SII-SWORD/CoKE huggingface dataset:
Quinohemoprotein amine dehydrogenase, alpha subunit domain IV (QH-AmDH_asu_dom_IV)
Type: Domain

Members of this entry, which are predominantly found in the prokaryotic protein quinohemoprotein amine dehydrogenase, adopt an immunoglobulin-like β-sandwich fold, with seven strands arranged into two β sheets; the fold is possibly related to the immunoglobulin and/or fibronectin type III superfamilies. The precise function of this domain has not, as yet, been defined .
Exotoxin A, binding (Exotox-A_bind)
Type: Domain

This domain is found in Pseudomonas aeruginosa exotoxin A, and is responsible for binding of the toxin to the alpha-2-macroglobulin receptor, with subsequent internalisation into endosomes. It adopts a thirteen-strand antiparallel β jelly roll topology, which belongs to the concanavalin A-like lectins/glucanases fold superfamily .
Exotoxin A, middle domain (Exotox-A_middle_dom)
Type: Domain

This domain, found in Pseudomonas aeruginosa exotoxin A, is responsible for transmembrane targeting of the toxin, as well as transmembrane translocation of the catalytic domain into the cytoplasmic compartment. A furin cleavage site is present within the domain: cleavage generates a 37kDa carboxy-terminal fragment, which includes the enzymatic domain, which is then is translocated into the cytoplasm. It adopts a helical structure, with six α-helices forming a bundle .
BRCA2, OB1 (BRCA2_OB_1)
Type: Domain

BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks . It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein . Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility . BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA) .

This entry represents OB1, which consists of a highly curved five-stranded β-sheet that closes on itself to form a β-barrel. OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome .
BRCA2, OB3 (BRCA2_OB_3)
Type: Domain

BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks . It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein . Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility . BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA) .

This entry represents OB3, which consists of a highly curved five-stranded β-sheet that closes on itself to form a β-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between β1 and β2 and another between β4 and β5, which allows for strong ssDNA binding .
Translation elongation factor SelB, winged helix, type 1 (Elong_fac_SelB-wing-hlx_typ-1)
Type: Domain

This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small β-sheet wing . Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 1".
Translation elongation factor SelB, winged helix, type 2 (Elong_fac_SelB-wing-hlx_typ-2)
Type: Domain

This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small β-sheet wing . Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2".
Elongation factor SelB, fourth winged-helix domain (SelB_WHD4)
Type: Domain

This domain is found in Elongation factor SelB from Moorella thermoacetica (

) and similar bacterial proteins. SelB is a selenocysteine(Sec)-specific elongation factor that brings the selenocysteinyl-tRNA(Sec) to the ribosome. It consists of three EF-Tu-like domains followed by four winged-helix domains (WHD1-4). This entry represents the fourth winged-helix domains (WHD4).

Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognises this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). The SelB C-terminal part comprises the four winged-helix domains that are arranged in tandem into 'L' shape.
Switch protein XOL-1, N-terminal (Xol-1_N)
Type: Domain

This domain, found in sex-determining protein Xol-1, adopts a secondary structure consisting of five α helices and six antiparallel β sheets, in a β-α-β-β-β-α-β-α-α-α-β arrangement. The fold of this family is similar to that found in ribosomal protein S5 domain 2-like . The active site of the enzyme is found at the interface between this domain and the C-terminal GHMP-like domain.
Switch protein XOL-1, GHMP-like (Xol-1_GHMP-like)
Type: Domain

This domain, found in sex-determining protein Xol-1, adopts a secondary structure consisting of five α helices and seven antiparallel β sheets, in a β-α-β-α-α-α-β-β-α-β-β-β arrangement. The fold of this family is structurally similar to that found in the C-terminal domain of GHMP Kinase . The active site of the enzyme is found at the interface between this domain and the N-terminal domain.
ISWI, HAND domain (ISWI_HAND-dom)
Type: Domain

Nucleosome remodelling is an energy-dependent process that alters histone-DNA interactions within nucleosomes, thereby rendering nucleosomal DNA accessible to regulatory factors. The ATPases involved belong to the SWI2/SNF2 subfamily of DEAD/H-helicases, which contain a conserved ATPase domain characterised by seven motifs. Proteins within this family differ with regard to domain organisation, their associated proteins and the remodelling complex in which they reside.
SLIDE domain (SLIDE)
Type: Domain

The SLIDE domain adopts a secondary structure comprising a main core of three α-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb repeats or homeodomains .
Peptide-N-glycosidase F, N-terminal (PngaseF_N)
Type: Domain

This domain adopts an eight-stranded antiparallel β jelly roll configuration, with the β strands arranged into two sheets. It is similar in topology to many viral capsid proteins, as well as lectins and several glucanases. This domain allows the protein to bind sugars and catalyses the complete removal of N-linked oligosaccharide chains from glycoproteins .
Peptide-N-glycosidase F, C-terminal (PngaseF_C)
Type: Domain

This domain adopts an eight-stranded antiparallel β jelly roll configuration, with the β strands arranged into two sheets. It is similar in topology to many viral capsid proteins, as well as lectins and several glucanases. This domain allows the protein to bind sugars and catalyses the complete removal of N-linked oligosaccharide chains from glycoproteins .
Bacteriophage T4, MotA, transcription regulator N-terminal (Phage_T4_MotA_Tscrpt_reg_N)
Type: Domain

Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds . MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the β-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters.

Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely α-helical topology, with five α-helices and a short, two-stranded, β-ribbon. Four α helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 .
DNA polymerase III, delta subunit, C-terminal (DNA_pol_III_delta_C)
Type: Domain

This entry represents a domain which is predominantly found in prokaryotic DNA polymerase III, assuming an α helical structure with a core of five α helices and an additional small helix. This domain is essential for the formation of the polymerase clamp loader .
Sliding clamp, C-terminal (Sliding_clamp_C)
Type: Domain

This domain is essential for the interaction of the sliding clamp (also known as gp45) with the corresponding polymerase. It adopts a DNA clamp fold, consisting of two α-helices and two β-sheets - the fold is duplicated and has internal pseudo two-fold symmetry .
Antimicrobial protein MiAMP1 (Antimicrobial_MiAMP1)
Type: Family

MiAMP1 is a highly basic protein from the nut kernel of Macadamia integrifolia (Macadamia nut), which inhibits the growth of several microbial plant pathogens in vitro while having no effect on mammalian or plant cells. It consists of eight β-strands which are arranged in two Greek key motifs. These Greek key motifs then associate to form a Greek key β-barrel .
Galactose oxidase-like, Early set domain (GO-like_E_set)
Type: Domain

E or 'early' set domains are associated with the catalytic domain of galactose oxidase at the C-terminal end. Galactose oxidase is an extracellular monomeric enzyme which catalyzes the stereospecific oxidation of a broad range of primary alcohol substrates, and possesses a unique mononuclear copper site essential for catalyzing a two-electron transfer reaction during the oxidation of primary alcohols to corresponding aldehydes. The second redox active centre necessary for the reaction was found to be situated at a tyrosine residue. The C-terminal domain of galactose oxidase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end, and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase, among others .
Secreted effector protein SptP, N-terminal domain (SptP_N)
Type: Domain

The domain is found in the Salmonella effector protein SptP, which interacts with SicP chaperone dimers mainly through four regions of its chaperone-binding domain. The structure of the SptP-SicP complex contains four molecules of SicP, aligned in a linear fashion and arranged in two sets of tightly bound homodimers that bind two SptP molecules. The SicP homodimers do not interact with each other, but are held together by a molecular interface formed between two SptP molecules. Each SptP molecule is wrapped around by three SicP chaperones (two chaperones from one homodimer and a third one from the opposite homodimer pair) .
Tower domain (Tower_dom)
Type: Domain

This domain adopts a secondary structure consisting of a pair of long, antiparallel α-helices (the stem) that support a three-helix bundle (3HB) at their end. The 3HB contains a helix-turn-helix motif and is similar to the DNA binding domains of the bacterial site-specific recombinases, and of eukaryotic Myb and homeodomain transcription factors. The Tower domain has an important role in the tumour suppressor function of BRCA2, and is essential for appropriate binding of BRCA2 to DNA .
3-mercaptopyruvate sulfurtransferase, C-terminal domain (SulfurTase_C)
Type: Domain

This entry represents a domain found in putative 3-mercaptopyruvate sulphurtransferases from Trypanosomatida (kinetoplastids). This domain adopts a structure consisting of a four-stranded antiparallel β-sheet and an α-helix, arranged in a β(2)-α-β(2) fashion, and bearing a remarkable structural similarity to the FK506-binding protein class of peptidylprolyl cis/trans-isomerase . It may be involved in mediating protein folding and sulfurtransferase-protein interactions .
Protein of unknown function DUF1931 (DUF1931)
Type: Family

This entry represents a set of hypothetical bacterial proteins containing a core of six α-helices, where one central helix is surrounded by the other five. The exact function of this family has not, as yet, been determined .
T4 recombination endonuclease VII, dimerisation (T4_recomb_endonuclease_dimer)
Type: Domain

This entry represents a dimerisation domain predominantly found in Bacteriophage T4 recombination endonuclease VII. It adopts a helical secondary structure, with three α helices oriented parallel to each other. As well as mediating dimerisation of the protein, this domain is also involved in binding to the DNA major groove .
Cytochrome C oxidase subunit IIa, transmembrane domain (Cyt_c_oxidase_su2a_TM_dom)
Type: Domain

This N-terminal domain forms the transmembrane region in subunit II of cytochrome c oxidase from Thermus thermophilus. This domain adopts a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold .
Type II restriction enzyme NaeI (NaeI)
Type: Domain

This restriction endonuclease NaeI domain adopts a secondary structure consisting of nine α-helices, six 3-10 helices and 13 β-strands. NaeI binds two GCC-CGG recognition sequences to cleave DNA into blunt-ended products .

There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , as summarised below:

Type I enzymes (

) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (

) activities.

Type II enzymes (

) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.

Type III enzymes (

) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (

).

Type IV enzymes target methylated DNA.

Type II restriction endonucleases (

) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four β-strands and one α-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin . However, there is still considerable diversity amongst restriction endonucleases . The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone .
Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal (Peptidase_M1_C)
Type: Domain

This C-terminal domain is found in peptidases belonging to MEROPS peptidase family M1, particularly: aminopeptidase-1 of Caenorhabditis elegans, aminopeptidase O, aminopeptidase B and the bifunctional leukotriene A4 (LTA-4) hydrolase/aminopeptidase.
Regulator of G protein signalling-like domain (RGS-like_dom)
Type: Domain

This entry represents a domain consisting of twelve helices that fold into a compact structure that contains the overall structural scaffold observed in other regulator of G protein signalling (RGS) proteins and three additional helical elements that pack closely to it. Helices 1-9 comprise the RGS fold, in which helices 4-7 form a classic antiparallel bundle adjacent to the other helices. Like other RGS structures, helices 7 and 8 span the length of the folded domain and form essentially one continuous helix with a kink in the middle. Helices 10-12 form an apparently stable C-terminal extension of the structural domain, and although other RGS proteins lack this structure, these elements are intimately associated with the rest of the structural framework by hydrophobic interactions. This domain binds to active G-alpha proteins, promoting GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways .
Cholesterol oxidase, substrate-binding (Cholesterol_OX_subst-bd)
Type: Domain

The substrate-binding domain found in cholesterol oxidase is composed of an eight-stranded mixed β-pleated sheet and six α-helices. This domain is positioned over the isoalloxazine ring system of the FAD cofactor bound by the FAD-binding domain (

) and forms the roof of the active site cavity, allowing for catalysis of oxidation and isomerisation of cholesterol to cholest-4-en-3-one .
Pesticidal crystal protein, central domain, Cry2A/18 (Pest_cryst_cen_dom_Cry2A/18)
Type: Domain

The crystal proteins of Bacillus thuringiensis have been extensively studied because of their pesticidal properties and their high natural levels of production . When an insect ingests these proteins, they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C-terminal extension is cleaved in some members. Once activated, the endotoxin binds to the gut epithelium and causes cell lysis by the formation of cation-selective channels, which leads to death. The activated region of the toxin is composed of three distinct structural domains: an N-terminal helical bundle domain (

) involved in membrane insertion and pore formation; a β-sheet central domain involved in receptor binding; and a C-terminal β-sandwich domain (

) that interacts with the N-terminal domain to form a channel .

This entry represents the central β-sheet domain, which consists of three four-stranded β-sheets, each with a Greek key fold, with internal pseudo threefold symmetry. Thus, it acts as a receptor binding β-prism, binding to insect-specific receptors of gut epithelial cells .

The sequences matched by this entry are predominantly from the Cry2A and Cry18 subgroups .
BmKX domain (BmKX_dom)
Type: Domain

This entry represents a domain that is often, thought not exclusively, found in short-chain scorpion toxins. It forms a structure consisting of a cysteine-stabilised α/β scaffold consisting of a short 3-10-helix and a two-stranded antiparallel β-sheet. The biological method of action of the toxins has not yet been defined, and the function of this domain remains unknown .
SANT associated (SANTA)
Type: Domain

The SANTA domain (SANT associated) is approximately 90 amino acids in length and is conserved in eukaryotes. It is sometimes found in association with the SANT domain (

, also known as the Myb-like DNA-binding domain) implying a putative function in regulating chromatin remodelling. Sequence analysis has showed that the SANTA domain is likely to form four central β-sheets with three flanking α-helices. Many conserved hydrophobic residues are present which implies a possible role in protein-protein interactions.
Invasin, domain 3 (Invasin_dom_3)
Type: Domain

This domain adopts a structure consisting of an immunoglobulin-like β-sandwich, with seven strands in two β-sheets, arranged in a Greek-key topology. It forms part of the extracellular region of the protein, which can be expressed as a soluble protein (Inv497) that binds integrins and promotes subsequent uptake by cells when attached to bacteria .
Glucodextranase, N-terminal (Glucodextranase_N)
Type: Domain

This domain is found in bacterial and archaeal glucoamylases and glucodextranases, and adopts a structure consisting of 17 antiparallel β-strands . These β-strands are divided into two β-sheets, and one of the β-sheets is wrapped by an extended polypeptide, which appears to stabilise the domain. This domain, together with glycoside hydrolase domain A (

), is mainly involved with catalytic activity, hydrolysing alpha-1,6-glucosidic linkages of dextran to release beta-D-glucose from the non-reducing end via an inverting reaction mechanism .
Ubiquitin-related modifier 1 (Urm1)
Type: Family

Ubiquitin related modifier 1 (Urm1) is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like urmylation pathway . Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily . Urm1 acts as a sulfur carrier required for 2-thiolation of mcm5S2U at tRNA wobble positions of cytosolic tRNA(Lys), tRNA(Glu) and tRNA(Gln) .
Phosphatidate cytidylyltransferase, mitochondrial (Tam41)
Type: Family

Tam41 is a mitochondrial phosphatidate cytidylyltransferase (CDP-DAG synthase) that catalyzes the formation of CDP-diacylglycerol (CDP-DAG) from phosphatidic acid (PA) in the mitochondrial inner membrane. It is required for the biosynthesis of the dimeric phospholipid cardiolipin, which stabilizes supercomplexes of the mitochondrial respiratory chain in the mitochondrial inner membrane .
ATPase MipZ (MipZ)
Type: Family

Cell division in bacteria is facilitated by a polymeric ring structure, the Z ring, composed of tubulin-like FtsZ protofilaments. Correct positioning of the division plane is a prerequisite for the generation of daughter cells with a normal chromosome complement. In Caulobacter crescentus MipZ, an essential protein, coordinates and regulates the assembly of the FtsZ cytokinetic ring during cell division. MipZ, forms a complex with the partitioning protein ParB near the origin of replication and localizes with the duplicated origin regions to the cell poles. MipZ also directly interferes with FtsZ polymerisation, thereby restricting FtsZ ring formation to mid-cell, the region of lowest MipZ concentration.