SII-SWORD/CoKE huggingface dataset:
Alpha-A conotoxin PIVA-like (Toxin_14)
Type: Family

Alpha-A conotoxin PIVA (

) is the major paralytic toxin found in the venom produced by the piscivorous snail Conus purpurascens. This peptide acts by blocking the acetylcholine-binding site of the nicotinic acetylcholine receptor at the neuromuscular junction . The overall shape of the peptide is described as an "iron" with a highly charged hydrophilic loop of 15S-19R forming the "handle" domain that is exposed to the exterior of the protein. The stability of the conotoxin is primarily governed by three disulphide bonds. A triangular structural motif formed by residues 19R, 12H and 6Y is thought to constitute a "binding core" that is important in binding to the acetylcholine receptor .
Janus-atracotoxin (Toxin_16)
Type: Family

This family represents insect-selective, excitatory neurotoxins known as Janus atracotoxins or Lambda-hexatoxins, including the peptides secreted by the spider Hadronyche versuta (Blue mountains funnel-web spider) (

,

,

). These toxins selectively inhibit invertebrate calcium-activated potassium (KCa, Slo-type) channels with high-affinity, probably acting as a pore blocker . Janus atracotoxin-Hv1c (J-ACTX-Hv1c,

) is organised into a disulphide-rich globular core (residues 3-19) and a β-hairpin (residues 20-34). There are 4 disulphide bridges, one of which is a vicinal disulphide bridge; this is known to be unimportant in the maintenance of structure but critical for insecticidal activity .
Clostridium neurotoxin, translocation (Toxin_trans)
Type: Domain

The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein: a N-terminal catalytic domain (

), a central translocation domain and two receptor binding domains . Subsequent to cell surface binding and receptor mediated endocytosis of the neurotoxin, an acid induced conformational change in the neurotoxin translocation domain is believed to allow the domain to penetrate the endosome and from a pore, thereby facilitating the passage of the catalytic domain across the membrane into the cytosol . The structure of the translocation reveals a pair of helices that are 105 Angstroms long and is structurally distinct from other pore forming toxins .
Vacuolar protein sorting-associated protein 54, C-terminal (Vps54_C)
Type: Domain

This entry represents a domain found in vacuolar protein sorting-associated protein 54 (VPS54), which acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). VPS54 is required to tether the complex to the TGN. However, it is not involved in endocytic recycling .
WAPL domain (WAPL_dom)
Type: Domain

The D. melanogaster WAPL protein regulates heterochromatin structure . It is required to hold sister chromatids of meiotic heterochromatin together and is implicated in both heterochromatin pairing during female meiosis and the modulation of position-effect variegation (PEV). Although the high-sequence conservation is limited to a third of the protein sequence, a WAPL homologue has been identified in mammals. Mammalian WAPL may play a significant role in meiosis as does the Drosophila one. Human WAPL is overexpressed in invasive human cervical cancers and is often associated with cervical carcinogenesis .

This entry represents a domain found in the WAPL proteins.
WisP, N-terminal (WisP_N)
Type: Domain

This family is found at the N terminus of the Tropheryma whipplei WisP family proteins .
Spore protein YabP (Spore_YabP)
Type: Family

This protein family includes Spore protein YabP of the bacterial sporulation program, as found in Bacillus subtilis, Clostridium tetani, and other spore-forming members of the Firmicutes. In B. subtilis, a YabP single mutant appears to sporulate and germinate normally , but is in an operon with YabQ (essential for formation of the spore cortex), it near-universal among endospore-forming bacteria, and is found nowhere else. YabP is involved in spore coat assembly during the process of sporulation .

The structure of a fragment of the Spore protein YabP from Desulfitobacterium hafniense has been resolved using NMR spectroscopy, showing a homodimer with two monomeric subunits, each consisting of five anti-parallel β-strands .
YbbR-like (YbbR)
Type: Family

This entry includes a group of bacterial proteins, including YbbR and CdaR. Bacillus subtilis CdaR regulates CdaA, a diadenylate cyclase that contributes to cell division .
Lysoplasmalogenase-like (TMEM86B-like)
Type: Family

This entry represents a family of proteins that include lysoplasmalogenase from humans (also known as Transmembrane protein 86B, TMEM86B) and similar proteins found in eukaryotes and bacteria. TMEM86B catalyses the degradation of lysoplasmalogen, which is formed by the hydrolysis of membrane glycerophospholipids, plasmalogens. It may modulate cell membrane properties . Uncharacterised membrane protein YhhN from E. coli also belongs to this group (

). Putative conserved active site residues have been proposed for this family .
YibE/F-like (YibE_F)
Type: Family

The sequences featured in this family are similar to two proteins expressed by Lactococcus lactis, YibE (

) and YibF (

). Most of the members of this family are annotated as being putative membrane proteins, and in fact the sequences contain a high proportion of hydrophobic residues.
ATPase, A1 complex, epsilon subunit, archaeal (ATPase_A1-cplx_e-su)
Type: Family

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

A-ATPases (or A1A0-ATPase) (

) are found exclusively in Archaea and display a close resemblance in structure and subunit composition with V-ATPases, although their function in both ATP synthesis and ATP hydrolysis is closer to that of F-ATPases . A-ATPases are composed of two linked complexes: the A1 complex consisting of seven subunits contains the catalytic core that synthesizes/hydrolyses ATP, while the A0 complex consisting of at least two subunits forms the membrane-spanning pore . The rotary motor in A-ATPases is composed of only two subunits, the stator subunit I and the rotor subunit C . A-ATPases may have arisen as an adaptation to the different cellular needs and the more extreme environmental conditions faced by Archaeal species.

The epsilon subunit is the smallest (7kDa) of those found in the A1 complex. Unlike the A, B and C subunits, the epsilon subunit does not have a homologous counterpart in F- or V-ATPases .
Neurotoxin 3, Anemonia (Neurotoxin_3_Anemonia)
Type: Domain

This entry occurs within the Anemonia sulcata toxin III (ATX III) neurotoxin family. ATX III is a neurotoxin that is produced by sea anemone; it adopts a compact structure containing four reverse turns and two other chain reversals, but no regular α-helix or β-sheet. A hydrophobic patch found on the surface of the peptide may constitute part of the sodium channel binding surface .
Actin-binding, Xin repeat (Actin-binding_Xin_repeat)
Type: Repeat

The repeat has the consensus sequence GDV(K/Q/R)(T/S/G)X(R/K/T) WLFETXPLD. This repeat motif is typically found in the N terminus of the proteins, with a copy number between 2 and 28 repeats. Direct evidence for binding to and stabilising F-actin has been found in the human protein (

) . The homologues in mouse and chicken localise in the adherens junction complex of the intercalated disc in cardiac muscle and in the myotendon junction of skeletal muscle. mXin may co-localise with Vinculin which is known to attach the actin to the cytoplasmic membrane . It has been shown that the amino-terminus of human xin (CMYA1) binds the EVH1 domain of Mena/VASP/EVL, and the carboxy-terminus binds the, for the filamin family unique, domain 20 of filamin C . This confirms the proposed role of xin repeat containing proteins as F-actin-binding adapter proteins.
S-adenosyl-l-methionine decarboxylase leader peptide (AdoMetDC_leader)
Type: Family

This family consists of the S-adenosyl-l-methionine decarboxylase (AdoMetDC) leader peptides. AdoMetDC is a key regulatory enzyme in the biosynthesis of polyamines. All expressed plant AdoMetDC mRNA 5, leader sequences contain a highly conserved pair of overlapping upstream ORFs (uORFs) that overlap by one base. Sequences of the small uORFs are highly conserved between monocot, dicot and gymnosperm AdoMetDC mRNA species, suggesting a translational regulatory mechanism .
Albumin I (Albumin_I)
Type: Family

The albumin I protein, a hormone-like peptide, stimulates kinase activity upon binding a membrane bound 43kDa receptor. The structure of this region reveals a knottin like fold, comprise of three β strands .
Metchnikowin (Mtk)
Type: Family

This family consists of the metchnikowin family of antimicrobial peptides from Drosophila. Metchnikowin is a proline-rich peptide whose expression is immune-inducible. Induction of the metchnikowin gene expression can be mediated either by the TOLL pathway or by the imd gene product. The metchnikowin peptide is unique among the Drosophila antimicrobial peptides in that it is active against both bacteria and fungi .
Formaecin (Formaecin)
Type: Family

This entry consists of the formaecin family of antimicrobial peptides isolated from the bulldog ant Myrmecia gulosa in response to bacterial infection. Formaecins are inducible peptide antibiotics and are active against growing Escherichia coli but were inactive against other Gram-negative and Gram-positive bacteria. Formaecin peptides are 16 amino acids long, are rich in proline and have N-acetylgalactosamine O-linked to a conserved threonine .
Pleurocidin (Antimicrobial12)
Type: Family

This family consists of the pleurocidin family of antimicrobial peptides. The first member identified in this family was Pleurocidin from the skin mucous secretions of the winter flounder (Pleuronectes americanus), peptides that exhibit antimicrobial activity against Gram-positive and Gram-negative bacteria . Pleurocidin is a 25-residue with an amphipathic α-helical conformation similar to other linear antimicrobial peptides and may play a role in innate host defence .
Halocidin (Antimicrobial13)
Type: Family

This family consists of the halocidin family of antimicrobial peptides. Halocidins are isolated from the haemocytes of the tunicate, Halocynthia aurantium (Sea peach). They are dimeric in structures, which are found via a disulphide linkage between cysteines of two different- sized monomers. Halocidins have been shown to have strong antimicrobial activities against a wide variety of pathogenic bacteria and could be ideal candidates as peptide antibiotics against multidrug-resistant bacteria .
Lactocin 705 (Antimicrobial14)
Type: Family

This family consists of lactocin 705 which is a bacteriocin produced by Lactobacillus casei CRL 705. Lactocin 705 is a class IIb bacteriocin, whose activity depends upon the complementation of two peptides (705-alpha and 705-beta) of 33 amino acid residues each. Lactocin 705 is active against several Gram-positive bacteria, including food-borne pathogens and is a good candidate to be used for biopreservation of fermented meats .
Ocellatin (Antimicrobial15)
Type: Domain

This family consists of the ocellatin family of antimicrobial peptides. Ocellatins are produced from the electrical-stimulated skin secretions of the South American frog, Leptodactylus ocellatus (Argus frog). The family consists of three structurally related peptides, ocellatin 1, ocellatin 2 and ocellatin 3 . These peptides present haemolytic activity against human erythrocytes and are also active against Escherichia coli . This domain is found associated with the domain

, which contains a signal peptide .
Lantibiotic, type A, Pep5-type (Lantibiotic_typ-A_Pep5)
Type: Family

This family consists of the type A lantibiotic peptides. Both Pep5 and epicidin-280 are ribosomally-synthesised antimicrobial peptides produced by Gram-positive bacteria that are characterised by the presence of lanthionine and/or methyllanthionine residues. The lantibiotics family has a highly specific activity against multi-drug resistant bacteria and has potential to be utilised in a wide range of medical applications .
Frog antimicrobial peptide, brevinin-1 type (Antimicrobial_frog_1)
Type: Domain

This family includes antimicrobial peptides secreted from skins of frogs. The secretion of antimicrobial peptides from the skins of frogs plays an important role in self defence. Structural analysis of these peptides showed that they can be classified into eight families . This is the brevinin-1 family, which includes brevinin-1 but excludes brevinin-2. It also includes lividin-1, Ranalexin, Gaegurin-5 and -6, Jingdongin-1 and Ranatuerin-4. This domain is found associated with the domain

, which contains a signal peptide [

[.
Frog antimicrobial peptide, brevinin-2/esculentin type (Antimicrobial_frog_2)
Type: Domain

This family consists of the major classes of antimicrobial peptides secreted from the skin of frogs that protect the frogs against invading microbes. They are typically between 10-50 amino acids long and are derived from proteolytic cleavage of larger precursors. Major classes of peptides such esculentin, gaegurin, brevinin-2, rugosin and ranatuerin are included in this family .
Spider antimicrobial peptide (Antimicrobial_3)
Type: Family

This family includes antimicrobial peptides isolated from the crude venom of the wolf spider Oxyopes kitabensis (Wolf spider). These peptides, known as oxyopinins, are the largest linear cationic amphipathic peptides chemically characterised and exhibit disrupting activities towards biological membranes .
Ant antimicrobial peptide (Antimicrobial_4)
Type: Family

This family consists of the ponericin (also known as poneritoxin) family of antimicrobial peptides isolated from predatory ant Pachycondyla goeldii (Ponerine ant) and antimicrobial peptides from scorpion species . The ponericin peptides may adopt amphipathic α-helical structure in polar environments. In the ant colony, these peptides exhibit a defensive role against microbial pathogens arising from prey introduction and/or ingestion .
Abaecin, antimicrobial peptide (Abaecin_antimicrobial_peptide)
Type: Family

This entry represents antimicrobial peptides produced by bees. These peptides have strong antimicrobial and some anti-fungal activity and has homology to abaecin which is the largest proline-rich antimicrobial peptide isolated from European bumblebee Bombus pascuorum .
Scorpion antimicrobial peptide (Antimicrobial_7)
Type: Family

This family consists of antimicrobial peptides secreted by scorpions. Novel antimicrobial peptides have been isolated from scorpions, namely Opistoporin , Pandinin , Heterin , Vejovine and Hadrurin . These peptides show amphipathic helical structures and demonstrate high antimicrobial activity .
Uperin (Antimicrobial_8)
Type: Family

This family consists of the uperin family of antimicrobial peptides. Uperin is a wide-spectrum antibiotic peptide isolated from the Australian toadlet, Uperoleia mjobergii. Being only 17 amino acid residues long, it is smaller than most other wide-spectrum antibiotic peptides isolated from amphibians. Uperin adopts a well-defined amphipathic α-helix with distinct hydrophilic and hydrophobic faces .
Ponericin L (Antimicrobial_9)
Type: Family

This family consists of the ponericin L family (also known as poneritoxin) of antimicrobial peptides that are isolated from the venom of the predatory ant Pachycondyla goeldii (Ponerine ant). Ponericin L family shares similarities with dermaseptins. Ponericin L may adopt an amphipathic α-helical structure in polar environments and these peptides exhibit a defensive role against microbial pathogens arising from prey introduction and/or ingestion .
Attractin (Attractin)
Type: Family

This family consists of the attractin family of water-borne pheromone. Mate attraction in Aplysia involves a long-distance water-borne signal in the form of the attractin peptide that is released during egg laying. These peptides contain 6 conserved cysteines and are folded into 2 antiparallel helices. The second helix contains the IEECKTS sequence conserved in Aplysia attractins .
B melanoma antigen-like (BAGE-like)
Type: Family

This family consists of the B melanoma antigen (BAGE) peptides. The BAGE gene encodes a human tumour antigen that is recognised by a cytolytic T lymphocyte. BAGE genes are expressed in melanomas, bladder and lung carcinomas and in a few tumours of other histological types .

This entry also includes bacterial proteins from the Vibrionaceae family.
BDHCT (BDHCT)
Type: Domain

This is a C-terminal domain in RecQ-like DNA helicase BLM subfamily . The helicase participates in DNA replication and repair, exhibiting a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.
YncI, copper-binding domain (YcnI-copper_dom)
Type: Domain

The ycnKJI operon is responsible for regulating copper levels in the Gram-positive bacterium Bacillus subtilis . This operon encodes three Cu-related proteins: a copper-dependent transcriptional repressor (YcnK), a putative copper importer (YcnJ), and a copper-binding protein of unknown function (YcnI). YcnI's extracellular Domain of Unknown Function 1775, represented by this entry, uses a monohistidine brace consisting of an N-terminal histidine residue (H27), a glutamate side chain (E50), and a tryptophan residue (W137) . This domain can be found associated with

at the N-terminal.
Bombolitin (Bombolitin)
Type: Family

This family consists of the bombolitin peptides that are found in the venom of the bumblebee Megabombus pennsylvanicus (American common bumblebee). Bombolitins are structurally and functionally very similar. They lyse erythrocytes and liposomes, release histamine from rat peritoneal mast cells, and stimulate phospholipase A2 from different sources .
Cell division protein Cdc14 (Cell_div_Cdc14)
Type: Family

Cdc14 is a component of the septation initiation network (SIN) and is required for the localisation and activity of Sid1. Sid1 is a protein kinase that localises asymmetrically to one spindle pole body (SPB) in anaphase disappears prior to cell separation , .
Cytomegalovirus US glycoprotein (CMV_US)
Type: Family

This is a family of unique short (US) cytoplasmic glycoproteins which are expressed in cytomegalovirus . In human bodies, US11 participates in the inhibition of the host immune response. It redirects newly synthesized MHC class I heavy chains via the SEC61 translocon to the cytosol where they undergo proteasome-dependent destruction. In consequence, infected cells are masked for immune recognition by cytotoxic T-lymphocytes .
Chloramphenicol resistance gene leader peptide (Cmp-R_leader)
Type: Family

This family consists of chloramphenicol (Cm) resistance gene leader peptides. Inducible resistance to Cm in both Gram-positive and Gram-negative bacteria is controlled by translation attenuation. In translation attenuation, the ribosome-binding-site (RBS) for the resistance determinant is sequestered in a secondary structure domain within the mRNA. Preceding the secondary structure is a short, translated ORF termed the leader. Ribosome stalling in the leader causes the destabilisation of the downstream secondary structure, allowing initiation of translation of the Cm resistance gene .
Cytochrome c oxidase polypeptide 2A (Cyt_c_oxidase_su2a)
Type: Family

This family consists of the cytochrome c oxidase polypeptide 2A family. The ba3-type cytochrome c oxidase from Thermus thermophilus is known as a two subunit enzyme. From its crystal structure, it was discovered that an additional transmembrane helix, subunit IIa, spans the membrane. This subunit consists of 34 residues forming one helix across the membrane. The presence of this subunit seems to be important for the function of cytochrome c oxidases .
Crustacean cuticle (Cuticle_1)
Type: Family

This family consists of the cuticle proteins from the Cancer pagurus (Rock crab) and the Homarus americanus (American lobster). These proteins are isolated from the calcified regions of the crustacean and they contain two copies of an 18 residue sequence motif, which thus far has been found only in crustacean calcified exoskeletons .
Cuticle 7 isoform (Cuticle_2)
Type: Family

This family consists of cuticle protein 7 isoforms that are isolated from the carapace cuticle of a juvenile horseshoe crab, Limulus polyphemus. There are 3 isoforms of cuticle protein 7. The 3 isoforms are N-terminally blocked but could be deblocked by treatment with pyroglutaminase, showing that the N-terminal residue is a pyroglutamine residue .
DBP10, C-terminal (DBP10_C)
Type: Domain

This group of DEAD-box RNA helicases includes Dbp10 from fungi, DDX54 (also known as DP97) from mammals and RH29 from plants. DDX54 interacts in a hormone-dependent manner with nuclear receptors . It plays an important role in central nervous system myelination . Dbp10 has a role in ribosome biogenesis . RH29 is essential for the functional maturation of both male and female gametophytes .
DTHCT (DTHCT)
Type: Domain

The DTCHT region is the C-terminal part of DNA gyrases B / topoisomerase IV / HATPase proteins . This region is composed of quite low complexity sequence.
Protein of unknown function DUF1694 (DUF1694)
Type: Family

This family contains many hypothetical proteins.
Bacterial Pleckstrin homology domain (PHb)
Type: Domain

This domain can be found in many bacterial hypothetical proteins. The structures of

,

, and

,

, show similarities to the PH or pleckstrin homology domain. The first evidence of PH-like domains in bacteria suggests a role in cell envelope stress response .
Protein of unknown function DUF1697 (DUF1697)
Type: Family

This family contains many hypothetical bacterial proteins.
Protein of unknown function DUF1699 (DUF1699)
Type: Family

This family contains many archaeal proteins which have very conserved sequences.
PD-(D/E)XK nuclease superfamily 9 (PDDEXK_9)
Type: Family

This family contains many hypothetical bacterial proteins. It has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches. Proteins in this family have the predicted secondary structure pattern of the restriction endonuclease-like fold core and contains an additional β-strand at the C terminus .
Microtubule-associated tyrosine carboxypeptidase (MATCAP)
Type: Family

This entry includes microtubule-associated tyrosine carboxypeptidases, proteins that remove the C-terminal tyrosine residue of alpha-tubulin, thereby regulating microtubule dynamics and function . They are also able to remove the C-terminal phenylalanine residue of alpha-tubulin TUBA8 . These proteins recognise adjacent tubulin dimers along the same protofilament .
Phosphoethanolamine transferase, N-terminal (EptA-like_N)
Type: Domain

This entry represents a domain found in a group of bacterial phosphoethanolamine transferases, including EptA from Helicobacter pylori and Neisseria meningitidis , and EptA/EptB/EptC from Escherichia coli . This domain is found immediately N-terminal to the sulphatase domain in many sulphatases.

The structure of EptA from Neisseria meningitidis has been solved. This entry represents the N-terminal transmembrane domain of EptA .
Protein of unknown function DUF1706 (DUF1706)
Type: Family

This family contains many hypothetical proteins from bacteria and yeast. Proteins in this entry include Irc4 (increased recombination centres 4) from budding yeast .
DUF1707 SHOCT-like domain (DUF1707_SHOCT-like)
Type: Domain

This domain is found in a variety of actinomycetales proteins. All of the proteins containing this domain are uncharcterised and probably membrane bound or associated. Currently, it is unclear to the function of this domain.