SII-SWORD/CoKE huggingface dataset:
DVL (DVL)
Type: Family

This family consists of the DVL family of proteins. In a gain-of-function genetic screen for genes that influence fruit development in Arabidopsis, DEVIL (DVL) gene was identified. DVL (also known as Small polypeptide ROTUNDIFOLIA) is a small protein and over expression of the protein results in pleiotropic phenotypes featured by shortened stature, rounder rosette leaves, clustered inflorescences, shortened pedicles, and siliques with pronged tips. DVL family is a novel class of small polypeptides and the overexpression phenotypes suggest that these polypeptides may have a role in plant development playing a role as negative regulators of cell proliferation .
Defensin-like peptide (Defensin_3)
Type: Family

This family consists of the defensin-like peptides (DLPs) isolated from duckbill platypus (Ornithorhynchus anatinus) venom. These DLPs show similar three-dimensional fold to that of beta-defensin-12 and sodium-channel neurotoxin Shl. However the side chains known to be functionally important to beta-defensin-12 and Shl are not conserved in DLPs. This suggests a different biological function. Consistent with this contention, DLPs have been shown to possess no anti-microbial properties and have no observable activity on rat dorsal-root-ganglion sodium-channel currents .
Degradation enzyme regulation protein DegQ (DegQ)
Type: Family

This family consists of the DegQ (formerly sacQ) regulatory peptides. The DegQ family of peptides control the rates of synthesis of a class of both secreted and intracellular degradative enzymes in Bacillus subtilis and related bacteria . DegQ is 46 amino acids long and activates the synthesis of degradative enzymes. The expression of this peptide was shown to be subjected both to catabolite repression and DegS-DegU-mediated control. Thus allowing an increase in the rate of synthesis of DegQ under conditions of nitrogen starvation . DegQ also affects lipopeptide production and formation of secretory proteases .
Major transforming E5 (EPV_E5)
Type: Family

This family consists of the major transforming proteins (E5) of the bovine papilloma virus (BPV). The equine sarcoid is one of the most common dermatological lesion in equids. It is a benign, locally invasive dermal fibroblastic lesion and studies have shown an association of the lesions with BPV. E5 is a short hydrophobic membrane protein localising to the Golgi apparatus and other intracellular membranes. It binds to and constitutively activates the platelet-derived growth factor-beta in transformed cells. This stimulation activates a receptor signalling cascade which results in an intracellular growth stimulatory signal .
Entericidin A/B (Entericidin)
Type: Family

This family consists of the entericidin antidote/toxin peptides. The entericidin locus is activated in stationary phase under high osmolarity conditions by rho-S and simultaneously repressed by the osmoregulatory EnvZ/OmpR signal transduction pathway. The entericidin locus encodes tandem paralogous genes (ecnAB) and directs the synthesis of two small cell-envelope lipoproteins (EcnA and EcnB) which can maintain plasmids in bacterial population by means of post-segregational killing .

The product of the entericidin locus has been shown to have bactericidal activity against the fish pathogen Flavobacterium psychrophilum .
Heat stable enterotoxin, EAST1 (Heat-stable_enterotox_EAST1)
Type: Family

Heat-stable toxin 1 of entero-aggregative Escherichia coli (EAST1) is a small toxin. It is not, however, solely associated with entero-aggregative E. coli but also with many other diarrhoeic E. coli families. Some studies have established the role of EAST1 in some human outbreaks of diarrhoea. Isolates from farm animals have been shown to carry the astA gene coding for EAST1. However, the relation between the presence of EAST1 and disease is not conclusive .
Erythromycin resistance leader peptide-1 (Emycin-R_leader_pep1)
Type: Family

This family consists of erythromycin resistance gene leader peptides. These leader peptides are involved in the translational attenuation of erythromycin resistance genes. Interestingly, the consensus sequence of peptides conferring erythromycin resistance is similar to that of the leader peptides, thus indicating that a similar type of interaction between the nascent peptide and antibiotics can occur in both cases .
Erythromycin resistance leader peptide-2 (Emycin-R_leader_pep2)
Type: Family

This family consists of erythromycin resistance gene leader peptides. These leader peptides are involved in the transcriptional attenuation control of the synthesis of the macrolide-lincosamide -streptogramin B resistance protein. It acts as a transcriptional attenuator, in contrast to other inducible erm genes. The mRNA leader sequence can fold in either of two mutually exclusive conformations, one of which is postulated to form in the absence of induction, and to contain two rho factor-independent terminators .
Ferlin A-domain (Ferlin_A-domain)
Type: Domain

The ferlin gene family are characterised by multiple tandem C2 domains and a C-terminal transmembrane domain. They are found in a wide range of species and their function remains unknown, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease .

This is central domain A in proteins of the Ferlin family .
Ferlin B-domain (Ferlin_B-domain)
Type: Domain

The ferlin gene family are characterised by multiple tandem C2 domains and a C-terminal transmembrane domain. They are found in a wide range of species and their function remains unknown, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease .

This is central domain B in proteins of the Ferlin family .
GUCT (GUCT)
Type: Domain

This is the C-terminal domain found in the RNA helicase II / Gu protein family .
Gns (Gns)
Type: Family

This family consists of the Gns/GnsA/GnsB proteins. GnsA and GnsB are multicopy suppressors of the cold-sensitive secG null mutation. These proteins participate in the synthesis of phospholipids, suggesting the functional relationship between SecG and membrane phospholipids. Overexpression of gnsA and gnsB causes a remarkable increase in the unsaturated fatty acid content. However, the gnsA-gnsB double null mutant exhibits no effect. Both proteins are predicted to possess a helix-turn-helix structure .
Herpesvirus UL74, glycoprotein (Herpes_UL74)
Type: Family

Members of this family are viral glycoproteins that form part of an envelope complex .
Histidine operon leader peptide (His_leader)
Type: Family

This family consists of the leader peptide of the histidine (his) operon. The his operon contains all the genes necessary for histidine biosynthesis. The region corresponding to the untranslated 5'-end of the transcript, named the his leader region, displays the typical features of the T box transcriptional attenuation mechanism which is involved in the regulation of many amino acid biosynthetic operons .
IlvB leader peptide (IlvB_leader)
Type: Family

This family consists of the leader peptides of the ilvB operon. This operon contains the structural gene for acetohydroxy acid synthase I, an enzyme required for the biosynthesis of valine and isoleucine. The DNA sequence of the ilvB operon promoter-control region encodes a potential leader polypeptide containing 32 amino acids, 12 of which are valine or leucine. A model for the multivalent regulation of this operon by valyl- and leucyl-tRNA is proposed on the basis of the mutually exclusive formation of five strong stem-and-loop structures in the leader mRNA .
IlvGEDA operon leader peptide (IlvGEDA_leader)
Type: Family

This family consists of the leader peptides of ilvGEDA operon. The expression of the ilvGEDA operon of E coli K-12 is multivalently controlled by the three branched -chain amino acids. Regulation is thought to occur by attenuation of transcription in response to the changing levels of the cognate tRNAs. Transcription of this operon is usually terminated at the end of the leader (regulatory) region .
KI67R (KI67R)
Type: Repeat

This entry represents the KI67/Chmadrin repeat . It can be found in the human antigen KI-67 protein . The function of this repeat is unknown.
Internalin, Ig-like inter-repeat region (Inl_IR)
Type: Domain

These are small, all β-strand domains, structurally described for the protein Internalin (InlA) and related proteins InlB, InlC, InlH from the pathogenic bacterium Listeria monocytogenes, in which it has been described as Ig-like inter-repeat (IR) region. Their function appears to be mainly structural: they are fused to the C-terminal end of leucine-rich repeats (LRR), significantly stabilising the LRR, and forming a common rigid entity with the LRR. They are themselves not involved in protein-protein interactions but help to present the adjacent LRR-domain for this purpose. These domains belong to the family of Ig-like domains in that they consist of two sandwiched β-sheets that follow the classical connectivity of Ig-domains. The β-strands in one of the sheets is, however, much smaller than in most standard Ig-like domains, making it somewhat of an outlier .
Leucine operon leader peptide (Leu_leader)
Type: Family

This family consists of the leucine operon leader peptide. The leucine operon is involved in the control of the biosynthesis of leucine. Four adjacent leucine codons within the leucine leader RNA are critically important in transcription attenuation-mediated control of leucine operon expression in bacteria. The leader RNA contains translational start and stop signals, a cluster of four leucine codons and overlapping regions of dyad symmetry that are capable of forming stem-and-loop structures .
Mitochondrial distribution and morphology protein family 31/32, fungi (Mdm31/Mdm32)
Type: Family

Proteins in this family are yeast mitochondrial inner membrane proteins Mdm31 and Mdm32. They are required for the maintenance of mitochondrial morphology, and the stability of mitochondrial DNA . Mdm31 plays important roles in phospholipid biosynthesis in mitochondria .
Mad3/Bub1 homology region 2 (Mad3/Bub1_II)
Type: Domain

This domain is found in checkpoint proteins which are involved in cell division. This region has been shown to be necessary and sufficient for the binding of Mad3 to Bub3 in Saccharomyces cerevisiae. This domain is present in Bub1 which also binds Bub3 .
Meleagrin/Cygnin (Meleagrin/Cygnin)
Type: Family

This family consists of meleagrin and cygnin basic peptides that are isolated from turkey and black swan respectively. Both peptides are low in molecular weight and contain three disulphide bonds with high concentrations of aromatic residues. These peptides show similarity to transferrins and probably play some vital role in avian eggs but the exact function is still unknown .
ATP synthase subunit ATP5MJ, mitochondrial (ATP5MJ)
Type: Family

ATP5MJ (also known as ATP5MPL and MLQ) is a hydrophobic mitochondrial protein and a regulator of the mitochondrial ATP synthesis .
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 (NDUB1)
Type: Family

This family consists of the subunit 1 (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 NDUB1 or NDUFB1, also known as MNLL subunit) of NADH:ubiquinone oxidoreductase complex . This is an accessory subunit of complex I, not involved in catalysis .
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 (NDUFB3)
Type: Family

This family represents an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain .
NIPSNAP (NIPSNAP)
Type: Domain

Proteins containing this domain include many hypothetical proteins. It also includes members of the NIPSNAP family, which have putative roles in vesicular transport . This domain is often found in duplicate.
Nuclear pore complex component (Nucl_pore_cmplx)
Type: Family

Proteins containing this domain are components of the nuclear pore complex . One member of this domain is Nucleoporin POM34 (

) which is thought to have a role in anchoring peripheral Nups into the pore and mediating pore formation .
U3 small nucleolar RNA-associated protein NOL7, C-terminal (NOL7_C)
Type: Domain

This entry represents the C-terminal domain of human U3 small nucleolar RNA-associated protein NOL7 (also known as Nucleolar protein 7) and similar proteins from vertebrates. NOL7 is part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit and has been reported to act as a tumour suppressor . It plays a role in early pre-rRNA accumulation and processing
NUC153 (NUC153)
Type: Domain

This small domain is found in a novel nucleolar family .
DNA-dependent protein kinase catalytic subunit, CC3 (DNAPKcs_CC3)
Type: Domain

This domain represents a region of the Circular Cradle segment (CC) from DNA-PKcs that covers the complete CC3 and part of CC4. This domain contains the Ku-binding site A and a the highly conserved region (HCR) II .

DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is involved in DNA nonhomologous end joining (NHEJ), which is recruited by Ku70/80 heterodimer to DNA ends and required for double-strand break (DSB) repair. DNA-PKcs phosphorylates a number of protein substrates, including the heat shock protein 90 (HSP90), the transcription factors p53, specificity protein 1 (Sp1) and MYC23, and a majority of NHEJ factors. It folds into three well-defined large structural units, consisting of a N-terminal region (arranged in four supersecondary α-helical structures, N1 to N4), the Circular Cradle (consisting of five supersecondary α-helical structures CC1 to CC5), and the C-terminal Head (comprising FAT, FRB, kinase, and FATC). The N-terminal and CCs regions resemble HEAT repeats, and thus, they are also referred to as N-HEAT and M-HEAT ('middle'), respectively. The N-terminal region likely mediates DNA binding and, together with the CCs, forms a ring through which Ku70/80 may present DNA for repair. The CCs form a curved elliptical ring that serves as a scaffold to maintain the integrity of the whole complex. It has been suggested that the binding of Ku or DNA activates the allosteric mechanism required for communication between the N terminus and the CC with the kinase in the Head .
Pre-rRNA-processing protein RIX1, N-terminal (RIX1_N)
Type: Domain

Rix1 is a nucleoplasmic particle involved in rRNA processing/ribosome assembly . It associates with two other proteins, Ipi1 and Ipi3, to form the RIX1 complex that allows Rea1 - the AAA ATPase - to associate with the 60S ribosomal subunit. More than 170 assembly factors are involved in the construction and maturation of yeast ribosomes, and after these factors have completed their function they need to be released from the pre-ribosomes. Rea1 induces the release of the assembly protein complex in a mechanical fashion . This family is usually associated with NUC202,

.
Nucleolar protein 11, N-terminal domain (NOL11_N)
Type: Domain

This entry covers a section of the β-propeller found at the N terminus of NOL11 .

NOL11 is a nucleolar protein and a component of the human ribosomal small subunit (SSU) processome. It is required for the early stages of ribosome biogenesis in humans . It interacts with the C-terminal region of the known t-UTP/UTPA subcomplex member, hUTP4/Cirhin, the protein mutated in North American Indian childhood cirrhosis (NAIC) . In Xenopus, it is required for optimal rDNA transcription and craniofacial development .
Anticodon nuclease activator Stp (Stp)
Type: Family

This family represents the anticodon nuclease activator protein Stp. Pre-existing host tRNAs are reprocessed during Bacteriophage T4 infection of certain Escherichia coli strains. In this pathway, tRNA(Lys) is cleaved 5, by the anticodon nuclease to the wobble base and is later restored in polynucleotide kinase and RNA ligase reactions . The second function of Stp is the inhibition of EcoprrI restriction .
28S rRNA (cytosine-C(5))-methyltransferase repeat (NOP2_rpt)
Type: Repeat

This entry represents a characteristic repeat of 28S rRNA (cytosine-C(5))-methyltransferase (NOP2, also known as proliferating cell nuclear antigen p120), which is found in three copies . NOP2 is involved in ribosomal large subunit assembly . It is an S-adenosyl-L-methionine-dependent methyltransferase that specifically methylates the C5 position of cytosine 4447 in 28S rRNA.
RNA helicase p68 repeat (P68_rpt)
Type: Repeat

This short region is found in two copies in RNA helicase p68 (DDX5), which is involved in the alternative regulation of pre-mRNA splicing; its RNA helicase activity is necessary for increasing tau exon 10 inclusion and occurs in a RBM4-dependent manner .
Exosome-associated factor Rrp6, N-terminal (Exosome-assoc_fac_Rrp6_N)
Type: Domain

Exosomes are nano-compartments that function in the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA) . Exosomes occur in both archaea and eukaryotes, and have a similar overall structure to each other and to bacterial/organelle PNPases (polynucleotide phosphorylases;

) , consisting of a barrel structure composed of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber . There are two types of exosomes in eukaryotes, cytoplasmic exosomes that are responsible for 3'-5' exoribonuclease degradation of mRNAs, and nuclear exosomes that degrade pre-mRNAs (such as nonsense transcripts) and degrade rRNAs, snRNAs and snoRNAs. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel .
Plasma membrane ATPase proteolipid (Pmp1/Pmp2)
Type: Family

Pmp1 and its paralogue, Pmp2, are small single-spanning membrane proteins functioning as a regulatory subunit of the yeast plasma membrane H(+)-ATPase . Pmp1 forms a unique helix and exhibits a positively charged cytoplasmic domain that is able to specifically segregate phosphatidylserines (PSs) .
POPLD domain (POPLD_dom)
Type: Domain

Ribonucleases P/MRP protein subunit POP1 is a subunit common to both ribonuclease P, a ribonucleoprotein complex that generates mature tRNA molecules by cleaving their 5'-ends , and MRP ribonuclease complex, which cleaves pre-rRNA sequences . This domain is found towards the C-terminal of POP1 .
PRO8NT domain (PRO8NT)
Type: Domain

The PRO8NT domain is found at the N terminus of pre-mRNA splicing factors of PRO8 family . The NLS or nuclear localisation signal for these spliceosome proteins begins at the start and runs for 60 residues. N-terminal to this domain is a highly variable proline-rich region .
PROCN domain (PROCN)
Type: Domain

The PROCN domain is the central domain in pre-mRNA splicing factors of PRO8 family .
Pea-VEAacid (Pea-VEAacid)
Type: Family

This family consists of the PEA-VEAacid neuropeptides family. These neuropeptides are isolated from the abdominal perisympathetic organs of the American cockroach. These peptides are found together with Pea-YLS-amide and Pea-SKNacid, giving a unique neuropeptide pattern in abdominal perisympathetic organs. The functions of these neuropeptides are unknown .
PetM of cytochrome b6/f complex subunit 7 (PetM_cyt_b6/f_cplx_su7)
Type: Family

This family consists of the PetM family of cytochrome b6f complex subunit IV. The cytochrome b6f complex consists of 7 subunits and contains 2 beta haem's and 1 chlorophyll alpha per cytochrome f. It is highly active in transferring electrons from decylplastoquinol to oxidised plastocyanin .
Bacteriophage T4, Y12G (Phage_T4_Y12G)
Type: Family

Proteins in this family are bacteriophage Y12G proteins. Gene Y12G encodes a 17.1kDa protein in Gp30-rIII intergenic region, which in T4 is a 75 amino acid basic peptide which has a C terminus rich in charged amino acids .
Fungal mating-type pheromone (Pheromone)
Type: Family

This family corresponds to mating-type pheromone proteins. The homobasidiomycetes, or mushroom fungi, have arguably the most complex mating system of all known organisms. Many species possess a mating system known as bifactorial incompatibility, where two unlinked loci control the mating-type of an individual incompatibility loci (the A and B mating-type loci). Each A mating-type sublocus encodes a pair of divergently transcribed homeodomain transcription factors while the genes responsible for B mating-type activity encode lipopeptide pheromones and G-protein -coupled pheromone receptors .
Plasmodium-MYXSPDY (Plasmod_MYXSPDY)
Type: Repeat

This repeat is found in hypothetical Plasmodium proteins.
Peptidase C1A, propeptide (Propeptide_C1A)
Type: Domain

This domain is found at the N-terminal of cathepsin B and cathepsin B-like peptidases that belong to MEROPS peptidase subfamily C1A. Cathepsin B are lysosomal cysteine proteinases belonging to the papain superfamily and are unique in their ability to act as both an endo- and an exopeptidases. They are synthesized as inactive zymogens. Activation of the peptidases occurs with the removal of the propeptide .
Gingipain propeptide (Propeptide_C25)
Type: Domain

Gingipains are proteinases from Porphyromonas gingivalis, a major pathogen associated with chronic periodontitis. They belong to MEROPS peptidase family C25. There are three types: Arg-specific proteinases RgpA, and RgpB, and the Lys-specific proteinase Kgp. All three gingipain precursors contain a propeptide of around 200 amino acids in length that is removed during maturation. It has been shown that gingipain propeptides are capable of inhibiting their mature cognate proteinases . Proteins homologous to the gingipain precursor are known from many other bacteria, some archaea and some eukaryotes.
Spermatozal protamine type (Spermatozal_protamine_typ)
Type: Family

This entry consists of the spermatozal protamines. Spermatozal protamines play an important role in remodelling of the sperm chromatin during mammalian spermiogenesis. Nuclear elongation and chromatin condensation are concomitant with modifications in the basic protein complement associated with DNA. Somatic histones are initially replaced by testis-specific histone variants, then by transitional proteins, and ultimately by protamines .
PyrBI operon leader peptide (PyrBI_leader)
Type: Family

This family consists of the pyrBI operon leader peptides. The expression of the pyrBI operon, which encodes the subunits of the pyrimidine biosynthetic enzyme aspartate transcarbamylase. is regulated primarily through a UTP-sensitive transcriptional attenuation control mechanism. In this mechanism, the concentration of UTP determines the extent of coupling between transcription and translation within the pyrBI leader region, hence determining the level of rho-independent transcriptional termination at an attenuator preceding the pyrB gene .
ARID4A/B, PWWP domain (ARID4A/B_PWWP)
Type: Domain

This is the PWWD domain which is found N-terminal to the ARID/BRIGHT domain in proteins of the Retinoblastoma-binding protein 1 family .

Retinoblastoma-binding protein 1 (RBBP1, also known as (ARID4A) AT-rich interactive domain-containing protein 4A) and RBBP1-like 1 (RBBP1L1, also known as (ARID4B) AT-rich interactive domain-containing protein 4B) are homologous proteins involved in cell cycle control . RBBP1 contributes to suppression of cancers such as leukemia and regulates the epigenetics of several genetic diseases including Prader-Willi's syndrome. Together with retinoblastoma protein (RB) and Sin3, RBBP1 and RBBP1L1 form the Sin3 complex involved in gene regulation and epigenetic regulation functions . They also function as transcriptional coactivators for the androgen receptor (AR) and RB, being important for the AR and RB regulatory pathways, involved in the regulation of Sertoli cell function and male fertility . These proteins contain five domains, namely Tudor, PWWP, ARID, chromobarrel and R2 domains, connected by intrinsically disordered regions.
RBM1CTR (RBM1CTR)
Type: Domain

This region is found in RBM1-like RNA binding hnRNPs .