SII-SWORD/CoKE huggingface dataset:
Ribosome-binding factor A domain superfamily (RbfA_dom_sf)
Type: Homologous_superfamily

The structural domain of RbfA has an α-β fold containing three helices and three β-strands: α1-β1-β2-α2-α3-β3. The structure has type-II KH-domain fold topology, related to conserved KH sequence family proteins whose β-α-α-β subunits are characterised by a helix-turn-helix motif with sequence signature GxxG at the turn. In RbfA, this β-α-α-β subunit is characterised by a helix-kink-helix motif in which the GxxG sequence is replaced by a conserved AxG sequence .

Ribosome-binding factor A (gene rbfA) is a bacterial protein that associates with free 30S ribosomal subunits. It does not associate with 30S subunits that are part of 70S ribosomes or polysomes. It is essential for efficient processing of 16S rRNA. Ribosome-binding factor A is a protein of from 13 to 15 Kd which is found in most bacteria. A putative chloroplastic form seems to exist in plants.

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 .
Histone deacetylase domain (His_deacetylse_dom)
Type: Domain

This entry represents the structural domain found in histone deacetylases. It consists of a 3-layer(α-β-α) sandwich.

Histone deacetylases (HDACs)

are a class of enzymes that remove acetyl groups from N(6)-acetyl-lysine residues on histones. This process plays a critical role in transcription regulation, as HDACs facilitate tighter wrapping of DNA around histones. DNA expression is regulated in part by the balance between acetylation and deacetylation. The reaction catalyzed by HDACs is the reverse of

, which transfers acetyl groups to histones. In general, HDACs suppress gene expression because the removal of acetyl groups from the ε-amino group of lysine side chains at the N-terminal of histones restores the positive charge of lysine residues. This stabilization strengthens histone-DNA interactions and prevents transcription factors from binding to promoter elements . HDACs, along with acetoin utilization proteins and acetylpolyamine amidohydrolases, belong to an ancient protein superfamily .
HDAC can be divided by different classes :

Class I:
Includes HDAC1, HDAC2, HDAC3, and HDAC8. Generally nuclear and involved in transcriptional repression.

Class II:
Includes HDAC4, HDAC5, HDAC6, HDAC7, HDAC9, and HDAC10. Can shuttle between the nucleus and cytoplasm and are involved in diverse cellular processes. Subdivided into IIa (HDAC4, 5, 7, 9) and IIb (HDAC6, 10).

Class III:
Sirtuins (SIRT1-7 in mammals). NAD+-dependent deacetylases with different enzymatic mechanisms, involved in aging, metabolism, and stress response. Often considered a separate family.

Class IV:
Includes HDAC11. Has characteristics of both Class I and II.
Small ribosomal subunit protein bS16 domain superfamily (Ribosomal_bS16_dom_sf)
Type: Homologous_superfamily

This superfamily represents the structural domain of ribosomal bS16 proteins, consisting of an α-β 2 layer sandwich.

Ribosomal protein S16 (also known as bS16) is one of the proteins from the small ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups:

Eubacterial S16.

Algal and plant chloroplast S16.

Cyanelle S16.

Neurospora crassa mitochondrial S24 (cyt-21).

S16 proteins have about 100 amino-acid residues. There are two paralogues in Arabidopsis thaliana, RPS16-1 (chloroplastic) and RPS16-2 (targeted to the chloroplast and the mitochondrion) .

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 .
Protein of unknown function DUF3792, transmembrane (DUF3792_TM)
Type: Family

Members of this family of strongly hydrophobic putative transmembrane protein average about 125 amino acids in length and occur mostly, but not exclusively, in the Firmicutes. Members are quite diverse in sequence. Their function is unknown.
Uncharacterised protein family, spore photo-product lyase-related (Uncharacterised_Spl-rel)
Type: Family

This uncharacterised radical SAM domain protein occurs rarely and sporadically in species that include select Alphaproteobacteria and Actinobacteria, and in Deinococcus deserti VCD115. It is a distant but full-length homologue to the Bacillus subtilis spore photo-product lyase (Spl), which monomerises thymine dimers created as DNA damage by UV radiation.
Conserved hypothetical protein CHP03905 (CHP03905)
Type: Family

This entry describes a family of conserved hypothetical proteins of small size with four invariant Cys residues. This small protein is distantly homologous to a C-terminal domain found in proteins identified by N-terminal homology as ribonucleotide reductases.
Peptide modification radical SAM enzyme (Peptide_mod_rSAM)
Type: Family

Members of this protein family are radical SAM (rSAM) enzymes similar in sequence to others with known or postulated roles in peptide modification, and regularly found adjacent to members of the family described by

.
Nitrile hydratase accessory protein, putative (Nitrile_Hydratase_acc_put)
Type: Family

Members of this protein family are found in operons with the alpha and beta subunits of nitrile hydratase and appear to be accessory proteins for maturation or activation of the enzyme.
Thiopeptide-type bacteriocin biosynthesis domain (Thiopep_bacteriocin_synth_dom)
Type: Domain

This domain is often found within longer proteins that contain lantibiotic dehydratase domains (see

), such as Epidermin biosynthesis protein EpiB, Subtilin biosynthesis protein SpaB and Nisin biosynthesis protein NisB . It occurs also in bacteriocin biosynthesis single-domain proteins , including the pyridine synthases GE2270A (PbtD,

) and TbtD (

) .
Conserved hypothetical protein CHP03894 (CHP03894)
Type: Family

This protein family is restricted to the Prochlorococcus and Synechococcus lineages of the Cyanobacteria, and is sporadic in those lineages. Members average 100 amino acids in length, including a 30-residue, highly polar, low complexity region sandwiched between an N-terminal region of about 60 residues and a C-terminal [KR]VVR[KR]RS motif, both well-conserved. Their function is unknown.
Conserved hypothetical protein CHP04076 (CHP04076)
Type: Family

Members of this protein family are uncharacterised. The only invariant residue, and one of three other residues better than 90 percent conserved are both Cys. Phylogenetic profiling results and occasional fusion genes suggest a role for members of this family in redox reactions or iron cluster metabolism. Species occasionally have two or three copies.
Conserved hypothetical protein CHP04002 (CHP04002)
Type: Family

This family of proteins occur strictly as part of a tandem gene pair where one of the two represents an uncharacterised radical SAM protein.
Heme sensing membrane protein HsmA-like (HsmA-like)
Type: Family

This entry represents a group of bacterial proteins, including Heme sensing membrane protein HsmA from Clostridioides difficile, part of a heme-sensing membrane protein system (HsmRA) that induces a protective response that repurposes heme to counteract antimicrobial oxidative stress responses .
His-Xaa-Ser system protein (His-Xaa-Ser_sys)
Type: Family

Members of this rare protein family occur in the presence of

and

, which in turn occur only in the context of radical SAM protein families

and

. Their function is unknown .
CRISPR-associated protein Csx19 (CRISPR-assoc_Csx19)
Type: Family

Members of this protein family are found exclusively in CRISPR-containing organisms, in operon contexts with RAMP (repeat-associated mystery protein) proteins also linked to CRISPR. The Csx19 family previously was known as the TIGR03984 family CRISPR-associated protein .
CRISPR-associated protein CYA0889 (CRISPR-assoc_CYA0889)
Type: Family

Members of this protein family belong to CRISPR-associated (Cas) gene clusters. The majority of members are Cyanobacterial.
Frankia-40 domain (Frankia_40_dom)
Type: Domain

This entry describes a paralogous domain of 40 amino acids, restricted to smaller proteins of the genus Frankia, a member of the Actinobacteria. The function of the domain is unknown.
Conserved hypothetical protein CHP03890, nif11/cupin domain-containing (Nif11_cupin)
Type: Family

Members of this protein family occur exclusively in the Cyanobacteria and contain both a nif11 and a cupin domain. The function is unknown.
Peptide-modifying radical SAM enzyme putative, AF0577 (Pep-mod_rSAM_AF0577)
Type: Family

This radical SAM family contains a C-terminal region motif CXXCX5CX3C that is found in PqqE and other radical SAM enzymes that act on peptide substrates. Members of this family are found primarily in the Archaea, but also several eukaryotes (Trichomonas vaginalis G3, Entamoeba dispar SAW760, Giardia intestinalis ATCC 50581, etc.). The function is unknown .
Radical SAM GDL-associated (rSAM_GDL-assoc)
Type: Family

This narrowly distributed protein family contains an N-terminal radical SAM domain. It occurs in Pseudomonas fluorescens Pf0-1, Ralstonia solanacearum, and numerous species and strains of Burkholderia. Members always occur next to a trio of three mutually homologous genes, all of which contain the domain

as the whole of the protein (about 60 amino acids) or as the C-terminal domain. The function is unknown, but the fact that all phylogenetically correlated proteins are mutually homologous with prominent invariant motifs (an invariant tyrosine and a GDL motif) and as small as 60 amino acids suggests that post-translational modification of

domain-containing proteins may be its function. This view is supported by closer homology to the PqqE radical SAM protein involved in PQQ biosynthesis from the PqqA precursor peptide than to other characterised radical SAM proteins.
Radical SAM, TatD-associated (rSAM_TatD-assoc)
Type: Family

Members of this family are radical SAM proteins found in about 5 percent of microbial genomes. A portion occur as gene fusions with, or adjacent to, members of the TatD family of hydrolases (

). The TatD family may have several paralogs per genome, including TatD itself from E. coli (a soluble protein not actually part of the twin-arginine translocation complex), which appears to act in quality control for TAT, directing turnover of misfolded TAT substrates. The functions of TatD family hydrolases in general (other than TatD itself, which may be exceptional within its larger family), and of this radical SAM domain protein modeled here, are unknown.
Radical SAM, TatD-associated, bacteria (rSAM_TatD-assoc_bac)
Type: Family

Members of this protein family are radical SAM enzymes that appear paired with members of

, a family of small (~170 residue), mostly hydrophobic proteins. This family of radical SAM enzymes belongs to a larger family

, in which some members show regularly in contexts with TatD.
Conserved hypothetical protein CHP04066, peptide maturation system (CHP04066_peptide_maturation)
Type: Family

Members of this protein family occur in various Clostridial genomes, always in the context of a short peptide, which is likely to be a bacteriocin, and a radical SAM protein that is predicted to modify the short peptide. Sequence analysis suggests a relationship between family members and archaeal proteins designated as subunits of an H+-transporting two-sector ATPase. Family members are candidates to act in either maturation or immunity.
Conserved hypothetical protein CHP04073, exosortase-affiliated (CHP04073_exosortase-affil)
Type: Family

Members of this protein family are found in beta, gamma, and delta proteobacteria, and in the verrucomicrobia. Twenty-two of twenty-four species encountered contain the PEP-CTERM/exosortase system for modulating extracellular polysaccharide biosynthesis production, suggesting a role in protein sorting. There is a distant sequence relationship between a region of this protein of about 100 amino acids and a corresponding region of the very large eukaryotic protein Vps13, associated with vacuolar protein sorting in yeast.
CRISPR-associated RAMP BGP1436 (CRISPR-assoc_RAMP_BGP1436)
Type: Family

Members of this protein family, part of the larger Repeat-Associated Mystery Protein (RAMP) family, are found in local contexts containing other RAMPs. They occur exclusively in species with CRISPR systems.
Rhomboid-like serine protease, proteobacteria (Rhom-like_SP_proteobac)
Type: Family

This entry describes a rhomboid-like intramembrane serine protease. Its species distribution closely matches that of GlyGly-CTERM (

), a protein targeting domain analogous to LPXTG and PEP-CTERM. In a number of species (Ralstonia eutropha, R. metallidurans, R. solanacearum, Marinobacter aquaeolei, etc) with just one GlyGly-CTERM protein (i.e., a dedicated system), the rhombosortase and GlyGly-CTERM genes are adjacent .
Peptidase S8, subtilisin, Asp-active site (Peptidase_S8_Asp-AS)
Type: Active_site

Subtilases are an extensive family of serine proteases belonging to the MEROPS peptidase family S8 (subtilisin, clan SB). Members of this family have a catalytic triad in the order Asp, His and Ser in the sequence, which is a different order to that of families S1, S9 and S10. The catalytic activity is provided by a charge relay system similar to that of the trypsin family of serine proteases but which evolved by independent convergent evolution. The sequence around the residues involved in the catalytic triad (Asp, Ser and His) are completely different from that of the analogous residues in the trypsin serine proteases and can be used as signatures specific to that category of proteases. If a protein includes at least two of the three active site signatures, the probability of it being a serine protease from the subtilase family is 100%.

This entry represents the conserved sequence around the aspartic acid (Asp) active site.
Peptidase S8, subtilisin, Ser-active site (Peptidase_S8_Ser-AS)
Type: Active_site

This entry represents the conserved sequence around the Ser active site.

Subtilases are an extensive family of serine proteases belonging to the MEROPS peptidase family S8 (subtilisin, clan SB). Members of this family have a catalytic triad in the order Asp, His and Ser in the sequence, which is a different order to that of families S1, S9 and S10. The catalytic activity is provided by a charge relay system similar to that of the trypsin family of serine proteases but which evolved by independent convergent evolution. The sequence around the residues involved in the catalytic triad (Asp, Ser and His) are completely different from that of the analogous residues in the trypsin serine proteases and can be used as signatures specific to that category of proteases. If a protein includes at least two of the three active site signatures, the probability of it being a serine protease from the subtilase family is 100%.
Poly-beta-1,6-N-acetyl-D-glucosamine biosynthesis protein PgaD (PGA_PgaD)
Type: Family

This entry represents the poly-beta-1,6-N-acetyl-D-glucosamine (PGA) biosynthesis protein PgaD. This cytoplasmic membrane protein appears to be an auxiliary subunit to the PGA synthase PgaC (

) . PgaD is esential for the process of PGA synthesis and export. PGA serves as an adhesin for the maintenance of biofilm structural stability in bacteria.
Peptidase S8A, PatG (Peptidase_S8A_PatG)
Type: Family

Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) .

Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes . The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route . The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus.

This entry contains serine endopeptidases belonging to the MEROPS peptidase family S8 (subtilisin family , clan SB); which include PatA and C-terminal peptidase domain of the PatG protein of Prochloron didemni, TenA and a region of TenG from Nostoc spongiaeforme var. tenue, etc. These peptidases are associated with the maturation of various members of the cyanobactin family of ribosomally produced, heavily modified bioactive metabolites.
Serine peptidase MXAN_5808-like (MXAN_5808-like)
Type: Family

This entry represents a group of protein sequences mainly found in the order Myxococcales in the Deltaproteobacteria, including MXAN_5808 from Myxococcus xanthus (

). Members are multidomain proteins of about 1070 residues that contain a PDZ domain, an S41 family peptidase domain belonging to MEROPS peptidase family S41A, and an SH3 domain.
Histidine triad protein (His_triad_protein)
Type: Family

This entry represents a family of Streptococcal proteins that contain a number of repeated His-X-X-His-X-His (histidine triad) motifs. Members of the family are suggested to cleave human complement component 3, and family member PhpA has been shown in vaccine studies to be a protective antigen in mice .
SipW-dependent-type signal peptide (Signal_pept_SipW-depend-type)
Type: Domain

This entry describes an N-terminal domain found regularly in proteins encoded near a variant form of signal peptidase I such as the SipW protein of Bacillus subtilis. Many though not all members are homologues of camelysin (a casein-cleaving metalloprotease) and TasA (CotN), a metalloprotease that is secreted, along with extracellular polysaccharide (EPS), to be the major protein constituent of the Bacillus subtilis biofilm matrix. Sequencing from several known TasA/CotN proteins shows the cleavage location to be near the centre of the alignment and typical of type I signal peptidases, with small residues at -3 and -1.
Type VII secretion system peptidase S8A, mycosin (T7SS_pept_S8A_mycosin)
Type: Family

Members of this family are subtilisin-related serine proteases belonging to MEROPS peptidase family S8A, mycosin-1 clan SB. They are found strictly in the Actinobacteria and associated with type VII secretion operons . The designation mycosin is used for members from Mycobacterium .
Type VII secretion system AAA-ATPase, EccA (T7SS_EccA)
Type: Family

This entry represents the AAA family ATPase, EccA, of the type VII secretion system from the actinobacteria. Species such as Mycobacterium tuberculosis have multicopies of this secretion system with genes designated: EccA1, EccA2, etc.
EccCa-like, Actinobacteria (EccCa-like_Actinobacteria)
Type: Family

This entry represents the EccCa subunit of the type VII secretion system from Actinobacteria. In many proteins it forms the N-terminal domain being fused to EccCb as the C-terminal domain. Type VII secretion is defined more broadly as including secretion systems for ESAT-6-like proteins in the Firmicutes as well as in the Actinobacteria , but this family does not show close homologues in the Firmicutes.