SII-SWORD/CoKE huggingface dataset:
Sucrose-phosphate synthase, glycosyltransferase domain (SucroseP_synth_GlycoTrfase_dom)
Type: Domain

This family consists of the N-terminal regions, or in some cases the entirety, of bacterial proteins closely related to plant sucrose-phosphate synthases (SPS). The C-terminal domain (

), found with most members of this family, resembles both bona fide plant sucrose-phosphate phosphatases (SPP) and the SPP-like domain of plant sucrose phosphate synthase (SPS). At least two members of this family lack the SPP-like domain, which may have binding or regulatory rather than enzymatic activity by analogy to plant SPS. This enzyme produces sucrose 6-phosphate and UDP from UDP-glucose and D-fructose 6-phosphate, and may be encoded near the gene for fructokinase.
Flagellar export FliJ (Flagell_FliJ)
Type: Family

The bacterial flagellum consists of three major parts: the basal body (including the rod), the hook, and the filament. Outer components of the flagellum are transported to the assembly site by a specialised type III export apparatus, which is related to the type III secretion system (T3SS). FliJ is a soluble regulatory component of the flagellar export apparatus . The function of FliJ is not clear.
Zinc chaperone CobW (CobW)
Type: Family

Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase .

This entry represents CobW proteins, which are generally found proximal to the trimeric cobaltochelatase subunit CobN, an essential protein for vitamin B12 (cobalamin) biosynthesis . They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids.
5,6-dimethylbenzimidazole synthase BluB (BluB)
Type: Family

A previously published hypothesis that BluB, involved in cobalamin biosynthesis , is cob(II)yrinic acid a,c-diamide reductase (

) has now been contradicted by newer work ascribing a role in 5,6-dimethylbenzimidazole (DMB) biosynthesis . The BluB protein is related to the nitroreductase family.
Flagellar motor switch FliN (FliN)
Type: Family

The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour . The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN . The proteins are not particularly hydrophobic and may be peripheral to the membrane, possibly mounted on the basal body M ring .

This entry represents the flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY.
Hemerythrin, metal-binding domain (Hemerythrin_metal-bd)
Type: Domain

The hemerythrin family is composed of hemerythrin proteins found in invertebrates, and a broader collection of bacterial and archaeal homologues. Hemerythrin is an oxygen-binding protein found in the vascular system and coelomic fluid, or in muscles (myohemerythrin) in invertebrates . Many of the homologous proteins found in prokaryotes are multi-domain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (

) and methyl-accepting chemotaxis protein (MCP) signalling domain (

). Most hemerythrins are oxygen-carriers with a bound non-haem iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. The prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium.

Hemerythrins and myohemerythrins are small proteins of about 110 to 129 amino acid residues that bind two iron atoms. They are left-twisted 4-α-helical bundles, which provide a hydrophobic pocket where dioxygen binds as a peroxo species, interacting with adjacent aliphatic side chains via van der Waals forces . In both hemerythrins and myohemerythrins, the active centre is a binuclear iron complex, bound directly to the protein via 7 amino acid side chains , 5 His, 1 Glu and 1 Asp . Ovohemerythrin , a yolk protein from the leech Theromyzon tessulatum seems to belong to this family of proteins, it may play a role in the detoxification of free iron after a blood meal .

This entry represents a metal-binding domain found in the haemerythrin family. In haemerythrin this domain binds iron.
ATP-dependent 6-phosphofructokinase, prokaryotic (PFKA_ATP_prok)
Type: Family

6-phosphofructokinase (

), a key regulatory enzyme in glycolysis, catalyses the addition of phosphate from ATP to fructose 6-phosphate to give fructose 1,6-bisphosphate. This represents a key control step in glycolysis. This entry contains bacterial ATP-dependent 6-phosphofructokinases, which lack a β-hairpin loop present in

family members.

contains members that are ATP-dependent as well as members that are pyrophosphate-dependent.

represents the pyrophosphate-dependent phosphofructokinase, diphosphate--fructose-6-phosphate 1-phosphotransferase (

).
Phosphofructokinase, mixed-substrate PFK group III (Phosphofructokinase_III)
Type: Family

This entry includes pyrophosphate--fructose 6-phosphate 1-phosphotransferase from Amycolatopsis methanolica and ATP-dependent 6-phosphofructokinase 2 from Streptomyces coelicolor . They catalyzes the phosphorylation of D-fructose 6-phosphate, the first committing step of glycolysis.
Citrate utilization protein B (Citrate_utilization_prot_B)
Type: Family

This entry identifies proteins that are decribed as citrate utilization protein B, restricted to the proteobacteria. CitB has been identified in Salmonella and Escherichia coli as the signal transduction component of a two-component system for citrate in which CitA acts as a citrate transporter.

This domain is also a C-terminal domain in the Rhodobacter capsulatus (Rhodopseudomonas capsulata) CobZ gene, which in most other species exists as the separate CitB gene (also known as TcuB) adjacent to CobZ . CobZ is essential for cobalamin biosynthesis (by knockout of the R. capsulatus gene ) and is complemented by the characterised precorrin 3B synthase CobG. The enzyme has been shown to contain flavin, haem and Fe-S cluster cofactors and is believed to require dioxygen as a substrate.
Precorrin 3B synthase CobZ (CobZ)
Type: Family

Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase .

This entry represents CobZ (also known as TcuA), which is essential for cobalamin biosynthesis and is complemented by precorrin 3B synthase CobG (

). The enzyme has been shown to contain flavin, haem and Fe-S cluster cofactors, and is believed to require dioxygen as a substrate. In Rhodobacter capsulatus, CobZ is found as a N-terminal domain, whereas in other species it exists as a separate protein. The C-terminal portion is homologous to the 2-component signal transduction system protein CitB/TcuB (

) .
Reductive dehalogenase (RDH)
Type: Family

This entry represents a family of corrin and 8-iron Fe-S cluster-containing reductive dehalogenase found primarily in halorespiring microorganisms such as Dehalococcoides ethenogenes which contains as many as 17 enzymes of this type with varying substrate ranges. One example of a characterised enzyme is the tetrachloroethene reductive dehalogenase (

) which also acts on trichloroethene converting it to dichloroethene.
Ribonucleoside-triphosphate reductase, anaerobic (NrdD)
Type: Family

This entry represents anaerobic, class III ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centred radical , a C-terminal zinc binding site , and a set of conserved active site cysteines and asparagines . This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (

). Together the two form an alpha-2/beta-2 heterodimer.

Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical . Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded α-β barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase) . The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit which contains the active and allosteric sites.
Flagellar basal-body rod FlgG (FlgG_G_neg)
Type: Family

This family consists of the FlgG protein of the flagellar apparatus in bacteria. The basal body constitutes a major portion of the flagellar organelle and consists of four rings (L,P,S, and M) mounted on a central rod . The rod consists of about 26 subunits of flgG in the distal portion, and flgB, flgC and flgF are thought to build up the proximal portion of the rod with about 6 subunits each.
Flagellar hook FlgE (FlgE_epsilon)
Type: Family

Members of this family are flagellar hook proteins, designated FlgE, as found in the epsilon subdivision of the proteobacteria (Helicobacter, Wolinella, and Campylobacter). These proteins differ significantly in architecture from proteins designated FlgE in other lineages; the N-terminal and C-terminal domains are homologous, but members of this family only contain a large central domain that is surface-exposed and variable between strains .
Flagellar basal-body rod FlgF (FlgF)
Type: Family

FlgF is a flagellar basal-body protein that along with FlgBCG composes the rod of bacterial flagellin . This entry contains proteins only from the proteobacteria, and not in the epsilon subdivision (where the architecture of the related FlgE protein differs substantially from other lineages).
Ribonucleoside-triphosphate reductase activating, anaerobic (NrdG)
Type: Family

This enzyme is a member of the radical-SAM protein and utilises S-adenosyl methionine, an iron-sulphur cluster and a reductant (dihydroflavodoxin ) to produce a glycine-centred radical in the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD,

). The two components form an alpha-2/beta-2 heterodimer.
Pyruvate formate-lyase 1 activating enzyme (PFL1_activating)
Type: Family

Pyruvate formate lyase-activating enzyme

is a 28kDa monomeric protein which is involved in the anerobic glucose metabolism pathway. It is a member of the radical S-adenosylmethionine family of enzymes which initiate radical catalysis. It is necessary to activate pyruvate formate lyase (PFL), which catalyses the conversion of pyruvate and coenzyme A to formate and acetyl CoA.

Pyruvate formate lyase activating enzyme functions by catalysing the formation of the Gly734 radical of PFL. It utilises a [4Fe-4S] cluster and adenosylmethionine to generate a putative adenosyl radical, which extracts a hydrogen atom from Gly734 on PFL, thus activating PFL for catalysis . Members of this family are iron-sulphur proteins with a radical-SAM domain.
Organic radical enzyme activase (Organic_radical_activase)
Type: Family

This subset of the radical-SAM domain includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centred radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA,

,

) and the anaerobic ribonucleotide reductase activating enzyme (

). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA, ), benzylsuccinate synthase (BssD, ), gycerol dehydratase (DhaB2, ), trans-4-hydroxy-L-proline dehydratase (pflE, ) as well as enzymes annotated in Escherichia coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterisation and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain, which follows a conserved group of three cysteines and contains a variable pattern of 0 to 8 additional cysteines.
Anaerobic ribonucleoside-triphosphate reductase activating protein (NrdG2)
Type: Family

This enzyme is a member of the radical-SAM family. It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD,

) and presumably fulfils the identical function as NrdG , which utilises S-adenosyl methionine, an iron-sulphur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centred radical in NrdD .
Type 3 secretion system stator protein SctL/SctL2 (T3SS_SctL/SctL2)
Type: Family

This entry represents Type 3 secretion system stator proteins (also referred to HrpE-like proteins), which are the cytoplasmic components of bacterial type III secretion systems . Type 3 secretion systems (T3SSs) are used by many different Gram-negative pathogens and symbionts to inject bacterial effector proteins into eukaryotic host cells and modulate the interaction with them. This entry includes Type 3 secretion system stator protein SCTL (also known as NolV) from Rhizobium, Type 3 secretion system stator protein SCTL (also known as Yop proteins translocation protein L) from Yersinia enterocolitica and SPI-2 type 3 secretion system stator protein SCTL2 (also known as Secretion system apparatus protein SsaK) from Salmonella typhimurium . SCTL and SCTL2 act as regulators of the YscN/SctN and SsaN/SctN2 ATPases activity, respectively. This entry excludes the related protein FliH of the bacterial flagellar apparatus (see

).
YscD (YscD)
Type: Family

This family represents YscD from proteobacteria and similar putative type III secretion system bacteria such as HrpQ in Pseudomonas syringae, and EscD in enteropathogenic Escherichia coli. In the Chlamydiae, this entry describes the C-terminal 400 residues of a longer protein.

YscD is a single-pass inner membrane protein required for the export process of the Yop proteins. It is an essential component of the type III secretion system. YscD contains an N-terminal cytoplasmic domain (

), a transmembrane linker and a large periplasmic region formed by the three BON domains (

), (

) and (

). YscD forms part of the inner membrane component of the bacterial type III secretion injectosome apparatus .
Dihydroxyacetone kinase phosphotransferase subunit, N-terminal domain (DhaM_N)
Type: Domain

In Escherichia coli and many other bacteria, unlike the yeasts and a few bacteria such as Citrobacter freundii, the dihydroxyacetone kinase (also called glycerone kinase) transfers a phosphate from a phosphoprotein rather than from ATP. The dihydroxyacetone kinase of Escherichia coli consists of three subunits: DhaK, DhaL and DhaM. DhaM consists of three domains. The N-terminal dimerisation domain has the same fold as the IIA domain of the mannose transporter of the bacterial phosphoenolpyruvate:sugar phosphotransferase system (PTS) . The middle domain is similar to HPr and the C terminus is similar to the N-terminal domain of enzyme I (EI) of the PTS.

This entry represents the N-terminal domain of DhaM.
RNA polymerase sigma factor, FliA/WhiG (RNA_pol_sigma_FliA_WhiG)
Type: Family

Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors .

The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors .
Acetolactate synthase, large subunit, biosynthetic (Acetolactate_synth_lsu)
Type: Family

Two groups of proteins form acetolactate from two molecules of pyruvate. The type of acetolactate synthase described in this entry also catalyzes the formation of acetohydroxybutyrate from pyruvate and 2-oxobutyrate, an early step in the branched chain amino acid biosynthesis; it is therefore also termed acetohydroxyacid synthase. In bacteria, this catalytic chain is associated with a smaller regulatory chain in an alpha2/beta2 heterotetramer. Acetolactate synthase is a thiamine pyrophosphate enzyme. In this type, FAD and Mg++ are also found. Several isozymes of this enzyme are found in Escherichia coli (strain K12), one of which contains a frameshift in the large subunit gene and is not expressed.
Sucrose phosphatase, plant/cyanobacteria (Sucrose_phosphatase_pln/cyn)
Type: Family

This entry describes the sucrose phosphate phosphohydrolase from plants and cyanobacteria (SPP). However, a closely related group of sequences from bacteria and archaea may prove to catalyze the same reaction. SPP is a member of the Class IIB subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. SPP catalyzes the final step in the biosynthesis of sucrose, a critically important molecule for plants.

Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain, which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.
Aspartic peptidase, N-terminal (Aspartic_peptidase_N)
Type: Domain

This entry represents the N-terminal domain of the aspartic peptidases.
Abl-interactor, homeo-domain homologous domain (Abl-interactor_HHR_dom)
Type: Domain

The region is found towards the N terminus of a number of adaptor proteins that interact with Abl-family tyrosine kinases . More specifically, it is termed the homeo-domain homologous region (HHR), as it is similar to the DNA-binding region of homeo-domain proteins . Other homeo-domain proteins have been implicated in specifying positional information during embryonic development, and in the regulation of the expression of cell-type specific genes . The Abl-interactor proteins are thought to coordinate the cytoplasmic and nuclear functions of the Abl-family kinases, and seem to be involved in cytoskeletal reorganisation, but their precise role remains unclear .
Alpha-amylase, C-terminal beta-sheet (A-amylase_bs_C)
Type: Domain

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.

This entry represents the β-sheet domain that is found in several alpha-amylases, usually at the C terminus. This domain is organised as a five-stranded anti-parallel β-sheet .

Alpha-amylase is classified as family 13 (

) of the glycosyl hydrolases and is present in archaea, bacteria, fungi, plants and animals. Alpha-amylase is an essential enzyme in alpha-glucan metabolism, acting to catalyse the hydrolysis of alpha-1,4-glucosidic bonds of glycogen, starch and related polysaccharides. Although all alpha-amylases possess the same catalytic function, they can vary with respect to sequence. In general, they are composed of three domains: a TIM barrel containing the active site residues and chloride ion-binding site (domain A), a long loop region inserted between the third β-strand and the α-helix of domain A that contains calcium-binding site(s) (domain B), and a C-terminal β-sheet domain that appears to show some variability in sequence and length between amylases (domain C) . Amylases have at least one conserved calcium-binding site, as calcium is essential for the stability of the enzyme. The chloride-binding functions to activate the enzyme, which acts by a two-step mechanism involving a catalytic nucleophile base (usually an Asp) and a catalytic proton donor (usually a Glu) that are responsible for the formation of the beta-linked glycosyl-enzyme intermediate.
Spore coat protein CotF-like (Spore_coat_CotF-like)
Type: Family

The Coat F proteins contribute to the Bacillales spore coat. They occur multiple times in the genomes in which they are found. Bacillus subtilis endospore protein coats protect them and may play a role in their germination . Spore coat protein F, on the outer surface of the endospore, is one of a suite of proteins that could be used to differentiate between members of the Bacillus genus .
Calcium binding and coiled-coil domain-like (CALCOCO1-like)
Type: Domain

Calcium-binding and coiled-coil domain-containing protein 1 (Calcoco1) from Mus musculus (

) binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 (

), and thus enhances transcriptional activation by a number of nuclear receptors. Calcoco1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region .