo-hepta-4-ene-1,7-dioic acid to form 4-hydroxy-2-oxo-heptane-1,7-dioic acid in the catabolism of 4-hydroxyphenylacetic acid. The gene for this enzyme is generally found adjacent to other genes of this pathway .
2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase variant (HpaI_NOT_DapA)
Type: Family

This entry represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see

). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus (strain HB27/ATCC BAA-163/DSM 7039). In both of these cases, one or more other DapA genes can be found and the members of this family are found in the operon for 4-hydroxyphenylacetic acid catabolism.
ABC transporter, phosphonate import, PhnC (ABC_transpr_PhnC)
Type: Family

The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions . Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette . More than 50 subfamilies have been described based on a phylogenetic and functional classification .

Members of this protein family are the ABC transporters of phosphonates. Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only prokaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system .

This entry also includes transporters of phosphite (an organophosphorous compound with the formula P(OR)
3
) and hypophosphite (H
2
PO
-
2
), including the phosphite import ATP-binding protein PxtA and hypophosphite import ATP-binding protein HtxD, both from Pseudomonas stutzeri .
Propionate--CoA ligase (Propion_PrpE)
Type: Family

This family contains one of three readily separable clades of proteins in the group of acetate and propionate--CoA ligases. Characterised members of this family act on propionate . From propionyl-CoA, there is a cyclic degradation pathway: it is ligated by PrpC to the TCA cycle intermediate oxaloacetate, acted upon further by PrpD and an aconitase, then cleaved by PrpB to pyruvate and the TCA cycle intermediate succinate.