SII-SWORD/CoKE huggingface dataset:
Influenza C non-structural protein NS1 (Flu_C_NS1)
Type: Domain

The influenza C virus genome consists of seven single-stranded RNA segments. The shortest RNA segment encodes a 286 amino acid non-structural protein NS1 . This protein contains 6 conserved cysteines that may be functionally important, perhaps binding to a metal ion.
Influenza C non-structural protein NS2 (Flu_C_NS2)
Type: Domain

The influenza C virus genome consists of seven single-stranded RNA segments. The shortest RNA segment encodes a 286 amino acid non-structural protein NS1

as well as the NS2 protein. The NS2 protein is only about 60 amino acids in length and of unknown function.
Focal adhesion kinase, targeting (FAT) domain (Focal_adhesion_kin_target_dom)
Type: Domain

Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signalling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal "focal adhesion targeting" (FAT) region is necessary and sufficient for localizing FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin . The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not.
Glutamate-ammonia ligase adenylyltransferase, repeated domain (GlnE_rpt_dom)
Type: Domain

This is a conserved repeated domain found in GlnE proteins. These proteins adenylate and deadenylate glutamine synthases:
ATP + {L-Glutamate:ammonia ligase (ADP-forming)} = Diphosphate + Adenylyl-{L-Glutamate:Ammonia ligase (ADP-forming)}.
The domain is related to the nucleotidyltransferase domain

.
Glycoside hydrolase, family 49, C-terminal (Glyco_hydro_49_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.

Dextranase (

) and isopullulanase (

) are members of glycoside hydrolase family 49 (

). Dextranase hydrolyses alpha-1,6-glycosidic bonds in dextran polymers.

This entry corresponds to the C-terminal of the pectate lyase like domain.
Glycoside hydrolase, family 62, arabinosidase (GH62_arabinosidase)
Type: Family

This is a family of alpha -L-arabinofuranosidases (

) which are all members of glycoside hydrolase family 62 (

). This enzyme hydrolyzed aryl alpha-L-arabinofuranosides and cleaves arabinosyl side chains from arabinoxylan and arabinan.

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.
Glycoside hydrolase family 65, C-terminal (Glyco_hydro_65_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.

Family 65 (

) contains this domain and includes vacuolar acid trehalase and maltose phosphorylases. Maltose phosphorylase (MP) is a dimeric enzyme that catalyses the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The C-terminal domain forms a two layered jelly roll motif. This domain is situated at the base of the catalytic domain, however its function remains unknown .
Glycoside hydrolase, family 65, central catalytic (Glyco_hydro_65_M)
Type: Domain

The family of glycosyl hydrolases (

) which contains this domain includes vacuolar acid trehalase and maltose phosphorylase. Maltose phosphorylase (MP) is a dimeric enzyme that catalyses the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The central domain is the catalytic domain, which binds a phosphate ion that is proximal the the highly conserved Glu. The arrangement of the phosphate and the glutamate is thought to cause nucleophilic attack on the anomeric carbon atom . The catalytic domain also forms the majority of the dimerisation interface.

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.
Glycoside hydrolase, family 65, N-terminal (Glyco_hydro_65_N)
Type: Domain

This entry represents the N-terminal domain of the glycoside hydrolase family 65 proteins. The family of glycosyl hydrolases (

) containing this domain includes vacuolar acid trehalase and maltose phosphorylase. Maltose phosphorylase (MP) is a dimeric enzyme that catalyses the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. This domain is believed to be essential for catalytic activity although its precise function remains unknown.

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.
Glycoside hydrolase family 71 (Glyco_hydro_71)
Type: Family

This is a family of alpha-1,3-glucanases belonging to glycoside hydrolase family 71 (

). Endo-1,3-alpha-glucanase Agn1 hydrolyses septum-edging material and acts in concert with endo-(1,3)-beta-glucanase Eng1 to achieve efficient cell separation in fission-yeast .

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.
Glycoside hydrolase, family 76 (Glyco_hydro_76)
Type: Family

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 is a family of alpha-1,6-mannanases belonging to glycoside hydrolase family 76 (

).
Glycoside hydrolase, family 79 (Glyco_hydro_79)
Type: Family

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 is a family of endo-beta-N-glucuronidase, or heparanase belonging to glycoside hydrolase family 79 (

). Heparan sulphate proteoglycans (HSPGs) play a key role in the self- assembly, insolubility and barrier properties of basement membranes and extracellular matrices. Hence, cleavage of heparan sulphate (HS) affects the integrity and functional state of tissues and thereby fundamental normal and pathological phenomena involving cell migration and response to changes in the extracellular microenvironment. Heparanase degrades HS at specific intrachain sites. The enzyme is synthesized as a latent approximately 65kDa protein that is processed at the N terminus into a highly active approximately 50kDa form. Experimental evidence suggests that heparanase may facilitate both tumor cell invasion and neovascularization, both critical steps in cancer progression. The enzyme is also involved in cell migration associated with inflammation and autoimmunity .
Endo-1,3(4)-beta-glucanase (Endo-beta-glucanase)
Type: Family

This is a family of endo-beta-1,3(4)-glucanases belonging to glycoside hydrolase family 81 (

) that are also known as Glucan endo-1,3-beta-D-glucosidases. Proteins in this entry include fission yeast Eng1/Eng2 and budding yeast Dse4 (also known as Eng1). They have been shown to hydrolyse linear beta-1,3-glucan chains . Eng1 is required for the degradation of the primary septum after completion of cytokinesis . Eng2 may couple the endocytic coat to the actin module . This entry also includes some uncharacterised proteins from plants and bacteria.

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.
Cytosolic endo-beta-N-acetylglucosaminidase, TIM barrel domain (TIM_ENGase)
Type: Domain

This describes the TIM barrel fold in ENGase, which contains a β/α fold .

Endo-β-N-acetylglucosaminidase (ENGase) is a glycosyl hydrolase that cleaves the β-1,4-glycosidic bond within the di-N-acetylchitobiose core of N-glycosylated proteins, leaving one N-acetylglucosamine residue attached to the protein and releasing the remainder of the glycan. It plays a key role in the cytosolic degradation of free oligosaccharides derived from the endoplasmic reticulum, aiding in the recycling of sugars. ENGases possess an eight-stranded α/β barrel structure and belong to glycosyl hydrolase family 85 (GH85), sharing sequence similarity with

chitinases .

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.
Transcription factor GRAS (TF_GRAS)
Type: Family

Sequence analysis of the products of the GRAS (GAI, RGA, SCR) gene family indicates that they share a variable N terminus and a highly conserved C terminus that contains five recognizable motifs . Proteins in the GRAS family are major players in gibberellin (GA) signaling, which regulates various aspects of plant growth and development . Mutation of the SCARECROW (SCR) gene results in a radial pattern defect, loss of a ground tissue layer, in the root. The PAT1 protein is involved in phytochrome A signal transduction .

A sequence, structure and evolutionary analysis showed that the GRAS family emerged in bacteria and belongs to the Rossmann-fold, AdoMET (SAM)-dependent methyltransferase superfamily . All bacterial, and a subset of plant GRAS proteins, are predicted to be active and function as small-molecule methylases. Several plant GRAS proteins lack one or more AdoMet (SAM)-binding residues while preserving their substrate-binding residues. Although GRAS proteins are implicated to function as transcriptional factors, the above analysis suggests that they instead might either modify or bind small molecules .

Some proteins known to belong to the GRAS family are listed below:

Arabidopsis thaliana SCARECROW (SCR) protein. It regulates asymetric cell divisions of cortex/endodermal initial cells during root development.

Arabidopsis thaliana SCARECROW-LIKE (SCL) protein.

Arabidopsis thaliana GIBBERELLIN-ACID INSENSITIVE (GAI) and REPRESSOR OF GA1 (RGA), two closely related proteins involved in gibberellin signaling.

Arabidopsis thaliana SHORT ROOT (SHR) protein. It is necessary for cell division and endodermis specification.

Arabidopsis thaliana PAT1 protein. It inhibits light signaling via the phytochrome A (phyA).

LATERAL SUPPRESSOR (LS), a protein from tomato that controls the formation of lateral branches during vegetative development.
Hemocyanin, C-terminal (Hemocyanin_C)
Type: Domain

This entry represents the C-terminal domain of hemocyanin and hexamerin proteins.

Crustacean and cheliceratan hemocyanins (oxygen-transport proteins) and insect hexamerins (storage proteins) are homologous gene products, although the latter do not bind oxygen .

Haemocyanins are found in the haemolymph of many invertebrates. They are divided into 2 main groups, arthropodan and molluscan. These have structurally similar oxygen-binding centres, which are similar to the oxygen-binding centre of tyrosinases, but their quaternary structures are arranged differently. The arthropodan proteins exist as hexamers comprising 3 heterogeneous subunits (a, b and c) and possess 1 oxygen-binding centre per subunit; and the molluscan proteins exist as cylindrical oligomers of 10 to 20 subunits and possess 7 or 8 oxygen-binding centres per subunit . Although the proteins have similar amino acid compositions, the only real similarity in their primary sequences is in the region corresponding to the second copper-binding domain, which also shows similarity to the copper-binding domain of tyrosinases.
Hemocyanin, N-terminal (Hemocyanin_N)
Type: Domain

This entry represents the N-terminal domain of hemocyanin and hexamerin proteins.

Crustacean and cheliceratan hemocyanins (oxygen-transport proteins) and insect hexamerins (storage proteins) are homologous gene products, although the latter do not bind oxygen .

Haemocyanins are found in the haemolymph of many invertebrates. They are divided into 2 main groups, arthropodan and molluscan. These have structurally similar oxygen-binding centres, which are similar to the oxygen-binding centre of tyrosinases, but their quaternary structures are arranged differently. The arthropodan proteins exist as hexamers comprising 3 heterogeneous subunits (a, b and c) and possess 1 oxygen-binding centre per subunit; and the molluscan proteins exist as cylindrical oligomers of 10 to 20 subunits and possess 7 or 8 oxygen-binding centres per subunit . Although the proteins have similar amino acid compositions, the only real similarity in their primary sequences is in the region corresponding to the second copper-binding domain, which also shows similarity to the copper-binding domain of tyrosinases.
Herpesvirus ICP4-like protein, C-terminal (Herpes_ICP4_C)
Type: Domain

The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection. ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer. ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the C-terminal region that probably acts as an enhancer for the N-terminal region .
Herpesvirus ICP4-like protein, N-terminal (Herpes_ICP4_N)
Type: Domain

The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection. ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer. ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the N-terminal region that contains sites for DNA binding and homodimerisation .
Herpesvirus UL14-like (Herpes_UL14)
Type: Family

This is a family of Herpesvirus proteins including UL14. UL14 protein is a minor component of the virion tegument and is expressed late in infection. UL14 protein can influence the intracellular localization patterns of a number of proteins belonging to the capsid or the DNA encapsidation machinery .
Herpesvirus tripartite terminase subunit 2 (Herpes_TT2)
Type: Family

This is a family of Herpesvirus proteins including UL33 (

) and UL51 (

) . These proteins constitute the T-terminase subunit of the tripartite terminase complex that assembles in the cytoplasm of infected cells and uses the host nuclear import machinery to enter the nucleus, where capsid assembly and genome-packaging occur .
Herpesvirus large tegument protein deneddylase (Herpes_LT_deneddylase)
Type: Domain

BPLF1, the Epstein-Barr-virus-encoded member of this protease family, is a deneddylase that regulates virus production by modulating the activity of cullin-RING ligases. Homologues encoded by other herpesviruses share the deneddylase activity .
Herpesvirus envelope glycoprotein N domain (Herpes_glycoprotein_N_domain)
Type: Domain

This entry represents a conserved region found in a number of viral proteins: BLRF1, U46, 53, and UL73, collectively known as glycoprotein N. These UL73-like envelope glycoproteins, which associate in a high molecular mass complex with their counterpart protein gM, induce neutralizing antibody responses in the host. These glycoproteins are highly polymorphic, particularly in the N-terminal region .
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose 2,3-dehydratase (EvaA-like)
Type: Domain

This domain occurs in a range of proteins from antibiotic production pathways. These include the gra-ORF27

product that probably functions at an early step, most likely as a dTDP-4-keto-6- deoxyglucose-2,3-dehydratase . Its homologues include dnmT from the daunorubicin biosynthetic gene cluster in S. peucetius , a similar gene from the daunomycin biosynthetic cluster in Streptomyces sp. (strain 5)

, eryBVI from the erythromycin cluster in S. erythraea and snoH from the nogalamycin cluster in S. nogalater. This domain is a 200 amino acid long region, which may be a structural unit, that occurs twice within the proteins that contain it.

This entry also includes sugar 2,3-dehydratase, EvaA, that belongs to the "Nudix" hydrolase family, members of which often function as "housekeeping" enzymes. EvaA is organised as a dimer, each subunit of the dimer folds into two domains, which are related by a 2-fold rotational axis and which arose via gene duplication. Two binding sites for the dTDP-sugar ligands, pockets A and B, have been identified in each subunit. Site-directed mutagenesis experiments and activity assays strongly suggest that pocket A represents the active site and pocket B is a vestige of the gene duplication event .
HGWP repeat (HGWP_repeat)
Type: Repeat

This short (30 amino acids) repeat is found in a number of plant proteins. It contains a conserved HGWP motif, hence its name. The function of these proteins is unknown.
IBV 3A protein (IBV_3A)
Type: Family

The gene product of gene 3 from Infectious bronchitis virus (strain CL190). Currently, the function of this protein remains unknown.
Trigger factor (Trig_fac)
Type: Family

The trigger factor is found in several prokaryotes, and is involved in protein export. Trigger factor is a ribosome-associated molecular chaperone and is the first chaperone to interact with nascent polypeptide. It acts as a chaperone by maintaining the newly synthesised protein in an open conformation. It consists of three domains, an N-terminal ribosome-binding domain (RBD), a central peptidyl-prolyl cis/trans isomerase (PPIase) domain and a C-terminal substrate-binding domain (SBD) which is stabilised by a linker between the RBD and PPIase domains . The association between its N-terminal domain with the ribosomal protein L23 located next to the peptide tunnel exit is essential for the interaction with nascent polypeptides and its in vivo function. Trigger factor can bind at the same time as the signal recognition particle (SRP), but is excluded by the SRP receptor (FtsY) .

The trigger factor-like protein included in this entry can be found in plant chloroplasts, where it may be involved in protein export.
Citrate lyase ligase (Citrate_lyase_ligase)
Type: Family

[Citrate (pro-3S)-lyase] ligase (

), also known as citrate lyase ligase, is responsible for acetylation of the prosthetic group (2-(5''-phosphoribosyl)-3'-dephosphocoenzyme-A) of the gamma subunit of citrate lyase. It converts the inactive thiol form of the enzyme to the active form. In Clostridium sphenoides, citrate lyase ligase actively degrades citrate. In Clostridium sporosphaeroides and Lactococcus lactis, however, the enzyme is under stringent regulatory control. The enzyme's activity in anaerobic bacteria is modulated by phosphorylation and dephosphorylation .
Iron permease EfeU/FTR1-like (EfeU/FTR1-like)
Type: Family

Fungi uptake extracellular ferrous iron (Fe2+) using a bipartite high-affinity transporter consisting of a multicopper ferroxidase associated with a membrane permease which translocates generated ferric iron (Fe3+) into the cytosol. The Saccharomyces cerevisiae (Baker's yeast) iron permease FTR1 is a plasma membrane permease for high-affinity iron uptake . FTR1, together with multicopper oxidase FET3, mediate high-affinity iron uptake.

Many bacteria possess Fe2+ transporters with functional similarities to the FET3-FTR1 system. Escherichia coli encodes an EfeUOB transporter where EfeU is homologous to the high-affinity iron permease FTR1 of S. cerevisiae .

This entry includes the iron permeases from some bacteria and yeast (Enterobacteria and budding yeasts mainly).
Diacylglycerol/lipid kinase (Diacylglycerol/lipid_kinase)
Type: Family

This protein family include proteins predominantly from bacteria but also from some archaeal and eukaryotic species.

The Escherichia coli member of this family, YegS, has been purified and shown to have phosphatidylglycerol kinase activity . DagK from Bacillus subtilis catalyses the phosphorylation of diacylglycerol (DAG) into phosphatidic acid. It is a key enzyme involved in the production of lipoteichoic acid by reintroducing DAG formed from the breakdown of membrane phospholipids into the phosphatidylglycerol biosynthetic pathway. It is more active toward long-chain DAG compared with short-chain DAG and is not able to phosphorylate substrates other than DAG, such as monoacylglycerol, ceramide, undecaprenol, phosphatidylinositol, or sphingosine .

Sphingoid long-chain bases kinase 2, mitochondrial from Arabidopsis thaliana (Mouse-ear cress) is involved in the production of sphingoid long-chain base (LCB). This protein is required for the cold-induced accumulation of phytosphingosine-phosphate, the regulation of the cold-responsive MPK6 and reduction of root growth at moderate low temperature .
Intermembrane transport protein PqiA-like, proteobacteria (PqiA-like_proteobact)
Type: Family

This family consists of proteins from proteobacteria, including intermembrane transport proteins PqiA and YebS, which are components of transport pathways that contribute to membrane integrity . The promoter for the pqiA gene is inducible by paraquat, a superoxide radical-generating agent, and other known superoxide generators .