SII-SWORD/CoKE huggingface dataset:
Importin repeat (Importin_rep_5)
Type: Repeat

The importin subunit beta-3 has a superhelical structure composed of tandem repeats structurally similar to HEAT repeats . This entry includes a single repeat unit and includes sequences not captured by

.
Archaellum regulatory network B, C-terminal (ArnB_C)
Type: Domain

This is the C-terminal domain found in archeal proteins that carry a von Willebrand factor type A domain such as ArnB from Sulfolobus acidocaldarius. ArnB is involved in negative regulation of the archaellum (former: archaeal flagellum), and the C-terminal domain is phosphorylated by ArnC and ArnD on serine and threonine residues affecting docking of ArnA .
AF-9, ANC1 homology domain (AF-9_AHD)
Type: Domain

This entry corresponds to the ANC1 homology domain (AHD) found in AF-9 . AF-9 is a chromatin reader component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA . Proteins containing this domain also include ENL (also known as MLLT1), which is also a component of the super elongation complex .
Cadmium carbonic anhydrase repeat (CDCA)
Type: Repeat

This entry represents the cadmium carbonic anhydrase repeat unit of the beta-carbonic anhydrase of a marine diatom , that uses both zinc and cadmium for catalysis of the reversible hydration of carbon dioxide for use in inorganic carbon acquisition for photosynthesis (thus being a cambialistic enzyme). Compared with alpha-and gamma-carbonic anhydrases that use three histidines to coordinate the zinc-atom, this beta-carbonic anhydrase has two cysteines and one histidine, and rapidly binds cadmium .
Csm4, C-terminal (Csm4_C)
Type: Domain

Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA.

This entry represents the C-terminal domain found in Csm4. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Studies indicate that Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Structural analysis show , Csm3 and Csm4 have one and two ferredoxin-like folds (also known as an RRM-like fold), respectively. The long β-hairpin inserted into the C-terminal ferredoxin-like fold of Csm4, is well-conserved in the Cmr3 structure. The corresponding β-hairpin of Cmr3 binds the D1 domain of Cmr2, as observed in the Cmr2-Cmr3 complex structure. Furthermore, it is suggested that the hairpin of Csm4 is responsible for the interaction with Csm1 (ortholog of Cmr2) .
Photosystem II Psb31 protein (PSII_Pbs31)
Type: Domain

This domain can be found in Psb31, an extrinsic protein found in photosystem II (PSII) present in Chaetoceros gracilis . Photosystem II (PSII) is a multisubunit, membrane protein complex located in the thylakoid membranes of oxygenic photosynthetic organisms from cyanobacteria to higher plants. The four helices in the N-terminal domain are arranged in an up-down-up-down fold and are similar in structure to PsbQ protein in Spinach, despite low sequence homology .
Mit1, C-terminal Zn finger 2 (Znf-CCCH_6)
Type: Domain

Mit1 is part of the Snf2/Hdac Repressive Complex (SHREC), the fission yeast nucleosome remodeling and deacetylation (NuRD) equivalent that plays a major role in transcriptional gene silencing (TGS) within heterochromatin. SHREC consists of the chromatin remodeler Mit1, the HDAC Clr3, and Clr1 and Clr2 proteins .
Subtilisin-like protease 2, prodomain (Pro_sub2)
Type: Domain

Subtilisin-like protease 2 (Sub2) is a multidomain protein that plays an important role in malaria infection. This domain is a conserved region of the inhibitory prodomain of Sub2 from Plasmodium falciparum, termed prosub2 which has structural similarity to bacterial and mammalian subtilisin-like prodomains .
Large polyvalent protein associated domain 26 (LPD26)
Type: Domain

This is a small α-helical domain with two acidic residues conserved in a predicted loop between two of its helices . The domain is mainly found in polyvalent proteins of conjugative elements .
Argonaute, N-terminal (Ago_N_1)
Type: Domain

The AGO (Argonaute) proteins have four domains: an N-terminal domain, the PAZ domain, the MID domain and the PIWI domain. This entry is for the N-terminal domain. The N-terminal domain of AGOs is the most variable domain. Compared with prokaryotic Argonautes, KpAGO (Kluyveromyces polysporus Argonaute) has numerous surface-exposed insertion segments, with a cluster of conserved insertions re-positioning the N domain, contributing to the formation of nucleic-acid-binding channel to enable full propagation of the 3' end of the guide RNA guide-target pairing. The guide strand is used by the RISC complex to specify interactions with target RNAs. If sequence complementarity between guide and target is extensive, AGO catalyses cleavage, resulting in slicing of the target RNA .
Legionella ubiquitin-specific protease A domain (LupA)
Type: Domain

This domain is found in Legionella ubiquitin-specific protease A (LupA). LupA removes a ubiquitin modification from LegC3 which inactivates the cognate effector. This domain is typical of eukaryotic ubiquitin proteases involved in deconjugation of ubiquitin or ubiquitin-like proteins from their targets .
Vacuolar protein sorting 38 (Vps38)
Type: Family

This entry includes Vps38 from budding yeasts. Vps38 is involved in endosome-to-Golgi retrograde transport as part of the VPS34 PI3-kinase complex II .

The class III phosphatidylinositol-3-kinase (PI3K) known as Vps34 regulates intracellular membrane trafficking in endocytic sorting, cytokinesis and autophagy. Vps34 forms complexes with other proteins: Vps15, Vps30 (encoded by VPS30/ATG6 in yeast, equivalent to mammalian Beclin 1, encoded by BECN1) and either Vps38 (UVRAG) or Atg14 (ATG14L). Although the N-terminal domains of Vps30, Vps38 and Atg14 differ, the overall similarity of their domain organizations suggests that these proteins may have evolved from a common ancestor .
DNA polymerase nu, pseudo-exo domain (DNA_pol_P_Exo)
Type: Domain

This domain, known as the Pseudo-exo domain, is found DNA polymerase Nu protein in species such as Homo sapiens. Residues 192-416 of Nu formed a degenerate 3'-5'-exonuclease domain, which deviates from the equivalent .
Exuperantia, SAM-like domain (SAM_Exu)
Type: Domain

Exuperantia (Exu) is associated with localization of bicoid (bcd) mRNA and required for its localization at the anterior pole of the oocyte. Crystal structure of Exu reveals a dimeric assembly with each monomer consisting of a 3'-5' EXO-like domain and a sterile alpha motif (SAM)-like domain. The SAM-like domain interacts with its target RNA as a homodimer and is required for RNA binding activity .
Minimal CRISPR polymerase domain (Minimal_Cpol)
Type: Domain

This entry represents the minimal version of the CRISPR polymerase domain. It is predicted to generate cyclic nucleotides, potentially sensed by CARF domains which in turn activate various effector domain including HEPN RNases, CARF sensor and effectors are found in conserved genome contexts. It is part of a broader class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivatives. This implicates CRISPR polymerase of the Type III CRISPR/Cas systems in a nucleotide synthetase functional role .
Protein of unknown function DUF5571 (DUF5571)
Type: Family

This entry includes a group of vertebrate proteins, including C12orf50 from humans.
Importin 13 repeat 2 (Importin_rep_2)
Type: Repeat

Importin 13 serves as receptor for nuclear localization signals (NLS) in cargo substrates . It mediates docking of the importin/substrate complex to the nuclear pore complex (NPC). It contains several repeats structurally similar to the HEAT repeat . This Pfam entry represents a single repeat unit.
Domain of unknown function DUF5621 (DUF5621)
Type: Domain

This is a domain of unknown function found in gammaproteobacteria.
Endoglucanase B, carbohydrate binding domain (CBM46)
Type: Domain

This entry represents the carbohydrate binding domain (also known as the CBM46 domain) found in endoglucanase B (CelB) from Paenibacillus lautus and Cel5B from Bacillus halodurans.
Short myomegalin-like EB1 binding protein, N-terminal (SMYLE_N)
Type: Domain

This N-terminal region is found in SMYLE (for short myomegalin-like EB1 binding protein). It includes the SMYLE homology (SmyH) domain found in the first 100 residues at the N terminus. This conserved SmyH domain is required and sufficient for PKA scaffolding protein AKAP9, and the pericentrosomal protein CDK5RAP2 binding .
Domain of unknown function DUF5639 (DUF5639)
Type: Domain

This is a domain of unknown function which is mainly found in Deinococcus-Thermus.
HetR, C-terminal Hood domain (HetR_C)
Type: Domain

This is the C-terminal hood domain found in Heterocyst differentiation control protein (HetR). HetR-C binds to PatS peptide. Two PatS6 peptides bind to the lateral clefts of HetR-Hood domain, and trigger significant conformational changes of the flap domain, resulting in dissociation of the auxiliary α-helix and eventually release of HetR from the DNA major grove and termination of transcription .
ADGRG1, GAIN subdomain A (ADGRG1_GAIN_A)
Type: Domain

ADGRG1/GPR56 is a a cell-surface G protein-coupled receptor (GPCR) which belongs to the adhesion G protein-coupled receptor (aGPCR) family, a large family of chimeric proteins that have both adhesion and signaling functions and play critical roles in diverse neurobiological processes including brain development, synaptogenesis, and myelination. This entry represents GPCR-Autoproteolysis-INducing (GAIN) subdomain A, including PLL-GAIN linker (F161-D175) region .
Interleukin-2 receptor subunit beta, N-terminal (IL2RB_N1)
Type: Domain

IL-2Rbeta is a member of the class I cytokine receptor superfamily . It carries a cytokine-binding homology region, which is divided in two fibronectin type-III (FN-III) domains termed D1 and D2. Each domain contains seven β-strands that form a sandwich of two antiparallel β-sheets. The N-terminal D1 domain of IL-2Rbeta includes two highly conserved disulfide bridges . This entry describes D1 of the N-terminal region of IL2Rbeta.
Domain of unknown function DUF5594 (DUF5594)
Type: Domain

This domain was first discovered in BPSL1050, a highly immunoreactive protein found in Burkholderia pseudomallei. The domain's structure consists of three helical regions which pack onto an antiparallel β sheet, formed by four strands. The β sheet is solvent exposed on one side and packs tightly against the three helices on the other side, generating a network of hydrophobic and aromatic interactions that contribute to tight packing of the protein. It is thought that the small loop L1, the main loop L2, and part of helix α3 extending until Leu120 are the three main immunogenic sequences .
ZAP, zinc finger (Znf-CCCH_8)
Type: Domain

Zinc-finger antiviral protein (ZAP) is a host factor that specifically inhibits the replication of certain viruses, such as HIV-1, by targeting viral mRNA for degradation. N-terminal domain of ZAP is the major functional domain which contains four zinc-finger motifs. This entry represents the third zinc finger type CCCH .
Immune mapped protein 2, N-terminal (IMP2_N)
Type: Domain

This domain is conserved across both IMP1 and IMP2 families. It is suggested that the globular domain likely contributes to a shared function, hence it is termed 'IMP1-like domain' .
Lower baseplate protein, N-terminal (BppL_N)
Type: Domain

This domain is found in the N-terminal region of the receptor-binding protein of bacteriophage TP901-1, which infects Lactococcus lactis. The receptor-binding protein of phage TP901-1 is termed the lower baseplate protein (BppL) and is trimeric in nature. The N-terminal domain of BppL plugs into the upper baseplate protein (BppU) .
Anosmin-1, cysteine rich domain (Anosmin-1_Cys_box)
Type: Domain

This is the Cys-box (cysteine-rich) domain found on the N-terminal of anosmin-1 proteins. It is suggested that the Cys-box domain may resemble the cysteine-rich region of the insulin-like growth factor receptor .
Secreted Novel AID/APOBEC-like Deaminase 1 (SNAD1)
Type: Family

This is a family of secreted AID/APOBEC like deaminases found sporadically across vertebrates .
Cellulose-binding protein CttA, N-terminal (CttA_N)
Type: Domain

This is the N-terminal domain of cellulose-binding protein CttA present in Ruminococcus flavefaciens. CttA mediates attachment of the bacterial substrate via two carbohydrate-binding modules. The domain is known as the X-module and lacks a true hydrophobic core. Unlike the X-modules in other types of CohE-XDoc complexes it does not contribute to the binding surface. This X-module appears to serve as an extended spacer, which separates the cellulose-binding modules at the N terminus of CttA and the bacterial cell wall. The domain does not share structural similarity with other known X-modules from cellulolytic bacteria but does show similarity to G5-1 module of StrH from S. pneumoniae .
Homeobox-cysteine loop-homeobox (HOCHOB)
Type: Domain

This domain is considered a double homeodomain, termed HOCHOB, present in the C. elegans genome. Proteins containing this domain include CEH-91/92/93 that share extended sequence similarity with each other upstream of their typical HDs (Homeodomains). CEH-92 has three copies of this domain. The domain consists of two divergent HDs that are separated by a linker of about 17 residues. The linker has a number of conserved positions, two of which are cysteine residues suggesting that they could be involved in metal binding. Hence, the name HOCHOB (Homeobox-cysteine loop-homeobox). Furthermore, there are two conserved histidine residues, one in each HD (in CEH-91 displaced by two positions), and there is also a conserved aspartic acid. It is speculated that the HOCHOB domain is an evolutionary novelty that is derived from two HDs and may have gained metal-binding capacity .
Cop9 signalosome subunit 5 C-terminal domain (CSN5_C)
Type: Domain

The COP9 (Constitutive photomorphogenesis 9) signalosome (CSN), a large multiprotein complex that resembles the 19S lid of the 26S proteasome, plays a central role in the regulation of the E3-cullin RING ubiquitin ligases (CRLs) . The catalytic activity of the CSN complex is carried by subunit 5 (CSN5), also known as c-Jun activation domain-binding protein-1 (Jab1) . This entry is the C-terminal domain found in CSN5 proteins. CSN5, whose two C-terminal helices form an antiparallel hairpin, inserts its final C-terminal helix (helix II) into the central CSN6 framework at the core of the bundle. Deletion of the C-terminal helices has a pronounced effect on CSN integrity .
Tetratricopeptide-like repeat (TPR_22)
Type: Repeat

This entry includes outlying tetratricopeptide-like repeats (two repeat units) that are not matched by

.
Magnetochrome domain (MCR)
Type: Domain

Magnetotactic bacteria (MTB) align along the Earth's magnetic field using an organelle called the magnetosome. The magnetosome-associated protein MamP is conserved in all MTB and has a PDZ domain, a small c-type cytochrome domain (the first magnetochrome domain, MCR1), a 17-residue linker and a second magnetochrome domain (MCR2). This entry describes the two tandem magnetochrome domains carrying c-type cytochrome motifs CX2CH .
OAA-family lectin sugar binding domain (SBD)
Type: Domain

This domain is found in agglutinin family of lectins. Oscillatoria agardhii agglutinin (OAA)- family lectins comprise either one or two homologous domains, with a single domain possessing two glycan binding sites. OAA is one of the lectins with anti-HIV activity. This sugar binding domain is also found in Pseudomonas fluorescens agglutinin (PFA) and myxobacterial hemagglutinin (MBHA), where MBHA contains two sugar-binding domains (i.e. 4 sugar binding sites), whereas OAA and PFA are single-domain proteins (i.e. 2 sugar binding sites) .
Protein of unknown function DUF5559 (DUF5559)
Type: Family

This is a family of unknown function found in primates.
Metalloprotease StcE, C-terminal (StcE_C)
Type: Domain

This is the C-terminal domain found in mucin glycoproteins such as secreted protease of C1 esterase inhibitor from EHEC (StcE). This domain adopts a beta/gamma crystallin fold and has been shown to be dispensable for substrate binding. Furthermore, deletion analysis suggest that lack of the C-terminal resulted in impaired association with the cell surface .
Domain of unknown function DUF5595 (DUF5595)
Type: Domain

This domain is found in Nude C 80 (Ndc80) proteins which can be found in species such as Homo sapiens. Ndc80 protein complexes are a core component of the end-on attachment sites for kinetochore microtubules. Ndc80 is also known as Hec1, for highly expressed in cancer 1 .
EZH2, MCSS domain, fungal (EZH2_MCSS_fung)
Type: Domain

Polycomb repressive complex 2 (PRC2) carries out the methylation of lysine 27 of histone H3, a hallmark of repressive chromatin. Three core subunits make up the catalytic core of PRC2; the SET domain containing EZH2, the zinc-finger containing SUZ12 and the WD40 repeat protein EED. The complex forms a compact arrangement of three lobes. The middle lobe largely comprises two domains that mark the beginning of the carboxy (C)-terminal region of EZH2 (MCSS and SANT2) and the helical, C-terminal, component of the Suz12 Vefs domain. This entry describes the MCSS (also known as SANT2L) domain. There is one zinc binding (Zn1Cys3His1) which is formed solely by MCSS .
Insulin receptor, trans-membrane domain (Insulin_TMD)
Type: Domain

This entry represents the trans-membrane domain (TMD) found in insulin receptor proteins. The TMD of the insulin receptor is within the beta-subunit and contains 23 amino acids. Mutations in the TMD were shown to have effects on receptor biosynthetic processing and kinase activation. Substitution of the entire TMD of the insulin receptor (IR) resulted in constitutive kinase activation in vitro, while replacing the TMD with that of glycophorin A inhibited insulin action. Structural studies show that TMD contains a helix and a kink when it is purified in dodecylphosphocholine (DPC) micelles. The residues 942-948 preceding the TMD have a propensity to be a short helix and may interact with membrane .
CadC C-terminal domain 1 (CadC_C1)
Type: Domain

CadC is an integral membrane protein of 512 amino acids comprising an N-terminal cytoplasmic DNA-binding domain, a transmembrane helix, and a C-terminal periplasmic domain. CadC belongs to the ToxR-like regulators that encompass biochemically non-modified one-component systems with similar gross topology, including several low pH-induced transcription regulators. Structural analysis of the C-terminal periplasmic domain indicates that it resembles the sensory domain of a (pH-activated) ToxR-like regulator. Furthermore, it is composed of two subdomains with a cavity at their interface that is suited to accommodate cadaverine, the feedback inhibitor of the Cad system. This is the N-terminal subdomain of the C-terminal periplasmic domain. It is composed of five-stranded β-sheets .
Pleurotolysin B, C-terminal (PlyB_C)
Type: Domain

This a trefoil C-terminal β-rich domain found in PlyB, one of the components of pleurotolysin (Ply) pore-forming protein. Ply is a membrane attack complex/perforin-like family (MACPF) protein consisting of two components, PlyA and PlyB. PlyB and PlyA act together to form relatively small and regular pores in liposomes. The PlyB C-terminal trefoil sits on top of the PlyA dimer .
ALMS repeat (ALMS_repeat)
Type: Repeat

This entry contains a single repeat unit of approximately 47 amino acids. It is found in Centrosome-associated protein ALMS1 and homologues .
Inactive serine protease scarface, clip-domain (CLIP_SPH_Scar)
Type: Domain

The clip domain is a structural/regulatory unit in many arthropod serine proteases . The clip domain superfamily also includes serine protease homologues (SPHs) . This entry describes clip domains in the SPHs (CLIP subfamily A), which belong to group-3. SPHs usually carry between 1 to 5 clip domains . The most prominent family member of carrying this clip domain is Scarface proteins in drosophila, which bear an inactive catalytic site, representing a subgroup of serine protease homologues (SPH). Loss-of-function induces defects in JNK-controlled morphogenetic events such as embryonic dorsal closure and adult male terminalia rotation .
Purple acid phosphatase, Fn3-like domain (Fn3_PAP)
Type: Domain

This entry represents an Fn3-like domain found at the N terminus of purple acid phosphatase enzymes .
RnaseLS-like HEPN (HEPN_RnaseLS)
Type: Family

This entry represents RnaseLS-like HEPN . Its function is not clear.
Fungal-type protein kinase (Pkinase_fungal)
Type: Domain

This domain is a variant of the protein kinase domain that is found in fungi (mostly in Basidiomycota and Ascomycota). Proteins containing this domain include CRN8 (crinkler effector protein 8) from Phytophthora infestans . CRN8 is a secreted effector and a kinase that induces cell death when expressed in host plants .
HP1451, C-terminal (HP1451_C)
Type: Domain

HP1451 modulates the ATPase activity of HP0525 H. pylori. It is suggested that HP1451 acts as an inhibitory factor of HP0525 to regulate Cag-mediated secretion. It consists of two domains. The two HP1451 domains (referred to as the KH-domain and S8-domain) interact with each other via two salt bridges. The second domain is structurally homologous to other nucleic acid-binding proteins such as the NTD of ribosomal protein S8 and DNaseI .
Isocitrate dehydrogenase/Hypothetical protein TT1725, C-terminal domain (Isocitrate_DH_TT1725_C)
Type: Domain

This entry represents the C-terminal domain of Isocitrate dehydrogenase [NADP] from Rickettsia typhi and similar bacterial proteins. It is also found in the hypothetical protein TT1725 from Thermus thermophilus HB8. The sequence is conserved in three predicted prokaryotic proteins with unknown functions, including Deinococcus radiodurans, Stigmatella aurantiaca, and Mycobacterium leprae. The presence of positively-charged residues in the α1 helix suggests this region binds to a protein with a negatively charged region or to nucleic acids .
Vid27, N-terminal (Vid27_N)
Type: Domain

This entry represents the N-terminal domain of Vid27. This region may contain a PH domain .

Vid27 is a cytoplasmic protein of unknown function, possibly regulates import of fructose-1,6-bisphosphatase into Vacuolar Import and Degradation (Vid) vesicles and is not essential for proteasome-dependent degradation of fructose-1,6-bisphosphatase (FBPase) .
SWI2/SNF2 ATPase (SWI2_SNF2)
Type: Domain

This is a SWi2/SNF2 ATPase found in type I restriction enzymes .
Fatty acid synthase subunit PfaD, N-terminal (PfaD_N)
Type: Domain

This domain is found in N-terminal region of PfaD, an enoyl reductase enzyme present in Bacillus subtilis. PfaD plays a role in the biosynthesis of polyunsaturated fatty acids. The domain is typically found just before the N-terminal region of a nitronate monooxygenase domain .
DNA polymerase III alpha subunit finger domain (DNA_pol3_finger)
Type: Domain

The shape of DNA polymerases can be described as resembling a right hand with thumb, finger, and palm domains. This entry represents the finger domain of the alpha subunit of DNA pol III .
Bacterial archaeo-eukaryotic release factor family 5 (Bact_RF_family5)
Type: Family

This entry represents the bacterial family of the archaeo-eukaryotic release factor superfamily. It is likely to play roles in biological conflicts or regulation under stress conditions at the ribosome. This family unusually lacks the fusion to the C-terminal Pelota domain .