SII-SWORD/CoKE huggingface dataset:
Mediator of RNA polymerase II transcription subunit 20 (Med20)
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 represents the Med20 subunit of the Mediator complex in fungi.
Wound-induced protein 1/12, subgroup (Wound-induced_1/12_sub)
Type: Family

This group represents wound-induced protein 1 (Wun1) , and wound-induced protein 12 (also known as senescence associated gene 20).
Vacuolar protein sorting-associated protein 16 (VPS16)
Type: Family

This group represents a vacuolar protein sorting-associated protein 16 (Vps16). Vps16 may play a role in vesicle-mediated protein trafficking to endosomal/lysosomal compartments and in membrane docking/fusion reactions .
RFamide neuropeptide, ACEP-1 (RFamide_neuropeptide_ACEP-1)
Type: Family

This entry represents ACEP-1 (Achatina cardioexcitatory peptide-1) type RFamide neuropeptides .
Uncharacterised conserved protein UCP008159, (UCP008159_ABC)
Type: Family

This group represents a predicted uncharacterised ABC-type transport system, periplasmic component.
Uncharacterised conserved protein UCP008292 (UCP008292)
Type: Family

This group represents an uncharacterised protein with calcineurin-like phosphoesterase domain.
Uncharacterised conserved protein UCP008315 (UCP008315)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP008459 (UCP008459)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP008505 (UCP008505)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Phosphatidylinositol N-acetylglucosaminyltransferase, GPI19/PIG-P subunit (PIG-P_GPI19)
Type: Family

This entry represents the phosphatidylinositol N-acetylglucosaminyltransferase GPI19/PIG-P subunit. These proteins form part of the complex catalysing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis .
Mitochondria fission 1 protein (Fis1)
Type: Family

Fis1 is an outer mitochondrial membrane protein that plays a role in mitochondrial membrane fission . In Saccharomyces cerevisiae, it facilitates mitochondrial fission by forming protein complexes with Dnm1 and Mdv1 . It contains tetratrico-peptide repeat (TPR)-like domain and a C-terminal transmembrane region .
N-glycosylase/DNA lyase (AGOG)
Type: Family

Oxidative damage represents a major threat to genomic stability, as the major product of DNA oxidation, 8-oxoguanine (GO), frequently mispairs with adenine during replication. In order to prevent these mutagenic events, organisms have evolved GO-DNA glycosylases (or N-glycosylase/DNA lyases) that remove this oxidized base from DNA . GO is removed from DNA predominantly by the base excision repair (BER) pathway. This process is initiated by 8-oxoguanine-DNA glycosylases, which cleave the N-glycosidic bond between the aberrant base and the sugar-phosphate backbone to generate an apurinic (AP) site. Some DNA glycosylases possess also an intrinsic AP lyase activity, which cleaves the phosphodiester bond 3' from the AP site by beta- or beta, delta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate .

This group represents archaeal GO-DNA glycosylases (AGOG). Pyrobaculum aerophilum PAE2237 has been shown to remove GO from single- and double-stranded substrates with great efficiency . It has both GO-DNA glycosylase and AP-lyase (

) activities .

Archaeal GO-DNA glycosylases are not closely related to other DNA glycosylases. However, they share with the other HhH-GPD DNA glycosylase families the overall fold and the general active site architecture. AGOG possesses the principal hallmark of GO-DNA glycosylases: a helix-hairpin-helix motif and a glycine/proline-rich sequence followed by an absolutely conserved aspartate (HhH-GPD motif) . It contains two α-helical subdomains, with the 8-oxoguanine binding site located in a cleft at their interface . AGOG belongs to a new class within the helix-hairpin-helix (HhH) superfamily of DNA repair enzymes. Its hairpin structure differs substantially from that of other proteins containing an HhH motif, and is predicted that to interact with the DNA backbone in a distinct manner. Furthermore, the mode of 8-oxoguanine recognition, which involves several hydrogen-bonding and pi-stacking interactions, is unlike that observed in human OGG1, the prototypic 8-oxoguanine HhH-type DNA glycosylase. Despite these differences, the predicted kinked conformation of bound DNA and the catalytic mechanism are likely to resemble those of human OGG1 .
Uncharacterised conserved protein UCP009120, proteasome-type protease, Sll0069 (UCP009120_prtse)
Type: Family

This group represents a predicted proteasome-type protease, Sll0069 type.
Maltodextrose utilization protein MalA (Maltodextrose_util_MalA)
Type: Family

This group represents a maltodextrose utilization protein MalA .
Antitoxin TacA (TacA)
Type: Family

This entry represents a group of proteins from Mycobacterium, including Antitoxin TacA from Mycobacterium tuberculosis. TacA is the antitoxin component of a type II toxin-antitoxin (TA) system. It counteracts the toxic effect of cognate toxin TacT .
Uncharacterised conserved protein UCP009180 (UCP009180)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP009193 (UCP009193)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.

The designation as "holocarboxylase synthetase" appears to be faulty. It originally comes from the annotation for the Triticum aestivum (Wheat) member, which notes similarity to human holocarboxylase synthetase. However, such similarity does not appear to exist.
Guanidinoacetate N-methyltransferase (GuanidinoAc_N-MeTrfase)
Type: Family

Guanidinoacetate methyltransferase (GAMT;

) catalyses the last step of creatine biosynthesis. In humans, GAMT is believed to be the major enzyme involved in the metabolic conversion of S-adenosylmethionine (SAM) to S-adenosylhomocycteine (SAH). GAMT is found in abundance in the liver of all vertebrates. The crystal structure of a truncated version of GAMT shows that it exists as a dimer , and the structure can be viewed as a ternary complex between protein arginine methyltransferase (one subunit) complexed with a protein substrate (the partner subunit) and the product SAH . Deficiency of GAMT in the liver causes a hereditary disease with extra pyramidal motor disorder and extremely low concentrations of creatine in the brain, serum and urine .
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa (Ndufb8_metazoa)
Type: Family

Image averaging of mitochondrial complex I reveals a complex that can be dissociated into two main sub-complexes. One sub-complex is thought to protrude from the membrane so is to be predominantly in the aqueous phase and contains the binding site for NAD(H), and the input electron transfer chain. The other sub-complex (the hydrophobic protein) is membrane bound, and contains a catalytic site at which ubiquinone is reduced, and inhibitors bind, and several iron sulphur centres .

This entry represents subunit 8 (also known as the ASHI subunit) of the NADH:ubiquinone oxidoreductase beta subcomplex from animals . This subunit is not believed to be involved in catalysis.
Protein tyrosine phosphatase receptor type C-associated protein (PTPRCAP)
Type: Family

This group represents protein tyrosine phosphatase receptor type C (PTPRC)-associated protein, also known as CD45-associated protein . It is a positive regulator of PTPRC (CD45), which activates Src family kinases implicated in tumorigenesis .
Runt-related transcription factor RUNX (TF_Runt-rel_RUNX)
Type: Family

This group represents runt-related transcription factors RUNX. The RUNX family of transcription factors plays important roles in hematopoiesis, neurogenesis, bone development, and segmentation in vertebrate embryos. RUNX1 and its Xenopus and Drosophila homologues appear to determine hematopoietic cell fate during development .
Phospholipase D, eukaryotic type (PLipase_D_euk)
Type: Family

This entry includes the lipid-signaling enzymes phospholipase D1 (PLD1) and D2 (PLD2) . They have roles in immune cell migration and phagocytosis . PLD1 is selectively required during extravasation of macrophages from the bloodstream to sites of damage .
Cyclic 2, 3-diphospoglycerate synthetase (Cyc_diphosphoglycerate_synth)
Type: Family

Cyclic 2,3-diphospoglycerate (cDPG) is a low molecular weight compound that accumulates to high levels in some hyperthermophilic methanogens, suggesting that it may play a thermoadaptive role. In support of this, cDPG has been shown to protect proteins from heat denaturation in vitro. This entry represents cDPG synthetase, which catalyzes the synthesis of cDPG by the formation of an intramolecular phosphoanhydride bond in 2,3-diphosphoglycerate .
DNA primase, large subunit, eukaryotic (DNA_primase_lsu_euk)
Type: Family

DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. Primases are grouped into two classes, bacteria/bacteriophage and archaeal/eukaryotic. The proteins in the two classes differ in structure and the replication apparatus components. Archaeal/eukaryotic core primase is a heterodimeric enzyme consisting of a small catalytic subunit (PriS or Pri1) and a large subunit (PriL or Pri2). In the yeast Saccharomyces cerevisiae the small subunit is 48kDa and the large subunit 58kDa . In eukaryotic organisms, a heterotetrameric enzyme formed by DNA polymerase alpha, the B subunit and two primase subunits has primase activity. Although the catalytic activity and the the ATP binding site reside within PriS , the PriL subunit is essential for primase function as disruption of the PriL gene in yeast is lethal. PriL is composed of two structural domains. Several functions have been proposed for PriL such as stabilization of the PriS, involvement in synthesis initiation, improvement of primase processivity, determination of product size and transfer of the products to DNA polymerase alpha . Primase function has also been demonstrated for human and mouse primase subunits .

This group represents the eukaryotic DNA primase, large subunit.
Uncharacterised conserved protein UCP009597 (UCP009597)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
T-cell leukemia translocation-altered gene protein (TCTA)
Type: Family

This entry represents the T-cell leukemia translocation-altered gene protein. It may be required for cellular fusion during osteoclastogenesis .
Dynein light chain roadblock-type 1/2 (DYNLRB1/2)
Type: Family

Dynein light chain roadblock proteins (DYNLRB1 and DYNLRB2) are non-catalytic accessory components of the cytoplasmic dynein 1 complex. The dynein light chains are required for the correct assembly of the dynein complex and have been implicated in controlling its association with cargo molecules. DYNLRB1 and DYNLRB2 can also be found in the dynein-2 complex .

Dynein-1 is comprised of a dimer of heavy chain subunits, which associate with two copies of an intermediate chain two copies of one of two light intermediate chains and a number of light chain subunits [including the dynein light chain (DYNLL1), roadblock (DYNLRB1 and DYNLRB2) and Tctex families (DYNLT1, DYNLT3) .
Proteasome assembly chaperone 2, eukaryotic (Proteasome_assmbl_chp_2_euk)
Type: Family

This PAC2 (Proteasome assembly chaperone) family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 247 and 307 amino acids in length. Its C-terminal segment containing the potential proteasome-activating HbYX motif. These proteins function as a chaperone for the 26S proteasome, which is about 2000 kilodaltons (kDa) in molecular mass and contains one 20S core particle structure and two 19S regulatory caps. The 26S proteasome mediates ubiquitin-dependent proteolysis in eukaryotic cells. A number of studies including very recent ones have revealed that assembly of its 20S catalytic core particle is an ordered process that involves several conserved proteasome assembly chaperones (PACs). Two heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4, promote the assembly of rings composed of seven alpha subunits .

This entry represents PAC2 family members found in eukaryotes.
Nuclear protein localization protein 4 (Npl4)
Type: Family

Npl4 forms the Cdc48-Ufd1-Npl4 complex, which is a segregase complex that is involved in several ubiquitin-related processes. By coupling the ubiquitin-binding properties of Ufd1-Npl4 with the ATPase activity of Cdc48 (p97 in mammals), Cdc48-Ufd1-Npl4 is believed to aid in the extraction of ubiquitylated proteins from higher order complexes . It also plays a role in the regulated destruction of resident ER membrane proteins .
Uncharacterised conserved protein UCP010056 (UCP010056)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Proteasome assembly chaperone 1 (Proteasome_assmbl_chp_1)
Type: Family

This entry represents proteasome assembly chaperone 1 (PAC1).

The 26S proteasome plays a critical role in a number of cellular processes including cell-cycle control, transcription, signal transduction and DNA repair . This complex is composed of a catalytic 20S proteasome and two axially positioned 19S regulatory complexes. The overall structure is highly conserved among eukaryotes and is essential for cell viability. Assembly of the catalytic 20S proteasome CP (core particle) initiates with the formation of rings composed of seven alpha subunits and involves proteasome-assembly chaperones PAC1-PAC2, PAC3-PAC4 and UMP1 . Two heterodimeric proteasome-assembly chaperones, PAC1-PAC2 and PAC3-PAC4, interact with alpha subunits and promote the correct assembly of alpha rings. PAC3-PAC4 leaves the complex during subsequent assembly of beta subunits, while PAC1-PAC2 remains bound until the assembly of the CP is completed .
Uncharacterised conserved protein UCP010219 (UCP010219)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be integral membrane proteins (with several transmembrane segments). Homologues are predominantly from Actinobacteria.
Cysteine-rich protein, furovirus (Cys-rich_furovirus)
Type: Family

This group represents a cysteine-rich protein of unknown function found in the ssRNA positive strand Furovirus group.
Sulphur oxidation, SoxY (Sulphur_oxidation_SoxY)
Type: Family

SoxY is encoded by one of the genes in the sulphur oxidizing gene cluster of alpha-proteobacteria. In the sulphur oxidation process, SoxY (which covalently binds sulphur) and SoxZ (which chelates sulphur) combine with each other to form the SoxYZ complex. The conserved cysteine residue in the sulphate-binding motif [(V/I)KV(T/S)(V/I)GGC] at the C terminus of SoxY is involved in forming a covalent S-S linkage with the sulphate ion to form SoxY-thiocysteine-S-sulphate, the first covalently bound sulphur adduct in sulphur anion oxidation by the proteins of the sox operon .

SoxY is a sulfate carrier protein with the GGCGG ir GGCG swinging arm C-terminal sequence. The Cys in the swinging arm is the residue to which the inorganic sulfate moiety becomes covalently attached. In some species, a closely related paralogue occurs as well (TIGR04487), with a swinging arm sequence AACIE. More distantly related forms have an additional C-terminal SoxZ-related domain. All members are periplasmic and have an N-terminal twin-arginine translocation (TAT) signal sequence .
Methyltransferase, trithorax (MeTrfase_trithorax)
Type: Family

This entry includes a group of histone methyltransferases. The enzyme activity has been mapped to the SET domain , originally identified in Drosophila melanogaster (Fruit fly) Su(var)3-9, E(z) and Trithorax proteins .

The mixed lineage leukemia (MLL) gene encodes a very large nuclear protein homologous to Drosophila trithorax (Trx). MLL is required for the proper maintenance of HOX gene expression during development and hematopoiesis . The Trithorax group of proteins has been implicated in a variety of processes, including centromeric and telomeric silencing and cell-cycle regulation .
Uncharacterised conserved protein UCP010361, membrane (UCP010361)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be integral membrane proteins (with several transmembrane segments).
Spore coat assembly protein CotJB (Spore_coat_assembly_CotJB)
Type: Family

This group represents a spore coat peptide assembly protein CotJB.
Uncharacterised conserved protein UCP010611 (UCP010611)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Meiosis-specific protein Hop1 (Hop1)
Type: Family

Hop1 is a key structural component of Saccharomyces cerevisiae synaptonemal complex, a complex found at synapses between homologous chromosomes during meiosis, and form when sister chromatids condense upon axial elements . Hop1 is involved in both gene conversion and crossing over between homologues, as well as enforces meiotic recombination checkpoint control over the progression of recombination intermediates. It interacts with the Holliday junction, changes its global conformation and blocks the dissolution of the junction by a RecQ helicase in vitro .
Nicalin (Nicalin)
Type: Family

Nicalin is a Nodal signalling antagonist and a distant homologue of the gamma-secretase component Nicastrin . In humans, Nicalin forms a complex with NOMO (Nodal modulator) and controls the assembly and stability of this complex . It is a component of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes .
Bardet-Biedl syndrome 7 protein (Bardet-Biedl_syndrome_7_prot)
Type: Family

This group represents a Bardet-Biedl syndrome 7 protein from Caenorhabditis elegans and similar animal proteins. This component of the BBSome complex plays a role in guanylyl cyclase localisation in the ring-like structures at the base of the finger compartment in AFD sensory neurons .
In ciliated sensory neurons, it is required for the sensation of nitric oxide and avoidance of NO-producing organisms like P.aeruginosa .

Bardet-Biedl syndrome is a member of genetic ciliopathies, but the link between cilia/centrosome deficits and metabolic abnormalities is not completely clear . Bardet-Biedl syndrome (BBS) is a heterogeneous genetic disorder characterised by many features, including retinal degeneration, obesity, cognitive impairment, polydactyly, renal abnormalities, and hypogenitalism. BBS genes play an important role in maintaining leptin sensitivity in proopiomelanocortin neurons . A relatively high incidence of BBS is found in the mixed Arab populations of Kuwait and in Bedouin tribes throughout the Middle East, most likely due to the high rate of consaguinity in these populations and a founder effect.

Primary cilia are ubiquitous cellular appendages that provide important sensory and signalling functions and their dysfunction underlies numerous human genetic disorders. The proteins disrupted in the human ciliary disorder Bardet-Biedl syndrome (BBS) are required for the localisation of G protein-coupled receptors to primary cilia on central neurons. The alteration of signalling caused by mislocalisation of ciliary signalling proteins underlies the BBS phenotype . Of the 12 known BBS genes, BBS1 is the most commonly mutated .
Large ribosomal subunit protein mL63 (Ribosomal_mL63)
Type: Family

This entry represents the large ribosomal subunit protein mL63 from animals, which was previously known as Mitochondrial ribosomal protein 63 or Mrpl57. This protein is present in the intact 55S subunit of the mitochondrial ribosome. It is not known if it belongs to the 28S or to the 39S subunit .
Adenylate cyclase, type 10 (Adenylate_cyclase_typ10)
Type: Family

This entry represents type 10 adenylate cyclases (also known as soluble adenylyl cyclase;

), which produces cAMP and phosphate from ATP. This enzyme has a critical role in mammalian spermatogenesis by producing cAMP to mediate the cAMP-responsive nuclear factors indispensable for maturation of sperm in the epididymis . This induces capacitation, the maturational process that sperm undergo prior to fertilization. Soluble adenylyl cyclase binds 2 magnesium ions per subunit, and is activated by manganese or magnesium ions. The enzyme is activated by bicarbonate in the presence of magnesium ions, and inhibited by bicarbonate i nthe presence of manganese ions. Genetic variations in the gene that encodes this enzyme (ADCY10) are associated with absorptive hypercalciuria type 2 (HCA2) .
SODIUM POTASSIUM ROOT DEFECTIVE 2/3 (NAKR2/3)
Type: Family

This family represents a group of heavy metal-associated plant proteins (HPPs) , which includes Arabidopsis SODIUM POTASSIUM ROOT DEFECTIVE 2 (NAKR2) and 3 (NAKR3). NAKR3 is involved in the salt stress response in Arabidopsis .
Synaptogyrin (Synaptogyrin)
Type: Family

This entry represents synaptogyrin1-4. They are conserved components of the exocytic apparatus and function as regulators of Ca(2+)-dependent exocytosis . Synaptogyrin-1 is involved in the regulation of short-term and long-term synaptic plasticity .
HUS1 (HUS1)
Type: Family

HUS1 is a component of the 9-1-1 cell-cycle checkpoint response complex (which consists of Rad9, Hus1, Rad1), a key complex in the coordination of DNA damage sensing, cell cycle progression and DNA repair pathways. In humans, the 9-1-1 complex is recruited to DNA lesions upon damage by the RAD17-replication factor C (RFC) clamp loader complex. It activates checkpoint response and acts as a sliding clamp platform on DNA for several proteins involved in DNA repair. The 9-1-1 complex is necessary for the recruitment of C12orf32/RHINO to sites of double-stranded breaks (DSB) occurring during the S phase .