SII-SWORD/CoKE huggingface dataset:
Glycosyl transferase, family 31 (Glyco_trans_31)
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 31 (

) comprises enzymes with a number of known activities; N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase (

); beta-1,3-galactosyltransferase (

); fucose-specific beta-1,3-N-acetylglucosaminyltransferase (

); globotriosylceramide beta-1,3-GalNAc transferase (

) .
Herpesvirus portal protein (Herpes_Portal)
Type: Family

This family consists of various proteins from the Herpesviridae that are similar to Human herpesvirus 1 (HHV-1) UL6 virion protein. UL6 is essential for cleavage and packaging of the viral genome . UL6 forms the DNA entry portal; it exists at a unique site in the capsid and forms a channel for entry of DNA into the capsid .
Ribosome recycling factor (Ribosome_recyc_fac)
Type: Family

The ribosome recycling factor or ribosome release factor (RRF) dissociates ribosomes from mRNA after termination of translation, and is essential for bacterial growth . Thus ribosomes are 'recycled' and ready for another round of protein synthesis.

RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear .
Birnavirus VP2 protein (Birna_VP2)
Type: Family

Infectious pancreatic necrosis virus (IPNV), a birnavirus, is an important pathogen in fish farms. Analyses of viral proteins showed that VP2 is the major structural and immunogenic polypeptide of the virus . All neutralizing monoclonal antibodies are specific to VP2 and bind to continuous or discontinuous epitopes. The variable domain of VP2 and the 20 adjacent amino acids of the conserved C-terminal are probably the most important in inducing an immune response for the protection of animals .

The large RNA segment of the Birnaviridae codes for a polyprotein (N-VP2-VP4-VP3-C), most of which is then processed to generate the constituent polypeptides. VP4 protein is involved in generating VP2 and VP3 . Recombinant VP3 is more immunogenic than recombinant VP2 .
Birnavirus VP3 protein (Birna_VP3)
Type: Family

Birnavirus VP3 is involved in virus morphogenesis. It interacts with the structural protein VP2, with the double-stranded RNA genome, and with the virus-encoded, RNA-dependent RNA polymerase (RdRP), VP1, playing a role in both viral capsid formation, recruitment of VP1 into the capsid and encapsidation of the viral genome .
Reduced folate carrier (Folate_carrier)
Type: Family

This entry represents the reduced folate carrier family, including folate transporter 1 (SLC19A1), thiamine transporter 1 (SLC19A2) and thiamine transporter 2 (SLC19A3). Despite their protein sequence/structure similarity, they have different functions.

The transporter 1 (SLC19A1, also known as the reduced folate carrier protein, RFC) transports reduced folate into mammalian cells via the carrier mediated mechanism (as opposed to the receptor mediated mechanism) it also transports cytotoxic folate analogues used in chemotherapy , such as methotrexate (MTX). It also transports cyclic dinucleotides (CDNs) into cells which is involved in the modulation of the immune response . Mammalian cells have an absolute requirement for exogenous folates which are needed for growth, and biosynthesis of macromolecules .

Thiamine transporter 1 (SLC19A2) and thiamine transporter 2 (SLC19A3) are high-affinity transporters for the intake of thiamine . They do not transport reduced or oxidized folates.

Also included in this entry is Putative solute carrier family 19 member 4 which has been defined as pseudogene in HGNC. It lacks the transmembrane region, suggesting that it has probably no transporter function.
Concentrative nucleoside transporter N-terminal domain (CNT_N_dom)
Type: Domain

The concentrative nucleoside transporter (CNT) (TC 2.A.41) family includes

, which is a purine-specific Na
+
-nucleoside cotransporter localised to the bile canalicular membrane . It also includes

, a Na
+
-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine, which also transports the anti-viral nucleoside analogues AZT and ddC .

This domain lies towards the N terminus of this family of transporters.
Urease accessory protein UreD (UreD)
Type: Family

UreD is a urease accessory protein. Urease hydrolyses urea into ammonia and carbamic acid . UreD is involved in activation of the urease enzyme via the UreD-UreF-UreG-urease complex and is required for urease nickel metallocentre assembly . This entry includes UreH from Helicobacter pylori, which is an orthologue of UreD .

This entry also includes the URE4 from Cryptococcus neoformans which is a fungal homologue of UreD and pays a role in host brain invasion causing meningoencephalitis .
Large ribosomal subunit protein eL22 (Ribosomal_eL22)
Type: Family

This entry represents the large ribosomal subunit protein eL22 family.

Ribosomal protein eL22 forms part of the 60S ribosomal subunit found in eukaryotes. Rattus norvegicus (Rat) eL22 is related to ribosomal proteins from other eukaryotes and is identical in amino acid sequence to human EAP, the EBER 1 (Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) encoded RNA) associated protein .

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 .
Large ribosomal subunit protein eL28 (Ribosomal_eL28)
Type: Family

This entry represents the large ribosomal subunit protein eL28 family.

Ribosomal protein eL28 forms part of the 60S ribosomal subunit . This entry is found in eukaryotes. In rat there are 9 or 10 copies of the eL28 gene. The eL28 protein contains a possible internal duplication of 9 residues .

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 .
Large ribosomal subunit protein eL29 (Ribosomal_eL29)
Type: Family

This entry represents the large ribosomal subunit protein eL29 family.

Ribosomal protein eL29 forms part of the 60S ribosomal subunit . This family is found in eukaryotes. There are there are 20 to 22 copies of the eL29 gene in Rattus norvegicus (Rat). Rat eL29 is related to yeast ribosomal protein YL43 .

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 .
Large ribosomal subunit protein eL43 (Ribosomal_eL43)
Type: Family

This entry represents the large ribosomal subunit protein eL43 family. This ribosomal protein is found in archaebacteria and eukaryotes . Ribosomal protein eL43, also known as L37A, has a single zinc finger-like motif of the C2-C2 type .

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 .
Large ribosomal subunit protein eL38 (Ribosomal_eL38)
Type: Family

Ribosomal protein eL38 forms part of the 60S ribosomal subunit . This family is found in eukaryotes.

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 .
RimM, N-terminal (RimM_N)
Type: Domain

The RimM protein is essential for efficient processing of 16S rRNA . It was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes . RimM contains a characteristic N-terminal domain and a PRC-barrel C-terminal domain, linked by an unstructured region . The N-terminal domain folds into a closed β-barrel structure.
Large ribosomal subunit protein bL32 (Ribosomal_bL32)
Type: Family

This entry represents the 50S large ribosomal subunit protein bL32 family. This family is found in prokaryotes and eukaryotic organelles. Structurally well characterised protein as a part of ribosome particle .

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 .
DUF34/NIF3 (DUF34/NIF3)
Type: Family

This family includes DUF34/metal-binding proteins from bacteria, NIF3 from budding yeasts and NIF3-like proteins from animals.

This entry includes the DUF34/metal-binding protein/NIF3 proteins, which are widely distributed across superkingdoms. They were previously annotated as GTP cyclohydrolase 1 type 2 and, recently, through a comprehensive literature review and integrative bioinformatic analyses it was revealed that annotations for these members are misleading as they were based on a single set of in vitro results examining the NIF3 homolog of Helicobacter pylori . Actually, they have varied phenotypes with the unifying functional role as metal-binding proteins .

NIF3 interacts with the yeast transcriptional coactivator Ngg1p which is part of the ADA complex, the exact function of this interaction is unknown .

The structure of the Methanocaldococcus jannaschii MJ0927 NIF3 protein has been determined . It binds to both single-stranded and double-stranded DNA .
Closterovirus coat protein (Closter_coat)
Type: Family

This family consist of coat proteins from closterovirus, which belong to the Closteroviridae, which have a positive strand ssRNA genome with no DNA stage during replication. The viral coat protein encapsulates and protects the viral genome. Both the large cp1 and smaller cp2 coat protein originate from the same primary transcript . Members of the Closterovirus include Beet yellows virus (BYV) (Sugar beet yellows virus) and Grapevine leafroll-associated virus 7.
Alternative oxidase (AOX)
Type: Family

The alternative oxidase (AOX) is an enzyme that forms part of the electron transport chain in mitochondria of different organisms . Proteins homologous to the mitochondrial oxidase have also been identified in bacterial genomes . The oxidase provides an alternative route for electrons passing through the electron transport chain to reduce oxygen. However, as several proton-pumping steps are bypassed in this alternative pathway, activation of the oxidase reduces ATP generation. This enzyme was first identified as a distinct oxidase pathway from cytochrome c oxidase as the alternative oxidase is resistant to inhibition by the poison cyanide .

The alternative oxidase (also known as ubiquinol oxidase) is used as a second terminal oxidase in the mitochondria, electrons are transferred directly from reduced ubiquinol to oxygen forming water . This is not coupled to ATP synthesis and is not inhibited by cyanide, this pathway is a single step process . In Oryza sativa (rice) the transcript levels of the alternative oxidase are increased by low temperature . It has been predicted to contain a coupled diiron centre on the basis of a conserved sequence motif consisting of the proposed iron ligands, four Glu and two His residues . The EPR study of Arabidopsis thaliana (mouse-ear cress) alternative oxidase AOX1a shows that the enzyme contains a hydroxo-bridged mixed-valent Fe(II)/Fe(III) binuclear iron centre . A catalytic cycle has been proposed that involves a di-iron centre and at least one transient protein-derived radical, most probably an invariant Tyr residue .
Coat protein, Ilarvirus (Coat_Ilarvirus)
Type: Family

This family consists of various coat proteins from the
Ilarviruses which belong to the Bromoviridae, members include
Apple mosaic virus and
Prune dwarf virus. The Ilarvirus coat protein is required to initiate replication of the viral genome in host plants . Members of the
Bromoviridae have a positive stand ssRNA genome with no DNA stage in their replication.