Classification I Classification II Subsystem Functional Role Occurrence Amino Acids and Derivatives Alanine, serine, and glycine Alanine Biosynthesis Cysteine desulfurase (EC 4.4.1.-) 2 Amino Acids and Derivatives Alanine, serine, and glycine Glycine cleavage system Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2) 4 Amino Acids and Derivatives Alanine, serine, and glycine Glycine cleavage system Dihydrolipoamide dehydrogenase (EC 1.8.1.4) 3 Amino Acids and Derivatives Alanine, serine, and glycine Glycine cleavage system Aminomethyltransferase (glycine cleavage system T protein) (EC:2.1.2.10) 1 Amino Acids and Derivatives Alanine, serine, and glycine Glycine synthesis Serine hydroxymethyltransferase (EC 2.1.2.1) 2 Amino Acids and Derivatives Alanine, serine, and glycine Glycine synthesis Low- specificity L-threonine aldolase (EC 4.1.2.5) 2 Amino Acids and Derivatives Alanine, serine, and glycine Serine Biosynthesis Phosphoserine aminotransferase (EC 2.6.1.52) 1 Amino Acids and Derivatives Alanine, serine, and glycine Serine Biosynthesis Phosphoserine phosphatase (EC 3.1.3.3) 1 Amino Acids and Derivatives Alanine, serine, and glycine Serine Biosynthesis Serine hydroxymethyltransferase (EC 2.1.2.1) 2 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Urease accessory protein UreF 3 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Agmatine deiminase (EC 3.5.3.12) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation 4-aminobutyrate aminotransferase (EC 2.6.1.19) 4 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Arginine decarboxylase (EC 4.1.1.19) 9 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Urease accessory protein UreE 7 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Ornithine aminotransferase (EC 2.6.1.13) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation 3-polyprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.-) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Ornithine carbamoyltransferase (EC 2.1.3.3) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Urease alpha subunit (EC 3.5.1.5) 9 Amino Acids and Derivatives Arginine; urea cycle, polyamines Polyamine Metabolism Spermidine Putrescine ABC transporter permease component potC (TC_3.A.1.11.1) 2 Amino Acids and Derivatives Arginine; urea cycle, polyamines Polyamine Metabolism Arginine decarboxylase (EC 4.1.1.19) 9 Amino Acids and Derivatives Arginine; urea cycle, polyamines Polyamine Metabolism Putrescine transport system permease protein potH (TC 3.A.1.11.2) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Polyamine Metabolism Spermidine Putrescine ABC transporter permease component potB (TC_3.A.1.11.1) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Polyamine Metabolism Ornithine decarboxylase (EC 4.1.1.17) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urea ABC transporter, permease protein UrtC 6 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urease alpha subunit (EC 3.5.1.5) 9 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urease accessory protein UreF 3 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urea ABC transporter, permease protein UrtB 2 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urea ABC transporter, ATPase protein UrtD 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urea carboxylase 2 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urea ABC transporter, urea binding protein 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urease accessory protein UreE 7 Amino Acids and Derivatives Aromatic amino acids and derivatives Central meta-cleavage pathway of aromatic compound degradation 2-hydroxymuconic semialdehyde hydrolase (EC 3.7.1.9) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis 3- phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) 10 Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis Prephenate dehydrogenase (EC 1.3.1.12) 7 Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis Shikimate kinase (EC 2.7.1.71) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis Shikimate 5-dehydrogenase (EC 1.1.1.25) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) 5 https://static-content.springer.com/esm/art%3A10.1186%2F1471-2164-7-57/MediaObjects/12864_2005_440_MOESM3_ESM.txt[9/25/2019 2:46:04 PM] Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis Chorismate mutase (EC 5.4.99.5) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis 3- dehydroquinate synthase (EC 4.2.3.4) 5 Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis Chorismate synthase (EC 4.2.3.5) 2 Amino Acids and Derivatives Aromatic amino acids and derivatives Phenylalanine synthesis Aspartate aminotransferase (EC 2.6.1.1) 6 Amino Acids and Derivatives Aromatic amino acids and derivatives Phenylalanine synthesis Chorismate mutase (EC 5.4.99.5) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Tryptophan synthesis Tryptophan synthase beta chain like (EC 4.2.1.20) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Tryptophan synthesis Indole-3-glycerol phosphate synthase (EC 4.1.1.48) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Tryptophan synthesis Anthranilate synthase, aminase component (EC 4.1.3.27) 2 Amino Acids and Derivatives Aromatic amino acids and derivatives Tryptophan synthesis Tryptophan synthase beta chain (EC 4.2.1.20) 3 Amino Acids and Derivatives Aromatic amino acids and derivatives Tyrosine synthesis Chorismate mutase (EC 5.4.99.5) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Tyrosine synthesis Aspartate aminotransferase (EC 2.6.1.1) 5 Amino Acids and Derivatives Aromatic amino acids and derivatives Tyrosine synthesis Prephenate dehydrogenase (EC 1.3.1.12) 7 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis Dihydroxy-acid dehydratase (EC 4.2.1.9) 6 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis 3-isopropylmalate dehydrogenase (EC 1.1.1.85) 3 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis Acetolactate synthase large subunit (EC 2.2.1.6) 4 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis 2-isopropylmalate synthase (EC 2.3.3.13) 12 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis Threonine dehydratase (EC 4.3.1.19) 1 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33) 1 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis Ketol-acid reductoisomerase (EC 1.1.1.86) 3 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis Branched-chain amino acid aminotransferase (EC 2.6.1.42) 45 Amino Acids and Derivatives Branched-chain amino acids HMG CoA Synthesis Isovaleryl- CoA dehydrogenase (EC 1.3.99.10) 2 Amino Acids and Derivatives Branched-chain amino acids HMG CoA Synthesis Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) 1 Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation Branched- chain alpha-keto acid dehydrogenase, E1 component, beta subunit (EC 1.2.4.4) 5 Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation Dihydrolipoamide dehydrogenase (EC 1.8.1.4) 3 Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation 3- hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) 1 Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation Branched- chain amino acid aminotransferase (EC 2.6.1.42) 45 Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation Branched- chain alpha-keto acid dehydrogenase, E1 component, alpha subunit (EC 1.2.4.4) 2 Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation Acyl-CoA dehydrogenase (EC 1.3.99.3) 1 Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation Enoyl-CoA hydratase (EC 4.2.1.17) 1 Amino Acids and Derivatives Branched-chain amino