SII-SWORD/CoKE huggingface dataset:
Succinyldiaminopimelate transaminase, DapC (DapC)
Type: Family

Two lysine biosynthesis pathways evolved separately in organisms, the diaminopimelic acid (DAP) and aminoadipic acid (AAA) pathways. The DAP pathway synthesizes L-lysine from aspartate and pyruvate, and diaminopimelic acid is an intermediate. This pathway is utilised by most bacteria, some archaea, some fungi, some algae, and plants. The AAA pathway synthesizes L-lysine from alpha-ketoglutarate and acetyl coenzyme A (acetyl-CoA), and alpha-aminoadipic acid is an intermediate. This pathway is utilised by most fungi, some algae, the bacterium Thermus thermophilus, and probably some archaea, such as Sulfolobus, Thermoproteus, and Pyrococcus. No organism is known to possess both pathways .

There four known variations of the DAP pathway in bacteria: the succinylase, acetylase, aminotransferase, and dehydrogenase pathways. These pathways share the steps converting L-aspartate to L-2,3,4,5- tetrahydrodipicolinate (THDPA), but the subsequent steps leading to the production of meso-diaminopimelate, the immediate precursor of L-lysine, are different .

The succinylase pathway acylates THDPA with succinyl-CoA to generate N-succinyl-LL-2-amino-6-ketopimelate and forms meso-DAP by subsequent transamination, desuccinylation, and epimerization. This pathway is utilised by proteobacteria and many firmicutes and actinobacteria.

The acetylase pathway is analogous to the succinylase pathway but uses N-acetyl intermediates. This pathway is limited to certain Bacillus species, in which the corresponding genes have not been identified.

The aminotransferase pathway converts THDPA directly to LL-DAP by diaminopimelate aminotransferase (DapL) without acylation. This pathway is shared by cyanobacteria, Chlamydia, the archaeon Methanothermobacter thermautotrophicus, and the plant Arabidopsis thaliana.

The dehydrogenase pathway forms meso-DAP directly from THDPA, NADPH, and NH4 _ by using diaminopimelate dehydrogenase (Ddh). This pathway is utilised by some Bacillus and Brevibacterium species and Corynebacterium glutamicum.

Most bacteria use only one of the four variants, although certain bacteria, such as C. glutamicum and Bacillus macerans, possess both the succinylase and dehydrogenase pathways.

The four sequences which make up the seed for this model are not closely related, although they are all members of the

family of aminotransferases and are more closely related to each other than to anything else. Additionally, all of them are found in the vicinity of genes involved in the biosynthesis of lysine via the diaminopimelate pathway (

), although this amounts to a separation of 12 genes in the case of Sulfurihydrogenibium azorense Az-Fu1. None of these genomes contain another strong candidate for this role in the pathway. Note: the detailed information included in the

record includes the assertions that the enzyme uses the pyridoxal pyrophosphate cofactor, which is consistent with the

family, and the assertion that the amino group donor is L-glutamate, which is undetermined for the sequences in this clade.
Succinyldiaminopimelate transaminase, DapC, beta/gammaproteobacteria (DapC_beta/gammaproteobac)
Type: Family

Two lysine biosynthesis pathways evolved separately in organisms, the diaminopimelic acid (DAP) and aminoadipic acid (AAA) pathways. The DAP pathway synthesizes L-lysine from aspartate and pyruvate, and diaminopimelic acid is an intermediate. This pathway is utilised by most bacteria, some archaea, some fungi, some algae, and plants. The AAA pathway synthesizes L-lysine from alpha-ketoglutarate and acetyl coenzyme A (acetyl-CoA), and alpha-aminoadipic acid is an intermediate. This pathway is utilised by most fungi, some algae, the bacterium Thermus thermophilus, and probably some archaea, such as Sulfolobus, Thermoproteus, and Pyrococcus. No organism is known to possess both pathways .

There four known variations of the DAP pathway in bacteria: the succinylase, acetylase, aminotransferase, and dehydrogenase pathways. These pathways share the steps converting L-aspartate to L-2,3,4,5- tetrahydrodipicolinate (THDPA), but the subsequent steps leading to the production of meso-diaminopimelate, the immediate precursor of L-lysine, are different .

The succinylase pathway acylates THDPA with succinyl-CoA to generate N-succinyl-LL-2-amino-6-ketopimelate and forms meso-DAP by subsequent transamination, desuccinylation, and epimerization. This pathway is utilised by proteobacteria and many firmicutes and actinobacteria.

The acetylase pathway is analogous to the succinylase pathway but uses N-acetyl intermediates. This pathway is limited to certain Bacillus species, in which the corresponding genes have not been identified.

The aminotransferase pathway converts THDPA directly to LL-DAP by diaminopimelate aminotransferase (DapL) without acylation. This pathway is shared by cyanobacteria, Chlamydia, the archaeon Methanothermobacter thermautotrophicus, and the plant Arabidopsis thaliana.

The dehydrogenase pathway forms meso-DAP directly from THDPA, NADPH, and NH4 _ by using diaminopimelate dehydrogenase (Ddh). This pathway is utilised by some Bacillus and Brevibacterium species and Corynebacterium glutamicum.

Most bacteria use only one of the four variants, although certain bacteria, such as C. glutamicum and Bacillus macerans, possess both the succinylase and dehydrogenase pathways.

This family of succinyldiaminopimelate transaminases (DapC) includes the experimentally characterised enzyme from Bordetella pertussis . The majority of genes in this family are proximal to genes encoding components of the lysine biosynthesis via succinylase diaminopimelate pathway (

) .
Ammonium transporter, marine subtype (Ammonium_transptr_marine)
Type: Family

This protein family is a well conserved subclass of putative ammonimum transporters. Species with this transporter tend to be marine bacteria. This transporter family may represent an important adaptation to the marine environment.
4-dedimethylamino-4-oxo-anhydrotetracycline transaminase OxyQ (OxyQ)
Type: Family

This family of actinobacterial proteins are involved in the biosynthesis of the tetracycline antibiotic, oxytetracycline. The minimum set of enzymes required for the biosynthesis of anhydrotetracycline, the first intermediate in the synthesis of oxytetracycline, are OxyL, OxyQ, and OxyT. OxyQ catalyzes the conversion of 4-dedimethylamino-4-oxoanhydrotetracycline to yield 4-amino-4-de(dimethylamino)anhydrotetracycline (4-amino-ATC) .

Two lysine biosynthesis pathways evolved separately in organisms, the diaminopimelic acid (DAP) and aminoadipic acid (AAA) pathways. The DAP pathway synthesizes L-lysine from aspartate and pyruvate, and diaminopimelic acid is an intermediate. This pathway is utilised by most bacteria, some archaea, some fungi, some algae, and plants. The AAA pathway synthesizes L-lysine from alpha-ketoglutarate and acetyl coenzyme A (acetyl-CoA), and alpha-aminoadipic acid is an intermediate. This pathway is utilised by most fungi, some algae, the bacterium Thermus thermophilus, and probably some archaea, such as Sulfolobus, Thermoproteus, and Pyrococcus. No organism is known to possess both pathways .

There four known variations of the DAP pathway in bacteria: the succinylase, acetylase, aminotransferase, and dehydrogenase pathways. These pathways share the steps converting L-aspartate to L-2,3,4,5- tetrahydrodipicolinate (THDPA), but the subsequent steps leading to the production of meso-diaminopimelate, the immediate precursor of L-lysine, are different .

The succinylase pathway acylates THDPA with succinyl-CoA to generate N-succinyl-LL-2-amino-6-ketopimelate and forms meso-DAP by subsequent transamination, desuccinylation, and epimerization. This pathway is utilised by proteobacteria and many firmicutes and actinobacteria.

The acetylase pathway is analogous to the succinylase pathway but uses N-acetyl intermediates. This pathway is limited to certain Bacillus species, in which the corresponding genes have not been identified.

The aminotransferase pathway converts THDPA directly to LL-DAP by diaminopimelate aminotransferase (DapL) without acylation. This pathway is shared by cyanobacteria, Chlamydia, the archaeon Methanothermobacter thermautotrophicus, and the plant Arabidopsis thaliana.

The dehydrogenase pathway forms meso-DAP directly from THDPA, NADPH, and NH4 _ by using diaminopimelate dehydrogenase (Ddh). This pathway is utilised by some Bacillus and Brevibacterium species and Corynebacterium glutamicum.

Most bacteria use only one of the four variants, although certain bacteria, such as C. glutamicum and Bacillus macerans, possess both the succinylase and dehydrogenase pathways.
Diaminopimelate aminotransferase, DapL, Desulfovibrio-type (DAP-NH2Trfase_DapL_Desulfo)
Type: Family

Two lysine biosynthesis pathways evolved separately in organisms, the diaminopimelic acid (DAP) and aminoadipic acid (AAA) pathways. The DAP pathway synthesizes L-lysine from aspartate and pyruvate, and diaminopimelic acid is an intermediate. This pathway is utilised by most bacteria, some archaea, some fungi, some algae, and plants. The AAA pathway synthesizes L-lysine from alpha-ketoglutarate and acetyl coenzyme A (acetyl-CoA), and alpha-aminoadipic acid is an intermediate. This pathway is utilised by most fungi, some algae, the bacterium Thermus thermophilus, and probably some archaea, such as Sulfolobus, Thermoproteus, and Pyrococcus. No organism is known to possess both pathways .

There four known variations of the DAP pathway in bacteria: the succinylase, acetylase, aminotransferase, and dehydrogenase pathways. These pathways share the steps converting L-aspartate to L-2,3,4,5- tetrahydrodipicolinate (THDPA), but the subsequent steps leading to the production of meso-diaminopimelate, the immediate precursor of L-lysine, are different .

The succinylase pathway acylates THDPA with succinyl-CoA to generate N-succinyl-LL-2-amino-6-ketopimelate and forms meso-DAP by subsequent transamination, desuccinylation, and epimerization. This pathway is utilised by proteobacteria and many firmicutes and actinobacteria.

The acetylase pathway is analogous to the succinylase pathway but uses N-acetyl intermediates. This pathway is limited to certain Bacillus species, in which the corresponding genes have not been identified.

The aminotransferase pathway converts THDPA directly to LL-DAP by diaminopimelate aminotransferase (DapL) without acylation. This pathway is shared by cyanobacteria, Chlamydia, the archaeon Methanothermobacter thermautotrophicus, and the plant Arabidopsis thaliana.

The dehydrogenase pathway forms meso-DAP directly from THDPA, NADPH, and NH4 _ by using diaminopimelate dehydrogenase (Ddh). This pathway is utilised by some Bacillus and Brevibacterium species and Corynebacterium glutamicum.

Most bacteria use only one of the four variants, although certain bacteria, such as C. glutamicum and Bacillus macerans, possess both the succinylase and dehydrogenase pathways.

This group of the superfamily of aminotransferases includes several which are adjacent to elements of the lysine biosynthesis via diaminopimelate pathway (

). Every member of this group is from a genome which possesses most of the lysine biosynthesis pathway but lacks any of the known aminotransferases, succinylases, desuccinylases, acetylases or deacetylases typical of the acylated versions of this pathway nor do they have the direct, NADPH-dependent enzyme (ddh). Although there is no experimental characterisation of any of the sequences in this group, a direct pathway is known in plants and Chlamydia so it seems quite reasonable that these enzymes catalyse the same transformation.
Conserved hypothetical protein CHP03643 (CHP03643)
Type: Family

This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Lactoylglutathione lyase (Lactoylglutathione_lyase)
Type: Family

Members of this protein family share homology with lactoylglutathione lyase (glyoxalase I) and are found mainly in marine members of the gammaproteobacteria, including

from Colwellia psychrerythraea (strain 34H / ATCC BAA-681). This family excludes a well-separated, more narrowly distributed paralogous family, exemplified by

from C. psychrerythraea. The function is of this protein family is unknown.
YtoQ family protein (YtoQ_family_protein)
Type: Family

This entry represents a family of uncharacterised proteins, including YtoQ from Bacillus subtilis. This family shows some sequence similarity to a family of nucleoside 2-deoxyribosyltransferases (COG3613 as iterated through CDD), but sufficiently remote that PSI-BLAST starting from YtoQ and exploring outwards does not discover the relationship.
Transcription regulator HTH, AsnC-type, conserved site (Tscrpt_reg_HTH_AsnC-type_CS)
Type: Conserved_site

The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily . The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes .

This entry represents a conserved site that spans the complete helix-turn-helix motif and extends one residue downstream and one upstream of the HTH extremities.
Sodium symporter small subunit (Na_symporter_ssu)
Type: Domain

Proteins matched by this entry are highly hydrophobic bacterial proteins of about 90 amino acids in length. They are usually found immediately upstream (sometimes fused to) a member of the solute:sodium symporter family, and are therefore putative sodium:solute symporter small subunits. They tend to be found in aquatic bacteria, especially those from marine or other high salt environments.
Transcription regulator AsnC/Lrp, ligand binding domain (Tscrpt_reg_AsnC/Lrp_C)
Type: Domain

The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily . The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes .

This entry represents the C-terminal regulatory ligand binding domain of the transcription regulator AsnC/Lrp. Structurally this domain has a dimeric α/β barrel fold . This domain binds almost exclusively amino acids, but also 4-hydroxyphenylpyruvate and kynurenine (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Transcription regulator AsnC-like (Tscrpt_reg_AsnC-like)
Type: Family

The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily . The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes .

This entry also includes some siroheme decarboxylases, which contain the AsnC-like ligand binding domain.
DNA helicase, DnaB-like, phage (DNA_helicase_DnaB-like_phg)
Type: Family

Proteins in this entry are phage (or prophage-region) homologues of the bacterial homohexameric replicative DNA helicase DnaB. Some phages rely on host DnaB while others encode their own versions. This entry represents the largest phage-specific clade among the close homologues of DnaB, but there are other phage DnaB homologues not present in this entry.
Bacteriocin, heterocycloanthracin/sonorensin family (Bacteriocin/sonorensin)
Type: Family

Numerous bacteria encode systems for producing bacteriocins by extensive modification of ribosomally produced precursors. Members of the TOMM class (thiazole/oxazole-modified microcins) are recognizable by association with cyclodehydratase (and often dehydrogenase) maturation proteins. This family consists of a special subclass, the heterocycloanthracin family, that share a homologous leader peptide region and then a repeat region with Cys as every third residue. In Bacillus anthracis and Bacillus cereus, the RiPP (ribosomally translated and post-translationally modified natural product) precursor is encoded far from its maturase genes, and every strain has the system. In other species (e.g. B. licheniformis, B. sorenensis), precursor and maturase genes are close together. Sonorensin, from B. sonorensis MT93, was shown to have broad spectrum antimicrobial activity, affecting Gram-positive and Gram-negative bacteria .
Bacteriocin, streptolysin S, precursor (Bacteriocin_streptolysin_S_pre)
Type: Family

This entry represents a family of heterocycle-containing bacteriocin precursors. It includes the hemolytic polypeptide streptolysin S from Streptococcus pyogenes. These small, ribosomally produced polypeptide precursors are extensively processed post-translationally. Bacteriocin genes in general are small, highly diverse, and have unusual sequence composition, so they are easily missed by many gene-finding programs.
Thiazole/oxazole-forming peptide maturase, SagC family component (Cyclo_dehy_ocin)
Type: Family

Members of this protein family include enzymes related to SagC, a protein involved in thiazole/oxazole cyclodehydration modifications during biosynthesis of streptolysin S in Streptococcus pyogenes from the protoxin polypeptide (product of the sagA gene). Recent evidence suggests that the YcaO/SagD-like component, not this component, performs an ATP-dependent cyclodehydration . This protein family serves as a marker for widely distributed prokaryotic systems for making a general class of heterocycle-containing bacteriocins . Note that this model does not find all possible examples of bacteriocin biosynthesis cyclodehydratases, an in particular misses the E. coli plasmid protein McbB of microcin B17 biosynthesis.
PQQ-dependent dehydrogenase SndH-like (SndH-like)
Type: Family

PQQ, or pyrroloquinoline-quinone, serves as a cofactor for a number of sugar and alcohol dehydrogenases in a limited number of bacterial species. Most characterised PQQ-dependent enzymes have multiple β-propeller repeats (

). This entry, however, represents a family of PQQ-dependent dehydrogenases that lack this repeat , including L-sorbosone dehydrogenase from Ketogulonicigenium vulgare (SndH,

), which directly converts l-sorbosone to l-ascorbic acid, an essential nutrient .
Patatin-related protein (Patatin-related_protein)
Type: Domain

Patatins are plant storage proteins capable of phospholipase activity (see

). This entry is found in a family of bacterial proteins of unknown function that contain an N-terminal patatin domain. Regions of strong sequence conservation are separated by regions of significant sequence and length variability. The proteins in this entry are distributed sporadically among bacteria.
Putative bacteriocin export ABC transporter, lactococcin 972 group (L_ocin_972_ABC)
Type: Family

A bacteriocin system gene pair with a fairly wide distribution in bacteria consists of a lactococcin 972 homologue (see

) and a multiple-membrane-spanning putative immunity protein (see

). This entry represents a small clade within the ABC transporters that are encoded adjacent to these bacteriocin system gene pairs and are likely to function as export proteins.
Polysaccharide pyruvyl transferase, CsaB (Polysacch_pyruvyl_Trfase_CsaB)
Type: Family

The cell surface anchoring B (CsaB) protein of Bacillus anthracis adds a pyruvyl group to peptidoglycan-associated polysaccharide . This addition is necessary for the non-covalent anchoring of proteins containing an S-layer homology (SLH) domain (

) to these pyruvylated polysaccharides. The proteins in this entry represent a distinct clade of polysaccharide pruvyl transferases that nearly exactly follows the phylogenetic distribution of the SLH domain.
RidA, conserved site (RidA_CS)
Type: Conserved_site

This entry represents a conserved site found towards the C-terminal of the YjgF family members. YjgF contains the enamine/imine deaminase activity and can accelerate the release of ammonia from reactive enamine/imine intermediates of the pyridoxal 5'-phosphate-dependent threonine dehydratase (IlvA). Therefore, YjgF is also known as RidA (reactive intermediate/imine deaminase A) . The RidA family members are widely distributed in eubacteria, archaea and eukaryotes. Although they share protein sequences and structures similarity, they may have different functions.
3-aminoacrylate deaminase RutC (RutC)
Type: Family

RutC from E. coli is essential for growth on uracil as sole nitrogen source. Its function is not known, but it is thought to reduce aminoacrylate peracid to aminoacrylate .
Sodium/solute symporter, VC2705 subfamily (Na/solute_symporter_VC_2705)
Type: Family

This family belongs to a larger family of transporters of the sodium:solute symporter superfamily, TC 2.A.21. Members of this strictly bacterial protein subfamily are found almost invariably immediately downstream from a member of family

. Occasionally, the two genes are fused.
Ergot alkaloid biosynthesis protein (Ergot_alkaloid_biosynthesis)
Type: Family

Proteins in this family are required in the final stages of the biosynthesis of secondary metabolite such as fungal alkaloids. These include agroclavine dehydrogenase (easG) from ergot (
Claviceps purpurea
), which is required for the biosynthesis of the ergot alkaloid agroclavine, converting the intermediate chanoclavine-I aldehyde to agroclavine non-enzymatically ; and festuclavine synthase I (ifgF1) from
Penicillium roqueforti
, which reduces the intermediate 6,8-dimethyl-6,7-didehydroergoline to form festuclavine .
Violacein biosynthesis enzyme, VioE (Violacein_biosynth_enz_VioE)
Type: Family

Violacein is a purple-coloured pigment produced by bacteria such as Chromobacterium violaceum. Violacein exhibits significant biological activities, such as strong inhibition of several tumor cell lines, as well as antibacterial and trypanocidal activities.

Violacein is synthesised from two molecules of tryptophan by the enzymes VioA-E.
VioE is important for formation of the intermediate prodeoxyviolacein in this biosynthetic pathway .

This entry represents the enzyme VioE.
Repair of iron centres family (RIC_family)
Type: Family

Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulphur clusters. The previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The new suggested name is RIC, for Repair of Iron Centres .
Peroxiredoxin OsmC (Peroxiredoxin_OsmC)
Type: Family

Osmotically inducible protein C (OsmC) is a stress-induced protein found in Escherichia coli. The transcription of the osmC gene of E. coli is regulated as a function of the phase of growth and is induced during the late exponential phase when the growth rate slows before entry into stationary phase. The transcription is initiated by two overlapping promoters, osmCp1 and osmCp2 .
Peroxiredoxin OsmC-like protein, Firmicutes (OsmC-like_firmicutes)
Type: Family

Osmotically inducible protein C (OsmC) is a stress-induced protein found in Escherichia coli. The transcription of the osmC gene of E. coli is regulated as a function of the phase of growth and is induced during the late exponential phase when the growth rate slows before entry into stationary phase. The transcription is initiated by two overlapping promoters, osmCp1 and osmCp2 .

This entry represents proteins belongs to the OsmC/Ohr family and is restricted to Firmicutes. Proteins in this family include YmaD from Bacillus subtilis.