SII-SWORD/CoKE huggingface dataset:
Peptidase S8A, DPH-A (Peptidase_S8A_DPH-A)
Type: Family

Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) .

Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes . The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route . The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus.

This entry contains serine peptidases belonging to MEROPS peptidase family S8A (subtilisin family, clan SB). This family of serine peptidases are highly similar in both structural and enzymatic feature to SAM-P45 peptidases, which are known as a target enzyme of Streptomyces subtilisin inhibitor (SSI), from Streptomyces albogriseolus.

DPH-A effectively forms chiral intermediates of 1,4-dihydropyridine calcium antagonists, and suggests the feasibility of developing DHP-A as a new commercial enzyme for use in the chiral drug industry .
Transcriptional regulator Ure2 (Ure2)
Type: Family

Ure2 is a yeast transcriptional regulator that plays an important role in the regulation of nitrogen metabolism . When easily utilised nitrogen sources are present, yeast cells down-regulate the synthesis of proteins involved in utilising poor nitrogen sources. Ure2 assists this process by interacting with, and repressing, the transcription factor Gln3, repressing the transcription of these proteins. Ure2 exists in two forms; a functional form and an infectious, non-functional prion form. Structurally, Ure2 is a homodimer where each monomer has a globular C-terminal region, and a poorly structured N-terminal region . The globular region, which is sufficient for its regulatory activity, forms a glutathione-S-transferase-like fold. The N-termnial region is known as the prion region and may interact with the globular region to prevent the protein from converting into its prion form.
DNA fragmentation factor 45 (DFF45)
Type: Family

One of the hallmarks of the terminal stages of apoptosis is internucleosomal DNA breakdown. DNA fragmentation factor (DFF) and endonuclease G (Endo G) are responsible for this process. DFF exists in the nucleus as a heterodimer composed of a 45kDa chaperone and inhibitor subunit (DFF45, also called ICAD-L) and a 40kDa latent nuclease subunit (DFF40/CAD). Apoptotic activation of caspase-3 or -7 results in the cleavage of DFF45 and release of active DFF40 nuclease, which forms homo-oligomers. DFF40's nuclease activity is further activated by proteins such as histone H1, HMGB1/2, and topoisomerase II .

This entry represents DFF45 .
Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 (NHERF-1/NHERF-2)
Type: Family

This entry includes NHERF-1 and NHERF-2. These proteins, which consist of two PDZ domains and a carboxy-terminal ezrin binding domain (EBD) , function as a scaffolding protein for the glutamate transporter GLAST. NHERF1 interacts with GLAST during ER export, while NHERF2 interacts with GLAST in the secretory pathway from the ER-Golgi intermediate compartment to the plasma membrane .
Neuronal migration protein doublecortin, chordates (DCX_chordates)
Type: Family

This family represents the neuronal migration protein doublecortin found in chordates.

Neuronal migration protein doublecortin (DCX; also known as Lissencephalin-X) is a microtubule-associated protein required for the initial steps of neuronal dispersion and cortex lamination during cerebral cortex development . This protein may act by competing with the putative neuronal protein kinase DCAMKL1 in binding to a target protein, and thereby participate in a signalling pathway that is crucial for neuronal interaction before and during migration, possibly as part of a calcium ion-dependent signal transduction pathway. It may also be involved with LIS-1 in an overlapping, but distinct, signalling pathways that promotes neuronal migration. Defects in neuronal migration protein doublecortin are the cause of lissencephaly X-linked type 1 (LISX1), a classic lissencephaly characterised by mental retardation and seizures that are more severe in male patients .
Mitochondrial import inner membrane translocase subunit Tim44 (Tim44)
Type: Family

Tim44 is an essential component of the PAM complex, which is required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. It recruits mitochondrial HSP70 to drive protein translocation into the matrix using ATP as an energy source .
Cytoplasmic protein NCK (NCK)
Type: Family

Cytoplasmic proteins Nck are non-enzymatic adaptor proteins composed of three SH3 (Src homology 3) domains and a C-terminal SH2 domain . They regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates . They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics . They associate with tyrosine-phosphorylated growth factor receptors or their cellular substrates . There are two vertebrate Nck proteins, Nck1 and Nck2.
Leupaxin/Paxillin/TGFB1I1 (Tgfb1i1/Leupaxin/TGFB1I1)
Type: Family

This entry includes the transforming growth factor beta-1-induced transcript 1 (TGFB1I1, also known as Hic-5) protein, paxillin and leupaxin.

Hic-5 functions as a molecular adapter coordinating multiple protein-protein interactions at the focal adhesion complex and in the nucleus . Leupaxin is a transcriptional coactivator for androgen receptor (AR) and serum response factor (SRF) .

Paxillin is a cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion) . Extensive tyrosine phosphorylation occurs during integrin-mediated cell adhesion, embryonic development, fibroblast transformation and following stimulation of cells by mitogens that operate through the 7TM family of G-protein-coupled receptors . Paxillin binds in vitro to the focal adhesion protein vinculin, as well as to the SH3 domain of c-Src, and, when tyrosine phosphorylated, to the SH2 domain of v-Crk . An N-terminal region has been identified that supports the binding of both vinculin and the focal adhesion tyrosine kinase, pp125Fak .

Paxillin is a 68kDa protein containing multiple domains, including four tandem C-terminal LIM domains (each of which binds 2 zinc ions); an N-terminal proline-rich domain, which contains a consensus SH3 binding site; and three potential Crk-SH2 binding sites . The predicted structure of paxillin suggests that it is a unique cytoskeletal protein capable of interaction with a variety of intracellular signalling and structural molecules important in growth control and the regulation of cytoskeletal organisation .
Peptidase S8A, fervidolysin-like (Peptidase_S8A_fervidolysi-like)
Type: Family

This entry contains serine peptidases belonging to MEROPS peptidase family S8A (subtilisin family, clan SB). They show protein sequence similarity with Fervidolysin.
Peptidase S8A, subtilisin-related, bacteroidetes (Pept_S8_subtilisin_bacteroid)
Type: Family

This entry contains predicted serine peptidases from bacteroidetes belonging to MEROPS peptidase family S8A (subtilisin family, clan SB).
Peptidase S8A, subtilisin-related, proteobacteria (Pept_S8A_subtilisin_proteobac)
Type: Family

Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) .

Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes . The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route . The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus.

This entry contains unassigned serine peptidases belonging to MEROPS peptidase family S8A (subtilisin family, clan SB).
Peptidase S8A, subtilisin-related, clostridia (Pept_S8A_subtilisin_clostridia)
Type: Family

This entry contains serine peptidases belonging to MEROPS peptidase family S8A (subtilisin family, clan SB), which include unassigned and non-peptidase homologues related to the peptidase CspB from Clostridium perfringens.

The CspA, CspB and CspC gene products are encoded by genes that are immediately upstream of two cortex lytic enzymes: SleC and SleM. CspA, CspB and CspC are germination specific peptidases that are required for the maturation of SleC and SleM. CspC has a secretion signal unlike CspA and CspB suggesting that they have different subcellular locations. The csp genes and sleM and sleC are conserved among many of the clostridia and are synthesized during stage II-III of sporulation .
Peptidase S8A, subtilisin-related, Sama-2696-type (Sama-2696)
Type: Family

This entry contains serine peptidases belonging to MEROPS peptidase family S8A (subtilisin family, clan SB). They represent unassigned subtilisin-related serine peptidases mainly from Shewanella and Pseudoalteromonas, including

.
Peptidase S8A, subtilisin-related, Alteromonadales (Subtilisin_Alteromonadales)
Type: Family

This entry contains serine peptidases belonging to MEROPS peptidase family S8A (subtilisin family, clan SB). They represent unassigned subtilisin-related serine peptidases mostly from Alteromonadales.
Peptidase S8A, subtilisin-related, Moth-2364-type (Moth2364)
Type: Family

Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) .

Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes . The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route . The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus.

This entry contains serine peptidases belonging to MEROPS peptidase family S8A (subtilisin family, clan SB), which include unassigned peptidases from Moorella thermoacetica (Clostridium thermoaceticum), Syntrophomonas wolfei and Pelotomaculum thermopropionicum.
Peptidase S8A, subtilisin-like peptidase 1, plasmodium (Pept_S8A_PfSUB_1)
Type: Family

This entry contains serine peptidases belonging to MEROPS peptidase family S8A (subtilisin family, clan SB). All of the peptidases in this entry derive from Plasmodium spp. and are called 'subtilisin-like peptidase 1'.

The peptidase in Plasmodium falciparum (isolate 3D7) termed pfSUB1 is a component of the exoneme . PfSUB1 mediates the proteolytic maturation of at least two essential members of another enzyme family called SERA. This proteolytic processing event is required for the release of viable parasites from the host erythrocyte .
Peptidase S8A, subtilisin-related, proteobacteria-2 (Pep_S8A_subtilisin_pbac-2)
Type: Family

Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) .

Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes . The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route . The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus.

This entry contains unassigned serine peptidases belonging to MEROPS peptidase family S8A (subtilisin family, clan SB) from the proteobacteria.
Peptidase S8A, subtilisin-related, cyanobacteria-2 (Pept_S8A_subtilisin_cyanobac-2)
Type: Family

This entry contains predicted subtilisin-related peptidases, predominantly found in cyanobacterial species. The peptides belong to MEROPS peptidase family S8A (subtilisin family, clan SB), and are unassigned.
Peptidase S8A, subtilisin-related, bacteroidetes-2 (Pept_S8_subtilisin_bacteroid-2)
Type: Family

Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) .

Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes . The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route . The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus.

This entry contains unassigned serine peptidases belonging to MEROPS peptidase family S8A (subtilisin family, clan SB) from the Bacteroidetes.
Peptidase S8A, subtilisin-related, campylobacter (Pept_S8A_subtilisin_campylobac)
Type: Family

This entry contains unassigned serine peptidases belonging to MEROPS peptidase family S8A (subtilisin family, clan SB) from Campylobacter.
Subtilisin-like serine protease TK1689-type (Subtilisin_TK1689)
Type: Family

Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes . The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route . The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus.

This entry represents subtilisin-like serine proteases related to TK1689 from Thermococcus kodakaraensis. TK1689 has high resistance to heat, denaturants, detergents and chelating agents .
Histone deacetylase class II, yeast (Hist_deAcase_II_yeast)
Type: Family

This group represents a histone deacetylase class II from yeast.
Receptor-interacting serine/threonine-protein kinase 2 (Rcpt-int_Ser/Thr_kinase-2)
Type: Family

This entry represents receptor-interacting serine/threonine-protein kinase 2 (RIP2), which functions in the phosphorylation (

) of its protein target. This enzyme activates pro-caspase-1 and pro-caspase-8, and it thought to potentiate CASP8-mediated apoptosis . It also activates NF-kappa-B. RIP2 undergoes autophosphorylation; it is phosphorylated upon DNA damage, probably by ATM or ATR.
Lysyl endopeptidase (Lysyl_endo-pept)
Type: Family

This group represents a lysyl endopeptidase.
Transmembrane protease serine 9 (Tmprss9)
Type: Family

This entry represents transmembrane serine protease 9 (also known as polyserase-1) (

), which belongs to MEROPS peptidase family S1A (clan PA(S)). It is encoded by the TMPRSS9 gene on chromosome 19p13 in Homo sapiens. This protein is synthesised as a membrane-associated polyprotein which undergoes post-translational cleavage to generate 3 independent serine protease chains (serase-1, serase-2 and serase-3); however it is unclear whether cleavage always takes place . The cleaved chains may remain attached to the membrane via disulphide bonds. Two of these products, serase-1 and serase-2, are proteolytically active against synthetic peptides commonly used for assaying serine proteases and their activities, and are blocked by serine protease inhibitors. However, serase-3 lacks the essential Ser residue of the catalytic triad at position 1009 and is predicted to be inactive. The domain architecture includes a type II transmembrane motif, a low-density lipoprotein receptor A domain, and three tandem trypsin-like serine protease domains .