SII-SWORD/CoKE huggingface dataset:
Methionyl-tRNA synthetase, beta subunit, C-terminal (Met-tRNA-synth_bsu_C)
Type: Domain

The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .

The methionyl-tRNA synthetase (MetG) (

) is a class I amino acyl-tRNA ligase. This family describes a region of the methionyl-tRNA synthetase that is present at the C terminus of MetG in some species (Escherichia coli, Bacillus subtilis, Thermotoga maritima, Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum), and as a separate beta chain in Aquifex aeolicus . It is absent in a number of other species (e.g. Mycoplasma genitalium, Mycobacterium tuberculosis), while Pyrococcus horikoshii has both a full length MetG and a second protein homologous to the beta chain only. This domain has general tRNA binding properties. The functional unit of MetG and Aquifex aeolicus Trbp111 is a homodimer, this domain acts as the dimerization domain .
Ferredoxin-type protein NapF (NapF)
Type: Family

Periplasmic nitrate reductase (NapABC enzyme) is responsible for nitrate dissimilation . NapF protein is the auxiliary protein of the Nap systems. It interacts with the catalytic subunit, NapA, and may be an accessory protein for NapA maturation .
NAD(P)H-quinone oxidoreductase subunit I (NDHI)
Type: Family

NAD(P)H-quinone oxidoreductase subunit I (

) catalyses the conversion of plastoquinone and NADH to plastoquinol and NAD(+). The enzyme binds two 4Fe-4S clusters at iron-sulphur centres which are similar to those of the bacterial-type 4FE-4S ferredoxins.
Ribosomal protein L11 methyltransferase (Ribosomal_PrmA_MeTrfase)
Type: Family

Ribosomal protein L11 methyltransferase (PrmA) (

) is required for the methylation of ribosomal protein L11. It forms a bifunctional operon in Escherichia coli with panF (pantothenate transport). In E. coli, it trimethylates the N-terminal alpha-amino group and the ε-amino groups of Lys3 and Lys39 . In Arabidopsis is targeted to both mitochondria and chloroplasts. Structures comparison with the E. coli enzyme revealed that they share similar product specificity but display a difference in substrate site specificity .
Proline-tRNA ligase, class IIa, archaeal-type (Pro-tRNA-ligase_IIa_arc-type)
Type: Family

Proline-tRNA ligase (also known as Prolyl-tRNA synthetase) is a class II tRNA ligase and is recognised by

, which recognises tRNA ligases for Gly, His, Ser, and Pro. The proline-tRNA ligases are divided into two widely divergent families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi (Lyme desease spirochete). The other family,

, includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis sp. (strain PCC 6308), and one of the two proline-tRNA ligases of Saccharomyces cerevisiae (Baker's yeast).

The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .
Prolyl-tRNA synthetase, class IIa, bacterial-type (Pro-tRNA-synth_IIa_bac-type)
Type: Family

The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .

Prolyl-tRNA synthetase belongs to class IIa. Prolyl-tRNA synthetase (

) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. This entry contains the first form of prolyl-tRNA synthetase.
Phosphotransferase system, EIIC component, type 3 (PTS_EIIC_3)
Type: Domain

The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) is a major carbohydrate transport system in bacteria. The PTS catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to enzyme I (EI) of PTS which in turn transfers it to a phosphoryl carrier protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease which consists of at least three structurally distinct domains (IIA, IIB, and IIC), which can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).

The first domain (IIA), carries the first permease-specific phosphorylation site, an histidine which is phosphorylated by phospho-HPr. The second domain (IIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. The IIC domain forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose .

According to sequence analyses , the PTS EIIC domain can be divided in five groups.

The PTS EIIC type 1 domain is found in the Glucose class of PTS and has an average length of about 80 amino acids.

The PTS EIIC type 2 domain is found in the Mannitol class of PTS and has an average length of about 90 amino acids.

The PTS EIIC type 3 domain is found in the Lactose class of PTS and has an average length of about 100 amino acids.

The PTS EIIC type 4 domain is found in the Mannose class of PTS and has an average length of about 160 amino acids.

The PTS EIIC type 5 domain is found in the Sorbitol class of PTS and has an average length of about 190 amino acids.
Thioredoxins/glutaredoxin (Thio_glut)
Type: Family

This group of proteins includes thioredoxins, glutaredoxins, protein-disulphide isomerases, amongst others, some of which have several such domains. The sequence of proteins in this group at the redox-active disulphide site, CPYC, matches glutaredoxins rather than thioredoxins, although overall the sequence seems closer to thioredoxins. Proteins may be involved in a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.
Serine-tRNA ligase type 2, archaea (Ser-tRNA-ligase_2_arc)
Type: Family

Serine-tRNA ligase (

) exists as monomer and belongs to class IIa .
The serine-tRNA ligases from a few of the archaea that belong to this group are different from the set of mutually more closely related serine-tRNA ligases from eubacteria, eukaryotes, and other archaea (

).

There are two distinct types of seryl-tRNA synthetase, as differentiated by primary sequence analysis, three-dimensional structure and substrate recognition mechanism: type 1 (

) is found in the majority of organisms (prokaryotes, eukaryotes and archaea), whereas type 2 (this entry) is confined to some methanogenic archaea . Methanosarcina barkeri possesses two seryl-tRNA synthetases, one of each type .

The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .
DNA repair protein RadA (DNA_repair_RadA)
Type: Family

RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in MEROPS peptidase family S16 (lon protease family, clan SJ).

RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks and in the integration of exogenous DNA into the genome during bacterial genetic transformation .
tRNA-specific 2-thiouridylase MnmA-like (MnmA-like)
Type: Family

This family represents tRNA-specific 2-thiouridylase MnmA (sometimes called tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase), which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine (mnm5s2U) present in the wobble position of some tRNAs . This family of enzyme only presents in bacteria and eukaryote. The archaeal counterpart of this enzyme performs same function, but is completely unrelated in sequence .
Flavin prenyltransferase UbiX-like (UbiX-like)
Type: Family

In Escherichia coli, the protein UbiX (

) is a flavin prenyltransferase that has been shown to be involved in the third step of ubiquinone biosynthesis . It is required for the reaction 3-octaprenyl-4-hydroxybenzoate = 2-octaprenylphenol + CO2 (

) catalyzed by UbiD and was initially believed to directly catalyse this reaction . The knockout of the homologous protein in yeast (Pad1) confers sensitivity to phenylacrylic acid, showing that this enzyme functions as a phenylacrylic acid decarboxylase .

E. coli strains also contain, in addition to UbiX, a second paralogue named Pad1. Its amino acid sequence shows 52% identity to UbiX and slightly higher sequence identity to Saccharomyces cerevisiae phenylacrylic acid decarboxylase Pad1. Despite its higher sequence similarity with yeast Pad1, E. coli Pad1 does not seem to have phenylacrylic acid decarboxylase activity. Its function is unknown, Pad1 may remove the carboxylate group from derivatives of benzoic acid but not from substituted phenolic acids .

This family also includes flavin prenyltransferase LpdB from Lactobacillus .
Thioredoxin-independent 5'-adenylylsulphate reductase (Thioredoxin-indep_APS_Rdtase)
Type: Family

This enzyme, involved in the assimilation of inorganic sulphate, is closely related to the thioredoxin-dependent PAPS reductase of Bacteria (CysH) and Saccharomyces cerevisiae. However, it has its own C-terminal thioredoxin-like domain and is not thioredoxin-dependent. Also, it has a substrate preference for 5'-adenylylsulphate (APS) over 3'-phosphoadenylylsulphate (PAPS) so the pathway does not require an APS kinase (CysC) to convert APS to PAPS. Arabidopsis thaliana appears to have three isozymes, all able to complement Escherichia coli CysH mutants (even in backgrounds lacking thioredoxin or APS kinase) but likely localized to different compartments in Arabidopsis.
Competence protein ComEA, helix-hairpin-helix domain (Competence_ComEA_HhH)
Type: Domain

Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions .

The development of genetic competence in Bacillus subtilis is a highly regulated adaptive response to stationary-phase stress. For competence to develop, the transcriptional regulator, ComK, must be activated. ComK is required for the expression of genes encoding proteins that function in DNA uptake. In log-phase cultures, ComK is inactive in a complex with MecA and ClpC. The comS gene is induced in response to high culture cell density and nutritional stress and its product functions to release active ComK from the complex. ComK then stimulates the transcription initiation of its own gene as well as that of the late competence operons .

This domain is found in competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This domain represents a region of two tandem copies of a helix-hairpin-helix domain, each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to this domain.
Phosphoadenosine phosphosulphate/adenosine 5'-phosphosulphate reductase (PAPS/APS_Rdtase)
Type: Family

This entry represents a family of phosphoadenosine phosphosulphate (PAPS) reductases and adenosine 5'-phosphosulphate (APS) reductases involved in the assimilatory reduction of inorganic sulphate. The APS reductases can be distinguished from the PAPS reductases by the presence of two additional cysteine pairs thought to form an iron-sulphur cluster . This family also includes APS reductases from plants, such as APR1-3 from Arabidopsis.
Ribosomal RNA methyltransferase E, gammaproteobacteria (rRNA_MeTrfase_gammaproteobac)
Type: Family

The ribosomal RNA large subunit methyltransferase E (

) methylates the 23S rRNA. It specifically methylates the uridine in position 2552 of 23s rRNA in the 50S particle using S-adenosyl-L-methionine as a substrate. It was previously known as cell division protein ftsJ.
Cell division protein FtsX (FtsX)
Type: Family

FtsX is an integral membrane protein encoded in the same operon as signal recognition particle docking protein FtsY and FtsE. FtsE is a hydrophilic nucleotide-binding protein that associates with the inner membrane by means of association with FtsX; FtsE mutants are viable only in high salt, supporting possible roles in cell division or in transport . FtsX belongs to a family of predicted permeases and may play a role in the insertion of proteins required for potassium transport, cell division, and other activities . FtsX is involved in sporulation in the Gram-positive bacterium Bacillus subtilis .
Glutamine-tRNA synthetase (Gln-tRNA-synth)
Type: Family

Glutamine-tRNA ligase (

) is a class Ic aminoacyl-tRNA ligase and shows several similarities with glutamine-tRNA ligase concerning structure and catalytic properties. It is an alpha2 dimer.
Glutamine-tRNA ligase is a relatively rare ligase, found in the cytosolic compartment of eukaryotes, in Escherichia coli and a number of other Gram-negative bacteria, and in Deinococcus radiodurans. In contrast, the pathway to Gln-tRNA in mitochondria, Archaea, Gram-positive bacteria, and a number of other lineages is by misacylation with Glu followed by transamidation to correct the aminoacylation to Gln.

The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .
Phosphoheptose isomerase (Phosphoheptose_Isoase)
Type: Family

Phosphoheptose isomerase is involved in lipopolysaccharide biosynthesis, more specifically in the synthesis of glyceromannoheptose 7-phosphate. It may also have a role in the virulence of Haemophilus ducreyi. In Salmonella typhimurium, phosphoheptose isomerase is the first enzyme in the biosynthesis of aldoheptose .
Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit (HisRS/HisZ)
Type: Family

This entry represents histidine-tRNA ligase (HisS or HisRS) and its paralogue, ATP phosphoribosyltransferase regulatory subunit (HisZ). Despite the significant sequential and structural similarity, HisRS and HisZ have different functions . HisRS is a class IIa aminoacyl-tRNA synthetase (ligase), while HisZ is a regulatory subunit of the hetero-octameric ATP phosphoribosyl transferase that regulate reactions initiating histidine biosynthesis .
ATP phosphoribosyltransferase regulatory subunit (HisZ)
Type: Family

Proteins in this entry are mostly annotated as the ATP phosphoribosyltransferase regulatory subunit (HisZ). However, this entry also includes some histidine-tRNA ligases (HisS or HisRS), which is the paralogue of HisZ. Despite the significant sequential and structural similarity, HisRS and HisZ have different functions . HisRS is a class IIa aminoacyl-tRNA synthetase (ligase), while HisZ is a regulatory subunit of the hetero-octameric ATP phosphoribosyl transferase that regulate reactions initiating histidine biosynthesis .
NTP pyrophosphohydrolase MazG-like domain (MazG-like_dom)
Type: Domain

This domain is found in a group of prokaryotic proteins which includes Escherichia coli MazG, which hydrolyses all canonical nucleoside triphosphates but it also might have a 'housecleaning' function by hydrolysing noncanonical NTPs, whose incorporation into the nascent DNA leads to the increased mutagenesis and DNA damage . Phylogenetic distribution studies of this domain revealed that it commonly appears as two domains in tandem, although there are single-domain analogs. In E. coli there are two tandem globular domains, in which the NTPase activity was observed only at the C-terminal domain .