SII-SWORD/CoKE huggingface dataset:
Proteasome activator Blm10, middle HEAT repeats region (Blm10_mid)
Type: Domain

This entry represents the middle HEAT repeats region of the yeast Blm10 and its homologues in plants and animals such as PA200 (also known as Proteasome activator complex subunit 4). Blm10 is a proteasome activator that binds the core proteasome and stimulates proteasome-mediated protein degradation by inducing gate opening .
Radical SAM, C-terminal extension (Radical_SAM_C)
Type: Domain

This domain is found as a C-terminal extension to a subset of Radical SAM domains

. It is found in archaeal, bacterial, fungal, plant and human proteins.
Putative virion glycoprotein, N-terminal (DiSB-ORF2_chro)
Type: Domain

This entry represents a short conserved region at the N terminus of putative glycoproteins from chroparaviruses. It carries two putative disulfide bridges. No similarity can be found with any other glycoproteins outside this region .
Emaravirus P4 movement protein (Emaravirus_P4)
Type: Family

This entry consists of movement proteins of the genus of negative-strand RNA viruses Emaravirus (related to the family Bunyaviridae), which infect plants. This entry includes P4 protein, which is a movement protein of the 30K superfamily .
STML2-like, C-terminal extension (STML2-like_C)
Type: Domain

This domain is found on a subset of proteins as a C-terminal extension of the Band 7 domain (

). It is found in proteins from bacteria to fungi, plants and mammals, including stomatin-like protein 2 from humans and its orthologue from S.pombe. STML2 is a mitochondrial protein that probably regulates the biogenesis and the activity of mitochondria .
Nucleolar pre-ribosomal-associated protein 1, C-terminal domain (NopRA1_C)
Type: Domain

Nucleolar pre-ribosomal-associated protein 1 (Npa1) is required for ribosome biogenesis and operates in the same functional environment as Rsa3p and Dbp6p during early maturation of 60S ribosomal subunits . The protein partners of Npa1p include eight putative helicases as well as the novel Npa2p factor. Npa1p can also associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase centre . The protein has also been referred to as Urb1.

This domain is found towards the C terminus of Npa1.
RecQ-like DNA helicase BLM, N-terminal domain (BLM_N)
Type: Domain

This is the very N-terminal region of chordate RecQ-like DNA helicase BLM proteins. BLM participates in DNA replication and repair . This domain, together with

, may play a role in regulation and oligomerization of BLM. These domains are also important in mediating interactions with partner proteins .
ERCC3/RAD25/XPB helicase, C-terminal domain (ERCC3_RAD25_C)
Type: Domain

This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases .

XPB, also known as Ssl2, Ercc3, RepB, Rad25 or haywire, is a core subunit of the eukaryotic basal transcription factor complex TFIIH, which plays a dual role in transcription and DNA repair . It is involved in nucleotide excision repair of DNA and in RNA transcription by RNA polymerase II . TFIIH is a multiprotein complex composed of a 7-subunit core, including XPB, p62, p52, p44, p34 and TTDA, associated with a 3-subunit CDK-activating kinase module consisting of MAT1, cyclin H and Cdk7 . XPB functions by opening DNA either around the RNA transcription start site or at sites of DNA damage . It is also required for spliced leader RNA gene transcription by RNA polymerase II, where TFIIH plays an essential role in transcription initiation . Once the pre-initiation complex has been established, TFIIH is necessary for promoter opening and promoter escape, processes that depend on the ATPase activity of XPB .
RecQ-like DNA helicase BLM, BDHCT-box associated domain (BDHCT_assoc)
Type: Domain

This domain is found on RecQ-like DNA helicase BLM in higher eukaryotes . It lies between the BDHCT (

), and DEAD-box domains (

). This domain, together with

, may play a role in regulation and oligomerization of BLM. These domains are also important in mediating interactions with partner proteins .
Small ribosomal subunit protein uS17, N-terminal (Ribosomal_uS17_N)
Type: Domain

This short N-terminal region is found in a number of eukaryotic small ribosomal subunit protein uS17 (also known as S11) .
Putative virion membrane protein (SP24)
Type: Family

SP24, or structural protein of 24kD, is a family of putative virion membrane proteins of plant and insect viruses. These viruses are ssRNA positive-strand viruses, with no DNA stage. The family corresponds to the central region of the ORF3 of insect chroparaviruses and negeviruses and plant cileviruses, higreviruses and blunerviruses. It contains four transmembrane regions. Chronic bee paralysis virus (CBPV) is one of the more common member virions. SP24 is probably one of the major structural components of the virions .
Cytoplasmic tRNA 2-thiolation protein 1, C-terminal (CTU1_C)
Type: Domain

This entry represents the C-terminal zinc-ribbon domain of cytoplasmic tRNA adenylyltransferase 1 (CTU1, NCS6), a protein required for uridine thiolation of Gln, Lys, and Glu tRNAs . CTU1 also carries an ATP-binding domain towards the N terminus.
RAWUL domain (RAWUL)
Type: Domain

The RAWUL domain is found at the C terminus of poly-comb group RING finger proteins. It contains a variant ubiquitin-like fold with a distinct conserved surface region. The conserved surface found in this domain is responsible for interaction with Cbx members of the PRC1 (polycomb repression complex 1) and homodimer formation .
Keratin type II head (Keratin_2_head)
Type: Domain

All intermediate filament proteins feature a central α-helical rod domain and variable nonhelical domains located at the N-terminal (head) and C-terminal (tail). The central rod domain is the main driver of self-assembly into filaments, whereas the N- and C-terminal domains are involved in post-translational modifications and interactions with other proteins . Type I and type II keratin form heteropolymeric intermediate filaments providing vital mechanical support in epithelia . This entry represents the N-terminal domain (head) of type II keratins.
Domain of unknown function DUF5059 (DUF5059)
Type: Domain

This domain is found in uncharacterised proteins together with a C-terminal copper-binding domain (

). Its function is not known, and it is largely found in the Halobacteriaceae family in Archaea.
S phase cyclin A-associated protein in the endoplasmic reticulum, N-terminal (SCAPER_N)
Type: Domain

This entry represents a short highly conserved region close to the N terminus of SCAPER. SCAPER is an ER-localised protein and a substrate for cyclin A/Cdk2. One theory suggests that SCAPER functions to create a local high concentration of cyclin A2 in the cytoplasm. Alternatively, SCAPER might be acting to sequester a portion of cellular cyclin A2 that could then be readily available for nuclear translocation, which may be needed for exit from G0 phase .
Cyclin-A, N-terminal APC/C binding region (Cyclin-A_N)
Type: Domain

This entry represents a disorder region. This region controls the stability of the region by recruiting the APC/C . This region includes the ABBA motif.
SMARCC, SWIRM-associated domain (SWIRM-assoc)
Type: Domain

This conserved domain can be found after the SWIRM and SANT domains in SWI/SNF complex subunits SMARCC1 (BAF155) and SMARCC2 (BAF170) . The function of this domain is not clear.
Keratin type II cytoskeletal 1, tail (Keratin_2_1_tail)
Type: Domain

All intermediate filament proteins feature a central α-helical rod domain and variable nonhelical domains located at the N-terminal (head) and C-terminal (tail). The central rod domain is the main driver of self-assembly into filaments, whereas the N- and C-terminal domains are involved in post-translational modifications and interactions with other proteins . Keratin 1 (KRT1) belongs to a large family of intermediate filament protein genes and is normally expressed in keratinocytes in the spinous layer of the epidermis . This entry represents the C-terminal domain (tail) of type II keratin KRT1.
SMARCC, N-terminal (SMARCC_N)
Type: Domain

This entry represents the N-terminal conserved domain found in the SWI/SNF complex subunits SMARCC1 (BAF155) and SMARCC2 (BAF170). The function of this domain is not clear.
SMARCC, C-terminal (SMARCC_C)
Type: Domain

This entry represents a conserved region found in the SWI/SNF complex subunit SMARCC 1/2, Ssr1/2 and SWI3 proteins. The function of this domain is not clear.
Sodium/calcium exchanger domain, C-terminal extension (Na_Ca_Ex_C-exten)
Type: Domain

This is a C-terminal extension of the eukaryote sodium/calcium exchanger domain, and is cytoplasmic.
Homeobox protein PKNOX/Meis, N-terminal (PKNOX/Meis_N)
Type: Domain

This domain is found towards the N terminus of the TALE/MEIS homeobox family members, including homeobox protein PKNOX and Meis.
Histone H2A, C-terminal domain (Histone_H2A_C)
Type: Domain

Histone H2A is a small, highly conserved nuclear protein that, together with two molecules each of histones H2B, H3 and H4, forms the eukaryotic nucleosome core ; the nucleosome octamer winds ~146 DNA base-pairs. In the mouse, histone H2A can be replaced by histone H2A-like 1 .

This entry represents the C-terminal domain of Histone H2A.
Cadherin, cytoplasmic C-terminal domain (Cadherin_C)
Type: Domain

This entry represents the cytoplasmic C-terminal domain of some proto-cadherins. It is this region of the cadherins that allows cell-adhesion and the essential feature of metazoan multicellularity. Cadherins are cell-surface receptors that function in cell adhesion, cell polarity, and tissue morphogenesis .
CAAX prenyl protease 1, N-terminal (Peptidase_M48_N)
Type: Domain

This entry represents the N-terminal five transmembrane α-helices domain of CAAX prenyl protease 1 (also known as Ste24 in budding yeast). Ste24 is a zinc metalloprotease catalysing two proteolytic steps in the maturation of yeast mating pheromone a-factor . The structures of Ste24 and its human homologue, ZMPSTE24, have been revealed .
Histone H2A conserved site (Histone_H2A_CS)
Type: Conserved_site

Histone H2A is a small, highly conserved nuclear protein that, together with 2 molecules each of histones H2B, H3 and H4, forms the eukaryotic nucleosome core ; the nucleosome octamer winds ~146 DNA base-pairs. This entry represents a conserved region in the N-terminal part of H2A. This region is conserved both in classical S-phase regulated H2A's and in variant histone H2A's which are synthesized throughout the cell cycle.
Putative oxidoreductase, C-terminal (Oxidoreduct_C)
Type: Domain

This is the C-terminal domain of a bacterial putative oxidoreductase.
Symplekin/Pta1, N-terminal (Symplekin/Pta1_N)
Type: Domain

This domain can be found in the symplekin protein from animals and Pta1 protein from budding yeasts. This domain is typically between 239 to 261 amino acids in length.

Symplekin is a scaffold protein that functions as a component of a multimolecular complex involved in histone mRNA 3'-end processing .

Pta1 is involved in pre-tRNA processing. Pta1 is a subunit of the cleavage and polyadenylation factor (CPF), which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB .
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (ACMSD)
Type: Family

2-amino-3-carboxymuconate-6-semialdehyde decarboxylase, also known as picolinate carboxylase or ACMSD, is a member of the amidohydrolase superfamily involved in tryptophan metabolism . It converts alpha-amino-beta-carboxymuconate-epsilon-semialdehyde (ACMS) to alpha-aminomuconate semialdehyde (AMS). ACMSD has medical importance as its substrate ACMS is unstable and dehydrates to quinolinic acid (QUIN, QA), not only a key precursor of NAD, but also a potent neurotoxin . Elevated levels of QUIN have been observed in several neuropsychiatric and neurodegenerative conditions .

The entry also includes decarboxylases OrsB, MacB and YanB, and salicylate decarboxylase.

YanB is a decarboxylase and part of the gene cluster that mediates the biosynthesis of yanuthone D, a fungal isoprenoid epoxycyclohexenone that acts as an antibiotic against fungi and bacteria . Salicylate decarboxylase has been shown to catalyse both the decarboxylation of salicylic acid to produce phenol, and the carboxylation of phenol to form salicylic acid .
Metal-dependent hydrolase (Metal_Hydrolase)
Type: Homologous_superfamily

The structural landmark of the metallo-dependent hydrolases (the amidohydrolase superfamily) is a (β/α)8-barrel fold (TIM barrel fold) with transition metal ions bound inside the barrel . This enzyme group comprises hundreds of hydrolytic enzymes with a diverse spectrum of substrates and reactions. Members have mono- or binuclear active-site metal centres, and play key roles in many fundamental processes .
Endophilin-A3, BAR domain (Endophilin-A3_BAR)
Type: Domain

BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This entry represents the Bar domain found in endophilin-A3.
AGRL2-4 , GAIN subdomain A (AGRL2-4_GAIN_subdom_A)
Type: Domain

This entry describes the GAIN subdomain A primarily found in adhesion G protein-coupled receptors L2-4 (AGRL2-4). It is also found in Latrophilin/CIRL, CELR1, AGRB1-3 and related G-protein-coupled receptors (GPCR). The GAIN domain consist of a stalk (consisting of subdomains A and B) and a GPS motif

, followed by a C-terminal transmembrane region

. The N-terminal subdomain A of the GAIN domain is composed of a variable number of α-helices (6, 5 or 3).

The ~320-residue GAIN domain is an ancient domain that exists in primitive ancestor organisms, and is conserved in all aGPCRs and all PKD1-related proteins. Functionally, the GAIN domain is both necessary and sufficient for autoproteolysis, suggesting an autoproteolytic mechanism whereby the overall GAIN domain fine-tunes the chemical environment. In contrast to most other autoproteolytic domains that cause the release of the cleaved mature protein, autoproteolysis of the GAIN domain does not lead to the dissociation of the cleaved extracellular sequences containing the GAIN domain from the membrane-embedded regions of the protein. The GAIN domain forms a tightly associated heterodimer upon proteolysis. Cleavage at the GAIN domain is not a feature that all GAIN domain-containing receptors possess and the GAIN domain likely has other functions (such as interacting with ligands or transmembrane helices) in addition to the autoproteolysis function.
Argonaute linker 2 domain (ArgoL2)
Type: Domain

ArgoL2 is the second linker domain in eukaryotic argonaute proteins. It starts with two α-helices aligned orthogonally to each other followed by a β-strand involved in linking the two lobes, the PAZ lobe and the Piwi lobe of argonaute to each other. Linker 2 together with the N, PAZ and L1 domains form a compact global fold . Numerous residues from Piwi, L1 and L2 linkers direct the path of the phosphate backbone of nucleotides 7-9, thus allowing DNA-slicing .
Protein argonaute, Mid domain (Argonaute_Mid_dom)
Type: Domain

This domain (Mid) is found to be part of the Piwi-lobe of the argonaute proteins. It is composed of a parallel four-stranded β-sheet core surrounded by four α-helices and two additional short α-helices. It most closely resembles the amino terminal tryptic core of the E.coli lactose repressor. There is an extensive interface between the Mid and the Piwi domains. The conserved C-terminal half or the Mid has extensive interactions with Piwi, with a deep basic pocket on the surface of the `Mid adjacent to the interface with Piwi. The Mid carries a binding pocket for the 5' phosphate overhang of the guide strand of DNA . The N, Mid, and Piwi domains form a base upon which the PAZ domain sits, resembling a duck. The 5' phosphate and the U1 base are held in place by a conserved network of interactions from protein residues of the Mid and Piwi domains in order to place the guide uniquely in the proper position observed in all Argonaute-RNA complexes .
Protein argonaute, N-terminal (Argonaute_N)
Type: Domain

This entry represents the N-terminal domain of argonaute proteins from eukaryotes. This domain is composed of an antiparallel four-stranded β-sheet core that has two α-helices positioned along one face of the sheet and an extended β-strand towards its N terminus. The core fold of the N domain most closely resembles the catalytic domain of replication-initiator protein Rep. The N domain is linked to the PAZ domain via linker 1 region, and together these three regions are designated the PAZ-containing lobe of argonaute .
Protealysin, N-terminal propeptide (Protealysin_N_PP)
Type: Domain

This entry represents the N-terminal propeptide of protealysin (

), a protease belongs the M4 family of peptidases that are commonly known as thermolysin-like proteases (TLPs) . All TLPs are synthesised as precursors containing N-terminal propeptides, and these propeptides are cleaved during maturation of the enzymes. The primary structure of these N-terminal propeptides can be used to classify TLP into two groups: the classical TLPs with long propeptide (approximately 200 amino acids) and the protealysin-type TLPs with short propeptide (approximately 50 amino acids). The propeptides of protealysin may act as an inhibitor that blocks the substrate-binding site and fixes the "open" conformation of the active site, which is unfavourable for catalysis . The PPL-motif (XXPP(Y/H)XL, where X is a hydrophobic residue) identified in this domain interacts with the S' subsites of the active centre being a critical element of the propeptide-catalytic domain interface .
Carnitine O-palmitoyltransferase, N-terminal (CPT_N)
Type: Domain

This domain is found at the N terminus of carnitine O-palmitoyltransferases. It functions as a regulatory domain and is linked to the catalytic domain via two transmembrane regions .
Glycoside hydrolase 64 (Glyco_hydro_64)
Type: Domain

This entry represents the glycoside hydrolase family 64 (GH64) domain (

), whose members are laminaripentaose-producing 'inverting' beta-1,3-glucanases (

). These enzymes cleave the beta-1,3-bonds found in a variety of beta-1,3-glucans such as laminarin or pachyman. 'Inverting' enzymes utilize a single-displacement reaction where an activated water molecule performs a nucleophilic attack at the sugar C-1 while concomitant aglycone departure is achieved by protonation of the glycosidic oxygen . This domain is composed of a barrel subdomain comprising mainly β-strands and a mixed (α/β) subdomain comprising helices and β-strands. It takes the form of a crescent, with a wide-open groove present for ligand binding. This wide groove is located between the β-barrel subdomain and the mixed α/β subdomain and the ligand-binding cleft in it is lined by negatively charged residues. Two strictly conserved catalytic residues, a Glu and an Asp, lie one-third of the way down the groove and act as an acid catalyst and a base catalyst, respectively .

This domain is found at the N-terminal of glucan endo-1,3-beta-glucosidase ; in Streptomyces matensis laminaripentaose hydrolase (SmLPHase), which cleaves a long-chain polysaccharide, beta-1,3-glucan, including laminarin, into a specific pentasaccharide oligomer laminaripentaose ; in beta-1,3-glucanase from Paenibacillus barengoltzii (PbBgl64A), a multi-domain protein which consists of an N-terminal CBM56 domain and a C-terminal GH64 domain and in Clostridium beijerinckii glucanallin, composed of a BetaGamma-crystallin domain, a GH64 domain, and a CBM56 domain .
Staufen, C-terminal (Staufen_C)
Type: Domain

This is the C-terminal domain of Staufen proteins. It consists of an N-terminal Staufen-swapping motif (SSM) comprising two α-helices, connected by a linker region to a dsRNA-binding-like domain ('RBD'). The 'RBD' has the fold of a functional dsRNA-binding domain, but lacks the residues required to bind RNA. This domain is responsible for dimerisation, the SSM from one molecule interacts with the 'RBD' of another .
Protein of unknown function DUF5058 (DUF5058)
Type: Family

This family consists of uncharacteried proteins around 250 residues in length and is mainly found in various Firmicutes species. The function of this family is unknown.
Domain of unknown function DUF5057 (DUF5057)
Type: Domain

This domain of around 360 residues in length is mainly found in proteins from various Firmicutes species. The function is unknown.
Protein of unknown function DUF5055 (DUF5055)
Type: Family

This family consists of several uncharacterised proteins around 100 residues in length and is mainly found in butyrate-producing bacteria. This family also includes sequences from phages. The function of this family is unknown.
Protein of unknown function DUF5054 (DUF5054)
Type: Family

This family consists of Glycosyl hydrolase family 38 proteins around 700 residues in length. The function of this family is unknown.
Protein of unknown function DUF5053 (DUF5053)
Type: Family

This family consists of uncharacterised proteins mainly from Bacteroides and Prevotella spp. The function of this family is unknown.
Protein of unknown function DUF5052 (DUF5052)
Type: Family

This family consists of uncharacterised proteins around 200 residues in length and is mainly found in various Firmicutes species. The function of this family is unknown.
Prolow-density lipoprotein receptor-related protein 1-like, beta-propeller domain (LRP1-like_beta_prop)
Type: Domain

This is a β-propeller domain found in Prolow-density lipoprotein receptor-related protein 1 (LRP1) from human, an endocytic receptor involved in endocytosis and in phagocytosis of apoptotic cells . LRP1 is involved in cellular lipid homeostasis and in the plasma clearance of chylomicron remnants and activated LRPAP1 (alpha 2-macroglobulin), as well as the local metabolism of complexes between plasminogen activators and their endogenous inhibitors. It acts as an LRPAP1 alpha-2-macroglobulin receptor .
JNK-interacting protein, leucine zipper II (JIP_LZII)
Type: Domain

This is the second leucine zipper domain (LZII) of several JNK-interacting proteins (JIP). It interacts with the small GTP-binding protein ARF6 .
Polyprotein allergen, nematode (ABA-1_nematode)
Type: Domain

The polyprotein allergens from certain nematoda, such as ABA-1 from Ascari and DvA-1 from Dictyocaulus viviparus, are lipid-binding proteins comprising multiple tandem repeats of this domain .
Protein of unknown function DUF5049 (DUF5049)
Type: Family

This family consists of some uncharacterised proteins around 60 residues in length. The function of this family is unknown.
Domain of unknown function DUF5048 (DUF5048)
Type: Domain

This domain is found at the C-terminal of several uncharacterised proteins of around 500 residues in length and is mainly found in tailed bacteriophages and Firmicutes prophages. The function of this domain is unknown.
Domain of unknown function DUF5047 (DUF5047)
Type: Domain

This entry represents the N-terminal domain of several uncharacterised proteins and peptidases around 360 residues in length. The function of this domain is unknown.
Domain of unknown function DUF5046 (DUF5046)
Type: Domain

This entry represents a domain found in several uncharacterised proteins from Faecalibacterium. The function of this domain is unknown.
Domain of unknown function DUF5045 (DUF5045)
Type: Domain

This domain is found in several uncharacterised proteins around 260 residues in length, mainly from various Bacteroides, Parabacteroides and Prevotella spp. The function of this domain is unknown.
Phage tail tube protein family (Phage_TTP_13)
Type: Family

This is a small family of Siphoviridae phage tail tube proteins. The tube protein polymerises to form the shaft through which the infecting DNA passes into the host .