SII-SWORD/CoKE huggingface dataset:
Cation channel sperm-associated targeting subunit tau, C2 domain (CTSRT_C2)
Type: Domain

This entry represents the C2 domain of CTSRT.

Cation channel sperm-associated targeting subunit tau (CTSRT, also known as Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 11 and C2 calcium-dependent domain-containing protein 6) has been identified in mice as an auxiliary component of the CatSper complex, which is involved in sperm cell hyperactivation. Sperm cell hyperactivation is required for sperm motility, essential late in the preparation of sperm for fertilization . This protein is key for CatSper flagellar targeting and trafficking into the quadrilinear nanodomains as it links the channel-carrying vesicles and motor proteins in elongating flagella.
Hikeshi-like, C-terminal domain (Hikeshi-like_C)
Type: Domain

This domain is found at the C-terminal of Hikeshi from humans and its orthologues OPI10 from yeast and arthropods. Hikeshi is an specific nuclear import carrier for HSP70 proteins following heat-shock stress, which is required to protect cells from heat-shock damages. The intrinsically flexible C-terminal domain is responsible for the asymmetric dimeric conformation adopted by the protein, which seems to be an important regulator of Hsp70 binding. It shows three α-helices and a short β-strand in a coiled-coil-like configuration .
Transposable element P transposase-like, RNase H domain, N-terminal (TNP-like_RNaseH_N)
Type: Domain

This entry represents the N-terminal segment of the RNase H domain of Transposable element P transposase (TNP) from Drosophila melanogaster and its homologue from human, DNA transposase THAP9. The catalytic RNase H domain in these proteins is interrupted by the GTP-binding insertion domain (GBD) . The C-terminal segment of the RNase H domain is represented in

.

TNP specifically mediates transposition of P-elements, being involved in both precise and imprecise excision. It has unique features such as the requirement for a guanosine triphosphate cofactor and the generation of long staggered DNA breaks during transposition. TNP structure revealed that it consists of several domains: THAP at the N-terminal, followed by a dimerisation domain, a HTH domain, the catalytic RNase H domain is interrupted by a GTP-binding insertion domain (GBD) and a C-terminal one . The HTH, GBD and C-terminal domains are involved in protein-DNA interactions.

THAP9 specifically recognises the bipartite 5'-TXXGGGX(A/T)-3' consensus motif and mediates transposition .
Transposable element P transposase-like, GTP-binding insertion domain (TNP-like_GBD)
Type: Domain

This entry represents a GTP-binding insertion domain (GBD) from Transposable element P transposase from Drosophila melanogaster (TNP) and its human homologue, DNA transposase THAP9 . This domain is inserted in the RNaseH domain and adopts a mostly α-helical fold, similar to that in Hermes, Tn5 or RAG1 proteins. This domain is involved in protein-DNA interactions .

TNP specifically mediates transposition of P-elements, being involved in both precise and imprecise excision. It has unique features such as the requirement for a guanosine triphosphate cofactor and the generation of long staggered DNA breaks during transposition. TNP structure revealed that it consists of several domains: THAP at the N-terminal, followed by a dimerisation domain, a HTH domain, the catalytic RNase H domain is interrupted by a GTP-binding insertion domain (GBD) and a C-terminal one . The HTH, GBD and C-terminal domains are involved in protein-DNA interactions.

THAP9 specifically recognises the bipartite 5'-TXXGGGX(A/T)-3' consensus motif and mediates transposition .
Transposable element P transposase-like, RNase H, C-terminal domain (TNP-like_RNaseH_C)
Type: Domain

This domain represents the C-terminal segment of the RNase H domain from Drosophila melanogaster transposable element P transposase (TNP) and its homologue from human, DNA transposase THAP9. The catalytic RNase H domain of these proteins is interrupted by the GTP-binding insertion domain (GBD,

) . The N-terminal segment of the RNase H domain is represented in

.

TNP specifically mediates transposition of P-elements, being involved in both precise and imprecise excision. It has unique features such as the requirement for a guanosine triphosphate cofactor and the generation of long staggered DNA breaks during transposition. TNP structure revealed that it consists of several domains: THAP at the N-terminal, followed by a dimerisation domain, a HTH domain, the catalytic RNase H domain is interrupted by a GTP-binding insertion domain (GBD) and a C-terminal one . The HTH, GBD and C-terminal domains are involved in protein-DNA interactions.

THAP9 specifically recognises the bipartite 5'-TXXGGGX(A/T)-3' consensus motif and mediates transposition .
Conserved oligomeric complex COG6, N-terminal (COG6_N)
Type: Domain

This entry represents the N-terminal coiled-coil region of COG6.

COG6 is a component of the peripheral membrane conserved oligomeric Golgi (COG) complex that is involved in intra-Golgi protein trafficking . COG is located at the cis-Golgi and it is required for normal Golgi morphology and localisation. It regulates tethering of retrograde intra-Golgi vesicles and consists of one octamer comprising two tetramers (COG1-4 and COG5-8) . COG subunits belong to the Complex Associated with Tethering Containing Helical Rods (CATCHRs) family which also includes subunits from the evolutionary related GARP (Golgi-Associated Retrograde Protein), exocyst and Dsl1 complexes. CATCHRs proteins share a structural fold consisting of α-helical bundles in tandem at the C-terminal and a coiled-coil region at the N-terminal .
Conserved Oligomeric Golgi complex subunit 6, C-terminal (COG6_C)
Type: Domain

This entry represents the α-helical bundle found at the C-terminal of COG6.

COG6 is a component of the peripheral membrane conserved oligomeric Golgi (COG) complex that is involved in intra-Golgi protein trafficking . COG is located at the cis-Golgi and it is required for normal Golgi morphology and localisation. It regulates tethering of retrograde intra-Golgi vesicles and consists of one octamer comprising two tetramers (COG1-4 and COG5-8) . COG subunits belong to the Complex Associated with Tethering Containing Helical Rods (CATCHRs) family which also includes subunits from the evolutionary related GARP (Golgi-Associated Retrograde Protein), exocyst and Dsl1 complexes. CATCHRs proteins share a structural fold consisting of α-helical bundles in tandem at the C-terminal and a coiled-coil region at the N-terminal .
ZSWIM4-8, C-terminal (ZSWIM4-8_C)
Type: Domain

This entry represents an α-solenoid structure found at the C-terminal of Zinc finger ZSWIM domain-containing proteins 4/5/6/8 (ZSWIM4/5/6/8).

ZSWIM8 is a substrate recognition component of a SCF-like E3 ubiquitin-protein ligase complex that promotes target-directed microRNA degradation (TDMD), a process that mediates degradation of microRNAs (miRNAs) .

ZSWIM4 has been associated with JAK2 inhibition resistance in breast cancer . ZSWIM5 was reported to suppress the invasion and migration of lung cancer cells by regulating the expression of cyclins and MMPs and may constitute a target for the diagnosis and therapy of non-small cell lung cancer (NSCLC) . ZSWIM6 plays a key role in neuronal development and mutations in this protein causes acromelic frontonasal dysostosis (AFND), an autosomal-dominant severe frontonasal and limb malformation syndrome . In ZSWIM6, this is termed the Sin3-like domain, in which a recurrent de novo missense variant causes AFND .
Zinc finger HIT domain-containing protein 3, C-terminal domain (ZNHIT3_C)
Type: Domain

This domain is found at the C-terminal of Zinc finger HIT domain-containing protein 3 from human (ZNHIT3) (

), a cofactor of the RNA-binding nuclear protein NUFIP1. This domain consists of five α-helices and is responsible for binding to NUFIP1 .
Cell-division protein ZapC, C-terminal (ZapC_C)
Type: Domain

This is the C-terminal domain which contains a pocket with a hydrophobic centre surrounded by conserved basic residues, critical for FtsZ binding . This domain is related to Tudor domains (

), whereas the N-terminal domain of ZapC has similarity to chromo domains (

).

ZapC is one of four FtsZ-binding components of the Z ring in bacteria. Formation of the Z ring on the cytoplasmic surface of the membrane is the starting process for assembly of the cell-division apparatus. It binds directly to the Z ring, and although it is not essential for absolute cell division it contributes to it by enhancing the interactions between the FtsZ protofilaments (or polymers) which aggregate to form the ring conformation in the Z ring .
Cell-division protein ZapC, N-terminal (ZapC_N)
Type: Domain

This entry represents the N-terminal α/β region which contains a pocket, termed the N-domain pocket, lined with residues important for ZapC function as an FtsZ bundler . This domain is related to chromo domains (

), whereas the C-terminal domain of ZapC has similarity to Tudor domains (

).

ZapC is one of four FtsZ-binding components of the Z ring in bacteria. Formation of the Z ring on the cytoplasmic surface of the membrane is the starting process for assembly of the cell-division apparatus. It binds directly to the Z ring, and although it is not essential for absolute cell division it contributes to it by enhancing the interactions between the FtsZ protofilaments (or polymers) which aggregate to form the ring conformation in the Z ring .
YuA phage, Gp49-like (YuA_Gp49-like)
Type: Family

This entry includes proteins from tailed bacteriophages such as Pseudomonas phage YuA. Gp49 shows an α-β fold. Its function is unknown.
YtxK-like, N-terminal helical domain (YtxK-like_N)
Type: Domain

This entry represents the N-terminal helical domain found in YtxK from B. subtilis (

), which is a restriction-modification system methylation subunit. Homologues of YtxK are primarily found in Firmicutes.
Inner membrane protein YqiJ, N-terminal domain (YqiJ_N)
Type: Domain

This entry represents a presumed helical domain found at the N terminus of several bacterial proteins, including the inner membrane protein YqiJ from E. coli (

), whose function is not clear.
TEX55, dimerization/docking domain (TEX55_DD)
Type: Domain

TEX55, also called testis-specific conserved cAMP-dependent type II PK-anchoring protein (TSCPA), is a putative A-kinase anchoring protein (AKAP) that is dispensable for male fertility. It contains a C-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1 .
Biogenesis factor required for ATP synthase 1-like, C-terminal domain (BFA1-like_C)
Type: Domain

This domain is predominantly found at the C-terminal end of proteins from cyanobacteria and plants, including Biogenesis factor required for ATP synthase 1 (BFA1,

) from Arabidopsis thaliana. BFA1 promotes the assembly of the CF1 subcomplex of the chloroplast ATP synthase by specifically interacting with the gamma and beta subunits. This domain consists of ten β-sheets and one α-helix forming a typical β-barrel, which locates perpendicularly to

.
Rad26-like, C-terminal domain (Rad26-like_C)
Type: Domain

This domain is found at the C-terminal end of Rad26 from Myceliophthora thermophila (

), a functional subunit of the Rad3-Rad26 complex that is responsible for bringing the kinase to sites of DNA damage. This domain consists of the last three helices in the structure. Together with the flexible C-terminal kinase-docking motif it plays a role in the binding of Rad3 .
Rad26-like, N-terminal domain (Rad26-like_N)
Type: Domain

This domain is found at the N-terminal end of Rad26 from Myceliophthora thermophila (

), a functional subunit of the Rad3-Rad26 complex that is responsible for bringing the kinase to sites of DNA damage. This domain consists of two α-helices that are arranged perpendicular to each other with an extended loop region in between. This coiled-coil domain is well-conserved in Rad26 orthologues. It seems to play a role in the formation of dimers .
NAD-specific glutamate dehydrogenase, C-terminal (GDH_C)
Type: Domain

Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia . The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises ACT-like and PAS-type domains which could act as metabolic sensors for allosteric regulation .

This entry represents the helical C-terminal domain.
BCAS3, WD40 domain (BCAS3_WD40)
Type: Domain

This is the WD40 repeat domain of BCAS3, which directly binds phosphatidylinositol-3-phosphate . This domain is also found in ATG18-like proteins from Arabidopsis.

BCAS3 microtubule associated cell migration factor (BCAS3, also known as Rhudira in mice) is involved in angiogenesis and metastasis . It participates in the regulation of cell polarity and directional endothelial cell migration by mediating both the activation and recruitment of CDC42 and and the reorganisation of the actin cytoskeleton at the cell leading edge . BCAS3 plays a regulatory role in autophagic activity; it forms a complex with PHAF1 (C16orf70) which associates with the preautophagosomal structure during both non-selective and selective autophagy .
Tripeptidyl-peptidase II, first Ig-like domain (TPPII_Ig-like-1)
Type: Domain

Tripeptidyl peptidase II (TPPII) is a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides. This protein adopts a dimeric assembly. Each monomer is organised into three main parts: the N-terminal subtilisine-like domain (

) a central domain and C-terminal domain (

). The central domain can be subdivided into two Ig-like domains and a GBD-like domain (

). This entry represents the first Ig-like domain, while

represents the second one .
Tripeptidyl-peptidase II, galactose-binding domain-like (TPPII_GBD)
Type: Domain

Tripeptidyl peptidase II (TPP II) is a large eukaryotic protease that acts downstream of the 26S proteasome and releases N-terminal tripeptides from polypeptides . It consists of three main parts: the N-terminal subtilisin-like domain (

), a central domain and a C-terminal domain (

) . According to the structures, the central domain can be subdivided into two Ig-like domains (

and

) and a galactose-binding domain-like (GBD). This entry represents the GBD segment of TPPII central domain .
ARC105/Med15 mediator subunit, central domain (Med15_central)
Type: Domain

This domain is found centrally located in the Med15 subunit of the ARC-Mediator co-activator complex (which is also known as ARC105) and in similar animal proteins.

The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, MED15 is a critical transducer of gene activation signals that control early metazoan development .

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.
ARC105/Med15 mediator subunit, C-terminal domain (Med15_C)
Type: Domain

This domain is found at the C-terminal of the Med15 subunit of the ARC-Mediator co-activator. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. This domain is structurally similar to the RWD domain.
T-box transcription factor 2/3, repressor domain (TBX2_3_RD)
Type: Domain

This entry represents the repressor domain (RD) found at the C-terminal of T-box transcription factors 2 and 3 (TBX2 and TBX3), which are homologous . T-box genes are highly conserved and encode transcription factors that are involved in morphogenesis and organogenesis of both invertebrates and vertebrates . However, TBX2 is strongly re-expressed in adults which suggests a role in non-developmental processes .
Tail fibre protein gp37, trimerization region (Gp37_trimer)
Type: Domain

This entry represents part of the phage tail fibre. In T-even phages, gp37 and gp38 are components of the tail fibre that are critical for phage-host interaction . This region is also found in similar proteins from tailed bacteriophages and proteobacterial prophages.
Predicted membrane protein YciQ-like, C-terminal domain (YciQ-like_C)
Type: Domain

This domain, found in various hypothetical prokaryotic proteins, including the predicted membrane protein YciQ from Escherichia coli, has no known function. This domain is located C-terminal to a domain of unknown function (DUF2207,

).
Long-tail fiber proximal subunit, trimerization domain (Gp34_trimer)
Type: Domain

The long tail fibers of bacteriophage T4 consist of rigid proximal and distal parts, connected by a hinge region. The proximal half- fiber is formed by a parallel homo-trimer of the Long-tail fiber proximal subunit Gp34. This entry represents a region of the C-terminal domain, which forms a long triple β-helix made up of parallel β-strands and is responsible for trimerisation .
Long-tail fiber proximal subunit domain (Gp34_dom)
Type: Domain

This domain is found at the C-terminal end of Long-tail fiber proximal subunit from Bacteriophage T4 (Gp34), a structural component of the proximal-half of the long-tail fiber. This protein adopts a trimeric configuration. This domain shows a core antiparallel β-sheet .
Exosome RNA helicase MTR4-like, stalk (MTR4-like_stalk)
Type: Domain

This entry represents the helical stalk found at the N-terminal of KOW β-barrel from MTR4 . This entry also includes Ski2-like helicases which have an overall similar structure to MTR4 proteins. However, Ski2 from yeast does not have the KOW motif and the β-barrel is tightly packed against the helical stalk .

Exosome RNA helicase Mtr4 is a essential RNA helicase, and is an exosome-activating cofactor. It functions together with the nuclear exosome being involved in processing of structured RNAs, including snRNAs and snoRNAs. It also plays a role in nuclear RNA surveillance pathways involving the so-called TRAMP complex . It contains an arch domain, required for proper 5.8S rRNA processing, and appears to function independently of canonical helicase activity . The arch domain comprises an helical stalk/elbow that flanks a KOW module which adopts a β-barrel fold .
Fatty acid kinase subunit A-like, middle domain (FakA-like_M)
Type: Domain

This domain is found in fatty acid kinase subunit A (FakA) from a bacterial fatty acid kinase (Fak) system and it is localised between

and

. Two major human pathogens, Staphylococcus and Streptococcus, use this machinery to scavenge host fatty acids . The Fak complex consists of an ATP-binding subunit FakA, which interacts with varied FakB (fatty acid-binding protein) isoforms, and synthesises acyl-phosphate from extracellular fatty acids . FakA comprises three domains, denoted as FakA_N, FakA_M and FakA_C in of which the middle domain is represented by this entry. It consists of four α-helices, four β-strands and several long loops, containing a zinc finger motif. It shows similarities to the yeast copper chaperone ATX1, a metallochaperone/metal-binding protein.
Glycosyl hydrolase family 31, C-terminal domain (Glyco_hydro_31_C)
Type: Domain

This entry represents the C-terminal β-sandwich domain of proteins that belong to the glycosyl hydrolase 31 family. Glycosyl hydrolases are key enzymes of carbohydrate metabolism. Family 31 comprises of enzymes that are, or similar to, alpha-galactosidases.
Shedu protein SduA, N-terminal (SduA_N)
Type: Domain

This domain is found at the N terminus of Shedu protein SduA (

), the only component of antiviral defence system Shedu. Expression of Shedu in B.subtilis (strain BEST7003) confers resistance to phages phi105, phi29, rho14 and to a lesser extent to SPP1 .
Virus-capping methyltransferase, connector domain (Methyltrans_Mon_CD)
Type: Domain

This entry represents the connector domain (CD) from Mononegavirales single-stranded RNA viral RNA polymerase enzymes (L proteins). This domain flanks the methyltransferase domain (MT,

) and together with the C-terminal domain (

), in conjunction with its phosphoprotein cofactor, likely facilitates the structural rearrangements that appear to coordinate the enzymatic activities during transcription and replication .
Virus-capping methyltransferase, C-terminal domain (Methyltrans_Mon_C)
Type: Domain

This entry represents the C-terminal domain of the Mononegavirales single-stranded RNA viral RNA polymerase enzymes. This region, together with the connector domain (CD,

), flanks the methyltransferase domain (MT) and is likely involved in the structural rearrangements that appear to coordinate the enzymatic activities during transcription and replication .
DUF4438, C-terminal (DUF4438_C)
Type: Domain

This is the C-terminal domain of M_1086 from Thermotoga maritima (

) and related bacterial proteins with unknown function. This domain consists of a partly open β-barrel and a three-stranded antiparallel β-sheet packed on on the barrel wall (

).
SLS1, N-terminal domain (SLS1_N)
Type: Domain

This entry represents the N-terminal helical domain found in the yeast SLS1 protein.

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 .
SLS1, C-terminal domain (SLS1_C)
Type: Domain

This entry represents the C-terminal β-barrel domain found in the SLS1 protein.

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 .
Sporulation protein YpeB, N-terminal (YpeB_N)
Type: Domain

This is the N-terminal region of YpeB, a protein restricted to endospore-forming species in the Firmicutes lineage of bacteria, that have been found in all such species to date except Clostridium perfringens. YpeB and the spore-cortex-lytic enzyme SleB are required for normal germination . This protein is essential in stabilising SleB enzyme in Bacillus spores, and may regulate its activity during germination .