SII-SWORD/CoKE huggingface dataset:
Tyrosine-protein kinase, Ret receptor (Tyr_kinase_Ret_rcpt)
Type: Family

Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process.
Protein kinases fall into three broad classes, characterised with respect to substrate specificity :

Serine/threonine-protein kinases

Tyrosine-protein kinases

Dual specificity protein kinases (e.g. MEK -phosphorylates both Thr and Tyr on target proteins)

Protein kinase function is evolutionarily conserved from Escherichia coli to human . Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation . Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved , leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases .

Tyrosine-protein kinases can transfer a phosphate group from ATP to a tyrosine residue in a protein. These enzymes can be divided into two main groups :

Receptor tyrosine kinases (RTK), which are transmembrane proteins involved in signal transduction; they play key roles in growth, differentiation, metabolism, adhesion, motility, death and oncogenesis . RTKs are composed of 3 domains: an extracellular domain (binds ligand), a transmembrane (TM) domain, and an intracellular catalytic domain (phosphorylates substrate). The TM domain plays an important role in the dimerisation process necessary for signal transduction .

Cytoplasmic/non-receptor tyrosine kinases, which act as regulatory proteins, playing key roles in cell differentiation, motility, proliferation, and survival. For example, the Src-family of protein-tyrosine kinases .

This group represents a tyrosine-protein kinase, Ret receptor type.
Tyrosine-protein kinase, Fes/Fps type (Tyr-prot_kinase_Fes/Fps)
Type: Family

Tyrosine-protein kinases can transfer a phosphate group from ATP to a tyrosine residue in a protein. These enzymes can be divided into two main groups :

Receptor tyrosine kinases (RTK), which are transmembrane proteins involved in signal transduction; they play key roles in growth, differentiation, metabolism, adhesion, motility, death and oncogenesis . RTKs are composed of 3 domains: an extracellular domain (binds ligand), a transmembrane (TM) domain, and an intracellular catalytic domain (phosphorylates substrate). The TM domain plays an important role in the dimerisation process necessary for signal transduction .

Cytoplasmic/non-receptor tyrosine kinases, which act as regulatory proteins, playing key roles in cell differentiation, motility, proliferation, and survival. For example, the Src-family of protein-tyrosine kinases .

This entry represents Fes/Fps family of non-receptor tyrosine kinases.

Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process.
Protein kinases fall into three broad classes, characterised with respect to substrate specificity :

Serine/threonine-protein kinases

Tyrosine-protein kinases

Dual specificity protein kinases (e.g. MEK -phosphorylates both Thr and Tyr on target proteins)

Protein kinase function is evolutionarily conserved from Escherichia coli to human . Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation . Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved , leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases .
Serine/threonine-protein kinase SpkB (Ser/Thr_kinase_SpkB)
Type: Family

Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process.
Protein kinases fall into three broad classes, characterised with respect to substrate specificity :

Serine/threonine-protein kinases

Tyrosine-protein kinases

Dual specificity protein kinases (e.g. MEK -phosphorylates both Thr and Tyr on target proteins)

Protein kinase function is evolutionarily conserved from Escherichia coli to human . Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation . Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved , leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases .

This entry represents serine/threonine-protein kinases (

) with pentapeptide domains, such as SpkB from Synechocystis sp. (strain PCC 6803). SpkB is required for cell motility .
Serine/threonine-protein kinase, asfivirus (Ser/Thr_kinase_asfivir)
Type: Family

Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process.
Protein kinases fall into three broad classes, characterised with respect to substrate specificity :

Serine/threonine-protein kinases

Tyrosine-protein kinases

Dual specificity protein kinases (e.g. MEK -phosphorylates both Thr and Tyr on target proteins)

Protein kinase function is evolutionarily conserved from Escherichia coli to human . Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation . Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved , leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases .

This enry represents a serine/threonine-protein kinase (

) found in Asfivirus such as African swine fever virus (ASFV). These enzymes are essential for viral replication and may mediate the virus' progression through DNA replication .
eIF-2-alpha kinase Gcn2 (Gcn2)
Type: Family

This entry represents Gcn2, a protein kinase that regulates the G1/S cell cycle checkpoint in response to DNA damage . It stimulates Gcn4 translation in amino acid-starved cells by phosphorylating the alpha subunit of eIF-2 (SUI2) on 'Ser-52' . This entry also includes the probable serine/threonine-protein kinases ifkB and ifkC from
Dictyostelium discoideum
.
Serine/threonine-protein kinase Rad53 (Ser/Thr_kinase_Rad53)
Type: Family

Rad53 is a protein kinase required for cell-cycle arrest in response to DNA damage. Rad53 controls the S-phase checkpoint as well as G1 and G2 DNA damage checkpoints. It prevents entry into anaphase and mitotic exit after DNA damage via regulation of the Polo kinase Cdc5 . Rad53 also seems to be involved in the phosphorylation of Rph1, a zinc finger protein that acts as a damage-responsive repressor of the photolyase gene Phr1 in Saccharomyces cerevisiae (Baker's yeast) . The 2C type phosphatase, Ptc2, which is required for DNA checkpoint inactivation after double-strand breaks, appears to dephosphorylate Rad53 .
Ephrin receptor type-A /type-B (Tyr_kinase_ephrin_rcpt)
Type: Family

This entry represents type A and type B ephrin receptors. Ephrin receptors (Ephs) are a group of receptor tyrosine kinases that are activated in response to binding ephrin ligands residing on adjacent cells . This binding leads to contact-dependent bidirectional signaling into neighbouring cells . Eph receptors play critical roles in embryonic patterning , neuronal targeting , vascular development and adult neovascularization .

There are 10 EphA receptors and six EphB receptors, distinguished on sequence difference and binding preferences. They interact with the six glycosylphosphatidylinositol-linked ephrin-A ligands and the three transmembrane ephrin-B ligands, respectively .
Multiphosphoryl transfer protein FruB (FruB)
Type: Family

This group represents multiphosphoryl transfer protein fruB. It is part of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS), a major carbohydrate active -transport system, catalyses the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane.
Hygromycin-B kinase (Hygromycin-B_Kinase)
Type: Family

This entry represents a group of hygromycin-B kinases, including hygromycin-B 7''-O-kinase from Streptomyces hygroscopicus .
Folic acid synthesis protein FOL1 (Folic_acid_synth)
Type: Family

FOL1 catalyses three sequential steps of the tetrahydrofolate biosynthetic pathway and is therefore the central enzyme of this pathway .
RNA polymerase sigma factor, SigB/C/D/F, plastid (RNA_pol_sigma_SigB/C/D/F)
Type: Family

This entry represents certain plastid RNA polymerase sigma factors, including SigB, SigC, SigD and sigF . Development of plastids into chloroplasts is triggered by light. The coordination of light-induced plastid gene expression is directed by both nuclear and plastid genomes. Plastid DNA is transcribed by at least two types of RNA polymerase, plastid-encoded RNA polymerase (PEP) and nuclear-encoded RNA polymerase (NEP). Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. Sigma factor SigB appears to play a critical role in the coordination of the two genomes for chloroplast development .
DNA polymerase epsilon, subunit B (POLE2)
Type: Family

DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure .
UTP--glucose-1-phosphate uridylyltransferase (UDPGP_trans)
Type: Family

UDP-glucose is the universal activated form of glucose, employed in all organisms for glucosyl transfer reactions and as precursor for various activated carbohydrates . It is formed by the enzyme UDP-glucose pyrophosphorylase (UGPase, UDPGP), also known as UTP--glucose-1-phosphate uridylyltransferase, (

), which catalyses the reaction UTP + alpha-D-glucose 1-phosphate = diphosphate + UDP-glucose. The enzymatically active form of the protein is a homooctamer in Saccharomyces cerevisiae .
RNA-directed RNA polymerase, hantavirus (RNA-dir_pol_hantavirus)
Type: Family

RNA-directed RNA polymerase (RdRp) (

) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage . It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.
The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product .

This entry represents RNA-directed RNA polymerase (also known as the large or L protein) from various Hantaviruses. The L protein of hantaviruses is an RNA transcriptase and replicase that transcribes mRNAs and replicates the genomic RNA using antigenomic RNA as an intermediate . It also appears to have endonuclease activity.
RNA-directed RNA polymerase, paramyxovirus (RNA-dir_pol_paramyxovirus)
Type: Family

RNA-directed RNA polymerase (RdRp) (

) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage . It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.
The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product .

This entry represents RNA-directed RNA polymerase (also known as the large structural protein) from Mononegavirales including Paramyxoviruses . The large structural protein (or L protein) carries four enzymatic activities: RNA-directed RNA polymerase (

), mRNA (guanine-N(7)-)-methyltransferase (

), mRNA guanylyltransferase (

), and poly(A) synthetase. The viral mRNA guanylyl transferase displays a different biochemical reaction than the cellular enzyme. The template is composed of the viral RNA tightly encapsidated by the nucleoprotein (N). The protein can function either as transcriptase or as replicase. The transcriptase synthesises subsequently subgenomic RNAs, assuring their capping and polyadenylation by a stuttering mechanism. The transcriptase stutters on a specific sequence, resulting on a cotranscriptional editing of the phosphoprotein (P) mRNA. The replicase mode is dependent on intracellular N protein concentration. In this mode, the polymerase replicates the whole viral genome without recognizing the transcriptional signals. 5' GpppApGpG sequence is required for mRNA cap methylation by the enzyme.
CDP-alcohol phosphatidyltransferase class-II family (PGS1)
Type: Family

This entry represents the CDP-alcohol phosphatidyltransferase class-II family, whose members include Pgs1 from S. cerevisiae. Pgs1 is a phosphatidylglycerolphosphate synthase that catalyzes the committed step to the synthesis of of cardiolipin .
CDP-diacylglycerol--serine O-phosphatidyltransferase, fungal (CDP-diaglyc--ser_O-PTrfase_fun)
Type: Family

This group represents a CDP-diacylglycerol--serine O-phosphatidyltransferase, fungal type.
Lipase, LIPH-type (Lipase_LIPH)
Type: Family

This group represents LIPH (lipase H)-type lipases . It includes lipase H, lipoprotein lipase (LPL), and hepatic and pancreatic lipases.

LIPH hydrolyses specifically phosphatidic acid (PA) to produce 2-acyl lysophosphatidic acid (LPA; a potent bioactive lipid mediator) and fatty acid .
Erythromycin esterase, proteobacteria (Emycin_Estase_proteobac)
Type: Family

This group represents an erythromycin esterase.
Histidine acid phosphatase, eukaryotic (Histidine_acid_Pase_euk)
Type: Family

This family represents eukaryotic histidine acid phosphatases, including Phytase A from Aspergillus oryzae (PhyA) and human Multiple inositol polyphosphate phosphatase 1 (MINPP1). PhyA catalyses the phosphate monoester hydrolysis of phytic acid (myo-inositol hexakisphosphate) with the subsequent formation of myo-inositol pentakis-, tetrakis-, tris-, bis-, and monophosphates, as well as the liberation of inorganic phosphate . MINPP1 regulates intracellular inositol polyphosphates pools, which act as metal chelators, it may control the availability of intracellular calcium and iron, which are important for proper neuronal development and homeostasis .
Glucose-6-phosphatase (Glucose-6-phosphatase)
Type: Family

This family represents glucose-6-phosphatases, hydrolyzes glucose-6-phosphate to glucose in the endoplasmic reticulum. It forms, with the glucose-6-phosphate transporter (SLC37A4/G6PT), the complex responsible for glucose production in the terminal step of glycogenolysis and gluconeogenesis, being the key enzyme in homeostatic regulation of blood glucose levels . Mutations in the gene encoding this protein cause Glycogen storage disease type Ia. Patients manifest a wide range of clinical symptoms and biochemical abnormalities, including hypoglycemia, severe hepatomegaly due to excessive accumulation of glycogen, kidney enlargement, growth retardation, lactic acidemia, hyperlipidemia, and hyperuricemia .
Non-receptor tyrosine-protein phosphatase 22 (PTPN22)
Type: Family

Tyrosine-protein phosphatase non-receptor type 22 (PTPN22) acts as negative regulator of T-cell receptor (TCR) signalling by direct dephosphorylation of the Src family kinases LCK and FYN, ITAMs of the TCRz/CD3 complex, as well as ZAP70, VAV, VCP and other key signalling molecules .

Variations of the PTPN22 gene affects the susceptibility of systemic lupus erythematosus (SLE) .
Tyrosine-protein phosphatase 1 (Ptp1)
Type: Family

In the budding yeast Saccharomyces cerevisiae three protein tyrosine phosphatases (Ptp1 to 3) have been identified to date. This entry represents Ptp1 . Like Ptp2 and Ptp3, Ptp1 plays a downregulatory role on MAPK pathways .
Dual specificity protein phosphatase 12 (DUSP12)
Type: Family

Human YVH1, also known as dual specificity phosphatase 12 (DUSP12), is a cell survival phosphatase that prevents both thermal and oxidative stress-induced cell death. Furthermore, it associates with multiple ribonucleoprotein particles and may affect a variety of fundamental cellular processes . The enzyme is known as dual specificity protein phosphatase MPK-4 in
Drosophila
. Yeast YVH1, on the other hand, is required for a late maturation step in the 60S biogenesis pathway .
Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma (PLC-gamma)
Type: Family

Phospholipase C gamma (PLCg), also known as 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma, is a member of the family of phosphoinositide specific PLCs that convert phosphatidylinositol 4,5-bisphosphate into second messengers 1,2-diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3), thereby initiating and propagating numerous cellular signaling events .

There are two forms of phospholipase C-gamma, PLCg1 and PLCg2. PLCg1 is widely distributed but the expression of PLCg2 is primarily limited to cells of haematopoietic lineage . PLCg1 is critical in many cells, and in haematopoietic systems it is required for T cell and NK cell function, whereas PLCg2 is important in mast cells, NK cells, B cells, and platelets. A third form, plc-3, is known from Caenorhabditis elegans .
Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta (PLC-beta)
Type: Family

This group represents phospholipase C-beta, also known as 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta. PLC-beta isoforms mediate the production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) to propagate signals for several physiological responses . This entry also includes NorpA, a phospholipase C (PLC) from Drosophila expressed in the eye. NorpA is a essential component of the phototransduction pathway in Drosophila .
Crossover junction endodeoxyribonuclease, RusA (Endonuclease_RusA)
Type: Family

This group represents a crossover junction endodeoxyribonuclease, RusA type.
Glycoside hydrolase, family 5, endoglucanase B (Glyco_hydro_5_endoGlcnase_B)
Type: Family

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.

Glycoside hydrolase family 5

comprises enzymes with several known activities; endoglucanase (

); beta-mannanase (

); exo-1,3-glucanase (

); endo-1,6-glucanase (

); xylanase (

); endoglycoceramidase (

).

The microbial degradation of cellulose and xylans requires several types of enzymes. Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family A or as the glycosyl hydrolases family 5 . One of the conserved regions in this family contains a conserved glutamic acid residue which is potentially involved in the catalytic mechanism.

This group represents an endoglucanase B.
Glycoside hydrolase, family 19 (Glyco_hydro_19)
Type: Family

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.

Glycoside hydrolase family 19

comprises enzymes with only one known activity; chitinase (

).

Chitinases are enzymes that catalyze the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Chitinases belong to glycoside hydrolase families 18 or 19 . Chitinases of family 19 (also known as classes IA or I and IB or II) are enzymes from plants that function in the defence against fungal and insect pathogens by destroying their chitin-containing cell wall. Class IA/I and IB/II enzymes differ in the presence (IA/I) or absence (IB/II) of a N-terminal chitin-binding domain. The catalytic domain of these enzymes consist of about 220 to 230 amino acid residues. The At2g43600 protein from Arabidopsis thaliana is presumably inactive as a chitinase because it lacks the Glu residue that is essential for catalytic activity.
Bacteriophage PRD1, P15, lysozyme (Phage_PRD1_P15_lysozyme)
Type: Family

This group represents one of the lytic enzymes of bacteriophage PRD1 (protein P15): muramidase (lysozyme). Host peptidoglycan is digested after permeabilization of the cytoplasmic membrane by holin, liberating progeny phages. Hydrolysis of the cell wall peptidoglycan occurs at the (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues and between N-acetyl-D-glucosamine residues in chitodextrins .