SII-SWORD/CoKE huggingface dataset:
Chromatid cohesion factor MAU2 (MAU2)
Type: Family

This entry represents the chromatid cohesion factor Mau2 and its homologues, including Scc4 from budding yeasts and Ssl3 from fission yeasts. Scc4 is a subunit of the cohesin loading factor complex (Scc2-Scc4), which is required for the loading of cohesin complexes onto chromosomes . Ssl3 is in complex with Mis4 (Scc2 homologue) and is required in G1 for cohesin binding to chromosomes .
FMP27/BLTP2/Hobbit, GFWDK motif-containing RBG unit (FMP27/BLTP2/Hobbit_GFWDK_RBG)
Type: Domain

This entry represents a RBG module containing the conserved GFWDK sequence motif.

This entry includes Hobbit protein from Drosophila melanogaster and its homologues such as Bridge-like lipid transfer protein family member 2 from human (BLTP2/KIAA0100) and FMP27 from yeast, referred to the Hob proteins . These proteins are localised to endoplasmic reticulum-plasma membrane (ER-PM) contact sites described as conserved lipid-binding proteins. They are tube-forming transport proteins which bind to phosphatidylinositols and affect phosphatidylinositol-4,5-bisphosphate (PtdIns-4,5-P2) distribution , that have a long hydrophobic groove and can mediate bulk transport of lipids between organelles. This entry also includes maize protein APT1 and Arabidopsis homologues SABRE and KIP . The Hob family belongs to the repeating β-groove (RBG) superfamily together with VPS13, ATG2, SHIP164, Csf1/BLTP1, which are all conserved lipid transfer proteins containing long hydrophobic grooves . They all share the same structure consisting of multiple repeating modules consisting of five β-sheets followed by a loop.
THADA/TRM732, DUF2428 (THADA/TRM732_DUF2428)
Type: Domain

This conserved domain is found in Thyroid adenoma-associated protein (THADA) from animals and in the yeast homologue tRNA (cytidine(32)-2'-O)-methyltransferase non-catalytic subunit TRM732 . Trm732 forms a complex with the methyltransferase Trm7 to 2'- O- methylate tRNA residue 32 (Nm32), being required for Trm7 methylation activity. In humans, mutations of the Trm7 homologue FTSJ1, which interacts with THADA, impair Nm32 modifications, associated with non-syndromic X-linked intellectual disability . It has been suggested that these proteins may play a role in additional biological processes not related to translation. This domain contains a RRSAGLP conserved motif that is required for tRNA modification activity .
Uncharacterised protein family UPF0321 (UPF0321)
Type: Family

This is a family of short, 111 residue, proteins found in Schizosaccharomyces pombe (Fission yeast). Their function is not known.
25S rRNA (uridine-N(3))-methyltransferase BMT5-like (BMT5-like)
Type: Domain

This is the N-terminal domain found in proteins from plants, yeast and humans, including 25S rRNA (uridine-N(3))-methyltransferase BMT5 from S. cerevisiae and the poorly characterised Ferredoxin-fold anticodon-binding domain-containing protein 1 from human and Heavy metal-associated isoprenylated plant protein 41 from Arabidopsis. This domain has a characteristic Rossmann-like fold of S-adenosyl-L-methionine (SAM) binding domains . BTM5 is a SAM-dependent methyltransferase that specifically methylates the N3 position of uridine in 25S rRNA.
DNA/RNA-binding protein Kin17, WH-like domain (DNA/RNA-bd_Kin17_WH-like_dom)
Type: Domain

Kin17 is a highly conserved protein that participates in DNA replication, DNA repair and cell cycle progression .

Region 51-160 of human Kin17 folds into an atypical winged helix (WH) domain. It consists of a three-α-helix bundle packed against a three-stranded β-sheet. Structural comparison with analogous WH domains reveals that Kin17 WH module presents an additional helix. In addition, helix H3 is not positively charged as in classical DNA-binding WH domains . This domain may be involved in protein-protein interactions.
NT-type C2 domain (NT-C2)
Type: Domain

The C2 domain is one of the most prevalent eukaryotic lipid-binding domains deployed in diverse functional contexts. Many C2 domains bind directly to membrane lipids and display a wide range of lipid selectivity, with preference for anionic phosphatidylserine (PS) and phosphatidylinositol-phosphates (PIPs).

Despite their limited sequence similarity, all C2 domains contain at their core a compact β-sandwich composed of two four-stranded β sheets with highly variable inter-strand regions that might contain one or more alpha- helices.

The NT-type C2 domain shows a diverse range of domain architectures but it is nearly always found at the N-termini of proteins that contain it. Hence, it has been named the N-terminal C2 (NT-C2) family. It is typically coupled with a coiled-coil domain, that could mediate di/oligo-merization and the DIL (Dilute) domain. It is also coupled with the Calponin homology (CH) domain in EHBP1 proteins, Filamin/ABP280 repeats and Mg2+ transporter MgtE N-terminal domain in proteins from chlorophyte algae such as Micromonas and Ostreococcus tauri. Thus, a common theme across the NT-type C2 domain proteins is the combination to several different domains with microfilament-binding or actin-related roles (i.e. such as CH, DIL, and Filamin). Other conserved groups of the NT-type C2 proteins prototyped by EEIG1, PMI1, and SYNC1 have their own distinct C- terminal conserved extensions that are restricted to these groups and might mediate specific interactions. The primary function of the NT-type C2 domain appears to be the linking of actin/microfilament-binding adaptors to the membrane and to act as a link that tethers endosomal vesicles to the cytoskeleton in course of their intracellular trafficking .
FMP27, WPPW motif-containing RBG unit (FMP27_WPPW_RBG)
Type: Domain

This entry represents a RBG module within FMP27 that contains the conserved HQR and WPPW sequence motifs.

Fungal proteins FMP27 (also known as Hob1) and Hob2 (YPR117W) are tube-forming lipid transport proteins which bind to phosphatidylinositols and affects phosphatidylinositol-4,5-bisphosphate (PtdIns-4,5-P2) distribution . They belong to the repeating β-groove (RBG) superfamily together with VPS13, ATG2, SHIP164, Csf1/BLTP1 proteins, which are all conserved lipid transfer proteins containing long hydrophobic grooves . They all share the same structure consisting of multiple repeating modules comprising five β-sheets followed by a loop.
RNA polymerase II assembly factor Rtp1, C-terminal (Rtp1_C1)
Type: Domain

This domain is found towards the C-terminal of required for the nuclear transport of RNA pol II protein (Rtp1). Rtp1 is required for the nuclear localisation of RNA polymerase II .

This domain is also found in transport and Golgi organisation protein 6 (Tango6) .
Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 1 (VPS39/TGF_beta_rcpt-assoc_1)
Type: Domain

This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole . In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange . Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling . The precise function of this domain has not been characterised.
Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated zinc finger domain (VPS39/TGFA1_Znf)
Type: Domain

This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole . In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange . Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling . The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 .
Putative cell-wall binding lipoprotein YkyA-like (Lipoprot_YkyA-like)
Type: Family

The YkyA family of proteins contain a lipoprotein signal and a hydrolase domain. They are similar to cell wall binding proteins and might also be recognisable by a host immune defence system. It is thus likely that they function in pathways important for pathogenicity .
Acetolactate synthase, small subunit, C-terminal (Acetolactate_synth_ssu_C)
Type: Domain

This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides .
Pyruvate-flavodoxin oxidoreductase, EKR domain (Pyrv-flavodox_OxRtase_EKR)
Type: Domain

EKR is a short, 33 residue, domain found in bacterial and some lower eukaryotic species which lies between a POR (pyruvate ferredoxin/flavodoxin oxidoreductase) domain (

) and the 4Fe-4S binding domain (

). It contains a characteristic EKR sequence motif. The exact function of this domain is not known.
Diadenylate cyclase CdaS, N-terminal (CdaS_N)
Type: Domain

This entry represents an α-hairpin found at the N terminus of bacterial diadenylate cyclase CdaS. These proteins often contain

towards the C terminus.

CdaS is one of 3 paralogous diadenylate cyclases (DAC) in Bacillus subtilis and B. thuringiensis, catalysing the condensation of 2 ATP molecules into cyclic di-AMP (c-di-AMP). It has slow DAC activity with ADP as a substrate and may have weak ADPase activity . CdaS is required for efficient spore formation in B. thuringiensis, whereas in B.subtilis, it is required for efficient spore germination. It is produced under the control of different sigma factors in the two bacteria. It is also required for parasporal crystal formation .
Telomerase activating protein Est1-like, N-terminal (Est1-like_N)
Type: Domain

Est1 is directly involved in telomere replication. It associates with telomerase and, during its interaction with CDC13, telomerase activity is promoted . This entry also includes Est1 homologues, such as human EST1A (also known as SMG6), which is essential for the replication of chromosome termini and also plays a role in nonsense-mediated mRNA decay .
GRIP-related Arf-binding domain (GRAB)
Type: Domain

The GRIP-related Arf-binding (GRAB) domain is located towards the C terminus of Rud3 type proteins. It is related to the GRIP domain, but the conserved tyrosine residue found at position 4 in all GRIP domains is replaced by a leucine residue. The small GTPase Arf is localised to the cis-Golgi where it recruits proteins via their GRAB domain, as part of the transport of cargo from the endoplasmic reticulum to the plasma membrane .
Autophagy-related protein 11, C-terminal (Atg11_C)
Type: Domain

This entry represents a domain found in C terminus of Atg11. Proteins containing this domain include Taf1 and Atg11. In Schizosaccharomyces pombe (fission yeast) Taf1 (taz1 interacting factor) is part of the telomere cap complex. In Saccharomyces cerevisiae (baker's yeast) Atg11 is known to be involved in vacuolar targeting and peroxisome degradation .
DNA-directed RNA polymerase, beta subunit, external 1 domain (DNA-dir_RNA_pol_bsu_external_1)
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.

RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This entry represents a domain in prokaryotic polymerases that spans the gap between domains 4 and 5 of the protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region .
RNA polymerase II elongation factor ELL, N-terminal (ELL_N)
Type: Domain

This entry represents the N-terminal domain of EEL.
Conserved oligomeric Golgi complex subunit 5 (Cog5)
Type: Family

The COG complex, the peripheral membrane oligomeric protein complex involved in intra-Golgi protein trafficking, consists of eight subunits arranged in two lobes bridged by Cog1. Cog5 is in the smaller, B lobe, bound in with Cog6-8, and is itself bound to Cog1 as well as, strongly, to Cog7 .

Defects in COG5 are the cause of congenital disorder of glycosylation type 2I (CDG2I). A multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins .
Matrilin, coiled-coil trimerisation domain (Matrilin_CC_trimer)
Type: Domain

This entry represents a short domain found the matrilin (cartilage matrix) proteins. It forms a coiled coil structure and contains a single cysteine residue at its start which is likely to form a di-sulphide bridge with a corresponding cysteine in an upstream EGF domain, thereby spanning the VWA domain of the protein (

). This domain is likely to be responsible for protein trimerisation .

The Matrilin proteins are major components of the extracellular matrix, primarily found in cartilage. These proteins play a crucial role in the formation of extracellular filamentous networks and matrix assembly. Proteins such as Matrilin-1, Matrilin-2, Matrilin-3, and Matrilin-4 can form various oligomeric structures, including homooligomers and heterooligomers, which contribute to their functional diversity. They interact with other extracellular matrix proteins like COMP and collagen, facilitating the structural integrity and function of cartilage. Matrilin-1, also known as cartilage matrix protein, is specifically involved in non-articular cartilage and binds to collagen, further emphasising its role in maintaining cartilage structure .
Histone acetyl transferase HAT1 N-terminal (Hat1_N)
Type: Domain

This entry represents the N-terminal half of the structure of histone acetyl transferase HAT1. It is often found in association with the C-terminal part of

. It seems to be motifs C and D of the structure. Histone acetyltransferases (HATs) catalyse the transfer of an acetyl group from acetyl-CoA to the lysine E-amino groups on the N-terminal tails of histones. HATs are involved in transcription since histones tend to be hyper-acetylated in actively transcribed regions of chromatin, whereas in transcriptionally silent regions histones are hypo-acetylated .
Adenylosuccinate lyase C-terminal (AdenyloSucc_lyase_C)
Type: Domain

Adenylosuccinate lyase catalyses two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide (the fifth step of de novo IMP biosynthesis); the formation of adenosine monophosphate (AMP) from adenylosuccinate (the final step in the synthesis of AMP from IMP) .

This entry represents the seven α-helical, C-terminal domain of adenylosuccinate lyase . It is also found in other enzymes, like in 3-carboxy-cis,cis-muconate cycloisomerase.
Protein of unknown function DUF2443 (DUF2443)
Type: Family

This entry represents a small group of highly conserved proteins from bacteria, in particular Helicobacter species. The structure is a bundle of α helices. The function is not known.
Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal (Ubiq_cytC_Rdtase_Fe-S_su_TAT)
Type: Domain

This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane . This entry is associated with

,

and

.
Interferon regulatory factor-3 (Interferon_reg_factor-3)
Type: Domain

This is the interferon-regulatory factor 3 chain of the hetero-dimeric structure which also contains the shorter chain CREB-binding protein. These two subunits make up the DRAF1 (double-stranded RNA-activated factor 1). Viral dsRNA produced during viral transcription or replication leads to the activation of DRAF1. The DNA-binding specificity of DRAF1 correlates with transcriptional induction of ISG (interferon-alpha, beta-stimulated gene). IRF-3 pre-exists in the cytoplasm of uninfected cells and translocates to the nucleus following viral infection. Translocation of IRF-3 is accompanied by an increase in serine and threonine phosphorylation, and association with the CREB coactivator occurs only after infection .
Transcription factor TFIID, subunit 8, C-terminal (TFIID_su8_C)
Type: Domain

The TATA Binding Protein (TBP) Associated Factor 8 (TAF8) is one of several TAFs that bind TBP, and is involved in forming the Transcription Factor IID (TFIID) complex. TAF8 plays a role in the differentiation of preadipocyte fibroblasts to adipocytes; it is also required for the integration of TAF10 into the TAF complex. The mouse ortholog of TAF8 is called taube nuss protein (TBN), and is required for early embryonic development. TBN mutant mice exhibit disturbances in the balance between cell death and cell survival in the early embryo. TAF8 plays a role in the differentiation of preadipocyte fibroblasts to adipocytes; it is also required for the integration of TAF10 into the TAF complex. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF8 is also a component of a small TAF complex (SMAT), which contains TAF8, TAF10 and SUPT7L. Several TAFs interact via histone-fold motifs. The histone fold (HFD) is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamer. TAF8 contains an H4 related histone fold motif, and interacts with several subunits of TFIID, including TBP and the histone-fold protein TAF10. Currently, five HF-containing TAF pairs have been described or suggested to exist in TFIID: TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10 .

This entry represents the C-terminal region of subunit 8 (also known as TAF8) of the transcription factor TFIID . The adjacent N-terminal region generally contains a histone fold domain (

). This subunit is one of the key subunits of TFIID, being one of several general cofactors which are typically involved in gene activation to bring about the communication between gene-specific transcription factors and components of the general transcription machinery .
Ubiquitin conjugation factor E4, core (Ub_conjug_fac_E4_core)
Type: Domain

This entry represents the most conserved part of the core region of ubiquitin conjugation factor E4 (or Ub elongating factor, or Ufd2P), running from helix α11 to α38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C terminus, (

), which has ligase activity.
DNA primase, DnaB-helicase binding domain (DNA_primase_DnaB-bd)
Type: Domain

This entry represents the C-terminal region three-helical domain of DNA primase . Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase . It is associated with the Toprim domain

, which is the central catalytic core.
Type IV secretion system coupling protein TraD, DNA-binding domain (T4SS_TraD_DNA-bd)
Type: Domain

The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein. It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells . This protein forms hexamers from six structurally very similar protomers . This hexamer contains a central channel running from the cytosolic pole (formed by the all-α domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-α domain appears to be the DNA-binding domain of the structure.
Rhodopsin, N-terminal (Rhodopsin_N)
Type: Domain

Rhodopsin is the archetypal G-protein-coupled receptor. Such receptors participate in virtually all physiological processes as signalling molecules. They utilise heterotrimeric guanosine triphosphate (GTP)-binding proteins to transduce extracellular signals to intracellular events. Rhodopsin is important because of the pivotal role it plays in visual signal transduction. It is a dimeric transmembrane protein whose intradiskal surface consists of an N-terminal domain and three loops connecting six of the seven transmembrane helices. The N-terminal domain is a compact α-helical region with breaks and bends at proline residues outside the membrane . This entry represents the N-terminal domain. The N-terminal domain is extracellular is and is necessary for successful dimerisation and molecular stability .