SII-SWORD/CoKE huggingface dataset:
Antifungal protein domain superfamily (Antifungal-protein_dom_sf)
Type: Homologous_superfamily

Antifungal protein consists of five antiparallel β strands which are highly twisted creating a β barrel stabilised by four internal disulphide bridges . A cationic site adjacent to a hydrophobic stretch on the protein surface may constitute a phospholipid binding site .

This superfamily represents an antifungal protein lysine rich domain, that contributes to the correct folding of the protein, which is necessary for its specific antifungal activity. It has been suggested that this domain might contribute to the cell wall and/or nucleic acids binding activity .
Telomere-binding protein, beta subunit domain superfamily (TEBP_beta_dom_sf)
Type: Homologous_superfamily

Telomeres are specialised protein-DNA complexes that compose the ends of eukaryotic chromosomes. Telomeres protect chromosome termini from degradation and recombination and act together with telomerase to ensure complete genome replication. TEBP beta forms a complex with TEBP alpha and this complex is able to recognise and bind ssDNA to form a sequence-specific, telomeric nucleoprotein complex that caps the very 3' ends of chromosomes .

This superfamily represents a domain found in a family that consists of several telomere-binding protein beta subunits, which represents the OB-binding fold.
Translation initiation factor IF- 2, domain 3 (TIF_IF2_dom3)
Type: Domain

Initiation factor 2 (IF-2) is one of the three factors required for the initiation of protein biosynthesis in bacteria . IF-2 promotes the GTP-dependent binding of the initiator tRNA to the small subunit of the ribosome. IF-2 is a protein of about 70 to 95kDa that contains a central GTP-binding domain flanked by a highly variable N-terminal domain and a more conserved C-terminal domain. Some members of this group undergo protein self splicing that involves a post-translational excision of the intein followed by peptide ligation.

The function of IF-2 in facilitating the proper binding of initiator methionyl-tRNA to the ribosomal P site appears to be universally conserved .

This entry represents the domain 3 of IF-2. It consists of a α/β/α structure with a core formed by a parallel β-sheet of 4 strands .
Phosphonoacetate hydrolase, insert domain superfamily (Phosphonoacetate_hydro_insert)
Type: Homologous_superfamily

Phosphonates are organic compounds with a direct C-P bond that is far less labile than the C-O-P bonds of phosphate attachment sites. Phosphonoacetate hydrolase specifically cleaves the C-P bond in phosphonoacetate . This superfamily represents a short α/β 2 layer sandwich domain inserted towards the C terminus of the catalytic domain.
PA1123-like domain (PA1123-like_domain)
Type: Domain

This domain contains three α helices and six β strands. It is found in a protein that is produced from gene PA1123 of Pseudomonas. The protein PA1123 appears to be present in the biofilm layer and may be a lipoprotein.
YqaI domain superfamily (YqaI_dom_sf)
Type: Homologous_superfamily

This superfamily represents a domain consisting of an α helix and four β strands. It is found in the hypothetical protein YqaI, which is expressed in bacteria, particularly Bacillus subtilis.
Multihaem cytochrome, PRC subunit superfamily (Multihaem_cyt_PRC_cyt_su-like)
Type: Homologous_superfamily

This superfamily represents a multihaem-binding domain found in the cytochrome subunit of the photosynthetic reaction centre (PRC) and other cytochrome proteins . This domain is predominantly α-helical and, in the PRC cytochrome subunit, binds two haem groups.
Winged helix-turn-helix transcription repressor, HrcA, inserted dimerising domain superfamily (WHTH_transcript_rep_HrcA_IDD)
Type: Homologous_superfamily

Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer.

This superfamily represents the inserted dimerising domain of HrcA.
ApoC-II domain superfamily (ApoC-II_dom_sf)
Type: Homologous_superfamily

This domain superfamily is found in apolipoprotein CII (apoC-II). ApoC-II is a surface constituent of plasma lipoproteins and the activator for lipoprotein lipase (LPL). It is therefore central for lipid transport in blood. Lipoprotein lipase is a key enzyme in the regulation of triglyceride levels in human serum . It is the C-terminal helix of apoCII that is responsible for the activation of LPL . The active peptide of apoC-II occurs at residues 44-79 and has been shown to reverse the symptoms of genetic apoC-II deficiency in a human subject .

Micellar SDS, a commonly used mimetic of the lipoprotein surface, inhibits the aggregation of apoC-II and induces a stable structure containing approximately 60% α-helix. The first 12 residues of apoC-II are structurally heterogeneous but the rest of the protein forms a predominantly helical structure .
NE1680-like superfamily (NE1680-like_sf)
Type: Homologous_superfamily

This superfamily represents a domain of ~86 residues which consists of two α helices and four β strands. Its function is unknown.
Tubulin, C-terminal (Tubulin_C)
Type: Homologous_superfamily

Microtubules are polymers of tubulin, a dimer of two 55kDa subunits, designated alpha and beta . Within the microtubule lattice, α-β heterodimers associate in a head-to-tail fashion, giving rise to microtubule polarity. Fluorescent labelling studies have suggested that tubulin is oriented in microtubules with beta-tubulin toward the plus end .

For maximal rate and extent of polymerisation into microtubules, tubulin requires GTP. Two molecules of GTP are bound at different sites, termed N and E. At the E (Exchangeable) site, GTP is hydrolysed during incorporation into the microtubule. Close to the E site is an invariant region rich in glycine residues, which is found in both chains and is thought to control access of the nucleotide to its binding site .

Most species, excepting simple eukaryotes, express a variety of closely-related alpha- and beta-isotypes. A third family member, gamma tubulin, has also been identified in a number of species. Gamma tubulin is found at microtubule-organising centres, such as the spindle poles or the centrosome,
suggesting that it is involved in minus-end nucleation of microtubule assembly . Further eukaryotic tubulins (gamma, epsilon, zeta) that are restricted to certain lineages or species have been reported .

Bacterial and archaeal homologues of tubulin have been discovered. BtubA and BtubB, two bacterial homologues in the genus Prosthecobacter, have probably been derived by horizontal gene transfer .

This entry represents the extreme C-terminal structural domain of both alpha and beta tubulin. It forms a helix hairpin .
DUF3239 domain superfamily (DUF3239_dom_sf)
Type: Homologous_superfamily

This domain superfamily is found in the protein family defined by

; these are putative membrane proteins, however this cannot be confirmed. Currently they have no known function.
HP0242-like superfamily (HP0242-like_sf)
Type: Homologous_superfamily

This domain superfamily is found in proteins of unknown function related to HP0242. The crystal structure of HP0242, a hypothetical protein from Helicobacter pylori (Campylobacter pylori) has been determined. It reveals an acid-adaptive protein possibly of physiological significance when H. pylori colonises the human stomach. The protein adopts a unique four α-helical triangular conformations. The biologically active form is thought to be a tetramer. The gene exist in an operon along with 6 other genes where the gene products appear to be related to iron storage and haem biosynthesis .
Protein N-terminal glutamine amidohydrolase, alpha beta roll (Prot_N_Gln_amidohydro_ab_roll)
Type: Domain

This entry represents a structural domain found in the N-terminal glutamine amidohydrolase (Nt
Q
-amidase) family of proteins. These proteins contain a region of approximately 200 residues carrying several distinctive motifs including a WDYHV motif and one of three cysteines. Protein N-terminal glutamine amidohydrolase is responsible for degradation of N-terminal glutamine .
MTH889-like domain superfamily (MTH889-like_dom_sf)
Type: Homologous_superfamily

This domain superfamily is found in proteins of unknown function. It forms an α/β 2-layer sandwich.
Ta0600-like superfamily (Ta0600-like_sf)
Type: Homologous_superfamily

This domain superfamily is functionally uncharacterised and found primarily in the UPF0147 family of proteins, which have no known function.
Mth639-like domain superfamily (Mth639-like_dom_sf)
Type: Homologous_superfamily

This domain superfamily is found in an archaeal family of proteins UPF0147, which have no known function.
Sama2622-like superfamily (Sama2622-like_sf)
Type: Homologous_superfamily

This domain superfamily is found in a family of proteins, which have no known function.
N6 adenine-specific DNA methyltransferase, TaqI class, C-terminal (N6_DNA_MeTrfase_TaqI_C)
Type: Homologous_superfamily

In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. There are 2 major classes of DNA methyltransferase that differ in the nature of the modifications they effect. The members of one class (C-MTases) methylate a ring carbon and form C5-methylcytosine (see PRINTS signature C5METTRFRASE). Members of the second class (N-MTases) methylate exocyclic nitrogens and form either N4-methylcytosine (N4-MTases) or N6-methyladenine (N6-MTases). Both classes of MTase utilise the cofactor S-adenosyl-L-methionine (SAM) as the methyl donor and are active as monomeric enzymes .

N-6 adenine-specific DNA methylases (

) (A-Mtase) are enzymes that specifically methylate the amino group at the C-6 position of adenines in DNA. Such enzymes are found in the three existing types of bacterial` restriction-modification systems (in type I system the A-Mtase is the product of the hsdM gene, and in type III it is the product of the mod gene). All of these enzymes recognise a specific sequence in DNA and methylate an adenine in that sequence. It has been shown that A-Mtases contain a conserved motif Asp/Asn-Pro-Pro-Tyr/Phe in their N-terminal section, this conserved region could be involved in substrate binding or in the catalytic activity.
Api92-like domain superfamily (Api92-like_dom_sf)
Type: Homologous_superfamily

This domain superfamily is found in a family of hypothetical enterobacterial proteins of around 170 residues in length. Members of this family are found in Escherichia coli, Salmonella typhimurium and Shigella species. The function of this family is unknown.
BrxA superfamily (BrxA_sf)
Type: Homologous_superfamily

BrxA is part of the phage resistance system BREX (Bacteriophage Exclusion). It shares structural homology with the RNA-binding antitermination protein NusB .
NMB0513-like superfamily (NMB0513-like_sf)
Type: Homologous_superfamily

This domain is found in a family of proteins, which have no known function.
PBDC1-like domain superfamily (PBDC1-like_dom_sf)
Type: Homologous_superfamily

This domain superfamily can be found in the PBDC1 (polysaccharide biosynthesis domain-containing protein 1) proteins from fungi and animals.

Protein PBDC1 homolog from S. cerevisiae also known as Ypl225w (Chp1, Chaperone 1 for eEF1A) functions as a co-translational chaperone by forming dual interactions with the eEF1A G domain nascent chain and the UBA domain of ribosome-bound nascent polypeptide-associated complex . This protein primes the eEF1A nascent chains for binding to GTP as part of a folding mechanism which is tightly coupled to chaperone recycling .
Domain of unknown function DUF357 (DUF357)
Type: Domain

This domain is found in a family of proteins, which have no known function.

The members of this family fold into a three helical bundle that has some structural similarity to imunnoglobulin/albumin binding domains

.
Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily (NH3_CH4_mOase_suB_hlx_hairpin)
Type: Homologous_superfamily

Ammonia monooxygenase and the particulate methane monooxygenase are both integral membrane proteins, occurring in ammonia oxidisers and methanotrophs respectively, which are thought to be evolutionarily related . These enzymes have a relatively wide substrate specificity and can catalyse the oxidation of a range of substrates including ammonia, methane, halogenated hydrocarbons and aromatic molecules . These enzymes are composed of 3 subunits - A (

), B (

,

) and C (

) - and contain various metal centres, including copper. Particulate methane monooxygenase from Methylococcus capsulatus str. Bath is an ABC homotrimer, which contains mononuclear and dinuclear copper metal centres, and a third metal centre containing a metal ion whose identity in vivo is not certain.

The soluble regions of these enzymes derive primarily from the B subunit. This subunit forms two antiparallel β-barrel-like structures and contains the mono- and di- nuclear copper metal centres .

This superfamily represents the β hairpin that links the two β barrels.
Microtubule-associated serine/threonine-protein kinase, pre-PK domain superfamily (MAST_pre-PK_dom_sf)
Type: Homologous_superfamily

This superfamily represents a four α-helical bundle domain found N-terminal to the protein kinase domain in microtubule-associated serine/threonine-protein kinases.
Mycolic acid cyclopropane synthase-like domain superfamily (Cyclopro_synthase-like_dom_sf)
Type: Homologous_superfamily

Some bacteria synthesise betaine from glycine by a three-step methylation process. The first enzyme, glycine/sarcosine N-methyltransferase, leads to the formation of either sarcosine or N,N-dimethylglycine, which is further methylated to yield betaine (N,N,N-trimethylglycine) by the action of sarcosine/dimethylglycine N-methyltransferase. Both of these enzymes can catalyse the formation of N,N-dimethylglycine from sarcosine .

This superfamily represents a helix hairpin domain found in several putative sarcosine-dimethylglycine methyltransferases.
Phenylalanine ammonia-lyase, shielding domain superfamily (Phe_NH3-lyase_shielding_dom_sf)
Type: Homologous_superfamily

This superfamily represents the shielding domain at the C-terminal of PAL which is tightly connected to the core domain through the exceptionally long 55-residue helix α17. The shielding domain restricts the access to the active centre so that the risk of inactivation by nucleophiles in conjunction with dioxygen is minimised. This may help PAL to function, for instance, in stressed plant tissue. It should be noted that PAL forms its electrophilic prosthetic group autocatalytically from its own polypeptide, rendering it independent of any cofactor and thus facilitating its upregulation .

The ubiquitous higher plant enzyme phenylalanine ammonia-lyase (PAL;

) is a key biosynthetic catalyst in phenylpropanoid assembly. PAL catalyses the non-oxidative deamination of L-phenylalanine to trans-cinnamic acid. PAL contains a catalytic Ala-Ser-Gly triad that is post-translationally cyclised. PAL is structurally similar to the mechanistically related histidine ammonia lyase (HAL;

), with PAL having an additional approximately 160 residues extending from the common fold . Catalysis in PAL may be governed by the dipole moments of seven α-helices associated with the PAL active site. The cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) resides atop the positive poles of three helices, increasing its electrophillicity. Plant and fungal PAL enzymes contain a 100-residue-long C-terminal multi-helix domain, which might play a role in the rapid response of PAL in the regulation of phenylpropanoid biosynthesis by destabilising the enzyme . This entry also includes fungal proteins such as phenolylalanine ammonia-lyase CLZ10, which mediates the biosynthesis of squalestatin S1 with potent cholesterol-lowering activity by targeting squalene synthase (SS) , and phenolylalanine ammonia-lyase hkm12, involved in the biosynthesis of hancockiamides, an unusual new family of N-cinnamoylated piperazines .
YfbU, helix-hairpin domain superfamily (YfbU_helix-hairpin_sf)
Type: Homologous_superfamily

This superfamily represents a helix-hairpin domain found in a number of proteins of unknown function belonging to the UPF0304 family.
YfbU, alpha-helical bundle domain superfamily (YfbU_alpha-helical_sf)
Type: Homologous_superfamily

This superfamily represents a domain consisting of three α helices arranged in an orthogonal bundle, and found in a number of proteins of unknown function belonging to the UPF0304 family.
tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily (tRNA_m1G_MeTrfase_C_sf)
Type: Homologous_superfamily

In transfer RNA many different modified nucleosides are found, especially in the anticodon region. tRNA (guanine (N1))-methyltransferase TrmD

is one of several nucleases operating together with the tRNA-modifying enzymes before the formation of the mature tRNA. It catalyses the reaction:

S-adenosyl-L-methionine + guanine37 in tRNA ->S-adenosyl-L-homocysteine + tRNA containing N1-methylguanine

It methylates guanosine(G) to N1-methylguanine (1-methylguanosine (m1G)) at position 37 of tRNAs that read CUN (leucine), CCN(proline), and CGG (arginine) codons. The presence of m1G improves the cellular growth rate and the polypeptide steptime and also prevents the tRNA from shifting the reading frame .

This entry represents the C-terminal structural domain.
Trans-aconitate 2-methyltransferase, C-terminal (Trans_acon_MeTrfase_C)
Type: Homologous_superfamily

This entry represents the C-terminal α-orthogonal bundle domain.

Trans-aconitate methyltransferases in bacteria catalyse the monomethyl esterification of trans-aconitate. Trans-aconitate is an effective inhibitor of aconitase, with potentially toxic results, as aconitase plays an essential role in the conversion of citrate to isocitrate in the tricarboxylic acid cycle .
PEP-utilising enzyme, conserved site (PEP_util_CS)
Type: Conserved_site

A number of enzymes that catalyze the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) via a phospho-histidine intermediate have been shown to be structurally related . These enzymes are:

Pyruvate,orthophosphate dikinase (

) (PPDK). PPDK catalyzes the reversible phosphorylation of pyruvate and phosphate by ATP to PEP and diphosphate. In plants PPDK function in the direction of the formation of PEP, which is the primary acceptor of carbon dioxide in C4 and crassulacean acid metabolism plants. In some bacteria, such as Bacteroides symbiosus, PPDK functions in the direction of ATP synthesis.

Phosphoenolpyruvate synthase (

) (pyruvate,water dikinase). This enzyme catalyzes the reversible phosphorylation of pyruvate by ATP to form PEP, AMP and phosphate, an essential step in gluconeogenesis when pyruvate and lactate are used as a carbon source.

Phosphoenolpyruvate-protein phosphatase (

). This is the first enzyme of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), a major carbohydrate transport system in bacteria. The PTS catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is the following: a phosphoryl group from PEP is transferred to enzyme-I (EI) of PTS which in turn transfers it to a phosphoryl carrier protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease.

The entry signature pattern represents a conserved region in the C-terminal part of the PEP-utilizing enzymes. The biological significance of this region is not yet known.
Ras GTPase-activating protein, conserved site (RasGAP_CS)
Type: Conserved_site

This entry represents a conserved site in the RasGAPs (Ras GTPase-activating proteins).
Dual-action ribosomal maturation protein DarP superfamily (DarP_sf)
Type: Homologous_superfamily

This superfamily includes Dual-action ribosomal maturation protein DarP from Pseudomonas syringae and similar sequences from bacteria and some plant species. DarP is a member of a network of 50S ribosomal subunit biogenesis factors which assembles along the 30S-50S interface, preventing incorrect 23S rRNA structures from forming. It adopts an all-α configuration (

).
Jann4075-like superfamily (Jann4075-like_sf)
Type: Homologous_superfamily

This domain superfamily is found in a family of proteins that have no known function.
Cytochrome c-552/4 (Cyt_c-552/4)
Type: Domain

This domain contains a di-heme elbow motif. It is found among others in cytochrome c-554 and c-552. Cytochrome c554 is a tetra-heme cytochrome involved in the oxidation of NH3 by Nitrosomonas europaea .
AGR-C-984p-like superfamily (AGR-C-984p-like_sf)
Type: Homologous_superfamily

This domain superfamily is found in a family of conserved proteins of unknown function, DUF1217. Some members contain multiple copies of the domain.
YerB-like superfamily (YerB-like_sf)
Type: Homologous_superfamily

This domain superfamily is found in a family of proteins with unknown function. YerB interacts with PcrA helicase. The interaction is not essential for cell viability or repair of UV-induced lesions . The domain structure was determined from the crystal structure of the YerB protein from Bacillus subtilis.
SO1590-like superfamily (SO1590-like_sf)
Type: Homologous_superfamily

This superfamily represents a β-barrel domain that is found in a family of bacterial proteins of unknown function. The crystal structure of such an uncharacterised protein (YP563039) from Shewanella denitrificans (strain OS217/ATCC BAA-1090/DSM 15013) at 1.80A resolution and of a protein with unknown function (SO1590) from Shewanella oneidensis MR-1 at 1.84A resolution have been solved.
Ribonuclease HII, helix-loop-helix cap domain superfamily (RNase_HII_hlx-loop-hlx_cap_dom)
Type: Homologous_superfamily

This superfamily represents the helix-loop-helix cap domain of ribonuclease HII. This C-terminal domain forms a compact structure consisting of two α-helices: α8 and α9. Unlike the N-terminal domain, bacterial RNases HI do not possess this domain. In the full-length enzyme, the α9 helix is followed by 15 amino acid residues, of which conformation is likely to be flexible, as revealed from the susceptibility to trypsin digestion. It has been suggested that this domain confers substrate-specific binding capacity to the core nuclease architecture, thus accounting for the endonucleolytic specificity of the type 2 RNase H family members . It also has been suggested that this domain to be involved in the interaction with the DNA/RNA hybrid .
Apc36109-like domain superfamily (Apc36109-like_dom_sf)
Type: Homologous_superfamily

This domain superfamily was determined from the crystal structure of APC36109 from Bacillus stearothermophilus (Geobacillus stearothermophilus). It is found in a family of proteins of unknown function.
SMc04008-like domain (SMc04008-like_domain)
Type: Domain

This domain was determined from the crystal structures of the proteins of unknown function from Rhizobium meliloti (Sinorhizobium meliloti)

and Alcanivorax borkumensis

. The domain is found in a family, which consists of several short bacterial proteins of around 100 residues in length. The function of this domain is unknown.
YqgQ-like superfamily (YqgQ-like_sf)
Type: Homologous_superfamily

This domain superfamily was determined from the crystal structure of a protein of unknown fuction from Bacillus subtilis. The domain is found in a family of proteins whose function is unknown; however it is found in the family represented by

.