SII-SWORD/CoKE huggingface dataset:
RIB43A (RIB43A)
Type: Family

This family consists of several RIB43A-like eukaryotic proteins. Ciliary and flagellar microtubules contain a specialised set of protofilaments, termed ribbons, that are composed of tubulin and several associated proteins. RIB43A was first characterised in the unicellular biflagellate, Chlamydomonas reinhardtii although highly related sequences are present in several higher eukaryotes including humans. The function of this protein is unknown although the structure of RIB43A and its association with the specialised protofilament ribbons and with basal bodies is relevant to the proposed role of ribbons in forming and stabilising doublet and triplet microtubules and in organising their three-dimensional structure. Human RIB43A homologues could represent a structural requirement in centriole replication in dividing cells .
RNA polymerase III Rpc82, C -terminal (RNA_pol_III_Rpc82_C)
Type: Domain

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.

This entry describes the C-terminal region of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10kDa .
ROS/MUCR transcriptional regulator (ROS_MUCR)
Type: Family

This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid and is necessary for succinoglycan production . S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan .
Powdery mildew resistance protein, RPW8 domain (Powdery_mildew-R_dom)
Type: Domain

This entry represents the RPW8 domain found in several broad-spectrum mildew resistance proteins from Arabidopsis thaliana and other dicots. Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The R protein-mediated defences typically involve a rapid, localized necrosis, or hypersensitive response (HR), at the site of infection, and the localised formation of antimicrobial chemicals and proteins that restrict growth of the pathogen. The A. thaliana locus Resistance to Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes: RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance . RPW8.1 and RPW8.2 share similarity with an ~150 amino acid module forming the N terminus of a group of disease resistance proteins, which have a nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) .

The RPW8 domain sequences contain a predicted N-terminal transmembrane (TM) region or possibly a signal peptide, and a coiled-coil (CC) motif .
Rhodococcus equi virulence-associated protein (R_equi_Vir)
Type: Family

This family consists of several virulence-associated proteins, mainly from Corynebacterium equii (Rhodococcus equi, Rhodococcus hoagii). R. equi is an important pulmonary pathogen of foals and is increasingly isolated from pneumonic infections and other infections in Homo sapiens immunodeficiency virus-infected patients. Both virulent and avirulent strains of R. equi differ in the possession of a virulence-associated plasmid . The type of virulence plasmid carried is host specific; the pVapA is the plasmid type carried by R. equi isolates infecting equine. These virulence plasmids have four common regions known as the conjugation, replication, unknown function and the virulence or pathogenicity island (PAI) regions, where the members of the vap (virulence associated protein) family reside . The virulence protein VapA has been shown to inhibit the maturation of R. equi-containing phagosomes and promote intracellular bacterial survival .
Glycosyl hydrolases 36 (Glycosyl_hydrolases_36)
Type: Family

This family consists of several galactinol-sucrose galactosyltransferase proteins, also known as raffinose synthases, which is a widespread oligosaccharide in plant seeds and other tissues. Raffinose synthase (

) is the key enzyme that channels sucrose into the raffinose oligosaccharide pathway . Raffinose family oligosaccharides (RFOs) are ubiquitous in plant seeds and are thought to play critical roles in the acquisition of tolerance to desiccation and seed longevity. Raffinose synthases are alkaline alpha-galactosidases and are solely responsible for RFO breakdown in germinating maize seeds, whereas acidic galactosidases appear to have other functions . Glycoside hydrolase family 36 can be split into 11 families, GH36A to GH36K . This family includes enzymes from GH36C.
GTP-binding nuclear protein Ran-related (Ran_GTP-bd-rel)
Type: Family

The small Ras-like GTPase Ran plays an essential role in the transport of macromolecules in and out of the nucleus and has been implicated in spindle and nuclear envelope formation during mitosis in higher eukaryotes. The Saccharomyces cerevisiae ORF YGL164c encoding a novel RanGTP-binding protein, termed Yrb30p was identified. The protein competes with S. cerevisiae RanBP1 (Yrb1p) for binding to the GTP-bound form of S. cerevisiae Ran (Gsp1p) and is, like Yrb1p, able to form trimeric complexes with RanGTP and some of the karyopherins .
Plasmid replication protein, RepL (Plasmid_replication_RepL)
Type: Domain

This entry consists of proteins thought to be involved in plasmid replication.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit Swp1 (Swp1)
Type: Family

Swp1 is an essential subunit of the N-oligosaccharyl transferase (OST) complex which catalyses the transfer of a high mannose oligosaccharide from a lipid-linked oligosaccharide donor to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains . N-glycosylation occurs cotranslationally and the complex associates with the Sec61 complex at the channel-forming translocon complex that mediates protein translocation across the endoplasmic reticulum (ER). All subunits are required for a maximal enzyme activity .
Glycine zipper 2TM domain (Gly_zipper_2TM_dom)
Type: Domain

This domain includes a putative two transmembrane α-helical region that contains glycine zipper motifs . Most members of this group of proteins are found in Proteobacteria, including several Rickettsia genus specific 17kDa surface antigen proteins .
Rotavirus major outer capsid VP7 (Rotavirus_VP7)
Type: Family

This family consists of several Rotavirus major outer capsid protein VP7 sequences. The rotavirus capsid is composed of three concentric protein layers. Proteins VP4 and VP7 comprise the outer layer. VP4 forms spikes and is the viral attachment protein. VP7 is a glycoprotein and the major constituent of the outer protein layer .
Rubella capsid (Rubella_Capsid)
Type: Family

Rubella virus is an enveloped positive-strand RNA virus of the family Togaviridae. Virions are composed of three structural proteins: a capsid and two membrane-spanning glycoproteins, E2 and E1. During virus assembly, the capsid interacts with genomic RNA to form nucleocapsids. It has been discovered that capsid phosphorylation serves to negatively regulate binding of viral genomic RNA. This may delay the initiation of nucleocapsid assembly until sufficient amounts of virus glycoproteins accumulate at the budding site and/or prevent non-specific binding to cellular RNA when levels of genomic RNA are low. It follows that at a late stage in replication, the capsid may undergo dephosphorylation before nucleocapsid assembly occurs . This family is found together with

and

.
Rubella membrane glycoprotein E1 (Rubella_E1)
Type: Family

Rubella virus (RV), the sole member of the genus Rubivirus within the family Togaviridae, is a small enveloped, positive strand RNA virus. The nucleocapsid consists of 40S genomic RNA and a single species of capsid protein which is enveloped within a host-derived lipid bilayer containing two viral glycoproteins, E1 (58kDa) and E2 (42-46kDa). In virus infected cells, RV matures by budding either at the plasma membrane, or at the internal membranes depending on the cell type and enters adjacent uninfected cells by a membrane fusion process in the endosome, directed by E1-E2 heterodimers. The heterodimer formation is crucial for E1 transport out of the endoplasmic reticulum to the Golgi and plasma membrane. In RV E1, a cysteine at position 82 is crucial for the E1-E2 heterodimer formation and cell surface expression of the two proteins. E1 has been shown to be a type 1 membrane protein, rich in cysteine residues with extensive intramolecular disulphide bonds .

This family is found together with

and

.
Rubella membrane glycoprotein E2 (Rubella_E2)
Type: Domain

Rubella virus (RV), the sole member of the genus Rubivirus within the family Togaviridae, is a small enveloped, positive strand RNA virus. The nucleocapsid consists of 40S genomic RNA and a single species of capsid protein which is enveloped within a host-derived lipid bilayer containing two viral glycoproteins, E1 (58kDa) and E2 (42-46kDa). In virus infected cells, RV matures by budding either at the plasma membrane, or at the internal membranes depending on the cell type and enters adjacent uninfected cells by a membrane fusion process in the endosome, directed by E1-E2 heterodimers. The heterodimer formation is crucial for E1 transport out of the endoplasmic reticulum to the Golgi and plasma membrane. In RV E1, a cysteine at position 82 is crucial for the E1-E2 heterodimer formation and cell surface expression of the two proteins . This family is found together with

and

.
Holliday junction resolvase RusA-like (Endonuclease_RusA-like)
Type: Family

This family consists of several bacterial and phage Holliday junction resolvase (RusA) like proteins. The RusA protein of Escherichia coli is an endonuclease that can resolve Holliday intermediates and correct the defects in genetic recombination and DNA repair associated with inactivation of RuvAB or RuvC .
RuvB, winged helix, C-terminal domain (RuvB_wg_C)
Type: Domain

This entry represents the C-terminal region of the RuvB protein which is thought to be an helicase DNA-binding domain.

The RuvB protein makes up part of the RuvABC resolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein . RuvB is part of the AAA+ superfamily of ATPases.
RuvB-like, AAA+ ATPase domain (RuvB-like_N)
Type: Domain

This entry represents the N-terminal domain of RuvB-like proteins. It adotps a Rossman fold (αβα sandwich).

The RuvB protein makes up part of the RuvABC resolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein . RuvB is part of the AAA+ superfamily of ATPases.

The AAA+ superfamily of ATPases is found in all kingdoms of living organisms where they participate in diverse cellular processes including membrane fusion, proteolysis and DNA replication. Although the terms AAA+ and AAA are often used loosely and interchangeably, the classical AAA family members are distinguished by their possession of the SRH region in the AAA module. Many AAA+ proteins are involved in similar processes to those of AAA proteins (facilitation of protein folding and unfolding, assembly or disassembly of proteins complexes, protein transport and degradation), but others function in replication, recombination, repair and transcription. For a review see .
S-antigen (S-antigen)
Type: Domain

This domain is found at the N terminus of S-antigen proteins from Plasmodium falciparum. S-antigens are heat stable proteins that are found in the blood of individuals infected with malaria .
Selenium-binding protein (Se-bd)
Type: Family

This family consists of selenium binding proteins from eukaryotes, bacteria and archaea. Human selenium-binding protein 1 (SELENBP1) is a methanethiol oxidase (MTO) that converts methanethiol to H2O2, formaldehyde, and H2S . Bovine SBP56 has been shown to participate in late stages of intra-Golgi protein transport . The Lotus japonicus homologue of SBP56, LjSBP is thought to have more than one physiological role, and can be implicated in controlling the oxidation/reduction status of target proteins in vesicular Golgi transport .
Synaptonemal complex protein 1 (SYCP1)
Type: Family

Synaptonemal complex protein 1 (SYCP1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase .
TORC2 component Sin1/Avo1 (Sin1/Avo1)
Type: Family

This entry includes MAPKAP1/Sin1 from animals, Sin1 from fission yeast, Avo1 from budding yeast and Rip3 from Slime mold. They are part of the Target Of Rapamycin Complex 2 (TORC2) complex, which plays an essential role in signal transduction . The mammalian TORC2 consists of mTOR, MLST8, PRR5, RICTOR, MAPKAP1 and DEPTOR . Within TORC2, MAPKAP1 is required for complex formation and TORC2 kinase activity . The budding yeast TORC2 is composed of Avo1, Avo2, Tsc11, Lst8, Bit61, Slm, Slm2 and Tor2 .
SepSecS/SepCysS family (SepSecS/SepCysS)
Type: Family

Early annotation suggested this family, SepSecS, of several eukaryotic and archaeal proteins, was involved in antigen-antibodies responses in the liver and pancreas . Structural studies show that the family is O-phosphoseryl-tRNA(Sec) selenium transferase, an enzyme involved in the synthesis of the amino acid selenocysteine (Sec). Sec is the only amino acid whose biosynthesis occurs on its cognate transfer RNA (tRNA). SepSecS catalyses the final step in the formation of the amino acid . The early observation that autoantibodies isolated from patients with type I autoimmune hepatitis targeted a ribonucleoprotein complex containing tRNASec led to the identification and characterisation of the archaeal and the human SepSecS . SepSecS forms its own branch in the family of fold-type I pyridoxal phosphate (PLP) enzymes that goes back to the last universal common ancestor.

This entry also includes O-phosphoseryl-tRNA:Cys-tRNA synthase SepCysS. It is found in Methanogenic archaea, which have an alternative pathway for Cys-tRNACys formation .
Mediator complex, subunit Med31 (Mediator_Med31)
Type: Family

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.

This entry includes subunit Med31 of the Mediator complex and the Saccharomyces cerevisiae homologue, Soh1. Soh1 is responsible for the repression of temperature sensitive growth of the Hpr1 mutant and has been found to be a component of the RNA polymerase II transcription complex. Soh1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the Soh1 protein may serve to couple these two processes .

Med31 is organised as a four helix bundle and with the N-terminal part of subunit Med7 forms a submodule of the middle module of the mediator core which is unique in structure and function. In vivo, Med7N/31 has a predominantly positive function on the expression of a specific subset of genes, including genes involved in methionine metabolism and iron transport .
Signal recognition particle SRP9 (SRP9)
Type: Family

The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes . SRP recognises the signal sequence of the nascent polypeptide on the ribosome. In eukaryotes this retards its elongation until SRP docks the ribosome-polypeptide complex to the RER membrane via the SR receptor . Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukaryotic complex: SRP19 and SRP54 .

This entry represents the 9kDa SRP9 component. Both SRP9 and SRP14 have the same (β)-α-β(3)-α fold. The heterodimer has pseudo two-fold symmetry and is saddle-like, consisting of a curved six-stranded β-sheet that has four helices packed on the convex side and an exposed concave surface lined with positively charged residues. The SRP9/SRP14 heterodimer is essential for SRP RNA binding, mediating the pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP .
Surfeit locus protein 2 (Surf2)
Type: Family

Surfeit locus protein 2 is part of a group of at least six sequence unrelated genes (Surf-1 to Surf-6). The six Surfeit genes have been classified as housekeeping genes, being expressed in all tissue types tested and not containing a TATA box in their promoter region. The exact function of SURF2 is unknown .
Salmonella plasmid virulence SpvD (Sal_SpvD)
Type: Family

This family consists of Salmonella SpvD (also known as VsdE) plasmid virulence proteins. The structure of the protein from Salmonella typhimurium has been solved and shows a papain-like fold, with a predicted catalytic triad of Cys73, His162 and Asp182. The protein has been shown to have deubiquitinating-like activity, releasing aminoluciferin (AML) from Ub-AML .
Sclerostin/Sclerostin domain-containing protein 1 (Sclerostin/SOSTDC1)
Type: Family

This sclerostin family consists of sclerostin and sclerostin domain-containing protein 1. Sclerostin (SOST) is thought to suppress bone formation. Mutations of the SOST gene lead to sclerosteosis, a progressive sclerosing bone dysplasia with an autosomal recessive mode of inheritance. Radiologically, it is characterised by a generalised hyperostosis and sclerosis leading to a markedly thickened and sclerotic skull, with mandible, ribs, clavicles and all long bones also being affected. Due to narrowing of the foramina of the cranial nerves, facial nerve palsy, hearing loss and atrophy of the optic nerves can occur. Sclerosteosis is clinically and radiologically very similar to van Buchem disease, mainly differentiated by hand malformations and a large stature in sclerosteosis patients . Sclerostin domain-containing protein 1, also known as USAG1, is a bone morphogenetic protein antagonist .
Semenogelin (Semenogelin)
Type: Family

This family consists of several mammalian secreted seminal proteins including semenogelin I and II. Freshly ejaculated Homo sapiens semen has the appearance of a loose gel in which the predominant structural protein components are the seminal vesicle secreted semenogelins (Sg) .
Serendipity locus alpha (Serendipity_A)
Type: Family

The Drosophila serendipity alpha (sry alpha) gene is specifically transcribed at the blastoderm stage, from nuclear cycle 11 to the onset of gastrulation, in all somatic nuclei . SRY-A is required for the cellularisation of the embryo and is involved in the localisation of the actin filaments just prior to and during plasma membrane invagination .
Variable surface protein, Brachyspira (Variable_surface_protein_TREHY)
Type: Family

This entry represents a group of variable surface proteins from Brachyspira.
Mitochondrial distribution and morphology family 33, fungi (MDM33_fungi)
Type: Family

Members of this family are mitochondrial inner membrane proteins with a role in inner mitochondrial membrane organisation and biogenesis . The yeast Mdm33 protein assembles into an oligomeric complex in the inner membrane where it performs homotypic protein-protein interactions. It has been suggested that Mdm33 plays a distinct role, possibly involved in fission of the mitochondrial inner membrane .