SII-SWORD/CoKE huggingface dataset:
Exocyst complex component Sec3, C-terminal (Sec3_C)
Type: Domain

Sec3 (also known as ExoC1) is a component of the exocyst complex, which mediates the tethering of post-Golgi secretory vesicles to the plasma membrane and promotes the assembly of the SNARE complex for membrane fusion. The exocyst is also involved in cell polarization, primary ciliogenesis, cytokinesis, pathogen invasion, tumorigenesis and metastasis . This complex has an elongated shape consisting of packed long rods, a a structure that is shared among the Complex Associated with Tethering Containing Helical Rods (CATCHRs) proteins from related complex such as Conserved Oligomeric Golgi complex (COG) and Golgi-Associated Retrograde Protein complex (GARP) . Subunits of these complexes, apart of helical bundles, they usually have a coiled-coil (CC) region at the N-terminal.

Sec3 is described as a membrane-anchoring component. This entry represents the C-terminal domain of Sec3 which interacts with small GTPases , which consists of the conserved α-helical bundle . Sec3 is recruited to the sites of polarised membrane growth through its interaction with the small GTP-binding protein Rho1p .
Inositol-tetrakisphosphate 1-kinase, preATP-grasp domain (ITPK1_preATP-grasp)
Type: Domain

This entry represents the preATP-grasp domain of a smalll group of proteins from Entamoeba, including Inositol-tetrakisphosphate 1-kinase from Entamoeba histolytica (ITPK1) . ITPK1 can phosphorylate various inositol polyphosphate such as Ins(3,4,5,6)P4 or Ins(1,3,4)P3. Phosphorylates Ins(3,4,5,6)P4 at position 1 to form Ins(1,3,4,5,6)P5 which may play a regulatory function. It may also act as an isomerase .
Exocyst complex component Sec8, middle helical bundle (Sec8_M)
Type: Domain

Sec8 is a component of the exocyst complex, composed of Sec3, Sec5, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70 and Exo84, which mediates the tethering of post-Golgi secretory vesicles to the plasma membrane. The exocyst promotes the assembly of SNARE complex for membrane fusion and it is also involved in many cellular processes such as cell polarisation, primary ciliogenesis, cytokinesis, pathogen invasion, tumorigenesis and metastasis .

Subunits of the exocyst have a rod structure which is a shared feature for the Complex Associated with Tethering Containing Helical Rods (CATCHRs) proteins such as those of the Conserved Oligomeric Golgi complex (COG) and Golgi-Associated Retrograde Protein complex (GARP), consisting of a N-terminal long coiled-coil followed by a region of antiparallel short helical bundle units . This entry represents a domain found in the middle region of Sec8 subunit, consisting of α-helical bundles.
Protein translocase subunit SecDF, P1 domain, N-terminal (SecD_1st)
Type: Domain

This domain is found in protein translocase subunit SecDF from Thermus thermophilus, which belongs to the RND superfamily. SecDF shows 12 transmembrane (TM) regions and 6 periplasmic regions (P1-P6). This entry represents the N-terminal region of the base subdomain of the P1 domain, that is located in the N- terminal half of the polypeptide, also known as SecD region. This domain folds into a pseudo-symmetrical antiparallel β-sheet that rearranges to a β-barrel architecture during ion transport. This domain, which covers the TM region , is related to

and usually appears associated with

and

.
CsgH-like (CsgH-like)
Type: Domain

CsgH is a Curli-like protein found in proteobacteria . These proteins adopt a seven stranded β-sandwich fold . CsgH is a functional homologue of CsgC and is a potent inhibitor of CsgA amyloid formation .
Integrin alpha-X-like, third Ig-like domain (ITGAX-like_Ig_3)
Type: Domain

This entry represents a domain found in Integrin alpha-X from humans (ITGAX) and similar proteins predominantly from vertebrates. ITGAX is a receptor for fibrinogen. This region consists of an immunoglobulin-like domain .
Protein export membrane protein SecD/SecF, C-terminal (SecD_SecF_C)
Type: Domain

This entry represents the C-terminal domain of various prokaryotic SecD and SecF protein export membrane proteins and their archaeal homologues. These SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC . SecD and SecF are required to maintain a proton motive force .
Transcription-repair-coupling factor, D3 domain (MFD_D3)
Type: Domain

The transcription-repair coupling factor (TRCF, also known as MFD) couples transcription and DNA repair in bacteria. MFD removes transcription elongation complexes stalled at DNA lesions and recruits the nucleotide excision repair (NER) machinery to the site . This protein consists of eight domains , of which D3 is represented in this entry. D1-D3 module plays a critical role in unmasking of the UvrA binding site .
Csf1, N-terminal (Csf1_N)
Type: Domain

This entry represents the N-terminal region of Csf1.

This entry includes Csf1 protein from yeast, which is the orthologue of human BLTP1. These are tube-forming lipid transport proteins which provide phosphatidylethanolamine for glycosylphosphatidylinositol (GPI) anchor synthesis in the endoplasmic reticulum . They belong to the repeating β-groove (RBG) superfamily which are conserved lipid transfer proteins containing long hydrophobic grooves consisting of multiple repeating modules made of five β-sheets followed by a loop .
Maternal embryonic leucine zipper kinase, UBA domain (MELK_UBA)
Type: Domain

This domain is found in Maternal embryonic leucine zipper kinase from humans (MELK) and similar proteins from animals. MELK is a member of the snf1/AMPK family of serine-threonine kinases that has been associated with various cellular processes, including stem cell renewal, cell cycle progression, and pre-mRNA splicing. It is upregulated in several types of tumour. MELK is organised into three domains: an N-terminal kinase domain (

), a ubiquitin associated (UBA) domain (this entry) and a C-terminal kinase associated domain (KA1,

). This domain adopts a compact configuration consisting of three α-helices organised in a "U"-shaped fold, with the first helix antiparallel to the third one .
Elongation factor SelB-like, third winged-helix domain (SelB-like_WHD3)
Type: Domain

This domain is found in Elongation factor SelB from Aquifex aeolicus (

) and similar aquificaceae family proteins. SelB is a selenocysteine(Sec)-specific elongation factor that brings the selenocysteinyl-tRNA(Sec) to the ribosome. It consists of three EF-Tu-like domains (D1-3, where

is the first one), followed by four winged-helix domains (WHD1-4). This entry represents the third winged-helix domain (WHD3) .
MgtC-like, C-terminal domain (MgtC-like_C)
Type: Domain

This entry represents a domain found at the C-terminal of Protein MgtC from Salmonella typhimurium and similar bacterial proteins. MgtC is a virulence factor required for growth in low Mg2+ medium and for intramacrophage survival. It may be involved in regulating membrane potential by activating Na+/K+-ATPase . This domain adopts a ferredoxin-like fold and has a significant structural similarity to ACT-like domains. In contrast to the canonical ACT-like domains, this domain doesn't dimerise or bind to small molecules. It is probably involved in protein-protein interactions .
Dual-specificity RNA methyltransferase RlmN, N-terminal domain (RlmN_N)
Type: Domain

This entry represents the N-terminal domain from the dual-specificity RNA methyltransferase RlmN and similar sequences mainly found in bacteria.

Dual-specificity RNA methyltransferase RlmN specifically methylates position 2 of adenine 2503 in 23S rRNA, which serves to optimize ribosomal fidelity, and position 2 of adenine 37 in tRNAs. Unmodified tRNA is not a suitable substrate for RlmN, which suggests that RlmN works in a late step during tRNA maturation .
Type-I-A Cascade subunit Csa5 (Csa5_I-A)
Type: Family

This group of archaeal proteins includes CRISPR type I-A cluster 1/Apern-associated protein Csa5-1 from Saccharolobus solfataricus (Csa5), the small subunit of the archaeal-specific Type-I-A Cascade complex for CRISPR-mediated antiviral immunity. This protein consists of two domains: an all α-helical arrangement and an insertion that shows a single helix and six β-strands arranged as three antiparallel two-stranded β-sheets .
Intraflagellar transport protein 52, C-terminal domain (Itf52_C)
Type: Domain

This entry represents the C-terminal domain of Intraflagellar transport protein 52 homolog from humans (IFT52) and similar eukaryotic proteins. IFT52 is part the IFT-B complex, which is involved in intraflagellar transport (IFT), the bidirectional movement of particles required for the assembly, maintenance and functioning of primary cilia. IFT52 is responsible for the binding to the C-terminal domain of IFT46 and essential for the interaction between the subcomplexes. This domain adopts an all-α structure .
Isoamylase, C-terminal (Isoamylase_C)
Type: Domain

Isoamylase from Pseudomonas amyloderamosa hydrolyses alpha-1,6-glucosidic linkages of amylopectin and glycogen. It consists of three domains: the N-terminal (

), the catalytic domain (

) and the C-terminal all-β domain, presented in this entry (

,

) .
Cry1Ac-like, domain VII (Cry1Ac-like_dom-VII)
Type: Domain

This entry includes insecticidal protein Cry1Ac from Bacillus thuringiensis and related sequences, which contains a proteolytically labile protoxin segment (in the C-terminal region) and a three-domain toxic core at the N terminus (domains I-III) . The protoxin segment consists of domains IV-VII. This entry represents domain VII, which is a β-roll that closely resembles carbohydrate-binding modules.
Ribosomal RNA large subunit methyltransferase M, THUMP-like domain (RlmM_THUMP-like)
Type: Domain

This entry represents the THUMP-like domain of Ribosomal RNA large subunit methyltransferase M (RlmM), adjacent the ferredoxin-like domain (

), which together constitutes the N-terminal domain . RlmM specifically catalyses the 2'-O-methylation of nucleotide C2498 in the peptidyl transferase loop of 23S rRNA .
23S rRNA (guanine(745)-N(1))-methyltransferase, N-terminal (RlmA_N)
Type: Domain

This is the N-terminal zinc-binding domain of 23S rRNA (guanine(745)-N(1))-methyltransferase from Escherichia coli (RlmA) and similar proteins. This domain is involved in specific recognition and binding of its rRNA substrate. It adopts a has a novel Cys3His Zn-finger fold .
Cytokine receptor-like factor 2-like, D2 domain (CRLF2-like_D2)
Type: Domain

CRLF2 is a receptor for thymic stromal lymphopoietin (TSLP). It forms a functional complex with TSLP and IL7R which is capable of stimulating cell proliferation through activation of STAT3 and STAT5. CRFL2 is implicated in the development of the hematopoietic system . It consists of two FnIII-like domains, D1 and D2.

This entry represents the membrane-proximal D2 domain, which displays a an ABE/C'CFG topology with two disulfide bridges . This domain interacts with IL7R D2 domain and forms a compact network of interactions . This domain is also found in the cytokine receptor common subunit gamma (IL2RG), a common subunit for the receptors for a variety of interleukins .
Selenocysteine-specific elongation factor, first winged helix domain (SelB_WND1)
Type: Domain

This domain is found in Selenocysteine-specific elongation factor SelB from Escherichia coli (

) and in similar proteins mainly found in enterobacteria. SelB is a translation factor necessary for the incorporation of selenocysteine into proteins. SelB is composed of a N-terminal region, and a C-terminal extension that consists of four winged-helix (WH) domains arranged in tandem. This entry represents the first of these domains, each of which contains three α-helices flanked by a three-stranded antiparallel β-sheet .
Isoamylase 1-3-like, C-terminal (ISOA1-3-like_C)
Type: Domain

This entry represents the C-terminal β-sandwich domain from ISOA1-3 and similar proteins from plants and bacteria. In ISOA1 from Chlamydomonas reinhardtii (

), this domain is involved in dimerisation of homodimers and suggests a similar interaction to form ISOA1-ISOA2 heterodimers .

Isoamylases (ISOAs) are starch debranching enzymes, including ISOA1, ISOA2 and ISOA3. ISOA1-2 are known to form a large complex and being involved in the biosynthesis and crystallization of starch. ISOA3 is involved in starch catabolism and removes different branches than ISA1-ISA2, namely short chains that prevent amylopectin crystallization .
Cytokine receptor-like factor 2-like, D1 domain (CRLF2-like_D1)
Type: Domain

This entry represents the membrane-distal D1 domain from cytokine receptor-like factor 2-related sequences mainly found in fish. This domain is characterised by a ABED/C'CFG topology stabilized by a disulfide bridge similarly to that from mammals . This domain contains the three regions that grasp TSLP .
Iron-regulated surface determinant protein H/B, linker domain (Isd_H_B_linker)
Type: Domain

The bacterial pathogen Staphylococcus aureus uses two closely related receptors located on its surface, IsdH and IsdB, to capture from haemoglobin (Hb) the iron it needs to grow. Both proteins show conserved near iron transporter (NEAT) domains (

) that function synergistically. These domains, essential for the arrest of iron, are appropriately positioned by an α-helical linker domain (this entry), which does not interact with the heme group. In IsdH, this linker domain forms a three-helix bundle structure that is essential for efficient heme capture .
Alpha-L-rhamnosidase, domain D2 (RhaB_D2)
Type: Domain

This domain is found in Alpha-L-rhamnosidase from Bacillus sp. (RhaB,

), a member of glycoside hydrolase (GH) family 78 that catalyses the hydrolytic release of rhamnose from polysaccharides and glycosides, degrading the bacterial biofilm gellan. RhaB is organised into five domains:

, this entry,

,

and

. This domain shows a β-sandwich structure with 13 β-strands and two short helices .
RHA1_ro05818, N-terminal helical domain (RHA1_ro05818_N)
Type: Domain

This domain is found at the N terminus of the RHA08564 protein from Rhodococcus jostii (

) and similar sequences from actinomycetes. This protein is thought to be a thioesterase involved in the metabolism of cholate . This protein has a 4HBT domain (

) at the C-terminal. The N-terminal domain shows an helical fold.
Thiazolinyl imine reductase-like, C-terminal (Irp3-like_C)
Type: Domain

This entry represents the C-terminal domain of Thiazolinyl imine reductase Irp3 from Yersinia enterocolitica, PchG from Pseudomonas aeruginosa and similar bacterial sequences.

Thiazolinyl imine reductases catalyse the NADPH-dependent reduction of a thiazoline to a thiazolidine, a step involved in formation of the siderophores yersiniabactin (Yersinia spp.) and pyochelin (Pseudomonas aeruginosa) . These proteins consist of two domains, an N-terminal dinucleotide-binding domain (

) and a C-terminal α/β domain, involved in substrate binding and oligomerisation .
GREB1-like, circularly permuted SF2 helicase domain (GREB1-like_cpSF2)
Type: Domain

This entry represents a circularly-permuted Superfamily 2 helicase found N-terminal to the Glycosyltransferase domain in eukaryotic GREB1-like proteins. Some versions, such as the human GREB1 and GREB1L are predicted to be inactive .
Invasin, domain 4 (Invasin_D4)
Type: Domain

This domain is found in a group of proteins from Gammaproteobacteria, including Invasin from Yersinia pseudotuberculosis (

,

), a protein that allows this enteric bacteria to penetrate cultured mammalian cells by binding several beta-1 chain integrins. This domain is structurally similar to the C1 set of Ig-like domains having two additional β-strands .
GREB1-like, second domain (GREB1-like_2nd)
Type: Domain

GREB1 (gene regulated by estrogen in breast cancer 1) was first identified as an estrogen-regulated gene expressed in breast cancer . Its exact function is not known but its expression is regulated by the coordinated binding of estrogen-receptors to distal sites interacting with Pol II to activate gene transcription from core promoters located at a considerable distance from the greb1 gene . It acts as a regulator of hormone-dependent cancer growth in breast, ovarian and prostate cancers . This is a presumed domain found adjacent the N-terminal domain of GREB1 and GREB1-like proteins. Structure predictions suggest that it may adopt an α/β fold.
Integrator complex subunit 9-like, C-terminal domain (IntS9-like_C)
Type: Domain

This is the C-terminal domain of Integrator complex subunit 9 (IntS9) from animals. IntS9 interacts with the C-terminal of IntS11 (responsible for endonuclease activity of INT), a crucial interaction for the role of INT in snRNA 3'-end processing. IntS9 is a component of integrator complex (INT) which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing .
Protein CPL1-like (CPL1-like)
Type: Domain

This domain is found in CPL1 from Cryptococcus neoformans and similar fungal proteins. CPL1 is a virulence factor which promotes fungal virulence by enhancing type 2 inflammation in the mouse host .
Integrator complex subunit 11, C-terminal domain (IntS11_C)
Type: Domain

IntS11 is the catalytic component of integrator complex (INT), which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. This entry represents the C-terminal domain (CTD) of IntS11 which interacts with the C-terminal of IntS9 (

), which is a crucial interaction for the role of INT in snRNA 3'-end processing . The IntS9-IntS11 CTD complex is composed of a continuous nine-stranded β-sheet with four strands from IntS9 and five from IntS11 (

). IntS11 is responsible for the endonuclease activity of INT .
SWI/SNF Subunit INI1, DNA binding domain (INI1_DNA-bd)
Type: Domain

This entry represents the N-terminal winged helix DNA binding domain of the INI1/hSNF5/SMARCB1 subunit and similar sequences from animals.

SWI/SNF complexes use the energy of ATP hydrolysis to remodel chromatin. In mammals they play a central role in regulating gene expression during differentiation and proliferation .
Immune inhibitor A-like metallopeptidase, VEG domain (InhA-like_VEG)
Type: Domain

Immune inhibitor A(InhA)-type metallopeptidases are potential virulence factors secreted by members of the Bacillus cereus group (BCG) and belong to the thuringilysin family within the metzincin clan of metallopeptidases, M6 in the MEROPS database. The structure of these proteins consists of four domains: a pro-peptide, a catalytic domain, a domain reminiscent of viral envelope glycoproteins (VEG), and a MAM domain grafted into the latter . This entry represents the VEG domain found at the C-terminal of InhA and PrtV peptidases (a slightly more distant thuringilysin family members). It consists of a central parallel β-sandwich comprised by an upper five-stranded mixed sheet and a lower four-stranded antiparallel sheet .
NADPH-dependent reductive aminase-like, C-terminal domain (RedAm-like_C)
Type: Domain

This domain is found at the C-terminal end of NADPH-dependent reductive aminase from Aspergillus oryzae (RedAm) and similar proteins predominantly found in fungi and bacteria. RedAm catalyses the reductive coupling of a broad set of carbonyl compounds with a variety of primary and secondary amines. This protein folds into an N-terminal Rossman domain (

) and a C-terminal helical bundle (this entry) connected by a long inter-domain α-helix .
Imm-5-like (Imm5-like)
Type: Domain

This domain is similar to

, which is predicted to be an immunity protein in bacterial toxin-antitoxin systems. This suggests a similar immunity function for proteins in this family.
Cytokine receptor common subunit beta, N-terminal (IL3RB_N)
Type: Domain

This entry represents the first Ig-like domain of human IL3RB (

) and similar sequences from vertebrates.

Cytokine receptor common subunit beta (IL3RB) is a cell surface receptor that plays a role in immune response and controls the production and differentiation of haematopoietic progenitor cells into lineage-restricted cells. It participates in the signalling pathways of interleukin-3, interleukin-5 and granulocyte-macrophage colony-stimulating factor/CSF2 which have overlapping activities on haematopoietic cells and have been implicated in the pathogenesis of allergic diseases of the lung. IL3RB consists of four extracellular domains with an Ig-like fold.
Histone-lysine N-methyltransferase SET1, RNA-binding domain (SET1_RBD)
Type: Domain

This domain is found in Histone-lysine N-methyltransferase, H3 lysine -4 specific from Saccharomyces cerevisiae (SET1) and similar proteins from yeast. SET1 is the methyltransferase subunit of the COMPASS (Set1C) complex that plays a role in telomere length maintenance and transcription elongation regulation . This entry represents the RNA-binding domain (RBD), which adopts an α/β structure.
Translation initiation factor 5A-like, N-terminal (IF5A-like_N)
Type: Domain

This entry represents the N-terminal domain of Translation initiation factor 5A from eukaryotes and archaea, which has an SH3-like fold. These proteins are involved in translation elongation and eIF5A is specifically required to promote peptide-bond formation between consecutive proline residues . This entry also includes Woronin body major protein Hex1, which is similar to eIF5A.
RecQ-1-like, helix-turn-helix domain (RecQ-1-like_HTH)
Type: Domain

This domain is found in a group of bacterial DNA helicases, including RecQ-1 from Porphyromonas gingivalis, which shows an all-helical structure . This entry represents the helix-turn-helix (HTH) domain.
Nonstructural protein 13, zinc-binding domain, coronavirus (NSP13_ZBD_CoV)
Type: Domain

Nonstructural protein 13 (NSP13) is encoded by the replicase polyprotein 1a/ab of coronaviruses and released after a proteolytic process. It plays a critical role catalysing the unwinding of duplex oligonucleotides into single strands in an NTP-dependent manner. It In SARS-CoV, it has been shown that NSP12 directly interacts with NSP13 and enhances its helicase activity.

NSP13 is a multidomain protein consisting of a N-terminal zinc-binding domain (ZBD), a stalk domain that connects the ZBD with the 1B domain and the helicase domain (that contains two RecA1 and RecA2 domains). ZBD, stalk and 1B domains are unique to nidovirus helicases . NSP13 adopts a triangular pyramid shape in which the two RecA1 and A2 and 1B domains form the triangular base while N-terminal ZBD and stalk domains are arranged at the apex of the pyramid . Recently, it has been reported that SARS-CoV-2 NSP13 acts as an interferon antagonist. It is involved in type I interferon (IFN-I) response as it binds and blocks TBK1 phosphorylation to inhibit interferon regulatory factor 3 (IRF3) which results in decreased IRF3 activation .

This entry represents the ZBD of NSP13, which is critically involved in nidovirus replication and transcription, modulating the ATPase/helicase activity in cis . It includes conserved cysteines and histidines involved in three zinc-binding sites .