SII-SWORD/CoKE huggingface dataset:
CRISPR-associated protein Cas7, subtype I-B/Tneap (Cas7/Cst2/DevR_sub_I-B/Tneap)
Type: Family

This entry represents a family of DevR (Cas7)-type Cas proteins that includes DevR from Myxococcus xanthus. DevR is a key regulator of development. DevR mutants are incapable of fruiting body development . The expression of DevR appears to be regulated through a number of means, including both location and autorepression.

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
CRISPR-associated protein Cas5/Cmx5/DevS (Cas5_Cmx5_DevS)
Type: Family

This entry represents a family of Cas5 proteins that includes DevS from Myxococcus xanthus, as well as related proteins from Leptospira interrogans and Gemmata obscuriglobus. Cas5 is a key regulator of development that is encoded in a cluster of CRISPR-associated (cas) genes, and in the special case of M. xanthus has taken on a role in the control of fruiting body development. This entry is related to

,

, and

.

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Conserved hypothetical protein CHP02587, putative integral membrane (CHP02587_IM)
Type: Family

Members of this protein family are found in Anabaena sp. (strain PCC 7120), Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus in a conserved two-gene neighbourhood. The proteins appear to span the membrane seven times.
Conserved hypothetical protein CHP02588 (CHP02588)
Type: Family

The function of this protein is unknown. It often found as part of a two-gene operon with

, a protein that appears to span the membrane seven times. It has so far been found in the bacteria Anabaena sp. (strain PCC 7120), Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus.
Type I-C CRISPR-associated protein Cas7/Csd2 (CRISPR-assoc_prot_Cas7/Csd2)
Type: Family

This entry represents one of two closely related subfamilies that belong to the larger family of CRISPR-associated protein TM1801. Members are the type I-C CRISPR-associated protein Cas7/Csd2 of the Dvulg subtype of the CRISPR/cas system . A related entry is

, the Csh2 protein of the Hmari CRISPR subtype.

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Type I-B CRISPR-associated protein Cas7/Csh2 (CRISPR-assoc_prot_Cas7/Csh2)
Type: Family

This entry represents one of two closely related subfamilies that belong to the larger family of CRISPR-associated protein TM1801. Members are the type I-B CRISPR-associated protein Cas7/Csh2 of the Hmari subtype of the CRISPR/cas system. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. A related model is

, the Csd3 protein of the Dvulg CRISPR subtype.

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Type I-B CRISPR-associated protein Cas8b/Csh1, C-terminal (CRISPR-assoc_prot_Cas8b/Csh1_C)
Type: Domain

This entry is found in the C-terminal region of a family of type I-B CRISPR-associated protein Cas8b/Csh1 of the Hmari subtype, . Except for some sequences from halophilic archaea, this domain contains a pair of CXXC motifs.

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Type I-B CRISPR-associated protein Cas5, HALMA (CRISPR-assoc_prot_Cas5_HALMA)
Type: Family

This entry represents a Cas5 family of Cas proteins unique to the hmari subtype of cas genes and CRISPR repeats, which is the only subtype present in Haloarcula marismortui ATCC 43049. The hmari type, though uncommon, is also found in the Aquificae, Thermotogae, Firmicutes, and Dictyoglomi.

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
CRISPR-associated protein Cas5, N-terminal (CRISPR-assoc_prot_Cas5_N)
Type: Domain

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.

This entry represents a shared N-terminal region, of about 43 amino acids in length, found in a number of Cas proteins. This region is widely distributed and was designated Cas5. Proteins containing this region are generally 210 to 265 amino acids in length and show little or no homology between their C-terminal regions. The best characterised protein in this entry is DevS (

) from Myxococcus xanthus, a Cas protein that appears to participate in a species-specific developmental pathway. Cas5 is found within a cluster of three cas genes associated with CRISPR structures in many bacterial species, named cas1B, cas5 and cas6 .
Conserved hypothetical protein CHP02594 (CHP02594)
Type: Family

This entry is so far restricted mostly to proteobacteria, although it is found in some other bacteria. Its function is unknown.
PEP-CTERM protein-sorting domain (PEP_exosort_dom)
Type: Domain

This entry describes a 25-residue domain including an invariant Pro-Glu-Pro (PEP) motif, a thirteen residue strongly hydrophobic sequence likely to span the membrane, and a five-residue strongly basic motif that often contains four Arg residues. In most cases, this motif is found within nine residues of the C-terminal end of the protein. Proteins containing this motif typically have signal sequences at the N terminus .
Autotransporter-associated beta strand repeat (Autotrns_rpt)
Type: Repeat

This Autotransporter-associated β strand repeat model represents a core 32-residue region of a class of bacterial protein repeat found in one to 30 copies per protein. Most proteins with a copy of this repeat have domains associated with membrane autotransporters (

). The repeats occur with a periodicity of 60 to 100 residues. A pattern of sequence conservation is that every second residue is well-conserved across most of the domain. These repeats as likely to have a β-helical structure. This repeat plays a role in the efficient transport of autotransporter virulence factors to the bacterial surface during growth and infection. The repeat is always associated with the passenger domain of the autotransporter. For these reasons it has been coined the Passenger-associated Transport Repeat (PATR) . The mechanism by which the PATR motif promotes transport is uncertain but it is likely that the conserved glycines (see HMM Logo) are required for flexibility of folding and that this folding drives secretion . Autotransporters that contain PATR(s) associate with distinct virulence traits such as subtilisin (S8) type protease domains and polymorphic outer-membrane protein repeats, whilst SPATE (S6) type protease and lipase-like autotransporters do not tend to contain PATR motifs .
Exosortase, EpsH-like (EpsH-like)
Type: Family

Members of this family are designated exosortase, analogous to sortase in cell wall sorting mediated by LPXTG domains in Gram-positive bacteria. The phylogenetic distibution of the proteins in this entry is nearly perfectly correlated with the distribution of the proteins having the PEP-CTERM anchor motif

.

Members of this entry are integral membrane proteins with eight predicted transmembrane helices in common. Some members of this family have long trailing sequences past the region described by this model. This model does not include the region of the first predicted transmembrane region. The best characterised member is EpsH of Methylobacillus sp. 12S, where it is part of a locus associated with biosynthesis of the exopolysaccharide methanolan.
Haem-binding domain, putative (Haem-bd_dom_put)
Type: Domain

This entry represents a protein domain found predominantly in bacterial species. A large number of paralogues exist in some of the species that contain it. For example, more than twenty copies are found in Rhodopirellula baltica SH 1 and Verrucomicrobium spinosum DSM 4136. This domain is approximately 140 amino acids long and contains an absolutely conserved motif CxxCH, which is the cytochrome c family haem-binding site signature.
Putative membrane-bound dehydrogenase (Membrane-bound_put_N)
Type: Domain

Most proteins containing this domain also contain several hundred residues of highly variable sequence, and then a well-conserved C-terminal domain (

) that features a putative cytochrome c-type haem binding motif CXXCH. The membrane-bound L-sorbosone dehydrogenase from Acetobacter liquefaciens (Gluconacetobacter liquefaciens) (

) shows some homolgy to this domain but lacks additional sequence regions found in this entry and belongs to a different clade of the larger family of homologues.

This domain is predicted to adopt six-bladed β-propeller structure.
Putative regulatory protein FmdB, zinc ribbon domain (Regulatory_FmdB_Zinc_ribbon)
Type: Domain

This entry represents a putative zinc beta-ribbon domain of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB . Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Toxin-antitoxin system, antidote protein, HigA (Toxin_antidote_HigA)
Type: Family

Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is encoded by the upstream member of the gene pair .
Delta-60 repeat (Delta_60_rpt)
Type: Repeat

This repeat often occurs in tandem, up to as many as 13 times, in proteins from Bdellovibrio bacteriovorus, Azotobacter vinelandii, Geobacter sulfurreducens, Pirellula sp. 1, Myxococcus xanthus, amongst others, many of which are Deltaproteobacteria. The length of the repeat ranges from about 57 to 61 amino acids -this entry represents a core region of approximately 54 amino acids.
Putative addiction module antidote (Doc_partner)
Type: Family

Members of this family are putative addiction module antidote proteins encoded by genes that appear recurrently in two-gene operons, where the other gene encodes a Doc (death-on-curing) protein (

). Many family members contain an AbrB-like domain (

). Note that these proteins tend to be found on bacterial chromosomes, not on plasmids.
Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn)
Type: Family

Proteins in this entry are encoded by genes involved in either polyhydroxyalkanoic acid (PHA) biosynthesis or utilisation, including proteins at found at the surface of PHA granules. These proteins have so far been predominantly found in the Pseudomonadales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria.
Conserved hypothetical protein CHP02611 (CHP02611)
Type: Family

Proteins in this entry are Actinobacterial proteins of about 150 amino acids in length, with three predicted transmembrane helices and an unusual motif with consensus sequence PGPGW.
Mobile mystery protein A (Mobile_mystery_prot_A)
Type: Family

Proteins in this entry are more often encoded within mobilisation-related contexts than not. This includes a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and plasmids in Agrobacterium tumefaciens and Coxiella burnetii. They are found together with mobile mystery protein B, a member of the Fic protein family (

). Mobile mystery protein A is encoded by the upstream member of the gene pair and contains a helix-turn-helix domain.
Mobile mystery protein B (Mobile_mystery_prot_B)
Type: Family

Proteins in this family, designated mobile mystery protein B, are more often encoded within mobilisation-related contexts than not. This includes a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and plasmids in Agrobacterium tumefaciens and Coxiella burnetii. They are always found together with mobile mystery protein A (

), a helix-turn-helix putative DNA binding protein. This protein is encoded by the downstream member of the gene pair and belongs to the Fic protein family, where Fic (filamentation induced by cAMP) is a regulator of cell division. The characteristics of having a two-gene operon in a varied context, often on plasmids, with one member affecting cell division and the other able to bind DNA, suggests similarity to addiction modules.
Probable peptidoglycan glycosyltransferase FtsW (FtsW)
Type: Family

FtsW is an integral membrane protein with ten transmembrane segments . In general, it is one of two paralogues involved in peptidoglycan biosynthesis, the other being RodA, and is essential for cell division . In endospore-forming bacteria (e.g. Bacillus subtilis) three or more RodA/FtsW/SpoVE family paralogues are present . SpoVE acts in spore cortex formation and is dispensable for growth .

FtsW belongs to the so called SEDS (shape, elongation, division and sporulation) family, which are thought to be peptidoglycan polymerases .
Sporulation stage V, protein E (SpoVE)
Type: Family

Like FtsW, SpoVE proteins are encoded in a peptidoglycan operon context, but found only in endospore-forming bacteria such as Bacillus, Geobacillus and Oceanobacillus. In these genera they are part of a larger set of paralogs (not just the pair FtsW and RodA) and are required specifically for sporulation, not for viability.
Tryptophanase (TNase)
Type: Family

Proteins in this entry belong to the beta-eliminating lyase family and are thought to act as tryptophanases (

) (also known as L-tryptophan indole-lyases). The genes encoding these proteins are, as a rule, found with a tryptophanase leader peptide TnaC encoded upstream.
Tyrosine phenol-lyase (Tyr_phenol_ly)
Type: Family

Tyrosine phenol-lyases (

) (beta-tyrosinase), are pyridoxal-phosphate enzymes which are closely related to tryptophanase (

) (see

). Both belong to the beta-eliminating lyase family.
CRISPR system ring nuclease SSO1393-like (SSO1393-like)
Type: Domain

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.

This entry represents a conserved region of about 150 amino acids found in a family of Cas proteins, such as ring nuclease SSO1393 from Saccharolobus solfataricus .
CRISPR-associated protein Csx16 (CRISPR-assoc_prot_Csx16)
Type: Family

This entry represents the CRISPR-associated protein Csx16 which has not been experimentally characterised but seems to be distantly related to DUF1874 (AcrIII-1) family proteins, which are potent ring nucleases .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Helicase Cas3, CRISPR-associated, Anaes-subtype (Helicase_Cas3_CRISPR-ass_Anaes)
Type: Family

This entry represents a subfamily of Cas3 DEAH-box helicases found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. The proteins include both DEAH and HD motifs. Cas3 is one of four protein families (Cas1 to Cas4) that are associated with CRISPR elements and always occur near a repeat cluster, usually in the order cas3-cas4-cas1-cas2 .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
CDP-glucose 4,6-dehydratase (CDP_4_6_deHydtase)
Type: Family

This entry contains CDP-glucose 4,6-dehydratases from a variety of Gram-negative and Gram-positive bacteria. Members are typically encoded next to a gene that encodes a glucose-1-phosphate cytidylyltransferase, which produces the substrate CDP-D-glucose. This is used by the proteins in this entry to produce CDP-4-keto-6-deoxyglucose.
Glucose-1-phosphate cytidylyltransferase-like (G1P_cyt_trans-like)
Type: Family

Alpha-D-Glucose-1-phosphate cytidylyltransferase, also known as CDP-glucose pyrophosphorylase, is the product of the rfbF gene and produces CDP-D-glucose from alpha-D-Glucose-1-phosphate and MgCTP as substrate . CDP-D-Glucose is the precursor for synthesising four of the five naturally occurring 3,6-dideoxy sugars-abequose (3,6-dideoxy-D-Xylo-hexose), ascarylose (3,6-dideoxy-L-arabino-hexose), paratose (3,6-dideoxy-D-ribohexose), and tyvelose (3,6-dideoxy-D-arabino-hexose. Deoxysugars are ubiquitous in nature where they function in a variety of biological processes, including cell adhesion, immune response, determination of ABO blood groups, fertilisation, antibiotic function, and microbial pathogenicity .

This entry also includes the probable glucose-1-phosphate cytidylyltransferase from Bacillus subtilis.
Rhamnulose-1-phosphate aldolase (Rhamnulose-1-P_Aldolase)
Type: Family

Proteins in this entry match the enzyme RhaD, rhamnulose-1-phosphate aldolase (

).
L-rhamnose mutarotase (L-rhamnose_mutarotase)
Type: Family

This entry contains rhamnose mutarotase from Escherichia coli, previously designated YiiL as an uncharacterised protein, and close homologues associated with rhamnose dissimilation operons in other bacterial genomes. Mutarotase is a term for an epimerase that changes optical activity. This enzyme was shown experimentally to interconvert alpha and beta stereoisomers of the pyranose form of L-rhamnose . The crystal structure of this small (104 amino acid) protein shows a locally asymmetric dimer with active site residues of His, Tyr, and Trp .
Rhamnulokinase (Rhamnulokinase)
Type: Family

Rhamnulokinase (

) is an enzyme that catalyses the second step in rhamnose catabolism. It catalyses the ATP-dependent phosphorylation of L-rhamnulose to produce L-rhamnulose-1-phosphate and ADP. Rhamnulokinase exists as a monomer composed of two large domains. The ATP binding site is located in the cleft between the two domains. The presence of divalent Mg2+ or Mn2+ is required for catalysis.
L-fuculokinase (Fuculokinase)
Type: Family

Proteins in this entry are L-fuculokinases including the Escherichia coli enzyme

. They catalyse the second step in fucose catabolism and belong to the FGGY family of carbohydrate kinases. These enzymes are encoded by the kinase (K) gene of the fucose (fuc) operon.
L-rhamnose catabolism isomerase (L_rhamnose_iso)
Type: Family

These enzymes are isomerases in the pathway of L-rhamnose catabolism, as found in Pseudomonas stutzeri and in a number of the Rhizobiales, and are distinct from the L-rhamnose isomerases of Escherichia coli (see

). They catalyze the isomerisation step in rhamnose catabolism. Genetic evidence in Rhizobium leguminosarum bv. trifolii suggests that unlike the situation in E. coli, phosphorylation occurs first, then isomerisation of the phosphorylated sugar occurs.
Xylose isomerase, bacterial-type (Xylose_isom_bac)
Type: Family

Xylose isomerase (

) is an enzyme which interconverts D-xylose and D-xylulose.
Xylose isomerase, actinobacteria (XylA_actinobac)
Type: Family

This is an enzyme which as well as interconverting D-xylose and D-xylulose, is also active as a D-glucose isomerase. It is tetrameric and dependent on a divalent cation, either Mg2+, Co2+ or Mn2+, as characterised in Arthrobacter . Enzymes in this entry differ substantially from the D-xylose isomerases of

.
Bifunctional rhamnulose-1-phosphate aldolase/alcohol dehydrogenase (Bifunc_RhaD/ADH)
Type: Family

Rhamnose is a methyl-pentose sugar which is found as a constituent of pectin within the cell walls of dicotyledonous plants and has also been found in the mucilage of a number of legume plants . RhaD from Rhizobium leguminosarum bv. trifolii is encoded by a gene occurring in a rhamnose utilisation cluster, and is necessary for growth on this compound . This protein is predicted to be a bifunctional NAD-dependent aldolase/dehydrogenase.
D-xylose-binding periplasmic protein (XylF)
Type: Family

This entry represents the D-xylose-binding periplasmic protein XylF (also known as D-xylose ABC transporter substrate-binding protein) which is a periplasmic (when in Gram-negative bacteria) binding protein for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter .

Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. Most of the bacterial ABC (ATP-binding cassette) importers are composed of one or two transmembrane permease proteins, one or two nucleotide-binding proteins and a highly specific periplasmic solute-binding protein. In Gram-negative bacteria the solute-binding proteins are dissolved in the periplasm, while in archaea and Gram-positive bacteria, their solute-binding proteins are membrane-anchored lipoproteins .
Rhamnose isomerase-related (Rhamnose_iso-rel)
Type: Family

The proteins in this entry are closely related to the L-rhamnose isomerases (

) found in Pseudomonas stutzeri and in a number of the Rhizobiales. They are encoded in similar genomic contexts, close to genes apparently involved in rhamnose catabolism such as rhamnulose-1-phosphate aldolase (

), sugar kinases, and sugar transporters.
Aldose 1-epimerase, bacterial (Ald_epimerase_bac)
Type: Family

Aldose 1-epimerase (

) (also known as mutarotase) participates in the Leloir pathway for galactose/glucose interconversion. It is the enzyme responsible for the anomeric interconversion of D-glucose and other aldoses between their alpha- and beta-forms. The sequence of mutarotase from two bacteria, Acinetobacter calcoaceticus and Streptococcus thermophilus is available . The best conserved region in the sequence of mutarotase is centered around a conserved histidine residue which may be involved in the catalytic mechanism.

This family represents aldose 1-epimerases from bacteria (also known as galactose mutarotases/D-galactose 1-epimerase). These proteins belong to the aldose 1-epimerase family. However, the aldose 1-epimerase itself (

) has a relatively broad specificity and can utilise D-glucose, L-arabinose, D-xylose, D-galactose, maltose and lactose. The restricted genomic context of the genes suggests members should act primarily on D-galactose.
Rhamnose ABC transporter, substrate-binding protein RhaS (RhaS)
Type: Family

This sugar-binding component of ABC transporter complexes is found in rhamnose catabolism operon contexts. Mutation of the gene in Rhizobium leguminosarum abolishes rhamnose transport and prevents growth on rhamnose as a carbon source.

Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. Most of the bacterial ABC (ATP-binding cassette) importers are composed of one or two transmembrane permease proteins, one or two nucleotide-binding proteins and a highly specific periplasmic solute-binding protein. In Gram-negative bacteria the solute-binding proteins are dissolved in the periplasm, while in archaea and Gram-positive bacteria, their solute-binding proteins are membrane-anchored lipoproteins .
Lactaldehyde reductase (Lactal_redase)
Type: Family

The proteins in this entry form a distinct clade of iron-containing alcohol dehydrogenases. The genes encoding these proteins are generally found in apparent operons for the catabolism of rhamnose or fucose. Catabolism of both of these monosaccharides results in the production of lactaldehydes, which are reduced by these enzymes to 1,2 propanediol . These enzymes are also sometimes called 1,2 propanediol oxidoreductases. They are active under anaerobic conditions in Escherichia coli, while being inactivated by reactive oxygen species under aerobic conditions . Under aerobic conditions the lactaldehyde product of rhamnose and fucose catabolism is believed to be oxidized to lactate by a separate enzyme, lactaldehyde dehydrogenase.