SII-SWORD/CoKE huggingface dataset:
Transcriptional regulatory protein DpiA-like, helix-turn-helix domain (DpiA-like_HTH)
Type: Domain

This entry represents a DNA-binding helix-turn-helix domain found at the C-terminal of the DpiA transcriptional regulator protein and similar bacterial sequences. DpiA is a member of the two-component regulatory system DpiA/DpiB, which is essential for expression of citrate-specific fermentation genes and genes involved in plasmid inheritance .
CggR, N-terminal DNA binding domain (CggR_N)
Type: Domain

The central glycolytic genes repressor (CggR) controls the transcription of the gapA operon encoding five key glycolytic enzymes in Bacillus subtilis. CggR recognises a unique DNA target sequence comprising two direct repeats and fructose-1,6-bisphosphate (FBP) is the inducer that negatively controls this interaction. This entry represents the N-terminal DNA-binding domain .
Protein-tyrosine-phosphatase-like, N-terminal domain (Phosphatase-like_N)
Type: Domain

This domain is found at the N-terminal of a group of bacterial phosphatases and arsenate reductases, including Protein-tyrosine- phosphatase from Corynebacterium glutamicum. This domain, often found associated to

, forms a three-helical bundle that interacts with the active site of the other chain in the dimeric interface .
SidM, N-terminal domain (SidM_N)
Type: Domain

This domain is found in the type IV virulence effector SidM/DrrA from Legionella pneumophila. This protein has dual GEF and GDF activity specifically toward Rab1, a key regulator for endoplasmic reticulum (ER)-to-Golgi vesicle trafficking. SidM consists of an N-terminal helical domain, a Rab1-activation domain (

), and a C-terminal phosphatidylinositol 4-phosphate-binding (P4M) domain (

).

This entry represents the N-terminal domain which is mostly α-helical, having a short two-stranded β-sheet in addition .
SidM, Rab1-activation domain (SidM_Rab1_act)
Type: Domain

This domain is found in the type IV virulence effector SidM/DrrA from Legionella pneumophila and similar sequences from Legionella sp. This protein has dual GEF and GDF activity specifically toward Rab1, a key regulator for endoplasmic reticulum (ER)-to-Golgi vesicle trafficking. SidM consists of an N-terminal helical domain (

), a Rab1-activation domain, and a C-terminal phosphatidylinositol 4-phosphate-binding (P4M) domain (

).

This is the Rab1-activation domain, which strongly interacts with Rab1 switch regions leading to substantial conformational changes on SidM binding. This domain is organised into two layers of α-helices .
Complement factor I, KAZAL domain (CFAI_KAZAL)
Type: Domain

This entry represents the KAZAL domain from CFAI FIMAC domain.

Complement factor I (CFAI) is a trypsin-like serine protease that plays an essential role in regulating the immune response by controlling all complement pathways. It cleaves three peptide bonds in the alpha-chain of C3b and two in the alpha-chain of C4b which inactivate these proteins. It consists of an N-terminal FI and membrane attack domain (FIMAC or Factor I-like modules FIM), a scavenger receptor cysteine-rich (SRCR) domain (

), LDLRA1 and LDLRA2 (

) and a C-terminal catalytic serine protease domain (

) . FIMs are also present in complement proteins C6 and C7, and participate in protein-protein interactions that critical to the progress of a complement-mediated immune response. In CFAI, the FIMAC domain is important for the ability of FI to degrade C4b and C3b . It consists of a small N-terminal FOLN subdomain (

) and a larger C-terminal KAZAL domain.
PROPPIN (PROPPIN)
Type: Family

This entry includes PROPPIN family members, which are β-propellers that bind polyphosphoinositides, conserved from yeast to human. These are PI(3)P sensors that share a β-propeller fold and the presence of an FRRG motif required for phosphoinositide binding and autophagy, playing a key role in autophagosome biogenesis. Four PROPPINs are known in human (WIPI1-4) and three in yeast (Atg18, Atg21 and Hvs2) . EPG6 from C. elegans is an homologue of human WIPI4 .
Complement factor I, FIMAC N-terminal domain (CFAI_FIMAC_N)
Type: Domain

This entry represents the N-terminal region of FIMAC, referred to as FOLN subdomain, whose structure is a truncated form of the epidermal growth factor (EGF) domain .

Complement factor I (CFAI) is a trypsin-like serine protease that plays an essential role in regulating the immune response by controlling all complement pathways. It cleaves three peptide bonds in the alpha-chain of C3b and two in the alpha-chain of C4b which inactivate these proteins. It consists of an N-terminal FI and membrane attack domain (FIMAC or Factor I-like modules FIM), a scavenger receptor cysteine-rich (SRCR) domain (

), LDLRA1 and LDLRA2 (

) and a C-terminal catalytic serine protease domain (

) . FIMs are also present in complement proteins C6 and C7, and participate in protein-protein interactions that critical to the progress of a complement-mediated immune response. In CFAI, the FIMAC domain is important for the ability of FI to degrade C4b and C3b . It consists of a small N-terminal FOLN subdomain (

) and a larger C-terminal KAZAL domain.
26S proteasome regulatory subunit 7-like, OB domain (PRS7-like_OB)
Type: Domain

This entry represents the OB domain from the human 26S proteasome regulatory subunit 7 (PRS7, also known as PSMC2, Rpt1 or MSS1) and similar eukaryotic sequences. This domain mediates interactions with USP14 or Ubp6 .

The human 26S proteasome consists of a 20S core particle and two 19S regulatory particles. PRS7, a component of the 19S proteasome cap, is one of six ATPases of the regulatory particle that form a heterohexameric ring .
Nuclear mitotic apparatus protein 1, N-terminal hook domain (NuMA_N_HOOK)
Type: Domain

Mitotic progression is orchestrated by the microtubule-based motor dynein, which sustains all mitotic spindle functions . During cell division, cytoplasmic dynein acts with the high-molecular-weight complex dynactin and nuclear mitotic apparatus (NuMA) to organize and position the spindle . NuMA contains a hook domain contacting directly LIC1 and LIC2 chains through a conserved hydrophobic patch shared among other Hook adaptors . Hook adaptor proteins, including human Nuclear mitotic apparatus protein 1 (Numa1), share an N-terminal conserved globular hook domain (this entry), which folds as a variant of the helical calponin homology (CH) domain .
Fimbrial protein MyfA/ph 6 antigen (MyfA_PsaA)
Type: Family

This entry represents a family of proteins from Yersinia, including Fimbrial protein MyfA from Yersinia enterocolitica (also known as Myf antigen) and the ph 6 antigen from Yersinia pestis (PsaA, also known as adhesin or antigen 4). MyfA is a major pilus subunit that is expressed only in pathogenic serotypes . PsaA is part of fimbriae, necessary for full virulence . It mediates bacterial attachment to alveolar cells of the lung.
Nuclear mitotic apparatus protein 1, LGN binding domain (NuMA_LGNBD)
Type: Domain

Mitotic progression is orchestrated by the microtubule-based motor dynein, which sustains all mitotic spindle functions . During cell division, cytoplasmic dynein acts with the high-molecular-weight complex dynactin and nuclear mitotic apparatus (NuMA) to organise and position the spindle . NuMA contains a hook domain contacting directly LIC1 and LIC2 chains through a conserved hydrophobic patch shared among other Hook adaptors . Hook adaptor proteins, including human Nuclear mitotic apparatus protein 1 (Numa1), share an N-terminal conserved globular hook domain (

) . NuMA, in complex with LGN, forms NuMA:LGN hetero-hexamers that promote spindle orientation. This entry corresponds to the LGN binding domain (LGNBD) of NuMA. LGN (named for leu-gly-asn repeats) is also known as G protein signalling modulator 2 .
Ski2, beta-barrel domain (Ski2_beta-barrel)
Type: Domain

Ski2 from yeast is an helicase with an overall similar structure to MTR4 proteins. It has an arch domain with an α-helical stalk/elbow (

) that flanks a β-barrel (referred to as the KOW module in MTR4 homologues).

This entry represents the β-barrel of Ski2 and related proteins from Saccharomycetales. This domain does not have the KOW motif and is tightly packed against the α-helical stalk .
Partitivirus capsid protein (CP_partitivirus)
Type: Family

This entry represents a family of proteins from partitivirus, including Capsid protein (CP) from Penicillium stoloniferum virus (

), which associates only with itself in forming capsids, adopting a quasi- symmetrical dimeric fold. 60 dimers associate to form the capsid shell. CP is organized into two domains: the shell domain, which form the continuous capsid, and the arch domain, responsible for the dimeric surface protrusions .
Schlafen, GTPase-like domain (SLFN_GTPase-like)
Type: Domain

This domain is found in groups II and III of Schlafen (SLFN) proteins, which follows the AlbA_2 domain (

).

In group II, this is the C-terminal domain, while in group III members it localises in the central region, followed by a C-terminal helicase domain (

). This domain has been described as a GTPase-like domain and it contains the SLFN-specific SWADL motif .

SLFN proteins are involved in the control of cell proliferation, induction of immune responses, and the regulation of viral replication. Mouse and human members are regulated by interferons . In SLFN12, this is the C-terminal domain which contains crucial residues for interaction with PDE3A . By analogy with dynamin and MxB, this domain in SLFN12 may contribute to chromatin and actin cytoskeleton interactions, involved in cell differentiation . SLFN proteins share common domains and a high degree of homology, however, they have specific and sometimes, opposing effects in some cancer types .
T26-6p, C-terminal domain (T26-6p_C)
Type: Domain

This domain is found at the C-terminal end of T26-6P, a large protein encoded by a plasmid from the hyperthermophilic archaea Thermococcus. This protein, present in all members of a family of mobile elements, has homologues in archaeal genomes. T26-6p has three domains: two β- sandwich with two sheets made of four antiparallel β-strands (

and

) and a bundle of five α-helices (this entry) . Its function is unknown.
DNA polymerase III subunit delta', AAA+ ATPase lid domain, gammaproteobacteria (HolB_lid-gammaproteobact)
Type: Domain

DNA polymerase III subunit delta' is part of the beta sliding clamp loading complex, which hydrolyses ATP to load the beta clamp onto primed DNA to form the DNA replication pre-initiation complex . It consists of three domains, of which the N-terminal domain contains a nonfunctional nucleotide binding site. This entry represents the lid domain (or domain 2 in ).
Cilia- and flagella-associated protein 69 (CFA69)
Type: Family

Cilia- and flagella-associated protein 69 (CFA69) is required for sperm flagellum assembly/stability. Truncating mutations of this protein induce autosomal-recessive MMAF (multiple morphological abnormalities of the flagella) and primary male infertility . In mice, it regulates the speed of activation and termination of the odour response and, thus, contributes to the robustness of olfactory transduction pathways .
Cilia- and flagella-associated protein 69, ARM repeats domain (CFA69_ARM_dom)
Type: Domain

This entry represents the ARM repeats domain of CFA69.

Cilia- and flagella-associated protein 69 (CFA69) is required for sperm flagellum assembly/stability. Truncating mutations of this protein induce autosomal-recessive MMAF (multiple morphological abnormalities of the flagella) and primary male infertility . In mice, it regulates the speed of activation and termination of the odour response and, thus, contributes to the robustness of olfactory transduction pathways .
Hyaluronate lyase, N-terminal beta-sheet domain (HL_N-beta)
Type: Domain

This entry represents the N-terminal β-sheet domain which adopts a Ig-like fold and may serve as a connection of the α-domain with another structural domain .

Hyaluronate lyase degrades hyaluronan and certain chondroitin sulfates at beta-1,4 glycosidic linkages and constitutes a virulence factor of Streptococcus agalactiae . It consists of three structural domains, an N-terminal β-sheet domain (also referred as to beta1), a middle catalytic α-helical domain (

) and a C-terminal β-sheet domain (beta2,

) .
Ca2+-activated K+ channel Slowpoke-like, C-terminal domain (Slowpoke-like_C)
Type: Domain

This domain is found at the cytoplasmic C terminus of the Drosophila slowpoke K channel (dSlo) (

) and its homologues. This domain is related to the TrkA C-terminal domain (

).

dSlo is a potassium channel activated by both membrane depolarisation or increase in cytosolic Ca2 that mediates export of K+. Its activation dampens the excitatory events that elevate the cytosolic Ca2 concentration and/or depolarise the cell membrane .
S-layer protein SlpA, beta-barrel (SlpA_C)
Type: Domain

This entry represents the β-barrel domain found at the C-terminal of S-layer protein SlpA (

) and similar bacterial S-layer proteins. SlpA plays an important role in the structural organisation and integrity of the S-layer . In Deinococcus radiodurans, SlpA binds the carotenoid deinoxanthin, a strong protective antioxidant specific of this bacterium suggested to be part of the first lane of defence against UV radiation, especially under desiccation .
Tubulin-like CetZ, C-terminal (CetZ_C)
Type: Domain

This is the C-terminal domain of CetZ proteins, which are tubulin-like proteins involved in control cell shape in archaea and some bacteria . CetZ proteins are related with Tubulin/FtsZ, and has the Tubulin GTPase domain (

) at the N-terminal. This domain has a two-layer α/β structure with an α-helical extension.
Centrosomal protein CEP104, Zn finger domain (CEP104_Znf)
Type: Domain

This entry represents the zinc finger domain of CEP104, which interacts with kinase Nek1 which competes with CP110 . This domain is also found in the uncharacterised protein C40H1.3 from Caenorhabditis elegans.

Centrosomal protein CEP104 localises to the distal end of centrioles that interacts through its N- and C-terminal region, respectively, with the distal end proteins Cep97 and CP110 . It is required for ciliogenesis and for structural integrity at the ciliary tip, being involved in regulating microtubule length in cilia. This is a multidomain protein that consists of an N-terminal all-β domain, a central all α-helical HEAT repeat domain and a C-terminal array of four zinc finger domains .
Centrosomal protein CEP104, N-terminal domain (CEP104_N)
Type: Domain

This is the N-terminal all-β domain of CEP104, which is structurally similar to domains of intraflagellar transport protein 25 (IFT25), DNA repair protein XRCC1 (

) and anaphase-promoting complex APC subunit 10 , which is implicated in Cep97 binding.

Centrosomal protein CEP104 localises to the distal end of centrioles that interacts through its N- and C-terminal region, respectively, with the distal end proteins Cep97 and CP110 . It is required for ciliogenesis and for structural integrity at the ciliary tip, being involved in regulating microtubule length in cilia. This is a multidomain protein that consists of an N-terminal all-β domain, a central all α-helical HEAT repeat domain and a C-terminal array of four zinc finger domains .
PurT, C-terminal (PurT_C)
Type: Domain

Formate-dependent phosphoribosylglycinamide formyltransferase (PurT) is involved in de novo purine biosynthesis. PurT belongs to the ATP-grasp superfamily of enzymes and catalyses the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR) . This entry represents the C-terminal domain which has a rudiment single hybrid motif consisting of a sandwich of half-barrel shaped β-sheets .
Pus10-like, C-terminal (Pus10-like_C)
Type: Domain

This entry represents the C-terminal catalytic domain of tRNA pseudouridine synthase Pus10, conserved in archaea and eukaryotes . In archaea it catalyses the formation of the pseudouridine at positions 54 and 55 in tRNA, while human Pus10 has different functions depending on its subcellular location: it is involved in miRNA processing in the nucleus and acts as a tRNA pseudouridylate synthase in the cytoplasm .
Pus10, N-terminal, eukaryotes (Pus10_N_euk)
Type: Domain

This entry represents the N-terminal domain of eukaryotic tRNA pseudouridine synthase Pus10 . Pus10 has different functions depending on its subcellular location: involved in miRNA processing in the nucleus and acts as a tRNA pseudouridylate synthase in the cytoplasm . This domain functions as an accessory RNA-binding domain regarding the presence of a THUMP domain (

), similarly to other pseudouridine synthases . The N-terminal domain of eukaryotic Pus10 (this entry) is much larger than that of archaeal Pus10 , while both groups of proteins belong to

.
Inner kinetochore subunit AME1 (AME1)
Type: Domain

This entry includes the inner kinetochore subunit AME1 (also known as CEMPU), a protein that is part of the yeast kinetochore, a multiprotein complex that assembles on centromeric DNA and attaches chromosomes to spindle microtubules. This protein is a component of the inner kinetochore COMA complex, which connects centromere-associated proteins and the outer kinetochore .
Inner kinetochore subunit MCM16 (MCM16)
Type: Family

This entry includes the inner kinetochore subunit MCM16 (also known as CENPH), a protein that is part of the yeast kinetochore, a multiprotein complex that assembles on centromeric DNA and attaches chromosomes to spindle microtubules .
Toxin CdiA-like, helical domain (CdiA_helical)
Type: Domain

This entry represents the helical domain of deoxyribonuclease CdiA (also known as CdiA toxin), a toxin of the Contact-dependent growth inhibition (CDI) system . EC869 appears to function as a Zn2-dependent DNAse degrading the genome of target cells.
CCL2-like, lectin domain (CCL2-like_lectin)
Type: Domain

This entry includes CCL2 lectin from Coprinopsis cinerea and similar sequences from fungi. CCL2 is a fruiting body lectin that binds to Fuc-alpha-1,3-modified core N-glycans, which are characteristic for invertebrates but absent from fungi. This protein adopts a β-trefoil fold consisting of three β-β-β-β repeats .
CCDC93, N-terminal domain (CCDC93_N)
Type: Domain

This entry represents the N-terminal helical domain from the CCDC93 protein. This protein is part of the complex termed the CCC complex that is composed of CCDC22, CCDC93 and various COMMD proteins .
SLS1, second KH domain (SLS1_KH2)
Type: Domain

This entry represents the second KH-like domain in the SLS1 protein. The second KH-like domain is more divergent compared to the first KH-like domain.

SLS1 is a fungal protein found bound to the mitochondrial inner-membrane . It reacts physically with fungal Kar2p to promote translocation across the endoplasmic-reticulum membrane. This action seems to be mediated via the promotion of the Sec63p-mediated activation of Kar2p's ATPase activity. This indicates that the Sls1p protein is a GrpE-like protein in the endoplasmic reticulum. In S.cerevisiae, the SLS1 gene (ScSLS1) is not essential but is also involved in ERAD and folding .
Structure-specific endonuclease subunit SLX1, C-terminal domain (SLX1_C)
Type: Domain

This is the RING zinc finger domain of structure-specific endonuclease subunit SLX1 found in eukaryotes.

Slx1 is a catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. It has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA .
Coiled-coil domain-containing protein 138, C-terminal domain (CCDC138_C)
Type: Domain

This is the C-terminal domain of coiled-coil domain-containing protein 138 (CCDC138), which adopts an α-solenoid structure. CCDC138 function is not yet clear. However, it has been localised to basal bodies, suggesting to play a role in centrosomal and ciliary biology .
Coiled-coil-domain-containing protein 138, coiled-coil (CCDC138_CC)
Type: Domain

This is the coiled-coil region of coiled-coil domain-containing protein 138 (CCDC138), whose function is not yet clear. However, it has been localised to basal bodies, suggesting to play a role in centrosomal and ciliary biology .
Prokaryotic cation-chloride cotransporter, second C-terminal subdomain (CCC_C_2nd_subdom)
Type: Domain

This entry includes a group of prokaryotic cation-chloride cotransporters (CCCs), such as the Na-K-Cl cotransporter from Methanosarcina acetivorans (

). These proteins consist of an N-terminal transmembrane transport region (

) followed by a cytoplasmic regulatory domain. The C-terminal domain adopts a compact trapezoid-shaped elongated structure with a mixed α/β fold and can be divided in two structurally related subdomains. This entry represents the second subdomain, which shows a central five-stranded parallel β-sheet and three α-helices that pack on either face of the sheet .
Prokaryotic cation-chloride cotransporter, first C-terminal subdomain (CCC_C_1st_subdom)
Type: Domain

This entry includes a group of prokaryotic cation-chloride cotransporters (CCCs), such as the Na-K-Cl cotransporter from Methanosarcina acetivorans (

). These proteins consist of an N-terminal transmembrane transport region (

) followed by a cytoplasmic regulatory domain. The C-terminal domain adopts a compact trapezoid-shaped elongated structure with a mixed α/β fold and can be divided in two structurally related subdomains. This entry represents the first subdomain, which shows a central five-stranded parallel β-sheet and three α-helices that pack on either face of the sheet .
SMK1 alpha subunit (SMK1_alpha_su)
Type: Domain

This entry represents the alpha subunit of SMK killer toxins that are secreted by several strains of yeasts. SMK toxin is encoded by a single open reading frame of chromosomal DNA (the SMK1 gene) and is translated in the form of a 222 amino acid preprotoxin. This preprotoxin is converted to the alpha and beta heterodimeric mature toxin, with a molecular weight of 14 kDa, through stepwise proteolytic processing.

The killer toxin SMK (salt-mediated killer) acts to kill sensitive strains of yeast. SMK exhibits maximum activity under conditions of acidic pH and high salt concentration. It is composed of two distinct subunits, alpha and beta, which tightly interact with each other under acidic conditions, jointly folding into an ellipsoidal single domain structure belonging to the α/β-sandwich family. SMK assumes a similar folding topology to the fungal killer toxin KP4, forming two left-handed split β/α/β motifs which is rarely found in other toxins; hence, these toxins may be evolutionarily or functionally related . SMK appears to function by associating with the membranes of sensitive cells .
Alpha-amylase SusG, CBM58 domain (SusG_CBM58)
Type: Domain

This entry includes alpha-amylase SusG from Bacteroides thetaiotaomicron (

), a member of the glycoside hydrolase family 13 (GH13). It is located on the outer membrane of the cell, and cleaves starch into oligosaccharides before internalisation for degradation.

Typically, GH13 members show three domains A, B and C. In addition to these, SusG includes the insertion of a unique carbohydrate binding module family 58 (CBM58), represented in this entry, which gives the protein an elongated shape. CBM58 is approximately 120 residues in length and folds into a β-sandwich that adopts an immunoglobulin-like topology with a flat five-stranded antiparallel β-sheet opposing a four-stranded antiparallel β-sheet which features three protruding loops. Y260, W287, and W299 form the starch-binding site .
Pyrrolysine biosynthesis protein PylD, N-terminal domain (PylD_N)
Type: Domain

This domain is found at the N-terminal end of Pyrrolysine biosynthesis protein PylD from Methanosarcina acetivorans, also known as 3-methylornithyl-N6-L-lysine dehydrogenase, a dehydrogenase that catalyses the final step in the biosynthesis of the amino acid pyrrolysine .