SII-SWORD/CoKE huggingface dataset:
T-complex protein 1, delta subunit (Chap_CCT_delta)
Type: Family

Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1 or Tailless Complex Polypeptide 1) or TRiC . Chaperonins are involved in productive folding of proteins . They share a common general morphology, a double toroid of 2 stacked rings. The archaeal equivalent group II chaperonin is often called the thermosome . Both the thermosome and the TCP-1 family of proteins are weakly, but significantly , related to the cpn60/groEL chaperonin family (see

).

The TCP-1 protein was first identified in mice where it is especially abundant in testis but present in all cell types. It has since been found and characterised in many other animal species, as well as in yeast, plants and protists. The TCP1 complex has a double-ring structure with central cavities where protein folding takes place . TCP-1 is a highly conserved protein of about 60kDa (556 to 560 residues) which participates in a hetero-oligomeric 900kDa double-torus shaped particle with 6 to 8 other different, but homologous, subunits . These subunits, the chaperonin containing TCP-1 (CCT) subunit beta, gamma, delta, epsilon, zeta and eta are evolutionary related to TCP-1 itself . Non-native proteins are sequestered inside the central cavity and folding is promoted by using energy derived from ATP hydrolysis . The CCT is known to act as a molecular chaperone for tubulin, actin and probably some other proteins .

This family consists exclusively of the CCT delta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
T-complex protein 1, epsilon subunit (Chap_CCT_epsi)
Type: Family

Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1 or Tailless Complex Polypeptide 1) or TRiC . Chaperonins are involved in productive folding of proteins . They share a common general morphology, a double toroid of 2 stacked rings. The archaeal equivalent group II chaperonin is often called the thermosome . Both the thermosome and the TCP-1 family of proteins are weakly, but significantly , related to the cpn60/groEL chaperonin family (see

).

The TCP-1 protein was first identified in mice where it is especially abundant in testis but present in all cell types. It has since been found and characterised in many other animal species, as well as in yeast, plants and protists. The TCP1 complex has a double-ring structure with central cavities where protein folding takes place . TCP-1 is a highly conserved protein of about 60kDa (556 to 560 residues) which participates in a hetero-oligomeric 900kDa double-torus shaped particle with 6 to 8 other different, but homologous, subunits . These subunits, the chaperonin containing TCP-1 (CCT) subunit beta, gamma, delta, epsilon, zeta and eta are evolutionary related to TCP-1 itself . Non-native proteins are sequestered inside the central cavity and folding is promoted by using energy derived from ATP hydrolysis . The CCT is known to act as a molecular chaperone for tubulin, actin and probably some other proteins .

This family consists exclusively of the CCT epsilon chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
T-complex protein 1, gamma subunit (Chap_CCT_gamma)
Type: Family

Proteins in this entry consist exclusively of the CCT gamma chain from animals, plants, fungi, and other eukaryotes.

Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1 or Tailless Complex Polypeptide 1) or TRiC . Chaperonins are involved in productive folding of proteins . They share a common general morphology, a double toroid of 2 stacked rings. The archaeal equivalent group II chaperonin is often called the thermosome . Both the thermosome and the TCP-1 family of proteins are weakly, but significantly , related to the cpn60/groEL chaperonin family (see

).

The TCP-1 protein was first identified in mice where it is especially abundant in testis but present in all cell types. It has since been found and characterised in many other animal species, as well as in yeast, plants and protists. The TCP1 complex has a double-ring structure with central cavities where protein folding takes place . TCP-1 is a highly conserved protein of about 60kDa (556 to 560 residues) which participates in a hetero-oligomeric 900kDa double-torus shaped particle with 6 to 8 other different, but homologous, subunits . These subunits, the chaperonin containing TCP-1 (CCT) subunit beta, gamma, delta, epsilon, zeta and eta are evolutionary related to TCP-1 itself . Non-native proteins are sequestered inside the central cavity and folding is promoted by using energy derived from ATP hydrolysis . The CCT is known to act as a molecular chaperone for tubulin, actin and probably some other proteins .
T-complex protein 1, eta subunit (Chap_CCT_eta)
Type: Family

Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1 or Tailless Complex Polypeptide 1) or TRiC . Chaperonins are involved in productive folding of proteins . They share a common general morphology, a double toroid of 2 stacked rings. The archaeal equivalent group II chaperonin is often called the thermosome . Both the thermosome and the TCP-1 family of proteins are weakly, but significantly , related to the cpn60/groEL chaperonin family (see

).

The TCP-1 protein was first identified in mice where it is especially abundant in testis but present in all cell types. It has since been found and characterised in many other animal species, as well as in yeast, plants and protists. The TCP1 complex has a double-ring structure with central cavities where protein folding takes place . TCP-1 is a highly conserved protein of about 60kDa (556 to 560 residues) which participates in a hetero-oligomeric 900kDa double-torus shaped particle with 6 to 8 other different, but homologous, subunits . These subunits, the chaperonin containing TCP-1 (CCT) subunit beta, gamma, delta, epsilon, zeta and eta are evolutionary related to TCP-1 itself . Non-native proteins are sequestered inside the central cavity and folding is promoted by using energy derived from ATP hydrolysis . The CCT is known to act as a molecular chaperone for tubulin, actin and probably some other proteins .

This family consists exclusively of the CCT eta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
T-complex protein 1, theta subunit (Chap_CCT_theta)
Type: Family

Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1 or Tailless Complex Polypeptide 1) or TRiC . Chaperonins are involved in productive folding of proteins . They share a common general morphology, a double toroid of 2 stacked rings. The archaeal equivalent group II chaperonin is often called the thermosome . Both the thermosome and the TCP-1 family of proteins are weakly, but significantly , related to the cpn60/groEL chaperonin family (see

).

The TCP-1 protein was first identified in mice where it is especially abundant in testis but present in all cell types. It has since been found and characterised in many other animal species, as well as in yeast, plants and protists. The TCP1 complex has a double-ring structure with central cavities where protein folding takes place . TCP-1 is a highly conserved protein of about 60kDa (556 to 560 residues) which participates in a hetero-oligomeric 900kDa double-torus shaped particle with 6 to 8 other different, but homologous, subunits . These subunits, the chaperonin containing TCP-1 (CCT) subunit beta, gamma, delta, epsilon, zeta and eta are evolutionary related to TCP-1 itself . Non-native proteins are sequestered inside the central cavity and folding is promoted by using energy derived from ATP hydrolysis . The CCT is known to act as a molecular chaperone for tubulin, actin and probably some other proteins .

This family consists exclusively of the CCT theta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
T-complex protein 1, zeta subunit (Chap_CCT_zeta)
Type: Family

Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1 or Tailless Complex Polypeptide 1) or TRiC . Chaperonins are involved in productive folding of proteins . They share a common general morphology, a double toroid of 2 stacked rings. The archaeal equivalent group II chaperonin is often called the thermosome . Both the thermosome and the TCP-1 family of proteins are weakly, but significantly , related to the cpn60/groEL chaperonin family (see

).

The TCP-1 protein was first identified in mice where it is especially abundant in testis but present in all cell types. It has since been found and characterised in many other animal species, as well as in yeast, plants and protists. The TCP1 complex has a double-ring structure with central cavities where protein folding takes place . TCP-1 is a highly conserved protein of about 60kDa (556 to 560 residues) which participates in a hetero-oligomeric 900kDa double-torus shaped particle with 6 to 8 other different, but homologous, subunits . These subunits, the chaperonin containing TCP-1 (CCT) subunit beta, gamma, delta, epsilon, zeta and eta are evolutionary related to TCP-1 itself . Non-native proteins are sequestered inside the central cavity and folding is promoted by using energy derived from ATP hydrolysis . The CCT is known to act as a molecular chaperone for tubulin, actin and probably some other proteins .

This family consists exclusively of the CCT zeta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
Chaperone DnaJ (DnaJ)
Type: Family

Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle.

Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation . Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L-and D-peptides and is assumed to interact only with the side chains of the substrate.

DnaJ comprises a 70-residue N-terminal domain (the J-domain); a 30-residue glycine-rich region (the G-domain); a central domain containing 4 repeats of a CxxCxGxG motif (the CRR-domain); and a 120-170 residue C-terminal region. The J-and CRR-domains are found in many prokaryotic and eukaryotic proteins , either together or separately.

The three components of the DnaK-DnaJ-GrpE system are typically encoded by consecutive genes. DnaJ homologues occur in many genomes, typically not encoded near DnaK and GrpE-like genes. Only some homologues are included in this family.
Chaperone DnaK (Chaperone_DnaK)
Type: Family

Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. In prokaryotes, the grpE protein is a co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle.

Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for the Mycoplasma sequence) found clustered with other genes of this systems. This entry excludes DnaK homologues that are not DnaK itself, such as the heat shock cognate protein HscA (

). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of DnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; the lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved.
Thiazole biosynthesis ThiH (ThiH)
Type: Family

Members of this protein family are the ThiH proteins (also known as 2-iminoacetate synthase) involved in thiamine biosynthesis . They are homologues of the BioB protein of biotin biosynthesis. Genes encoding these proteins are generally found in operons with other thiamin biosynthesis genes .
Glycine oxidase ThiO (Gly_oxidase_ThiO)
Type: Family

This family consists of the homotetrameric, FAD-dependent glycine oxidase ThiO, from species such as Bacillus subtilis that use glycine in thiamine biosynthesis. In general, members of this family will not be found in species such as Escherichia coli that instead use tyrosine and the ThiH protein .
Pls/PosA non-ribosomal peptide synthetases, C-terminal (Pls/PosA_C)
Type: Domain

This domain is found exclusively in non-ribosomal peptide synthetases and always as the final domain in the polypeptide. This domain is roughly 700 amino acids in size and is found in polypeptides roughly twice that size.

This domains is found in PosA, a δ-poly-L-ornithine synthetase that produces δ-poly-L-ornithine and Pls, a ε-poly-L-lysine synthase that produces ε-Poly-L-lysine .
Thiamine biosynthesis protein ThiF (ThiF_fam2)
Type: Family

Members of the HesA/MoeB/ThiF family of proteins (

) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees. The Escherichia coli ThiF and MoeB proteins are seemingly more closely related than the E. coli ThiF and Campylobacter (for example) ThiF. This entry represents the divergent clade of putative ThiF proteins as found in Campylobacter.

Members of this family are members of the superfamily of activating enzymes (E1) of the ubiquitin-like proteins . The exact function of this family is unknown.
Molybdopterin synthase sulfurylase MoeB (Mopterin_Synthase_Sase_MoeB)
Type: Family

This entry describes the molybdopterin biosynthesis protein MoeB in Escherichia coli and related species. MoeB and MoaD are involved in molybdenum cofactor biosynthesis, an evolutionarily conserved pathway. The MoeB enzyme covalently modifies the molybdopterin synthase MoaD by sulphurylation. The crystal structure of the complex between the E. coli MoeB and MoaD proteins reveals a MoeB(2)-MoaD(2) heterotetramer in which the MoeB subunits form a mainly hydrophobic dimer .
Thiazole biosynthesis adenylyltransferase ThiF (Adenyl_ThiF)
Type: Family

Members of the HesA/MoeB/ThiF family of proteins (

) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees. The Escherichia coli ThiF and MoeB proteins are seemingly more closely related than the E. coli ThiF and Campylobacter (for example) ThiF. This entry represents the more widely distributed clade of ThiF proteins as found in E. coli.
Hydroxymethylpyrimidine transporter CytX (Thia_CytX)
Type: Family

On the basis of a phylogenomic study of thiamine biosynthetic, salvage, and transporter genes and a highly conserved RNA element THI, this protein family has been identified as a probable transporter of hydroxymethylpyrimidine (HMP). ThiD phosphorylates hydroxymethylpyrimidine and when joined (by ThiE) to hydroxyethylthiazole phosphate creates thiamine phosphate .
4-hydroxybenzoate 3-monooxygenase (HB_mOase)
Type: Family

4-hydroxybenzoate 3-monooxygenase is a flavoprotein that converts its substrate to 3,4-dihydroxybenzoate, which subsequently enters the beta-ketioadipate pathway of aromatic degradation, using molecular oxygen and NADPH as shown below .

4-hydroxybenzoate + NADPH + O(2) = 3,4-dihydroxybenzoate + NADP(+) + H(2)O

4-hydroxybenzoate is an intermediate in the degradation of lignin and other aromatic plant compounds, and this enzyme is found extensively in soil bacteria.

This enzyme is a homodimer where each subunit is composed of three distinct domains: an N-terminal flavin-binding domain with a β-α-β fold, a small substrate-binding domain composed of a single α helix and β-sheet, and a C-terminal helical domain . The active site is found at the interface of all three domains. Catalysis occurs by a two-step reaction. In the first step, flavin is reduced by NADPH. Subsequently, the reduced flavin is oxygenated to a hydroperoxide which transfers the hydroxyl group to the substrate, forming 3,4-dihydroxybenzoate.
Dihydroxyacetone kinase (DhaK_ATP)
Type: Family

This family consists of examples of the single chain form of dihydroxyacetone kinase (also called glycerone kinase) that uses ATP (

) as the phosphate donor, rather than a phosphoprotein as in Escherichia coli. This form has separable domains homologous to the K and L subunits of the E. coli enzyme, and is found in yeasts and other eukaryotes and in some bacteria, including Citrobacter freundii .

The member from tomato has been shown to phosphorylate dihydroxyacetone, 3,4-dihydroxy-2-butanone, and some other aldoses and ketoses . Members from mammals have been shown to catalyse both the phosphorylation of dihydroxyacetone and the splitting of ribonucleoside diphosphate-X compounds among which FAD is the best substrate . In yeast there are two isozymes of dihydroxyacetone kinase (Dak1 and Dak2). They are required for detoxification of dihydroxyacetone (DHA) .
Dihydroxyacetone kinase DhaK, subunit 1b (DhaK_1b)
Type: Family

Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated

. By contract, Escherichia coli and many other bacterial species have a multisubunit form with a phosphoprotein donor related to PTS transport proteins. This family represents a protein, unique to the firmicutes (low GC Gram-positives), that appears to be a divergent second copy of the K subunit of that complex; its gene is always found in operons with the other three proteins of the complex.

This entry also includes DhaKLM operon coactivator DhaQ from Streptococcus lactis. It forms a heterotetramer with DhaS and functions as a transcriptional regulator .
Dihydroxyacetone kinase DhaK, subunit 1 (DhaK_1)
Type: Domain

In bacteria, dihydroxyacetone is formed by the oxidation of glycerol or the aldol cleavage of fructose-6-phosphate. Dihydroxyacetone kinase converts this compound to the glycolytic intermediate dihydroxyacetone phosphate. Two forms of this enzyme have been shown to exist, using either ATP or a phosphoprotein of the phosphoenolpyruvate: sugar phosphotransferase system (PTS) as phosphate donor. The ATP-dependent kinases (

) are single-subunit enzymes that are composed of two domains . The phosphoprotein-dependent kinases are composed of three subunits: DhaK and DhaL, which are homologous to the domains from the ATP-dependent enzyme; and DhaM which is a component of the PTS system .

This entry represents the DhaK subunit of phosphoprotein-dependent dihydroxyacetone kinase. The model excludes the DhaK paralog DhaK2 (

) encoded in the same operon as DhaK in the firmicutes, with which it sometimes exists as a DhaK/DhaK2 fusion. This subunit is a homodimer which contains the dihydroxyacetone-binding site . The overall fold consists of two six-stranded mixed β-sheets surrounded by nine α-helices and a β-ribbon covering the exposed edge strand of one sheet.
Dihydroxyacetone kinase, subunit L (DhaK_L_YcgS)
Type: Domain

Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated

. By contrast, Escherichia coli and many other bacterial species have a multisubunit form (

) with a phosphoprotein donor related to PTS transport proteins. This entry represents the ADP-binding subunit of the PTS-dependent dihydroxyacetone kinase .
Transcription regulator DhaS (Tscrpt_reg_DhaS)
Type: Family

This entry represents a set of known and predicted TetR-like transcriptional regulators associated with operons encoding PEP-dependent dihydroxyacteone (Dha) kinases. The Lactococcus lactis DhaS protein has been shown to interact with the Dha-binding protein DhaQ to form a stable complex . In the presence of Dha this complex activates transcription of the Dha kinase operon, leading to the utilisation of this substrate. Thus, unlike most TetR-like regulators, DhaS acts as an activator of gene expression rather than a repressor. The DhaS protein is composed of two monomers which fold into a wedge-shaped homodimer. Each monomer is composed of nine α helices and is divided into two domains: an N-terminal DNA-binding domain with a typical TetR fold, and a core domain involved in dimerisation.
Pyrrolysyl-tRNA ligase (Pyrrolysyl-tRNA_ligase)
Type: Family

PylS is the archaeal enzyme responsible for charging the pyrrolysine tRNA, PylT, by ligating a free molecule of pyrrolysine . Pyrrolysine is encoded at an in-frame UAG (amber) at least in several corrinoid-dependent methyltransferases of the archaeal genera Methanosarcina and Methanococcoides, e.g. trimethylamine methyltransferase.
Trimethylamine methyltransferase, Methanosarcina (MttB_Methanosar)
Type: Family

This entry represents trimethylamine:corrinoid methyltransferases that contain a critical pyrrolysine residue incorporated during translation via a special tRNA for a TAG (amber) codon . Known members so far are from the genus Methanosarcina. It is one of a suite of three non-homologous enzymes with a critical UAG-encoded pyrrolysine residue in these species (along with dimethylamine methyltransferase and monomethylamine methyltransferase). It demethylates trimethylamine, leaving dimethylamine, and methylates the prosthetic group of its small cognate corrinoid protein, MttC. The methyl group is then transferred by methylcorrinoid:coenzyme M methyltransferase to coenzyme M. Note that the pyrrolysine residue is variously translated as K or X, or as a stop codon that truncates the sequence.