SII-SWORD/CoKE huggingface dataset:
RepA1 leader peptide Tap (RepA1_leader_peptide_Tap)
Type: Family

This entry represents of the RepA1 leader peptide known as Tap found in IncFII plasmids. The frequency of replication of IncFII plasmid NR1 during the cell division cycle is regulated by the control of the synthesis of the plasmid-specific replication initiation protein (RepA1). When RepA1 is synthesised, it binds to the plasmid replication origin (ori) and effects the assembly of a replication complex composed of host proteins that mediate the replication of the plasmid . The tap gene encodes a 24-amino acid peptide whose translation is required for the translation of repA.
Small ribosomal subunit protein uS15, N-terminal (Ribosomal_uS15_N)
Type: Domain

This domain is found at the N terminus of ribosomal uS15 proteins.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Ribosome hibernation factor SRA (SRA-like)
Type: Family

This family represents the stationary-phase-induced ribosome-associated protein SRA also known as protein D. This protein was originally thought to be a ribosomal protein . More recently it was shown that this is a bona fide ribosome hibernation factor that together with the factors Rmf, Hpf and RaiA is bound to the ribosomes during the onset and a few first days of the stationary phase when translation is strongly suppressed. In the prolonged stationary phase, these factors dissociate from the ribosomes .
Sex peptide (Sex_peptide)
Type: Family

This family consists of Sex Peptides (SP) that are found in Drosophila. On mating, Drosophila females decreases her remating rate and increases her egg-laying rate due, in part, to the transfer of SP from the male to the female. SP are found in seminal fluids transferred from the male to the female during mating. The male seminal fluid proteins are referred to as accessory gland proteins (Acps). The SP is one of the most interesting Acps and plays an important role in reproduction .
Sporulation stage V, protein M (Spore_V_M)
Type: Family

This family consists of the stage V sporulation (SpoV) proteins of Bacillus subtilis which includes SpoVM. SpoVM is an small, 26 residue-long protein that is produced in the mother cell chamber of the sporangium during the process of sporulation in B. subtilis. SpoVM forms an amphipathic α-helix and is recruited to the polar septum shortly after the sporangium undergoes asymmetric division. The function of SpoVM depends on proper subcellular localisation .
Small acid-soluble spore protein, SspH (SASP_SspH)
Type: Family

This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organism. The sspH genes are monocistronic and are recognised by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties .
Small acid-soluble spore protein, SspK (SASP_SspK)
Type: Family

This family consists of the small acid-soluble spore proteins (SASP) belonging to the K type (sspK). The sspK are unique to the spores of Bacillus subtilis and are expressed only in the forespore compartment of sporulating cells of this organism. The sspK gene is monocistronic and transcription is primarily by the RNA polymerase with the forespore-specific sigma factor, sigma-G. Mutation deleting sspK results in loss of SspK from the spore but had no discernible effect on sporulation, spore properties or spore germination .
Small acid-soluble spore protein, SspN (SASP_SspN)
Type: Family

This family consists of the small acid-soluble spore protein (SASP) N type (sspN). SspN is a 48 residues protein that is expressed only in the forespore compartment of sporulating Bacillus subtilis. The sspN gene is recognised equally by both sigma-G and sigma-F. The role of SspN is still not well-defined .
Small acid-soluble spore protein, SspO (SASP_SspO)
Type: Family

This family consists of the small acid-soluble spore proteins (SASP) O type (sspO). SspO (originally cotK) are unique to the spores of Bacillus subtilis and are expressed only in the forespore compartment of sporulating cells of this organism. The sspO is the first gene in a likely operon with sspP and transcription of this gene is primarily by RNA polymerase with the forespore-specific sigma factor, sigma-G. Mutation deleting sspO causes the loss of the SspO from the forespore but had no discernible effect on sporulation, spore properties or spore germination .
Small acid-soluble spore protein, SspP (SASP_SspP)
Type: Family

This family consists of the small acid-soluble spore proteins (SASP) P type (sspP). sspP is expressed only in the forespore compartment of the sporulating cell. sspP is also expressed under sigma-G control from the same promoter as sspO. Mutations deleting sspP causes no discernible effect on sporulation, spore properties or spore germination .
Trematode Eggshell Synthesis (TES)
Type: Family

Proteins in this family have been identified in a number of distantly related species of trematodes. This protein is crucial for eggshell synthesis in trematodes .
CDP-alcohol phosphatidyltransferase, C-terminal (CDP-OH_P_trans_C)
Type: Domain

This domain is found on CDP-alcohol phosphatidyltransferases. These enzymes catalyse the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond.
Apoptosis-antagonizing transcription factor, C-terminal (AATF_C)
Type: Domain

This C-terminal domain is found in apoptosis-antagonizing transcription factor (AATF) proteins . This is the domain of the AATF proteins that interacts with BLOS2 or Ceap, that functions as an adaptor in processes such as protein and vesicle processing and transport, and perhaps transcription.
Myoactive tetradecapeptides (Tetradecapep)
Type: Family

This entry consists of myoactive tetradecapeptides that are isolated from the gut of Earthworms, Eisenia foetida (Common brandling worm) and Pheretima vittata (Earthworm). These peptides were termed ETP and PTP respectively. Both peptides showed a potent excitatory action on spontaneous contractions of the anterior gut. These peptides show similarity to Molluscan tetradecapeptides and Arthropodan tridecapeptides .
Tryptophanese operon leader peptide (Trp_operon_leader_peptide)
Type: Family

This entry defines the apparent leader peptides of tryptophanase operons in Escherichia coli, Vibrio cholerae, Photobacterium profundum, Haemophilus influenzae, and related species. It has been suggested that these peptides act in cis to alter the behaviour of the translating ribosome .

The tryptophanese (tna) operon leader peptide catalyses the degradation of L-tryptophan to indole, pyruvate and ammonia, enabling the bacteria to utilise tryptophan as a source of carbon, nitrogen and energy. The tna operon of Escherichia coli contains two major structural genes, tnaA and tnaB. Preceding tnaA in the tna operon is a 319 -nucleotide transcribed regulatory region that contains the coding region for a 24-residue leader peptide, TnaC. The RNA sequence in the vicinity of the tnaC stop codon is rich in Cytidylate residues which is required for efficient Rho -dependent termination in the leader region of the tna operon .
Mitochondrial import receptor subunit TOM7 (Tom7)
Type: Family

This family consists of mitochondrial import receptor subunit TOM7. TOM7 forms part of the translocase of the outer mitochondrial membrane (TOM) complex and it appears to function as a modulator of the dynamics of the mitochondrial protein transport machinery by promoting the dissociation of subunits of the outer membrane translocase .
Potassium channel toxin gamma/Ergtoxin (Ergtoxin)
Type: Family

The Ergtoxin (ErgTx) family is a class of peptides from scorpion venom that specifically block ERG (ether-a-go-go-related gene) K+ channels of the nerve, heart and endocrine cells .
Conotoxin O-superfamily (Toxin_18)
Type: Family

This family consists of members of the conotoxin O-superfamily. The O-superfamily of conotoxins consists of 3 groups of Conus peptides that belong to the same structural group. These 3 groups differ in their pharmacological properties: the w-conotoxins which inhibit calcium channels, the delta-conotoxins which slow down the inactivation rate of voltage -sensitive sodium channels and the muO-conotoxins block the voltage sensitive sodium currents .
Conotoxin I-superfamily (Toxin_19)
Type: Family

This family consists of the I-superfamily of conotoxins. This is a new class of peptides in the venom of some Conus species. These toxins are characterised by four disulphide bridges and inhibit of modify ion channels of nerve cells. The I-superfamily conotoxins is found in five or six major clades of cone snails and could possible be found in many more species .
Huwentoxin-II-like (Hwtx-2-like)
Type: Family

This entry mainly consists of the huwentoxin-II (HWTX-II) family of toxins secreted by spiders. These toxins are found in venom that secreted from the bird spider Selenocosmia huwena Wang. The HWTX-II adopts a novel scaffold different from the ICK motif that is found in other huwentoxins. HWTX-II consists of 37 amino acids residues including six cysteines involved in three disulphide bridges .
Spider insecticidal peptide (Spider_insecticidal_peptide)
Type: Family

This family consists of insecticidal peptides isolated from venom of spiders of Aptostichus schlingeri (Trap-door spider) and Calisoga sp. Nine insecticidal peptides were isolated from the venom of the A. schlinger spider and seven of these toxins cause flaccid paralysis to insect larvae within 10 min of injection. However, all nine peptides were lethal within 24 hours . The structure of Aps III was solved and shown to be an atypical knottin peptide with four disulphide bridges .
Magi peptide toxin (Toxin_22)
Type: Family

This family consists of Magi peptide toxins from spiders, including Magi 1, 2 and 5 from Macrothele gigas (Japanese funnel web spider). These insecticidal peptide toxins bind to sodium channels and induce flaccid paralysis when injected into lepidopteran larvae. However, these peptides are not toxic to mice when injected intracranially at 20 pmol/g .
Magi 5 toxic peptide (Toxin_23)
Type: Family

This family consists of toxic peptides (Magi 5) found in the venom of the Hexathelidae spider. Magi 5 is the first spider toxin with binding affinity to site 4 of a mammalian sodium channel and the toxin has an insecticidal effect on larvae, causing paralysis when injected into the larvae.

This entry also includes some proteins from the omega-atracotoxin type 2 family.
Conotoxin TVIIAGS (Conotoxin_TVIIAGS)
Type: Family

This family consists of conotoxins isolated from the venom of cone snail Conus tulipa and Conus geographus. Conotoxin TVIIA, isolated from Conus tulipa displays little sequence homology with other well-characterised pharmacological classes of peptides, but displays similarity with conotoxin GS, a peptide from Conus geographus. Both these peptides block skeletal muscle sodium channels and also share several biochemical features and represent a distinct subgroup of the four-loop conotoxins .
Hefutoxin (Toxin_25)
Type: Family

This family consists of the hefutoxins that are found in the venom of the scorpion Heterometrus fulvipes (Indian black scorpion). These toxins, kappa-hefutoxin1 and kappa-hefutoxin2, exhibit no homology to any known toxins. The hefutoxins are potassium channel toxins .
Conotoxin T-superfamily (Toxin_26)
Type: Family

This family consists of the T-superfamily of conotoxins. Eight different T-superfamily peptides from five Conus species were identified. These peptides share a consensus signal sequence, and a conserved arrangement of cysteine residues. T-superfamily peptides were found expressed in venom ducts of all major feeding types of Conus, suggesting that the T-superfamily is a large and diverse group of peptides, widely distributed in the 500 different Conus species .
Scorpion calcine (Scorpion_calcine)
Type: Family

Toxins of the scorpion calcine family bind directly to ryanodine receptors (RyRs), intracellular channel targets of the endoplasmic reticulum, and induce long lasting channel openings in a mode of smaller conductance. They have the ability to translocate into cells by crossing the plasma membrane .

Toxins of scorpion calcine family are highly basic 33-amino acid peptides that present three disulphide bridges (C1-C4, C2-C5, and C3-C6) and fold along a knottin or inhibitor cystine knot motif (https://www.dsimb.inserm.fr/KNOTTIN/) . Their three dimensional structure consists of a compact disulphide-bonded core from which emerge loops and the N terminus. The main element of regular secondary structure is a double-stranded antiparallel β-sheet. A third peripheral extended strand is almost perpendicular to the double-stranded antiparallel β-sheet . Scorpion calcine mimic the activating segment of the dihydropyridine receptor II-III loop, which interacts with a region of the ryanodine receptor .
SFI toxin (Toxin_28)
Type: Family

This family consists of the SFI family of spider toxins. This family of toxins might share structural, evolutionary and functional relationships with other small, highly structurally constrained spider neurotoxins. These toxins are highly selective agonists/antagonists of different voltage-dependent calcium channels and are extremely valuable reagents in the analysis of neuromuscular function.
PhTx neurotoxin (Toxin_29)
Type: Family

This family consists of PhTx insecticidal neurotoxins that are found in the venom of Phoneutria nigriventer (Brazilian armed spider). The venom of the P. nigrivente contains numerous neurotoxic polypeptides of 30-140 amino acids, which exert a range of biological effects. While some of these neurotoxins are lethal to mice after intracerebroventricular injections, others are extremely toxic to insects of the orders Diptera and Dictyoptera but had much weaker toxic effects on mice .
Parabutoxin (Parabutoxin)
Type: Family

This entry represents proteins that are acidic alpha-KTx short chain scorpion toxins. These toxins are named parabutoxins, that binds and inhibit voltage-sensitive potassium channels and inhibit the vertebrate potassium channel Kv1.1 with low affinity. Furthermore, they lack the crucial pore-plugging lysine. In addition, the second important residue of the dyad, the hydrophobic residue (Phe or Tyr) is also missing .
Tamulustoxin (Toxin_32)
Type: Family

This family consists of the tamulustoxins, which are found in the venom of Mesobuthus tamulus (Eastern Indian scorpion) (Buthus tamulus). Tamulustoxin shares no similarity with other scorpion venom toxins, although the positions of its six cysteine residues suggest that it shares the same structural scaffold. Tamulustoxin acts as a potassium channel blocker .
Waglerin (Toxin_33)
Type: Family

This family consists of the lethal peptides (waglerins) that are found in the venom of Trimeresurus wagleri (Wagler's pit viper) (Tropidolaemus wagleri). Waglerins are 22-24 residue lethal peptides and are competitive antagonist of the muscle nicotinic receptor (nAChR). Waglerin-1 possesses a distinctive selectivity for the α-ε interface binding site of the mouse nAChR .
Tryptophan leader peptide (Trp_leader1)
Type: Family

This family consists of tryptophan (trp) leader peptides from Streptomyces spp . Tryptophan accumulation is the principal event resulting in down regulation of transcription of the structural genes of the trp operon. The leader peptide of the trp operon forms mutually exclusive secondary structures that would either result in the termination of transcription of the trp operon when tryptophan is in plentiful supply or vice versa .
Tryptophan operon leader peptide (Trp_leader2)
Type: Family

This family consists of the tryptophan operon leader peptides, which are important for the control of tryptophan biosynthesis. The tryptophan operon is regulated by transcription attenuation in response to changes in the level of tryptophan. The transcript of the leader peptide can adopt alternative mutually-exclusive secondary structures that would either result in termination of transcription of the tryptophan structural genes or in transcription of the entire operon .
Membrane lipoprotein, lipid attachment site (Membr_lipoprot_lipid_attach_CS)
Type: Conserved_site

In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognises a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached .

This lipid attachment site is found in homologues of the VirB proteins of type IV secretion systems (T4SS). Conjugal transfer across the cell envelope of Gram-negative bacteria is mediated by a supramolecular structure termed mating pair formation (Mpf) complex. Collectively, secretion pathways ancestrally related to bacterial conjugation systems are now known as T4SS. T4SS are involved in the delivery of effector molecules to eukaryotic target cells; each of these systems exports distinct DNA or protein substrates to effect a myriad of changes in host cell physiology during infection .
Cysteine rich domain, Polydnavirus (Polydnavirus_Cys-rich)
Type: Domain

This entry represents a cysteine rich motif found in a group of proteins from Polydnavirus . Some proteins have multiple copies of this domain.
Transcription regulator Wos2-domain (Tscrpt_reg_Wos2-domain)
Type: Domain

Proteins containing the Wos2 domain are involved in the regulation of the cell cycle and are Myb-related transcriptional activators.
Wound-inducible basic (Wound_ind)
Type: Family

This family consists of the wound-inducible basic proteins from plants. The metabolic activities of plants are dramatically altered upon mechanical injury or pathogen attack. A large number of proteins accumulates at wound or infection sites, such as the wound-inducible basic proteins. These proteins are small, 47 amino acids in length, has no signal peptides and are hydrophilic and basic .
Conserved hypothetical protein CHP02300, FYDLN acid (CHP02300_FYDLN_acid)
Type: Family

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Conserved hypothetical protein CHP02301 (CHP02301)
Type: Family

Members of this uncharacterised protein family are found in a number of alphaproteobacteria, including root nodule bacteria, Brucella suis, Caulobacter crescentus (Caulobacter vibrioides), and Rhodopseudomonas palustris. Conserved residues include two well-separated cysteines, suggesting a disulphide bond. The function is unknown.
RNA ligase, DRB0094 (RNA_ligase_DRB0094)
Type: Family

RNA repair, though not as well characterised as DNA repair, is an important component of many biological systems. These include the kinteoplastid RNA-editing process and the defence of Bacteriophage T4 against tRNA damage caused by host nucleases. RNA ligase is an essential enzyme in the process of RNA repair . It is part of the broader nucleotidyl transferase superfamily which includes DNA ligase and RNA capping enzymes, and has the same basic mechanism as other memebers of this family. The RNA ligase family is divided into two distinct branches: the Rnl-1 like proteins, found only in viruses and fungi so far, and the Rnl2-like proteins which have been found in all three kingdoms of life.

This entry represents a small group of known and predicted RNA ligases found in some bacterial and phage species. The best characterised memeber is found in Deinococcus radiodurans, a bacterium capable of withstanding a variety of adverse environmental conditions including extreme amounts of radiation. Ligase activity is apparently specific to nicks within either duplex RNA or an RNA:DNA hybrid and is dependenton divalent cations such as manganese . These proteins have a distinctive domain structure, lacking the C-terminal domain observed in other Rnl2-like ligases, and possesing a distinctive N-terminal domain not found in other ligases but which is important for catalytic activity.
RNA ligase, Rnl2 (RNA_lig_RNL2)
Type: Family

Members of this family ligate (seal breaks in) RNA. Members so far include phage proteins that can counteract a host defence of cleavage of specific tRNA molecules and trypanosome ligases involved in RNA editing .
T4 RNA ligase 1 (Rnl1)
Type: Family

Members of this family are phage proteins with ATP-dependent RNA ligase activity. Host defence to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage . The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL. The structure of T4 RNA ligase 1 ligase has been revealed .
Phosphonopyruvate hydrolase (PPH)
Type: Family

This family consists of phosphonopyruvate hydrolase (PPH), an enzyme closely related to phosphoenolpyruvate phosphomutase. It cleaves the direct C-P bond of phosphonopyruvate. The characterised example is from Variovorax sp. Pal2 .
Conserved hypothetical protein CHP02328 (CHP02328)
Type: Family

Members of this family are found in a small number of taxonomically well-separated species, yet are strongly conserved, suggesting lateral gene transfer. Members are found in Treponema denticola, Clostridium acetobutylicum, and several of the firmicutes. The function of this protein is unknown.