SII-SWORD/CoKE huggingface dataset:
Mitochondrial splicing suppressor 51-like, C-terminal domain (Mss51-like_C)
Type: Domain

This entry represents a domain found at the C-terminal of protein MSS51 (Mitochondrial splicing suppressor 51) from yeast and its putative mammalian orthologue Mss51/Zmynd17. MSS51 is a COX1 mRNA-specific translational activator and Cox1 chaperone .

This domain is also found at the C-terminal of mammalian Zinc finger MYND domain-containing protein 15 (Zmynd15), a transcriptional repressor that functions through interaction with histone deacetylases (HDACs) . The specific function of this domain is unknown.
Prephenate dehydrogenase, dimerization domain (PDH_C)
Type: Domain

This entry includes are prephenate dehydrogenases

(PDHs), involved in tyrosine biosynthesis and related proteins predominantly found in bacteria. This is the C-terminal helical dimerisation domain of PDHs .
Prephenate dehydrogenase, nucleotide-binding domain (PDH_N)
Type: Domain

This entry includes prephenate dehydrogenases (PDHs)

involved in tyrosine biosynthesis, and related proteins predominantly found in bacteria. This is the N-terminal nucleotide-binding domain of PDHs, which has a modified Rossmann nucleotide-binding fold with an extended β-sheet sandwiched by three helices on each face .
Replication initiator protein (RepSA)
Type: Family

This entry represents a family of proteins that can be found in (and are an essential part of) actinomycete integrative and conjugative elements (AICEs), including Replication initiator protein from Streptomyces ambofaciens (RepSA), which is essential for pSAM2 replication .
Calmodulin binding protein, C-terminal domain (Calmod_bind_C)
Type: Domain

Members of this family include putative or actual calmodulin binding proteins and other transcription factors expressed by various plant species. Some members (for example,

), are known to be involved in the induction of plant defence responses . However, their precise function in this regards is as yet unknown.

This entry represents de C-terminal domain.
Calmodulin binding protein, central domain (Calmod_bind_M)
Type: Domain

This entry represents the central domain.

Members of this family include putative or actual calmodulin binding proteins and other transcription factors expressed by various plant species. Some members (for example,

), are known to be involved in the induction of plant defence responses . However, their precise function in this regards is as yet unknown.
Calmodulin binding protein-like, N-terminal domain (Calmodulin_bind_N)
Type: Domain

This entry represents the N-terminal β-sandwich domain of Calmodulin-binding proteins A/B/C/D/E/F/G.

Members of this family include putative or actual calmodulin binding proteins and other transcription factors expressed by various plant species. Some members (for example,

), are known to be involved in the induction of plant defence responses . However, their precise function in this regards is as yet unknown.
DNA helicase E1, DNA-binding domain, papillomavirus (PPV_E1_DBD)
Type: Domain

This entry represents the DNA-binding domain (DBD) of papillomavirus E1 protein, a DNA helicase that is required for initiation of viral DNA replication. This protein forms a complex with E2 protein at the origin of replication (ori) . This domain is found in the central region of E1 and binds DNA at specific sites of viral origin, and also binds cooperatively with E2-DBD. This domain comprises a five-stranded antiparallel β-sheet flanked by α-helices on each side . This domain binds originally as a dimer in which each monomer binds to one half-site of the palindromic E1 binding site, and promotes the assembly of the hexameric helicase on the ori . E1 has a domain architecture and function similar to SV40 T-antigen .
ATPase of the ABC class, N-terminal (ABC_N)
Type: Domain

This is the N-terminal domain of various bacterial predicted ABC class ATPases which show sequence and structural similarities to the N-terminal domain of MRB1590 (

) from kinetoplastids, a core protein of the multiprotein mitochondrial RNA binding complex 1 (MRB1) involved in kinetoplastid RNA (kRNA) editing . MRB1590 is a dimer and contains a central ABC ATPase fold (

) between novel N- and C-terminal regions. The N-terminal domains combine and form a RNA-binding basic pore which involves an arginine patch that has been suggested to act as a chaperone to bind and stabilize ssRNA during kRNA editing processes. N-terminal MRB1590 shows structural similarity to chaperones .
ATPase of the ABC class, C-terminal (ABC_ATPase_C)
Type: Domain

This is the C-terminal ATPase domain from bacterial ABC class ATPases. This entry also includes MRB1590 (

) from Trypanosoma brucei brucei, which has a central ATPase domain homologous to this domain .
Retrotransposon hot spot protein, N-terminal (RHS_N)
Type: Domain

Members of this entry are retrotransposon hot spot (RHS) proteins. They are associated with polymorphic subtelomeric regions in Trypanosoma. These proteins contain a conserved box 1 with a P-loop motif and a retrotransposon insertion site at the C-terminal (

). This domain represents the N-terminal region of the conserved box 1 from RHSPs .
Retrotransposon hot spot protein,C-terminal (RHS_C)
Type: Domain

Members of this entry are retrotransposon hot spot proteins (RHSs). They are associated with polymorphic subtelomeric regions in Trypanosoma. These proteins contain a P-loop (ATP/GTP-binding) motif, represented in this entry, at the C-terminal of the conserved box 1 . This domain also includes the retrotransposon insertion site .
Laa1/Sip1/HEATR5-like, HEAT repeat region (Laa1/Sip1/HEATR5-like_HEAT)
Type: Repeat

This entry represents a region consisting of HEAT repeats that is found in a group of eukaryotic proteins, including HEAT repeat-containing protein 5A/B (HEATR5A/B) from vertebrates, Pof6 interactor protein 1 (SIP1), AP-1 accessory protein LAA1 from yeast and SWEETIE from Arabidopsis thaliana.
BREX system Lon protease-like BrxL, N-terminal (BrxL_N)
Type: Domain

This entry represents the N-terminal domain of BREX system Lon protease-like protein BrxL from Bacillus cereus and similar proteins. BrxL is part of a type 1 BREX system, which contains a C-terminal Lon-like protease domain (

). BREX systems (bacteriophage exclusion) provide immunity against bacteriophage, a system that allows phage adsorption but prevents phage DNA replication, without degradation of the phage DNA .
ABC toxin, N-terminal domain (ABC_toxin_N)
Type: Domain

This entry represents the region found N-terminal to the neuraminidase domain (

) in the pore forming ABC toxins from fungi and bacteria, including Toxin subunit YenA2 from Yersinia entomophaga. YenA2 is part of an orally active toxin complex (TC) with strong insecticidal effects on larvae of the Coleoptera Costelytra zealandica, Acrossidius tasmania and Adoryphorus couloni and some Lepidoptera larvae .
Sporulation stage IV protein A, C-terminal (SpoIVA_C)
Type: Domain

The stage IV sporulation protein A (

) is an ATPase that has a role at an early stage in the morphogenesis of the spore coat and is required for proper coat localisation to the forespore . A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. This protein contains an ATPase domain at the N-terminal, a structural middle domain and a C-terminal domain that is key for targeting SpoIVA to the outer forespore membrane .

This entry represents the C-terminal domain of SpoIVA, which plays a key role in targeting the protein to the outer forespore membrane, in particular the five hydrophobic residues at the extreme C-terminal are essential for this function . Structure predictions suggest that it has three conserved α-helices followed by a β-hairpin .
Stage IV sporulation protein A, middle domain (SpoIVA_middle)
Type: Domain

The stage IV sporulation protein A (

) is an ATPase that has a role at an early stage in the morphogenesis of the spore coat and is required for proper coat localisation to the forespore . A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. This protein contains an ATPase domain at the N-terminal, a structural middle domain and a C-terminal domain that is key for targeting SpoIVA to the outer forespore membrane .

This is the structural middle domain of Stage IV sporulation protein A (SpoIVA) which follows the ATPase domain and the predicted secondary structure suggests that it is composed of two symmetrical units containing α-helices and β-strands .
Stage IV sporulation protein A, ATPase domain (SpoIVA_ATPase)
Type: Domain

The stage IV sporulation protein A (

) is an ATPase that has a role at an early stage in the morphogenesis of the spore coat and is required for proper coat localisation to the forespore . A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. This protein contains an ATPase domain at the N-terminal, a structural middle domain and a C-terminal domain that is key for targeting SpoIVA to the outer forespore membrane .

This entry represents the ATPase domain located at the N-terminal of SpoIVA . It contains a conserved 'sensor' threonine residue that is involved in coordinating a Mg 2 ion .
LonB, AAA+ ATPase LID domain, archaeal-type (LonB_AAA-LID)
Type: Domain

The species-specific Lon-insertion domain (LID) is characteristic of Lon proteases (also known as endopeptidase La) and is fused to the AAA module . Bacterial and eukaryotic Lons (LonA) have a LID at the N-terminal of AAA module; in archaeal Lons (LonB) the LID, represented in this entry, is inserted within the AAA module in a series of transmembrane segments known as the membrane-anchoring region (MA). In the Lon-like protease LonC, which does not have ATPase activity, the LID is also within the AAA-like module similar to LonBs; in this case, it is predicted to contain coiled-coil regions rather than transmembrane segments .
Lon-like, helical domain (Lon-like_helical)
Type: Domain

This domain represents the helical domain found in the Lon-like proteases .
Meiosis-specific protein ASY3-like, coiled-coil (ASY3-like_CC)
Type: Domain

This entry represents coiled-coil domain of ASY3 and PAIR3.

This entry represents a group of plant meiosis-specific proteins, such as AtASY3 from Arabidopsis and PAIR3 from rice. They are coiled-coil domain proteins required for normal meiosis . PAIR3 is an axial element and part of the synaptonemal complex (SC) that forms between homologous chromosomes during meiosis . Members of this family are homologues of SYCP2 from vertebrates and fungal Red1/Red10 .
PKAT, KLD domain (PKAT_KLD)
Type: Domain

This is the Kringle-like domain (KLD) found in Melanocyte protein PMEL, Transmembrane glycoprotein NMB (GPNMB) and Transmembrane protein 130 (TMEM130), which is downstream the PKD domain. It contains six highly conserved cysteine residues that form the disulphide bonds of mature PMEL dimers and promotes PMEL functional amyloid formation . This domain is perfectly conserved in PMEL and GPNMB which suggests that GPNMB also forms dimers. PMEL and GPNMB, together with TMEM130 (its most ancient paralogue), have a conserved domain architecture and have been recently described as the PKAT (PKD- and KLD-Associated Transmembrane) protein family . PMEL and GPNMB share overlapping phenotypes and disease associations, such as melanin-based pigmentation, cancer, neurodegenerative disease and glaucoma.
Antitoxin Xre-like, helix-turn-helix domain (Xre-like_HTH)
Type: Domain

This entry represents the N-terminal domain of the antitoxin component Xre of a type II toxin-antitoxin (TA) system, which is the helix-turn-helix (HTH) DNA binding domain, structurally similar to the Cro repressor, therefore, also referred to as HTH/Cro-like DNA-binding domain . This domain is also found in other antitoxin components, associated with a C-terminal toxin-binding domain

.
E motif (E_motif)
Type: Repeat

This entry represents the E motif (also known as E1) found in plant pentatricopeptide repeat (PPR) proteins . These proteins contain a DYW deaminase domain required for RNA editing, a process that deaminates specific cytidines to uridines. This motif, together with the E motif, precedes the DYW domain and, although their role is not clear, they are essential in the RNA editing reaction . The E/E motifs may contain two degenerate PPR motifs that could be involved protein binding.
E2 motif (E2_motif)
Type: Repeat

This is the E + motif (also known as E2) found in some plant pentatricopeptide repeat (PPR) proteins . PPRs contain a C-terminal DYW deaminase domain required for RNA editing, a process that deaminates specific cytidines to uridines. This motif, together with the E motif

, precedes the DYW domain

and, although their role is not clear, they are essential in the RNA editing reaction . The E/E motifs may contain two degenerate PPR motifs that could be involved in protein binding.
Nuclear speckle splicing regulatory protein 1, RS-like domain (NRP1_C)
Type: Domain

This domain found at the C-terminal of Nuclear speckle splicing regulatory protein 1 (NRP1, also known as Nuclear speckle-related protein 70 and Coiled-coil domain-containing protein 55) from mammals and aves. This is the RS-like domain, that resembles the arginine/serine-rich (RS) domain in other SR proteins, interacts with two SR proteins and with target mRNA, being essential for NRP1 activity. NRP1 is a RNA-binding protein that mediates pre-mRNA alternative splicing regulation .
Neurobeachin, beta-propeller domain (NBCH_WD40)
Type: Domain

This entry represents the β-propeller domain found at the C-terminal of neurobeachin-like proteins mainly from animals and plants. Neurobeachin from mouse appears to have a role in membrane trafficking .
Neurobeachin, alpha-solenoid region (Neurobeachin_a-sol)
Type: Domain

This entry represents a domain found at the N-terminal of neurobeachin and its homologues from animals and plants. Neurobeachin from mouse appears to have a role in membrane trafficking . It forms an extended α-solenoid structure.
PilZN3 domain (PilZN3)
Type: Domain

This is a noncanonical PilZ domain found at the N-terminal of proteins from spirochaetales, such as B. burgdorferi BB0733 and Treponema denticola TDE0214 proteins. They have a PilZN3-PilZ domain architecture and affect the motility and virulence of these organisms. Secondary structure predictions suggest that this domain retains the C-terminal α-helix of PilZ and three additional α-helices .
Isocitrate dehydrogenase kinase/phosphatase (AceK), regulatory domain (AceK_regulatory)
Type: Domain

This is the N-terminal regulatory domain of bacterial isocitrate dehydrogenase kinase/phosphatase (AceK) proteins (

) . It has an α-helical fold, with two long, parallel α-helices that form a large hairpin structure followed by two short, parallel α-helices forming a small hairpin segment. This domain is linked to the C-terminal kinase domain by a short (27 residues) α-helix .
Isocitrate dehydrogenase kinase/phosphatase (AceK), kinase domain (AceK_kinase)
Type: Domain

This the C-terminal protein kinase domain of bacterial isocitrate dehydrogenase kinase/phosphatase (AceK) proteins (

) . It has a classic bi-lobe protein kinase fold with the ATP-binding cleft located at the interface between the two lobes. The N-terminal lobe comprises a twisted antiparallel β-sheet of five strands and two α-helices. The C-terminal lobe is larger and mainly α-helical, with some stretches of antiparallel β-strands .
Gem-associated protein 6, C-terminal domain (Gemin6_C)
Type: Domain

This entry corresponds to a putative domain found at the C-terminal of several animal Gemin6 proteins. This domain appears to be distantly related to

, suggesting it may have an RNA-binding function. The exact function of Gemin6 is unknown but it has been found to form part of the survival motor neuron (SMN) complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles .
Gem-associated protein 6, Sm-like domain (Gemin6_Sm-like_dom)
Type: Domain

This entry represents the N-terminal Sm-like domain from mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the SMN complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles .
ChrB, N-terminal (ChrB_N)
Type: Domain

This entry represents the N-terminal domain found in protein ChrB from Cupriavidus metallidurans, a protein involved in the reduction of chromate accumulation and essential for chromate resistance . This domain may be involved in DNA binding and contains two highly conserved arginine residues important for its function .
Ral GTPase-activating protein subunit alpha/beta, N-terminal domain (RGPA/RALGAPB_N)
Type: Domain

This putative domain is found at the N-terminal of the Ral GTPase-activating protein alpha and beta subunits and similar proteins found in animals and some fungal species. The function of this region is not known.
SnoaL-like domain 5 (SnoaL_5)
Type: Domain

This entry contains a large number of proteins that share the SnoaL fold. Members of this protein family are predominantly found in bacteria.
Kinase suppressor RAS 1, N-terminal helical hairpin (SAM_KSR1_N)
Type: Domain

Pseudokinases kinase suppressor of Ras 1 and 2 (KSR1/2) are scaffolds that bridge RAF isoforms and their substrate, mitogen-activated protein kinase kinase (MEK). They dimerize with kinase-competent RAFs (ARAF, BRAF and CRAF) to stimulate catalysis allosterically . This entry represents the N-terminal helical hairpin which, together with the SAM-like domain (

) constitutes the N-terminal regulatory region that mediates heterodimerization of BRAF with KSR1. Additionally, MEK binding to the kinase domain of KSR1 asymmetrically drives BRAF-KSR1 heterodimerization, resulting in the concomitant stimulation of BRAF catalytic activity towards free MEK molecules .
Rhomboid-like protein (Rhomboid_2)
Type: Family

This family of proteins is related to the Rhomboid proteins and, thus, is likely to be an intramembrane protein. Proteins in this family are found primarily in actinobacteria.
Copper-binding protein MbnP-like domain (MbnP-like_dom)
Type: Domain

This entry represents a domain found in MbnP from methanobactin producer Methylosinus trichosporium Strain OB3b (

) and similar bacterial proteins. MbnP is a copper-binding protein and may be a methanobactin copper release protein .
Toxin VasX, N-terminal region (VasX_N)
Type: Domain

This entry represents the N-terminal region of the Toxin VasX from Vibrio cholerae. VasX is a toxin secreted by the type VI (T6SS) secretion system that acts on prokaryotic target cells. Acts in conjunction with VasW, an accessory protein to VasX, to compromise the inner membrane of prokaryotic target cells .
Flagellar Assembly Protein A, beta solenoid domain (FapA_b_solenoid)
Type: Repeat

This entry represents the C-terminal β-solenoid domain of FapA (flagellar assembly protein A,

) from Vibrio vulnificus and its homologues. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction [

. This entry shows similarity to

, suggesting a similar functional role.
Flagellar Assembly Protein A , N-terminal region (FapA_N)
Type: Domain

This entry represents an N-terminal region of the FapA protein and its homologues. This region is found in multiple copies in some proteins such as

. Members of this family include FapA (flagellar assembly protein A,

) from Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction .
Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain (AldOxase/xan_DH_MoCoBD2)
Type: Domain

Aldehyde oxidase (AOX

) catalyses the conversion of an aldehyde in the presence of oxygen and water to an acid and hydrogen peroxide. The enzyme is a homodimer, and requires FAD, molybdenum and two 2FE-2S clusters as cofactors. Xanthine dehydrogenase (XDH

) catalyses the hydrogenation of xanthine to urate, and also requires FAD, molybdenum and two 2FE-2S clusters as cofactors. This activity is often found in a bifunctional enzyme with xanthine oxidase (

) activity too. The enzyme can be converted from the dehydrogenase form to the oxidase form irreversibly by proteolysis or reversibly through oxidation of sulfhydryl groups .

The aldehyde oxido-reductase (Mop) from the sulphate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas is a homodimer of 907 amino acid residues subunits and is a member of the xanthine oxidase family. The protein contains a molybdopterin cofactor (Mo-co) and two different [2Fe-2S] centres. It is folded into four domains of which the first two bind the iron sulphur centres and the last two are involved in Mo-co binding. Mo-co is a molybdenum molybdopterin cytosine dinucleotide. Molybdopterin forms a tricyclic system with the pterin bicycle annealed to a pyran ring. The molybdopterin dinucleotide is deeply buried in the protein. The cis-dithiolene group of the pyran ring binds the molybdenum, which is coordinated by three more (oxygen) ligands .

This entry represents the second molybdopterin cofactor (Mo-Co) binding domain .
SLM1/RGC1-like, BAR-like domain (BAR_4)
Type: Domain

This entry represents a BAR-like domain found in a variety of fungal proteins, including SLM1/2 and RGC1/2, which are structurally related.
SLM1/RGC1-like, PH domain (SLM1/RGC1-like_PH)
Type: Domain

This entry represents a PH domain found in a variety of fungal proteins, including SLM1/2 and RGC1/2 . This domain is known to bind phosphatidylinositides, however, in RGC1/2 (also known as Ask10 and Ypr115w, respectively) this domain is interrupted by long insertions which suggests that they bind different ligands .
ABC-three component systems, C-terminal domain 3 (ABC-3C_CTD3)
Type: Domain

C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminal of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serves as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector .
Putative carbonic anhydrase (Pro_CA_2)
Type: Family

This entry represents a family of proteins that are likely to be prokaryotic carbonic anhydrase enzymes related to

. This family of proteins is found in bacteria and archaea.