SII-SWORD/CoKE huggingface dataset:
Conserved virulence factor B, third S1 domain (CvfB_S1_3rd)
Type: Domain

This domain is found in the virulence regulatory factor CvfB from Streptococcus pneumoniae and in similar proteins predominantly found in Firmicutes. CvfB is composed of three consecutive S1 RNA-binding domains and a winged-helix (WH) domain (Pfam:PF17783). This entry represents the third S1 domain, an RNA-binding module that adopts the typical S1 fold that consists of a five-stranded, antiparallel β-sheet forming a β-barrel .
Conserved virulence factor B, second S1 domain (CvfB_S1_2nd)
Type: Domain

Conserved virulence factor B (CvfB) is a conserved regulatory protein important for the virulence of Staphylococcus aureus . This entry represents the second of three S1 OB-fold domains.
SAM domain-containing protein 1-like, WH domain (SAMD1-like_WH)
Type: Domain

This entry represents a novel distinct group of WH domains .

SAM domain-containing protein 1 (SAMD1, also known as Atherin) is an unmethylated CpG island (CGI)-binding protein that acts as a repressive chromatin regulator. It consists of a C-terminal SAM domain (

), a central unstructured region and an atypical winged helix N-terminal domain that directly recognises unmethylated CpG-containing DNA. This domain has also been found in the transcriptional regulators KAT6A, KAT6B, and ZMYND11 which were grouped together as a novel class of WH domains (represented here).
CusS-like sensor domain (CusS-like_sensor)
Type: Domain

This entry represents a periplasmic sensor domain found in CusS from E. coli and similar sequences. The overall structure of the domain shows a PAS-like topology.
WDHD1/CFT4, helical bundle (WDHD1/CFT4_hel)
Type: Domain

This domain is found at the C-terminal end of DNA polymerase alpha-binding protein CTF4 from Baker's yeast and its homologue MCL1 from budding yeast, while in its human orthologue WDHD1 it is found before the HMG box domain at the C-terminal. This domain folds into a helical extension that is linked to the β-propeller domain (

) which together form the SepB domain described in . The helical bundle protrudes from one face of the disk-shaped trimer formed by the protein. It is essential for binding of dynamic partner proteins, such as Pol alpha-primase .

WDHD1 is an adaptor molecule crucial for DNA replication . It is a core replisome component that acts as a replication initiation factor. It binds directly to the CMG complex and functions as a hub to recruit additional proteins to the replication fork .

CTF4 is an accessory factor for DNA replication that plays a role in accurately duplicating the genome in vivo .
Switch activating protein 1, N-terminal domain (Sap1_N)
Type: Domain

This entry represents the N-terminal DNA-binding domain of Sap1 and closely related proteins from Schizosaccharomyces . Sap1 is known to bind to sequences required for mating-type switching. It binds to DNA origins during cell growth cycles, preferentially to a DNA sequence of 5'-(A/T) n (C/G)(A/T)9-10(G/C)(A/T)n -3' (n>1).
Acyloxyacyl hydrolase, N-terminal domain (AOAH_Saposin_N)
Type: Domain

This entry represents a saposin-like domain found at the N-terminal of some SGNH hydrolase enzymes such as Acyloxyacyl hydrolase (AOAH). In this enzyme, the substrate's lipid moiety is accommodated in a large hydrophobic pocket formed by the saposin and catalytic domains with a secondary acyl chain inserted into a narrow lateral hydrophobic tunnel at the active site .
Spindle assembly abnormal protein 5, implico domain (Sas-5-like_implico)
Type: Domain

This entry represents the implico domain found in Spindle assembly abnormal protein 5 from Caenorhabditis elegans (Sas-5) and related proteins from Caenorhabditis species. Sas-5 is essential for daughter-centriole formation. This protein is composed of two independent domains, a coiled-coil domain that is followed by the implico domain. The implico domain consists of three α-helices and adopt a globular dimeric structure .
BTB/POZ domain-containing protein KCTD1/15-like, C-terminal domain (KCTD1-15-like_C)
Type: Domain

This entry represents the C-terminal domain of BTB/POZ domain-containing proteins 1 and 15 (KCTD1/15), characterised by β-sheets surrounded by α-helices (

) . Structural similarities of the C-terminal domain of KCTD proteins allowed their classification in clades and subclades described in . This domain is also found in similar animal proteins.
Reovirus core-spike protein lambda-2-like, N-terminal domain (Reovirus_L2_N)
Type: Domain

Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts . It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top . This entry represents the N-terminal domain which adopts an α/β topology.
Reovirus core-spike protein lambda-2-like, second methyltransferase domain (Reovirus_L2_MT2)
Type: Domain

Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts . It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the second methyltransferase domain (MT2), which catalyses the last reaction, 2'O-methylation .
Reovirus core-spike protein lambda-2-like, first methyltransferase domain (Reovirus_L2_MT1)
Type: Domain

Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts . It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the first methyltransferase (MT1) domain which adds a methyl group to the N7 of the guanosine added by the GTase .
BTB/POZ domain-containing protein KCTD1, BTB/POZ domain (BTB_POZ_KCTD1)
Type: Domain

This entry represents the BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in the human potassium channel tetramerization domain-containing protein 1 (KCTD1) (

,

) and similar sequences from vertebrates. This domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerisation or heterodimerisation. KCTD family BTB domains can adopt a wide range of oligomerisation geometries, including homodimerisation, tetramerisation, and pentamerisation. The KCTD1 BTB domains form pentamers .

KCTD1 is a nuclear BTB/POZ domain-containing protein that acts as a transcriptional repressor and mediates protein-protein interactions through a BTB domain. It represses the transcriptional activity of AP-2 family members, including TFAP2A, TFAP2B and TFAP2C to various extent. It also functions as a novel inhibitor of the Wnt signalling pathway. Mutations in KCTD1 cause scalp-ear-nipple (SEN) syndrome .
Spindle assembly abnormal protein 6, helical domain (Sas-6_helical)
Type: Domain

This entry represents a domain found in Spindle assembly abnormal protein 6 from Caenorhabditis elegans (Sas-6) and related proteins from Caenorhabditis species. Sas-6 is essential for centriole formation. This domain is C-terminal to

and adopts an α-helical conformation .
Reovirus core-spike protein lambda-2-like, GTase domain (Reovirus_L2_GTase)
Type: Domain

Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts . It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the second domain, which contains the nucleotide-binding histidine triad (HIT)-like motif from the GTase (guanylyltransferase) domain .
Reovirus core-spike protein lambda-2-like, 7th domain (Reovirus_L2_7th)
Type: Domain

Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts . It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top.

This entry represents the seventh domain which, together with the sixth (

) and eighth (

) domains forms a three-domain flap at the top of the turret, that may serve as a gate to retard exit of the 5' terminus of the mRNA . This domain has a Ig-like fold, resembling the C region of an antibody light chain .
Reovirus core-spike protein lambda-2-like, 6th domain (Reovirus_L2_6th)
Type: Domain

Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts . It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the sixth domain which, together with the seventh and eighth (

) domains forms a three-domain flap at the top of the turret, that may serve as a gate to retard exit of the 5' terminus of the mRNA . This domain has a Ig-like fold, resembling the V of an antibody light chain .
Reovirus core-spike protein lambda-2-like, ferredoxin-like domain (Reovirus_L2_4th)
Type: Domain

Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts . It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the fourth domain, which adopts a ferredoxin-like fold consisting of four β-strands protected by α-helices that probably functions as a structural support for the three enzymatic domains (two methyltransferases and GTase domains) .
Reovirus VP3 protein, bridge domain (Reov_VP3_bridge)
Type: Domain

Cytoplasmic polyhedrosis virus (CPV) has a turreted single-layer capsid consisting of 12 pentameric turrets on the five-fold vertices. Each turret has one Turret protein (TP), also known as VP3 (

), which shows a polyhedrin-binding domain (PBD), a guanylyltransferase (GTase) domain (

), two methylase domains (

and

) and a bridge domain (this entry), which has two discontinuous regions .
Reovirus VP3 protein, Methyltransferase domain 2 (Reov_VP3_MTase2)
Type: Domain

Cytoplasmic polyhedrosis virus (CPV) has a turreted single-layer capsid consisting of 12 pentameric turrets on the five-fold vertices. Each turret has one Turret protein (TP), also known as VP3 (

), which shows a polyhedrin-binding domain (PBD), a guanylyltransferase (GTase) domain (

), two methyltransferase domains and a bridge domain (

). This entry represents the second methyltransferase domain, which is found at the C-terminal end of the protein .
Reovirus VP3 protein, Methyltransferase domain 1 (Reov_VP3_MTase1)
Type: Domain

Cytoplasmic polyhedrosis virus (CPV) has a turreted single-layer capsid consisting of 12 pentameric turrets on the five-fold vertices. Each turret has one Turret protein (TP), also known as VP3 (

), which shows a polyhedrin-binding domain (PBD), a guanylyltransferase (GTase) domain (

), two methyltransferase domains and a bridge domain (

). This entry represents the first methyltransferase domain (MTase-1), which has the small brace domain inserted on it .
Reovirus VP3 protein, guanylyltransferase (Reov_VP3_GTase)
Type: Domain

This domain family is found at the N-terminal end of Turret protein (TP), also known as VP3 (

), from Reovirus. This guanylyltransferase (GTase) domain, responsible for the catalysis of the first step of RNA capping, consists of two subdomains, which form a deep and narrow cleft. This domain is rich in β-strands and adopts a pentameric assembly .
KNL (Kinetochore null) Binding Protein 5 (Kbp-5)
Type: Family

This entry represents a group of proteins from Caenorhabditis species, including KNL (Kinetochore null) Binding Protein 5 (Kbp-5) from C. elegans (

), which interacts with KNL-1 and is thought to be homologous to human Zwint and yeast Kre28 . Proteins in this family are part of the kinetochore network involved in chromosome segregation. Unlike its homologue Kre28, Kbp-5 has not essential mitotic function.
Cohesin subunit SCC3, C-terminal domain (SCC3_C)
Type: Domain

This domain is found at the C-terminal of Cohesin subunit SCC3 from Saccharomyces cerevisiae and similar proteins from yeasts. SCC3 is a component of cohesin complex, a complex required for the cohesion of sister chromatids after DNA replication. This domain is is composed of a continuously twisted tandem array of antiparallel α-helices resembling tandem HEAT repeats. It binds to two small sections within Scc1, the other component of the complex .
Katanin p60 ATPase-containing subunit A1, MIT domain (KATNA1_MIT)
Type: Domain

Katanin is an ATP-dependent microtubule severing protein composed of 60kDa (katanin-p60) and 80kDa (katanin-p80) subunits (KATNA1 and KATNB1, respectively) . In mammals, there are two additional A-like subunits (KATNAL1 and KATNAL2) and one additional B-like subunit (KATNBL1) . KATNA1 has the enzymatic activity for microtubule severing and plays a key role in cytoskeletal reorganisation, while KATNB is the regulatory subunit. Formation of the katanin A/B heterodimer is mediated by the N-terminal Microtubule Interacting and Trafficking domain (MIT, represented in this entry) of KATNA1/KATNAL1) and a conserved C-terminal domain of KATNB . This domain is organised in an antiparallel three-helix bundle .
Katanin p60 ATPase-containing subunit A1, AAA domain (KTNA1_AAA_dom)
Type: Domain

This entry represents the AAA domain of human Katanin p60 ATPase-containing subunit A1 (KATNA1) and similar sequences from animals.

Katanin p60 ATPase-containing subunit A1 (KTNA1) is the catalytic subunit of the Katanin complex which is severs microtubules in an ATP-dependent manner, and is implicated in multiple aspects of microtubule dynamics. In addition to the p60 catalytic ATPase subunit, Katanin contains an accessory subunit (p80 or p80-like). The microtubule-severing activity of the ATPase is essential for female meiotic spindle assembly, and male gamete production; and the katanin complex severing microtubules is under tight regulation during the transition from the meiotic to mitotic stage to allow proper embryogenesis. This group of proteins belongs to the RecA-like NTPase family .
SdbC, C-terminal domain (SdbC_C)
Type: Domain

This entry represents a domain found at the C-terminal of the SdbC protein from Legionella pneumophila and related proteins from Legionella species. SdbC protein is thought to be a virulence factor or effector of the pathogen . The structure of this domain suggests that this part of the protein forms a dimer of dimers (

). This domain consists mainly of β-strands that pack with a neighbouring chain to form a β-barrel structure. Two of these barrels pack side by side to form a dimer that is hold by the C-terminal β-strands of each domain.
CSS_CxxC domain (CSS_CxxC)
Type: Domain

This is a periplasmic sensor domain found at the N-terminal of c-di-GMP phosphodiesterases, which is a variation of the CSS motif sensor

. This domain, apart of the CSS motif, has an additional conserved CxxC motif, which presumably broaden its redox-sensing palette. It has been found in Shewanella spp. and members of Altermonadales, and Vibrionales .
Lysine-specific demethylase 5, C-terminal helical domain (KDM5_C-hel)
Type: Domain

This entry represents the C-terminal helical domain from Lysine-specific demethylase 5A-D (KDM5A-D) and similar eukaryotic sequences. This helical domain is located C-terminal to the Jumonji C (JmjC) domain (

), which gives it this name, and N-terminal to the C5HC2 zinc finger motif (

) .
Mediator of RNA polymerase II transcription subunit 16 , central helical bridge (MED16_bridge)
Type: Domain

This entry represents the central helical bridge domain of human Mediator of RNA polymerase II transcription subunit 16 (MED16) and similar proteins from animals. MED16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression .
Midasin, lid domain 4 (MDN1_AAA_lid_4)
Type: Domain

Mdn1 is an essential AAA (ATPase associated with various activities) protein that removes assembly factors from distinct precursors of the ribosomal 60S subunit . This entry represents an AAA domain lid domain.
Monodehydroascorbate reductase 3-like, C-terminal domain (MDHAR3-like_C)
Type: Domain

This domain is found at the C-terminal end of Monodehydroascorbate reductase 3 (MDHAR3) from Oryza sativa and similar plant sequences. MDHAR3 transfers an electron directly to its substrate, monodehydroascorbate (MDHA), which binds to its active site pocket. It consists of three domains: an NAD(P)-binding domain, an FAD-binding domain, and a C-terminal domain (this entry) . This domain shows an α-β structure.
Carboxysome Shell Carbonic Anhydrase, N-terminal (CsoSCA_N)
Type: Domain

Carboxysome Shell Carbonic Anhydrase (CsoSCA) is a bacterial carbonic anhydrase localised in the carboxysome, where it converts bicarbonate ions to carbon dioxide for use in carbon fixation. It contains three domains: an N-terminal domain composed primarily of four α-helices; a catalytic domain containing a tightly bound zinc ion and a C-terminal domain with weak structural similarity to the catalytic domain . This entry represents the N-terminal domain .
Carboxysome Shell Carbonic Anhydrase, C-terminal domain (CsoSCA_C)
Type: Domain

Carboxysome Shell Carbonic Anhydrase (CsoSCA) is a bacterial carbonic anhydrase localised in the carboxysome, where it converts bicarbonate ions to carbon dioxide for use in carbon fixation. It contains three domains: an N-terminal domain composed primarily of four α-helices (

); a catalytic domain containing a tightly bound zinc ion (

) and a C-terminal domain with weak structural similarity to the catalytic domain . This entry represents the C-terminal domain which consists of a central five-stranded mixed β-sheet with two helices flanking one side of the sheet and one helix flanking the other side and lacks all the necessary zinc ligand residues .
COP9 signalosome complex subunit 3, C-terminal helix (CSN3_C)
Type: Domain

This domain is found in COP9 signalosome complex subunit 3 from humans (CSN3) and similar proteins predominantly found in vertebrates. CSN3 is a component of the eight-subunit COP9 signalosome complex (CSN), which inactivate Cullin-RING E3 ubiquitin ligases (CRLs) by removing their covalently attached activator, NEDD8. This entry represents the C-terminal helical decoration of this protein .
BRSK1/2-like, UBA domain (BRSK1_2-like_UBA)
Type: Domain

This entry represents a UBA domain found C-terminal to the kinase domain in the brain-specific kinases BRSK1 and BRSK2. It is also found in Serine/threonine kinase SAD-1.

BRSK1 and BRSK2.are AMP-activated protein kinase (AMPK)-related kinases that are highly expressed in mammalian forebrain and crucial for establishing neuronal polarity. BRSK1, also called brain-selective kinase 1, serine/threonine-protein kinase SAD-B, or synapses of Amphids Defective homologue 1 (SAD1 homologue), is associated with synaptic vesicles and is tightly associated with the presynaptic cytomatrix in nerve terminals. It can regulate neurotransmitter release presynaptically. BRSK2, also called brain-selective kinase 2, serine/threonine-protein kinase 29, or serine/threonine-protein kinase SAD-A is an AMP-activated protein kinase (AMPK)-related kinase exclusively expressed in brain and pancreas. It plays an essential role in neuronal polarisation. It interacts with CDK-related protein kinase PCTAIRE1, a kinase involved in neurite outgrowth and neurotransmitter release, and further negatively regulates glucose-stimulated insulin secretion (GSIS) in pancreatic beta-cells through activation of p21-activated kinase-1 (PAK1). BRSK2 also regulates cell-cycle progression controlled by APC/C (Cdh1) through the ubiquitin-proteasome pathway. Moreover, BRSK2 is regulated by endoplasmic reticulum (ER) stress in protein level and involved in ER stress-induced apoptosis. Both BRSK1 and BRSK2 contain an N-terminal protein kinase catalytic domain

followed by an ubiquitin-associated (UBA) domain (this entry) .
Short chain dehydrogenase-like, proteobacteria (SDR-like_proteobact)
Type: Domain

This family of uncharacterised proteins from proteobacteria appear to be related to other short-chain dehydrogenase enzymes. They are rather short having a Rossmann fold domain which consists of only four β-strands. Proteins in this family are primarily found in Proteobacteria.
COP9 signalosome complex subunit 1, C-terminal helix (CSN1_C)
Type: Domain

This is the C-terminal helix from COP9 signalosome complex subunit 1 from higher eukaryotes, an essential component of the COP9 signalosome complex (CSN), which involved in various cellular and developmental processes .
Exocyst complex component Sec10, N-terminal (Sec10_N)
Type: Domain

This entry contains the Sec10 component of the eukaryotic 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. It is also involved in cell polarisation, primary ciliogenesis, cytokinesis, pathogen invasion, tumorigenesis and metastasis .

The exocyst is a member of the Complex Associated with Tethering Containing Helical Rods (CATCHRs) which also includes DSL1, COG and GARP complexes, evolutionary related. They share structural features comprising α-helical bundles towards the C-terminal and coiled-coil regions at the N-terminal.

This entry represents the N-terminal coiled-coil region (also referred to as CorEx motif) of Sec10 and its homologues from animals ECOC5 (Exocyst complex component 5), which participates in the central pairwise interactions by forming an intact antiparallel 'zipper' which Sec15 subunit. Sec10-Sec15 CorEx motifs interact with Exo70-Exo84 dimers and form a four-helical bundle .
Exosome complex component CSL4, N-terminal domain (CSL4_N)
Type: Domain

This domain is found at the N-terminal end of Exosome complex component CSL4 from Saccharomyces cerevisiae, a non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events .
Exocyst complex component Sec10-like, alpha-helical bundle (Sec10_HB)
Type: Domain

This entry contains the Sec10 component (approximately 650 residues long) of the eukaryotic 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. It is also involved in cell polarisation, primary ciliogenesis, cytokinesis, pathogen invasion, tumorigenesis and metastasis .

The exocyst is a member of the Complex Associated with Tethering Containing Helical Rods (CATCHRs) which also includes DSL1, COG and GARP complexes, evolutionary related. They share structural features comprising α-helical bundles towards the C-terminal and coiled-coil regions at the N-terminal.

This entry represents the α-helical bundles of Sec10 and related proteins, like Recyclin-1 which is involved in recycling plasma membrane proteins internalised by endocytosis and Pof6, that together with skp1, is essential for septum processing and cell separation .