SII-SWORD/CoKE huggingface dataset:
Legume-like lectin (Lectin_leg)
Type: Domain

Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 and ERGIC-53 lectins. These two proteins were the first members of the family of animal lectins similar to the leguminous plant lectins . The alignment for this family is towards the N terminus, where the similarity of VIP36 and ERGIC-53 is greatest. Although they have been identified as a family of animal lectins, this alignment also includes yeast sequences.
MobA/MobL protein (MobA_MobL)
Type: Domain

This entry represents a domain found at the N terminus of MobA in Escherichia coli, and MobL in Thiobacillus ferrooxidans (Acidithiobacillus ferrooxidans), as well as in conjugal transfer protein TraA. MobA and MobL are mobilisation proteins, which are essential for specific plasmid transfer.
Nepovirus coat protein (Nepo_coat)
Type: Domain

Nepoviruses are plant viruses that, together with comoviruses and picornaviruses, are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. Its genome consist of two single-stranded RNAs, both required for infection .

This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped β-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure .
Insect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 (A10/PebIII)
Type: Family

This entry represents the insect odorant-binding protein A10, also known as OS-D or pherokine-1, and ejaculatory bulb-specific protein 3 (PebIII), also known as pherokine-2 .
Matrix protein, N-terminal, pneumovirus (MATRX_N_pneumovirus)
Type: Domain

This entry represents the N-terminal domain of the pneumoviral matrix protein (MATRX). The N-terminal domain of the RSV M protein (residues 1-126) adopts a twisted β-sandwich fold comprised of two nearly perpendicular β-sheets - one with 3 β-strands and one with 4 β-strands . The overall topology is a curved horseshoe-like arrangement with the 3-stranded β-sheet forming the concave inner face flanked by loop regions, and the 4-stranded β-sheet forming the convex outer face. This domain is loosely associated with the C-terminal domain via weak hydrophobic interactions. The N-terminal domain contains a distinctive negatively charged surface lobe that may direct interactions with binding partners. Sequence alignments indicate that regions of diversity between RSV and other pneumoviruses map to external loop regions and sheet edges in this domain, likely mediating species-specific protein or RNA interactions.

The matrix proteins of Pneumovirus are transcriptional processivity and antitermination factor, and play a crucial role in viral assembly.
Poxvirus E8 (Poxvirus_E8)
Type: Family

This entry represents a family of poxvirus proteins that includes Protein E8 from Vaccinia virus, which is also known as Protein OPG070. This protein may play a role in the biogenesis of the viral factories by recruiting and wrapping DNA replication sites in endoplasmic reticulum derived membranes. It binds DNA in vitro with this binding likely to be modulated by phosphorylation by the viral kinase F10L .
Poxvirus P4A (Poxvirus_P4A)
Type: Family

This entry represents Major core protein 4a precursor from Vaccinia virus (P4A), also known as Major core protein OPG136 precursor, and similar proteins from poxvirus. P4a is one of the most abundant structural proteins in the Vaccinia virion. It undergoes proteolytic processing during the immature virion (IV) to mature virion (MV) transition .
DNA-directed RNA polymerase, 35kDa subunit, poxviral (DNA-dir_RNA_pol_35kDa_poxviral)
Type: Family

DNA-directed RNA polymerases

(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.

RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.

Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:

RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.

RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.

RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.

Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.

The DNA-dependent RNA polymerase from vaccinia virions has a molecular weight of approximately 500kDa and can be dissociated into putative subunits of 140, 137, 37, 35, 31, 22, and 17kDa. This group represents a DNA-directed RNA polymerase, 35kDa subunit.
Rhabdovirus matrix protein (Rhabdo_matrix)
Type: Family

The matrix (M) proteins of Rabies virus (RV) plays a key role in both assembly and budding of progeny virions. A PPPY motif (PY motif or late-budding domain) is conserved in the M proteins. These PY motifs are important for virus budding and for mediating interactions with specific cellular proteins containing WW domains.
Vacuolar protein sorting-associated protein Ist1 (Ist1)
Type: Family

Budding yeast Ist1 is involved in a late step in sorting of cargo proteins of the multivesicular body (MVB) for incorporation into intralumenal vesicles . This entry also includes Ist1 homologues from animals and plants. Human Ist1 functions in the ESCRT (endosomal sorting complexes required for transport) pathway and is required for efficient abscission during HeLa cell cytokinesis . Human Ist1 binds the transport (MIT) domain of VPS4, LIP5, and Spartin via its C-terminal MIT-interacting motif (MIM) .
SAC3/GANP/THP3, conserved domain (SAC3/GANP/THP3_conserved)
Type: Domain

This domain contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. Proteins containing this domain include the yeast nuclear export factor Sac3 , and mammalian GANP/MCM3-associated protein, which facilitates the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle . It also includes yeast Thp3 (THO-related protein 3), which may have a role in transcription elongation .
Transposase, IS1 (Transposase_27)
Type: Family

Transposase proteins are necessary for efficient DNA transposition. This family represents bacterial IS1 transposases .
Bordetella uptake gene (BUG)
Type: Family

Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth . Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors .

They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved β strand-β turn-α helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation .

BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity .
Moybdenum cofactor oxidoreductase, dimerisation (MoCF_OxRdtse_dimer)
Type: Domain

The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cis-dithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism .

This domain is found in molybdopterin cofactor oxidoreductases, such as in the C-terminal of Mo-containing sulphite oxidase, which catalyses the conversion of sulphite to sulphate, the terminal step in the oxidative degradation of cysteine and methionine . This domain is involved in dimer formation, and has an Ig-fold structure .
Fatty acid desaturase, type 2 (Fatty_acid_desaturase-2)
Type: Family

Fatty acid desaturases are enzymes that catalyse the insertion of a double bond at the delta position of fatty acids.

There seem to be two distinct families of fatty acid desaturases which do not seem to be evolutionary related.

Family 1 is composed of:

Stearoyl-CoA desaturase (SCD) (

) .

Family 2 is composed of:

Bacterial fatty acid desaturases.

Plant stearoyl-acyl-carrier-protein desaturase (

) , this enzyme catalyses the introduction of a double bond at the delta(9) position of steraoyl-ACP to produce oleoyl-ACP. This enzyme is responsible for the conversion of saturated fatty acids to unsaturated fatty acids in the synthesis of vegetable oils.

Cyanobacterial DesA , an enzyme that can introduce a second cis double bond at the delta(12) position of fatty acid bound to membranes glycerolipids. DesA is involved in chilling tolerance; the phase transition temperature of lipids of cellular membranes being dependent on the degree of unsaturation of fatty acids of the membrane lipids.

This entry contains fatty acid desaturases belonging to Family 2, also known as Acyl-ACP (Acyl Carrier Protein) desaturases.
Bacteriophage lambda, Tail fiber protein, repeat-2 (Phage_lambda_Stf-r2)
Type: Repeat

This entry represents repeat 2 of Tail fiber protein from Bacteriophage lambda (Stf or gp27) and similar proteins found in the tailed bacteriophages Caudovirales and in bacterial prophages. The repeats are about 40 residues long.

The strain of the Bacteriophage lambda used in most laboratories in the early 1990's carried some mutations respect to the wild type. Stf is the gene product of one of these mutations, which allow the virus to bind to an additional outer membrane receptor and accelerate the rate of adsorption onto the host cell surface but a higher failed infection frequency .
Nucleotide-diphospho-sugar transferase (Nucl-diP-sugar_transferase)
Type: Domain

This entry represents a domain found in a group of glycosyltransferases, including Arabidopsis arabinosyltransferase RRA1/2/3/XEG113 , beta-arabinofuranosyltransferase RAY1 and UDP-D-xylose:L-fucose alpha-1,3-D-xylosyltransferases .

The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates ([ec:2.4.1.-]) and related proteins into distinct sequence based families has been described . This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.
Foamy virus envelope protein (Foamy_env)
Type: Family

Expression of the envelope (Env) glycoprotein is essential for viral particle egress. This feature is unique to the Spumavirinae, a subclass of the Retroviridae.
Transmembrane glycoprotein (Glycoprotein)
Type: Family

This family of proteins has some GO annotations for positive regulation of growth rate and nematode larval development. This is probably a family of membrane glycoproteins .
Peptidase M44, metalloendopeptidase G1 (Peptidase_M44)
Type: Family

This entry includes metallopeptidases from poxvirus that belong to MEROPS peptidase family M44 (clan ME). The active site residues for members of this family occur in the motif HXXEH. This protein family inlcudes Metalloendopeptidase G1 from Vaccinia virus, also known as Metalloendopeptidase OPG085, which appears to play a role in the maturation of viral proteins by processing them preferentially at Ala-Gly-|-Ser/Thr/Lys motifs. Does not seem to be responsible for the cleavage of major core proteins .
Peptidase M74, penicillin-insensitive murein endopeptidase (Peptidase_M74)
Type: Family

This group of peptidases belong to MEROPS peptidase family M74 (murein endopeptidase family, clan MD). The type example is murein endopeptidase from Escherichia coli (MepA). The entry represents a family of penicillin-insensitive murein endopeptidases involved in the removal of murein from the sacculus by cleaving the peptide bonds between neighbouring strands in mature murein. The crystal structure of MepA has been determined revealing similarities to the D-Ala-D-Ala carboxypeptidases in MEROPS peptidase family M15 .
Glycosyl transferase, family 6 (Glyco_trans_6)
Type: Family

The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates ([ec:2.4.1.-]) and related proteins into distinct sequence based families has been described . This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.

Glycosyltransferase family 6

comprises enzymes with three known activities;
alpha-1,3-galactosyltransferase (

); alpha-1,3 N-acetylgalactosaminyltransferase (

);
alpha-galactosyltransferase (

).
Sigma-E processing peptidase SpoIIGA (SpoIIGA)
Type: Family

Sporulation in bacteria such as Bacillus subtilis involves the formation of a polar septum, which divides the sporangium into a mother cell and a forespore. The sigma E factor, which is encoded within the spoIIG operon, is a cell-specific regulatory protein that directs gene transcription in the mother cell. Sigma E is synthesised as an inactive proprotein pro-sigma E, which is converted to the mature factor by the processing enzyme SpoIIGA, releasing an N-terminal peptide .

The SpoIIGA peptidase (MEROPS peptidase family A36) is assumed to be an aspartic peptidase because of the presence of an Asp-Thr/Ser-Gly motif in which the Asp is an active site residue. The peptidase is active as a homodimer . SpoIIGA has five transmembrane helices at the N-terminal half of the molecule; the proteolytic activity is in the C-terminal half . Its tertiary structure is not known.
Peptidase U9, T4 prohead protease (Peptidase_U9_T4_prohead)
Type: Family

This group of peptidases belongs to MEROPS peptidase family U9 (phage prohead processing peptidase family, clan U-), which play a role in the head assembly of Bacteriophage T4.

The peptidases families associated with clan U-have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported.
Carbohydrate binding module family 6 (CBM6)
Type: Domain

This entry represents

which was previously known as cellulose-binding domain family VI (CBD VI). CBM6 bind to amorphous cellulose, xylan, mixed beta-(1,3)(1,4)glucan and beta-1,3-glucan .

CBM6 adopts a classic lectin-like β-jelly roll fold, predominantly consisting of five antiparallel β-strands on one face and four antiparallel β-strands on the other face. It contains two potential ligand binding sites, named respectively cleft A and B. These clefts include aromatic residues which are probably involved in the substrate binding. The cleft B is located on the concave surface of one β-sheet, and the cleft A on one edge of the protein between the loop that connects the inner and outer β-sheets of the jellyroll fold . The multiple binding clefts confer the extensive range of specificities displayed by the domain .

A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins.

CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose . However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology.

Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see .
Carbohydrate binding module family 25 (CBM25)
Type: Domain

This entry represents

, which has been shown to bind starch .

A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins.

CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose . However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology.

Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see .
Carbohydrate binding module family 17/28 (CBM17/28)
Type: Domain

A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins.

CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose . However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology.

Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see .

binds to amorphous cellulose and soluble beta-1,4-glucans, with a minimal binding requirement of cellotriose and optimal affinity for cellohexaose. Family 17 CBMs appear to have a very shallow binding cleft that may be more accessible to cellulose chains in non-crystalline cellulose than the deeper binding clefts of family 4 CBMs .

does not compete with CBM17 modules when binding to non-crystalline cellulose but does have a "β-jelly roll" topology, which is similar in structure to the CBM17 domains. Sequence and structural conservation in families 17 and 28 suggests that they have evolved through gene duplication and subsequent divergence .

This entry includes family 17 and 28 which show structural homology. The domain is found in a number of alkaline cellulases.