SII-SWORD/CoKE huggingface dataset:
Exo-oligoalginate lyase, C-terminal domain (Alg17C_C)
Type: Domain

This domain is found at the C-terminal of Exo-oligoalginate lyase from Saccharophagus degradans (Alg17C) and similar sequences from proteobacteria. Alg17C catalyses the depolymerisation of alginate through an exolytic mode of action, via a beta-elimination mechanism. This protein consists of two major domains, an N-terminal imperfect α-barrel (

) and a C-terminal β-sheet domain (

, followed by a smaller all-β domain which is represented in this entry.
BRCA2, TR2 domain (BRCA2_TR2)
Type: Domain

This domain is found near the C terminus of BRCA2 and similar proteins from vertebrates. It is likely that the TR2 domain is largely disordered and does not fold into a globular structure. It contains a highly conserved proline-rich region which is preceded by a conserved stretch of positively charged residues. This domain is known to interact with meiosis-specific recombinase DMC1 and RAD51 .
Cypovirus WIV domain (Cypovirus_WIV)
Type: Domain

This entry corresponds to the WIV domain found at the C-terminal end of Non-structural protein 3 from Lymantria dispar cypovirus 1 (NS3) and similar proteins from arthropod-infecting cypoviruses. The WIV domain probably facilitates viral infection of arthropods. WIV stands for 'Widespread, Intriguing, Versatile'.
POP1, C-terminal domain (POP1_C)
Type: Domain

This entry represents the C-terminal domain of human Ribonuclease P/MRP protein subunit POP1 and similar proteins mainly found in animals. POP1 is a component of Ribonuclease P that cleaves the 5' leader from precursor tRNAs. The C-terminal domain of POP1 interacts with H1 RNA and has a stabilizing role. This domain adopts a β-barrel structure that is structurally very similar to the C-terminal β-barrel domains of eIF2 gamma, EF-Tu and tRNA thiouridylase MnmA .
Gal80p-like, C-terminal domain (Gal80p-like_C)
Type: Domain

This domain is found in Gal80p and its homologues from fungi and bacteria. Gal80p is a yeast regulatory protein closely related to glucose-fructose oxidoreductase. In Gal80p, this domain is likely involved in the binding of Gal4p .
NLP1-9, GAF domain (NLP1-9_GAF)
Type: Domain

This entry represents a GAF-like domain found in plant NLP1-9 from Arabidopsis thaliana and similar proteins mainly found in plants. Several members of this group contain two copies of this domain, while most contain a RWP-RK domain (

), and a carboxy-terminal Phox and Bem1 (PB1) domain (

). Additionally, a nuclear export signal domain is predicted in the N terminus .
Induced by infection (IBIN)
Type: Family

This family includes the protein product of the immunity-related lncRNA-encoded Induced by infection (IBIN) from Drosophila melanogaster (

, ). Its specific function is unknown.
Male-specific sperm protein Mst87F (Mst87F)
Type: Family

This family includes Male-specific sperm protein Mst87F from Drosophila melanogaster, the product of a transcript expressed in the germline from late pupal stages onward that overlaps with one of the enhancers of the pri transcriptional unit, which encodes the smORF-encoded peptides represented in

.
Peptide tarsal-less 1A/2A (Tal-1A_2A)
Type: Family

This protein family includes the short small open-reading frames (smORF) encoded peptides Peptide tarsal-less 1A/2A from Drosophila melanogaster (Tal-1A_2A), which are involved in several developmental processes .
Major capsid protein, jelly-roll (Major_capsid_jelly-roll)
Type: Domain

This entry represents a jelly-roll domain found at the C-terminal end of the major capsid protein from Sulfolobus turreted icosahedral virus 1. The structure of this domain is similar to major capsid protein structures of the eukaryotic Paramecium bursaria Chlorella virus, and the bacteriophage PRD1, and shows a common fold with the mammalian adenovirus .
MG491, central domain (MG491_central)
Type: Domain

This domain is found in the organelle protein MG491 (also known as MG218.1) from Mycoplasma genitalium. MG491 plays a key role in the functioning, organisation and stabilisation of the terminal organelle, a protrusion of the bacterial cell membrane responsible for its flask-shaped morphology. This protein is organised into a 60-residue N-terminal, a central three α-helical bundle (this entry) and a C-terminal region .
Gliding motility protein GldL-like, N-terminal domain (GldL-like_N)
Type: Domain

This entry represents a domain found N-terminal in Gliding motility protein GldL from Capnocytophaga canimorsus (

) and similar proteins mainly found in bacteroidetes. GldL is a component of the motor complex used by the T9SS and the gliding motility apparatus to transport proteins and gliding adhesin movement at the outer membrane. This motor complex consists of five copies of GldL surrounding two copies of GldM. GldL consists of two transmembrane helices (this entry) and a cytoplasmic domain .
Fibulin, C-terminal Ig-like domain (Fibulin_C)
Type: Domain

This entry represents a C-terminal Ig-like domain found in fibulin proteins mainly from vertebrates. This Ig-like domain seems most closely related to the cadherin domain

. Fibulins are a family of extracellular matrix glycoproteins characterised by a fibulin-type C-terminal domain preceded by tandem calcium-binding epidermal growth factor (EGF)-like modules. They are involved in protein-protein interaction with the components of basement membrane and extracellular matrix proteins .
COP9 signalosome complex subunit 3, N-terminal helical repeats (COP9_N)
Type: Domain

This entry represents the N-terminal domain from COP9 signalosome complex subunit 3, which consists of α-helical repeats . COP9 is a component of the eight-subunit COP9 signalosome complex (CSN), which inactivate Cullin-RING E3 ubiquitin ligases (CRLs) by removing their covalently attached activator, NEDD8. The CSN complex has two organisational centres, one consisting of an open ring formed by association of the WH subdomains from the PCI proteins (CSN1-4 and CSN7-8) and a bundle comprising the C-terminal α-helices from each subunit. The N-terminal helical repeat domains of the PCI proteins radiate from the PCI ring at the base of the complex .
Nucleoporin NUP120, helical domain, saccharomycetes (NUP120_helical_saccharomycetes)
Type: Domain

This domain is found in Nucleoporin NUP120 from Saccharomyces cerevisiae and similar sequences from Saccharomycetes. NUP120 is a a component of the nuclear pore complex (NPC) involved in nuclear poly(A)+ RNA and pre-ribosome export, in GSP1 nuclear import, in NPC assembly and distribution, as well as in nuclear envelope organisation. This entry represents the α-helical domain of NUP120, which packs against the side of the β-propeller, located N-terminal of the protein .
Carrier-protein-independent halogenase WelO5-like (WelO5-like)
Type: Family

This entry represents includes carrier-protein-independent halogenase WelO5, an enzyme that chlorinates C13 of 12-epi-fischerindole U to yield 12-epi-fischerindole G. This enzymatic transformation constitutes the first step in the oxidative maturation to welwitindolinones. WelO5 adopts a cupin-like fold that is also characteristic of Fe/2OG enzymes .

This entry also includes structurally related Fe-dependent dioxygenases, such as L-isoleucine 3(1)-dioxygenase which hydroxylates L-isoleucine at the C-4' position to form L-4'-hydroxyisoleucine (4'-HIL) , L-gamma-glutamyl-L-propargylglycine hydroxylase which catalyses the hydroxylation of the dipeptide L-gamma-glutamyl-L-propargylglycine, leading to L-gamma-glutamyl-L-beta-ethynylserine .
Alpha-galactosidase, N-terminal (GalA_N)
Type: Domain

This domain is found at the N-terminal of Alpha-galactosidase from Thermotoga maritima (GalA), which hydrolyses the short-chain alpha-galactosaccharides raffinose, melibiose and stachyose. This GH36 enzyme is organised into three domains: an N-terminal β-sandwich fold domain (this entry), a canonical (β/α)8-fold domain housing the active site (

), and a C-terminal β-sandwich domain with a Greek-key motif .
EPS8, spectrin-like domain (EPS8_2nd)
Type: Domain

This entry represents a spectrin-like domain is the EPS8 proteins. Epidermal growth factor receptor kinase substrate 8 (EPS8) is a signalling adapter that possesses actin binding, bundling, and barbed-end capping activities. It forms a complex with Sos-1, Abi1 and the lipid kinase phosphoinositide 3-kinase (PI3-K) to regulate Rac activation that leads to actin cytoskeletal remodeling. It is critical for dendritic cell migration. It is involved in the initial growth of stereocilia in both inner hair cells and outer hair cells. It also regulates axonal filopodia in hippocampal neurons in response to brain-derived neurotrophic factor (BDNF). It has been linked to proliferation, metastasis and prognosis of many malignant tumours .
NUP210, Ig-like domain 15 (NUP210_Ig15)
Type: Domain

This domain is found in Nuclear pore membrane glycoprotein 210 (NUP210) and its homologues. The domain represented by this entry is one of these constituent Ig-like domains and has a significant structural similarity to cadherin domains.

NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobulin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen . There are eight copies of NUP210 per spoke. NUP210 is the only NUP that primarily resides in the NE lumen. This protein is not required for faithful NPC assembly .
NUP210, C-terminal Ig-like domain (NUP210_Ig_C)
Type: Domain

This domain is found at the C-terminal of Nuclear pore membrane glycoprotein 210 (NUP210) from human and its homologues. The domain represented by this entry is one of these constituent Ig-like domain and has a significant structural similarity to cadherin domains.

NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobulin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen . There are eight copies of NUP210 per spoke. NUP210 is the only NUP that primarily resides in the NE lumen. This protein is not required for faithful NPC assembly .
NUP210, Ig-like domain 1 (NUP210_Ig1)
Type: Domain

This domain is found in human Nuclear pore membrane glycoprotein 210 (NUP210) and its homologues. The domain represented by this entry is one of these constituent Ig-like domains and has a significant structural similarity to cadherin domains.

NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobulin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen . There are eight copies of NUP210 per spoke. NUP210 is the only NUP that primarily resides in the NE lumen. This protein is not required for faithful NPC assembly .
NUP210, Ig-like domain 2 (NUP210_Ig2)
Type: Domain

This domain is found in human Nuclear pore membrane glycoprotein 210 (NUP210) and its homologues. The domain represented by this entry is one of these constituent Ig-like domains and has a significant structural similarity to cadherin domains.

NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobulin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen . There are eight copies of NUP210 per spoke. NUP210 is the only NUP that primarily resides in the NE lumen. This protein is not required for faithful NPC assembly .
NUP210, Ig-like domain 3 (NUP210_Ig3)
Type: Domain

This domain is found in human Nuclear pore membrane glycoprotein 210 (NUP210) and its homologues. The domain represented by this entry is one of these constituent Ig-like domains and has a significant structural similarity to cadherin domains.

NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobulin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen . There are eight copies of NUP210 per spoke. NUP210 is the only NUP that primarily resides in the NE lumen. This protein is not required for faithful NPC assembly .
NUP210, Ig-like domain 7 (NUP210_Ig7)
Type: Domain

This domain is found in Nuclear pore membrane glycoprotein 210 (NUP210) and its homologues. The domain represented by this entry is one of these constituent Ig-like domains and has a significant structural similarity to cadherin domains.

NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobulin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen . There are eight copies of NUP210 per spoke. NUP210 is the only NUP that primarily resides in the NE lumen. This protein is not required for faithful NPC assembly .
LYC1, C-terminal domain (GNAT_LYC1-like)
Type: Domain

This domain is found C-terminal in Lysine acetyltransferase (LYC1) and other related fungal proteins. LYC1 catalyses the first step the lysine degradation pathway. The domain represented by this entry is predicted to adopt GNAT-like fold. It is found usually upstream Acetyltransferase GNAT domain (

) suggesting a possible duplication event in these proteins.
Abortive infection phage resistance protein, N-terminal domain (AIPR_N)
Type: Domain

This entry represents the N-terminal domain found in an abortive infection phage resistance protein often found in restriction modification system operons .
PDXDC1-like, third domain (PDXDC1-like_3rd)
Type: Domain

This entry represents a domain found towards the C-terminal of Pyridoxal-dependent decarboxylase domain-containing protein 1 (PDXDC1). PDXDC1 has been associated with the modulation of prepulse inhibition of acoustic startle, perhaps through the metabolism of catecholamine neurotransmitters . The function of this domain is unknown.
PDXDC1/PDXD2, second domain (PDXDC1-like_2nd)
Type: Domain

This entry represents the second domain found in the central region of Pyridoxal-dependent decarboxylase domain-containing protein 1 (PDXDC1) and at the C-terminal of PDXD2. PDXDC1 has been associated with the modulation of prepulse inhibition of acoustic startle, perhaps through the metabolism of catecholamine neurotransmitters . The function of this domain is unknown.
CCR4-NOT transcription complex subunit 1, N-terminal domain (CNOT1_1st)
Type: Domain

This domain is found at the N-terminal of human CCR4-NOT transcription complex subunit 1 (CNOT1) and similar sequences from animals. CNOT1 is a scaffolding component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. This domain adopts a structure of a HEAT-repeat .
FKRP, stem domain (FKRP_N)
Type: Domain

This entry represents the N-terminal domain of the fukutin-related protein (also known as ribitol 5-phosphate transferase FKRP). Alpha-Dystroglycan (alpha-DG) is a highly-glycosylated surface membrane protein. Defects in the O-mannosyl glycan of alpha-DG cause dystroglycanopathy, a group of congenital muscular dystrophies. The core M3 O-mannosyl glycan contains tandem ribitol-phosphate (RboP), a characteristic feature first found in mammals. Fukutin and fukutin-related protein (FKRP), whose mutated genes underlie dystroglycanopathy, sequentially transfer RboP from cytidine diphosphate-ribitol (CDP-Rbo) to form a tandem RboP unit in the core M3 glycan. FKRP is composed of two domains, the N-terminal stem domain and the C-terminal catalytic domain. The overall structure of the stem domain is similar to that of the catalytic domain of polypeptide GalNAc transferase 10 (ppGalNAcT-10). However, the HxD motif of ppGalNAcT-10, which is critical to its catalytic reaction, was not conserved. Therefore, the stem domain of FKRP would not have glycosyltransferase activity despite its overall structural similarity to ppGalNAcT-10 .
ELFN1/ELFN2, fibronectin type-III domain (ELFN_Fn3)
Type: Domain

This domain is found in human ELFN1 and ELFN2 proteins and its homologues. The postsynaptic ELFN1 regulates target-specific presynaptic properties which influences the timing of recruitment of inhibitory neuron subtypes . Both ELFN1 and ELFN2 inhibit the phosphatase activity of protein phosphatase 1 (PP1) complexes . This domain is predicted to adopt a Ig-like β-sandwich with significant similarity to fibronectin type III domains.
Mediator of RNA polymerase II transcription subunit 14, RM8 (Med14_RM8)
Type: Domain

This entry represents an α/β domain that is found tandemly repeated in human Mediator of RNA polymerase II transcription subunit 14 (Med14) and its homologues. This entry represents repeat RM8.

Med14 is a component of the Mediator complex, 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. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors . Med14 along with Med17 are scaffold subunits in nucleating Mediator . The major portion of Med14 exists in the Head-Shoulder module of the Mediator and consists of nine tandem repeats (RM1 to RM9), which are arranged in an atypical right-handed helix .
Syntrophin, C-terminal PH domain (Syntrophin_4th)
Type: Domain

This entry represents the C-terminal PH domain found in syntrophin proteins. The syntrophin family are intracellular membrane-associated proteins that interact with both ion channels and signalling proteins. As such, syntrophins appear to be important for linking ion channels to intracellular signalling pathways. Syntrophins are concentrated at postsynaptic sites at the neuromuscular junction and may be involved in clustering acetylcholine receptors. In muscle and non-muscle tissues, syntrophin is associated with dystrophin, utrophin, and two homologues of the dystrophin carboxy-terminal region.
SMCHD1, ribosomal S5 domain 2-like domain (SMCHD1_S5)
Type: Domain

This domain is found in human SMCHD1 protein and its homologues. SMCHD1 is an epigenetic repressor that may participate in structural manipulation of chromatin in an ATP-dependent manner as a part of its role in gene expression regulation. This domain follows the SMCHD1 ATPase module and adopts a globular α/β structure consisting of five-stranded mixed β-sheet with α-helices packed on both sides. This domain is involved in dimerisation .
Reversion-inducing cysteine-rich with Kazal motifs, N-terminal (RECK-like_N)
Type: Domain

This domain is found at the N-terminal of human Reversion-inducing cysteine-rich protein with Kazal motifs (RECK) and similar proteins mainly found in vertebrates. RECK is a membrane-anchored glycoprotein that plays a role in Wnt7-specific responses in the central nervous system angiogenesis and in the blood-brain barrier regulation. This domain adopts an α-helical structure .
RNF34/RFFL, HeH domain (RNF34_RFFL_HeH)
Type: Domain

This entry represents a domain found in human E3 ubiquitin-protein ligase rififylin (RNF34L), RFFL and similar eukaryotic proteins. This domain is predicted to adopt an helix-extended loop-helix (HeH) structure.

RNF34 and RFFL are of E3 ubiquitin-protein ligases that play a crucial role in various biological processes by mediating the ubiquitin-mediated proteasomal degradation of target proteins. They are involved in the regulation of apoptosis by ubiquitinating and promoting the degradation of caspases CASP8 and CASP10 . They also participate in the regulation of the tumour necrosis factor-mediated signalling pathway, mainly through the 'Lys-48'-linked polyubiquitination and degradation of RIPK1. Additionally, they have a role in the negative regulation of p53/TP53, either directly through ubiquitination or indirectly via the degradation of SFN . RNF34 is implicated in metabolic regulation by targeting PPARGC1A for degradation , influencing brown fat cell metabolism, and is thought to be involved in innate immunity by the ubiquitination of NOD1 . Additionally, RFFL is thought to be involved in endocytic recycling.
Mediator of RNA polymerase II transcription subunit 14, RM2 (Med14_RM2)
Type: Domain

This entry represents an α/β domain that is found tandemly repeated in human Mediator of RNA polymerase II transcription subunit 14 (Med14) and its homologues. This entry represents repeat RM2.

Med14 is a component of the Mediator complex, 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. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors . Med14 along with Med17 are scaffold subunits in nucleating Mediator . The major portion of Med14 exists in the Head-Shoulder module of the Mediator and consists of nine tandem repeats (RM1 to RM9), which are arranged in an atypical right-handed helix .
Mediator of RNA polymerase II transcription subunit 14, RM6 (Med14_RM6)
Type: Domain

This entry represents an α/β domain that is found tandemly repeated in the homologues of human Mediator of RNA polymerase II transcription subunit 14 (Med14). This entry represents repeat RM6.

Med14 is a component of the Mediator complex, 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. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors . Med14 along with Med17 are scaffold subunits in nucleating Mediator . The major portion of Med14 exists in the Head-Shoulder module of the Mediator and consists of nine tandem repeats (RM1 to RM9), which are arranged in an atypical right-handed helix .
PAV1-137, bromodomain-like (PAV1-137_bromodom-like)
Type: Domain

This entry represents a Bromodomain-like domain present in PAV1-137 protein from PAV1 virus. Its function is unknown and it has been suggested that this domain could be involved in protein-protein interactions .
DBF4, BRCT domain (DBF4_BRCT)
Type: Domain

This entry represents the BRCT domain found in DBF4 from S.cerevisiae, its orthologues from S.pombe and similar sequences from fungi. DBF4 is a conserved eukaryotic protein that functions as the regulatory subunit of the Dbf4-dependent kinase (DDK) complex. DDK plays essential roles in DNA replication initiation and checkpoint activation. During the replication checkpoint, Saccharomyces cerevisiae Dbf4 is phosphorylated in a Rad53-dependent manner, and this, in turn, inhibits initiation of replication at late origins . This entry represents the minimal region of Dbf4 required for the interaction with the checkpoint kinase Rad53 .
MINAR1, N-terminal helical domain (MINAR1_N)
Type: Domain

This entry represents a N-terminal conserved domain found in the Major intrinsically disordered Notch2-binding receptor 1 (MINAR1) family. MINAR1 is a Notch2-binding protein that has been shown to inhibit angiogenesis and breast cancer growth .