-REACTIONS # GLYCOLYSIS 2.7.1.2a : beta-D-glucose + ATP -> beta-D-glucose-6-phosphate + ADP 2.7.1.2b : alpha-D-glucose + ATP <-> alpha-D-glucose 6-phosphate + ADP 5.3.1.9a : alpha-D-glucose 6-phosphate <-> beta-D-glucose-6-phosphate 5.3.1.9b : beta-D-glucose-6-phosphate <-> fructose-6-phosphate 2.7.1.11 : ATP + fructose-6-phosphate -> ADP + fructose-1,6-bisphosphate 4.1.2.13a : fructose-1,6-bisphosphate <-> dihydroxy-acetone phosphate + D-glyceraldehyde-3-phosphate 3.1.3.11 : fructose-1,6-bisphosphate + H2O -> fructose-6-phosphate + phosphate O4P 5.3.1.1 : D-glyceraldehyde-3-phosphate <-> dihydroxy-acetone phosphate _1.2.1.59a : NAD+ + H+ + D-glyceraldehyde-3-phosphate + phosphate O4P -> NADH + 1,3-diphosphateglycerate _1.2.1.59b : NADPH + 1,3-diphosphateglycerate -> NADP+ + H+ + D-glyceraldehyde-3-phosphate + phosphate O4P 1.2.1.12 : D-glyceraldehyde-3-phosphate + phosphate O4P + NAD+ + H+ <-> 1,3-diphosphateglycerate + NADH 2.7.2.3 : 3-phosphoglycerate + ATP <-> 1,3-diphosphateglycerate + ADP 5.4.2.1 : 3-phosphoglycerate <-> 2-phosphoglycerate 4.2.1.11 : 2-phosphoglycerate <-> phosphoenolpyruvate + H2O 2.7.1.40a : ADP + phosphoenolpyruvate -> ATP + pyruvate 2.7.9.2 : H2O + pyruvate + ATP -> phosphate O4P + phosphoenolpyruvate + AMP # TCA CYCLE 6.2.1.5 : succinate + coenzyme A + ATP <-> succinyl-CoA + ADP + phosphate O4P _1.3.99.1 : succinate + UQ <-> fumarate + UQH2 4.2.1.2 : malate <-> fumarate + H2O 1.1.1.37 : malate + NAD+ + H+ <-> oxaloacetate + NADH 2.3.3.1 : oxaloacetate + acetyl-CoA + H2O <-> citrate + coenzyme A 4.2.1.3a : citrate <-> cis-aconitate + H2O 4.2.1.3b : cis-aconitate + H2O <-> D-isocitrate 1.1.1.42 : D-isocitrate + NADP+ + H+ <-> 2-ketoglutarate + CO2 + NADPH # GLYOXYLATE SHUNT 6.2.1.9 : coenzyme A + malate + ATP <-> phosphate O4P + L-malyl-CoA + ADP # not pres ! would made up glyoxylate shunt ~~IMPORTANT, following 2 reactions not in sequence!!~~ ·4.1.3.1 : D-isocitrate -> glyoxylate + succinate ·2.3.3.9 : acetyl-CoA + H2O + glyoxylate <-> malate + coenzyme A # PENTOSE PHOSPHATE PATHWAY 1.1.1.49 : beta-D-glucose-6-phosphate + NADP+ + H+ <-> D-glucono-delta-lactone-6-phosphate + NADPH 3.1.1.31 : D-glucono-delta-lactone-6-phosphate + H2O -> 6-phospho-D-gluconate 1.1.1.44 : 6-phospho-D-gluconate + NADP+ + H+ -> D-ribulose-5-phosphate + CO2 + NADPH 5.1.3.1 : D-ribulose-5-phosphate <-> D-xylulose-5-phosphate 5.3.1.6 : D-ribose-5-phosphate <-> D-ribulose-5-phosphate 5.3.1.9c : alpha-D-glucose 6-phosphate <-> fructose-6-phosphate 2.2.1.1a : D-ribose-5-phosphate + D-xylulose-5-phosphate <-> D-sedoheptulose-7-phosphate + D-glyceraldehyde-3-phosphate 2.2.1.1b : D-erythrose-4-phosphate + D-xylulose-5-phosphate <-> fructose-6-phosphate + D-glyceraldehyde-3-phosphate 2.2.1.2 : D-glyceraldehyde-3-phosphate + D-sedoheptulose-7-phosphate <-> fructose-6-phosphate + D-erythrose-4-phosphate 4.1.2.14 : 2-keto-3-deoxy-6-phospho-gluconate -> D-glyceraldehyde-3-phosphate + pyruvate 4.1.2.4 : deoxyribose-5-phosphate <-> acetaldehyde + D-glyceraldehyde-3-phosphate # CALVIN CYCLE ADDITION TO PPP 2.7.1.19 : D-ribulose-5-phosphate + ATP -> D-ribulose-1,5-bisphosphate + ADP 4.1.2.13b : dihydroxy-acetone phosphate + D-erythrose-4-phosphate -> D-sedoheptulose-1,7-bisphosphate 3.1.3.37 : H2O + D-sedoheptulose-1,7-bisphosphate -> phosphate O4P + D-sedoheptulose-7-phosphate # in "SPECIAL" 4.1.1.39 : D-ribulose-1,5-bisphosphate + CO2 + H2O -> 2 3-phosphoglycerate + 2 H+ # AMINO ACIDS # alanine - Ala 5.1.1.1 : L-alanine <-> D-alanine 1.4.1.1 : NAD+ + H+ + H2O + L-alanine <-> ammonia H3N + NADH + pyruvate 2.3.3.5 : oxaloacetate + H2O + propionyl-CoA -> (2S,3S)-2-methylcitrate + coenzyme A tRNA 6.1.1.7 : tRNAala + L-alanine + ATP -> L-alanyl-tRNAala + diphosphate + AMP # Asp, Arg, Asn, Lys and Thr # aspartate - Asp 1.4.3.16 : O2 + H2O + L-aspartate -> ammonia H3N + H2O2 + oxaloacetate 2.6.1.1a : L-aspartate + 2-ketoglutarate <-> L-glutamate + oxaloacetate 4.1.1.11 : L-aspartate -> beta-alanine + CO2 4.1.1.15b : L-aspartate -> beta-alanine + CO2 # - from fumarate to Asp 4.3.2.2a : adenylo-succinate <-> fumarate + AMP 6.3.4.4 : L-aspartate + inosine-5'-phosphate + GTP <-> adenylo-succinate + phosphate O4P + GDP # - from Asp to Arg 2.1.3.3 : L-ornithine + carbamoyl-phosphate <-> citrulline + phosphate O4P 6.3.4.5a : L-aspartate + citrulline + ATP <-> L-arginino-succinate + diphosphate + AMP 4.3.2.1 : L-arginino-succinate <-> L-arginine + fumarate # - from Asp to Asn 3.5.1.1 : L-asparagine + H2O <-> ammonia H3N + L-aspartate # - from Asp to Thr 2.7.2.4 : L-aspartate + ATP -> L-aspartyl-4-phosphate + ADP 1.2.1.11 : NADPH + L-aspartyl-4-phosphate -> NADP+ + H+ + phosphate O4P + L-aspartate-semialdehyde _1.1.1.3a : L-aspartate-semialdehyde + NADPH <-> homoserine + NADP+ + H+ _1.1.1.3b : homoserine + NAD+ <-> L-aspartate-semialdehyde + NADH + H+ 2.7.1.39 : homoserine + ATP -> O-phospho-L-homoserine + ADP 4.2.3.1a : O-phospho-L-homoserine + H2O -> phosphate O4P + L-threonine # - from Asp to Lys 4.2.1.52 : pyruvate + L-aspartate-semialdehyde -> 2 H2O + L-2,3-dihydrodipicolinate _1.3.1.26a : tetrahydrodipicolinate + NADP+ + H+ <-> L-2,3-dihydrodipicolinate + NADPH _1.3.1.26b : tetrahydrodipicolinate + NAD+ + H+ <-> L-2,3-dihydrodipicolinate + NADH 2.6.1.83 : L,L-diaminopimelate + 2-ketoglutarate <-> tetrahydrodipicolinate + L-glutamate + H2O 5.1.1.7 : L,L-diaminopimelate <-> meso-diaminopimelate 4.1.1.20 : meso-diaminopimelate -> CO2 + L-lysine tRNA 6.1.1.12 : tRNAasp + L-aspartate + ATP -> L-aspartyl-tRNAasp + diphosphate + AMP # arginine - Arg # - from Asp to Arg tRNA 6.1.1.19 : tRNAarg + L-arginine + ATP -> L-arginyl-tRNAarg + diphosphate + AMP # - from Arg to putrescine 4.1.1.19 : L-arginine -> CO2 + agmatine 3.5.3.11 : H2O + agmatine -> urea + putrescine # asparagine - Asn # - from Asp to Asn tRNA 6.1.1.22 : tRNAasn + L-asparagine + ATP -> L-asparaginyl-tRNAasn + diphosphate + AMP tRNA 6.3.5.6 : L-glutamine + L-aspartyl-tRNAAsn + ATP -> L-glutamate + L-asparaginyl-tRNAAsn + phosphate O4P + ADP # lysine - Lys # - from Asp to Lys # - Ile, Leu and Val degradation (mostly not pres) tRNA 6.1.1.6 : tRNAlys + L-lysine + ATP -> L-lysyl-tRNAlys + diphosphate + AMP 4.1.1.18 : L-lysine -> CO2 + cadaverine # threonine - Thr # - from Asp to Thr THREOSPON-RXN : 2-amino-3-oxobutanoate <-> aminoacetone + CO2 4.3.1.19a : L-threonine -> 2-oxobutanoate + ammonia H3N tRNA 6.1.1.3 : tRNAthr + L-threonine + ATP -> L-threonyl-tRNAthr + diphosphate + AMP # Ser, Cys and Gly # serine - Ser # - from 3PG to Ser 1.1.1.95 : 3-phosphoglycerate + NAD+ + H+ -> 3-phospho-hydroxypyruvate + NADH _4.3.1.19b : L-serine <-> pyruvate + ammonia H3N # - from Ser to Cys 2.3.1.30 : L-serine + acetyl-CoA -> O-acetyl-L-serine + coenzyme A 2.5.1.47 : O-acetyl-L-serine + hydrogen sulfide H2s <-> L-cysteine + acetate # - from Ser to Gly (& viceversa) 2.1.2.1 : L-serine + tetrahydrofolate <-> 5,10-methylene-THF + glycine + H2O tRNA 6.1.1.11 : tRNAser + L-serine + ATP -> L-seryl-tRNAser + diphosphate + AMP # cysteine - Cys # - from Ser to Cys tRNA 6.1.1.16 : tRNAcys + L-cysteine + ATP -> L-cysteinyl-tRNAcys + diphosphate + AMP # glycine - Gly # - from Ser to Gly (& viceversa) tRNA 6.1.1.14 : tRNAgly + glycine + ATP -> glycyl-tRNAgly + diphosphate + AMP # Glu, Gln, Pro and Trp # glutamate - Glu transport TRANS-RXN59G-639 : L-glutamate_extrac + H+_extrac -> L-glutamate + H+ 1.4.1.4 : L-glutamate + H2O + NADP+ + H+ <-> ammonia H3N + 2-ketoglutarate + NADPH # - from Glu to Pro 2.7.2.11 : L-glutamate + ATP -> L-glutamate-5-phosphate + ADP 1.2.1.41 : L-glutamate gamma-semialdehyde + phosphate O4P + NADP+ + H+ <-> L-glutamate-5-phosphate + NADPH SPONTPRO-RXN : L-glutamate gamma-semialdehyde <-> H2O + pyrroline 5-carboxylate _1.5.1.12a : pyrroline 5-carboxylate + NAD+ + H+ + 2 H2O <-> L-glutamate + NADH _1.5.1.2a1 : L-proline + NADP+ + H+ <-> pyrroline 5-carboxylate + NADPH _1.5.1.2a2 : L-proline + NAD+ + H+ <-> pyrroline 5-carboxylate + NADH # - from Glu to Gln 3.5.1.2a : L-glutamine + H2O <-> L-glutamate + ammonia H3N 6.3.1.2 : ammonia H3N + L-glutamate + ATP -> L-glutamine + ADP + phosphate O4P 1.4.1.14 : NAD+ + H+ + 2 L-glutamate <-> NADH + 2-ketoglutarate + L-glutamine 5.1.1.3 : L-glutamate <-> D-glutamate _3.5.1.2b : D-glutamine + H2O -> D-glutamate + ammonia H3N # not pres ! would interconvert D-Gln and L-Gln ~~IMPORTANT, following reaction not in sequence!!~~ ·5.1.1.9 : D-glutamine <-> L-glutamine # - from Glu to Trp - chorismate comes from Phe biosynthesis 4.1.3.27 : chorismate + L-glutamine -> L-glutamate + anthranilate + pyruvate 2.4.2.18 : N-(5'-phosphoribosyl)-anthranilate + diphosphate <-> anthranilate + 5-phosphoribosyl 1-pyrophosphate 5.3.1.24 : N-(5'-phosphoribosyl)-anthranilate <-> 1-(o-carboxyphenylamino)-1'-deoxyribulose-5'-phosphate 4.1.1.48 : 1-(o-carboxyphenylamino)-1'-deoxyribulose-5'-phosphate -> indole-3-glycerol-phosphate + CO2 + H2O 4.2.1.20a : indole-3-glycerol-phosphate + L-serine <-> L-tryptophan + H2O + D-glyceraldehyde-3-phosphate _4.2.1.20b : indole-3-glycerol-phosphate <-> indole 4.2.1.20c : indole + L-serine -> L-tryptophan + H2O 4.1.1.15a : L-glutamate -> CO2 + 4-aminobutyrate 2.6.1.1b : 3-sulfinoalanine + 2-ketoglutarate -> L-glutamate + 3-sulfinyl-pyruvate tRNA 6.1.1.17 : tRNAGlu + L-glutamate + ATP -> L-glutamyl-tRNAGlu + diphosphate + AMP # glutamine - Gln transport TRANS-RXN59G-245 : L-glutamine_extrac + H+_extrac -> L-glutamine + H+ # - from Glu to Gln tRNA _6.3.5.7 : L-glutamine + L-glutamyl-tRNAGlu + ATP -> L-glutamate + L-glutaminyl-tRNAGln + phosphate O4P + ADP # not pres ! would produce Gln's tRNA ~~IMPORTANT, following reaction not in sequence!!~~ tRNA ·6.1.1.18 : tRNAgln + L-glutamine + ATP <-> L-glutaminyl-tRNAgln + diphosphate + AMP # proline - Pro # - from Glu to Pro # - from Pro to pyruvate - not pres _1.5.1.12d : trans-4-Hydroxy-L-proline -> L-1 pyrroline-3-hydroxy-5-carboxylate _1.5.1.2b : L-1 pyrroline-3-hydroxy-5-carboxylate -> trans-4-Hydroxy-L-proline _1.5.1.12b : L-1 pyrroline-3-hydroxy-5-carboxylate -> L-erythro-4-hydroxy-glutamate _2.6.1.1c : L-erythro-4-hydroxy-glutamate -> D-4-hydroxy-2-keto-glutarate 4.1.3.16 : D-4-hydroxy-2-keto-glutarate <-> glyoxylate + pyruvate _pyrroline1 : L-1 pyrroline-3-hydroxy-5-carboxylate <-> L-4-hydroxy-glutamate semialdehyde _1.5.1.12c : L-4-hydroxy-glutamate semialdehyde <-> L-erythro-4-hydroxy-glutamate _1.5.99.8a : L-4-hydroxy-glutamate semialdehyde <-> L-erythro-4-hydroxy-glutamate tRNA 6.1.1.15 : L-proline + tRNApro + ATP -> L-prolyl-tRNApro + diphosphate + AMP 5.2.1.8 : peptidylproline (omega = 180) -> peptidylproline (omega = 0) # tryptophan - Trp # - from Glu to Trp tRNA 6.1.1.2 : ATP + tRNAtrp + L-tryptophan -> AMP + diphosphate + L-tryptophanyl-tRNAtrp # Phe and Tyr # phenylalanine - Phe # - chorismate production (common to Phe, Tyr and Trp) 2.5.1.54 : phosphoenolpyruvate + D-erythrose-4-phosphate + H2O -> 3-deoxy-D-arabino-heptulosonate-7-phosphate + phosphate O4P 4.2.3.4 : 3-deoxy-D-arabino-heptulosonate-7-phosphate -> 3-dehydroquinate + phosphate O4P 4.2.1.10 : 3-dehydroquinate -> H2O + 3-dehydro-shikimate 1.1.1.25 : NADP+ + H+ + shikimate <-> NADPH + 3-dehydro-shikimate 2.7.1.71 : shikimate + ATP -> shikimate-3-phosphate + ADP 2.5.1.19 : shikimate-3-phosphate + phosphoenolpyruvate <-> 5-enolpyruvyl-shikimate-3-phosphate + phosphate O4P 4.2.3.5 : 5-enolpyruvyl-shikimate-3-phosphate -> phosphate O4P + chorismate # - from chorismate to prephenate (common to Phe and Tyr) 5.4.99.5 : chorismate <-> prephenate # - from prephenate to Phe 4.2.1.51 : prephenate <-> phenylpyruvate + H2O + CO2 2.6.1.9b : phenylpyruvate + L-glutamate <-> L-phenylalanine + 2-ketoglutarate # - from Phe to Tyr (not pres) 4.2.1.96 : 4alpha-hydroxy-tetrahydrobiopterin -> dihydrobiopterin + H2O tRNA 6.1.1.20 : tRNAphe + L-phenylalanine + ATP -> L-phenylalanyl-tRNAphe + diphosphate + AMP # tyrosine - Tyr # - chorismate production (common to Phe, Tyr and Trp) # - from chorismate to prephenate (common to Phe and Tyr) # - from prephenate to Tyr I 1.3.1.12 : prephenate + NAD+ + H+ <-> 4-hydroxyphenylpyruvate + CO2 + NADH _2.6.1.1d : 4-hydroxyphenylpyruvate <-> L-tyrosine # - from prephenate to Tyr II - not pres # - from Phe to Tyr - not pres tRNA 6.1.1.1 : L-tyrosine + tRNAtyr + ATP -> L-tyrosyl-tRNAtyr + diphosphate + AMP # histidine - His # - 5-phosphoribosyl 1-pyrophosphate comes from Pirimidine biosynthesis 2.4.2.17 : phosphoribosyl-ATP + diphosphate <-> ATP + 5-phosphoribosyl 1-pyrophosphate 3.6.1.31 : phosphoribosyl-ATP + H2O -> phosphoribosyl-AMP + diphosphate 3.5.4.19 : phosphoribosyl-AMP + H2O -> phosphoribosylformiminoAICAR-phosphate 5.3.1.16 : phosphoribosylformiminoAICAR-phosphate -> phosphoribulosylformimino-AICAR-P 2.4.2.-a : phosphoribulosylformimino-AICAR-P + L-glutamine -> L-glutamate + D-erythro-imidazole-glycerol-phosphate + aminoimidazole carboxamide ribonucleotide 4.2.1.19 : D-erythro-imidazole-glycerol-phosphate -> imidazole acetol-phosphate + H2O 2.6.1.9a : imidazole acetol-phosphate + L-glutamate <-> L-histidinol-phosphate + 2-ketoglutarate # not pres ! would close His production ~~IMPORTANT, following reaction not in sequence!!~~ ·3.1.3.15 : L-histidinol-phosphate + H2O <-> histidinol + phosphate O4P 1.1.1.23a : histidinol + NAD+ + H+ -> histidinal + NADH 1.1.1.23b : histidinal + NAD+ + H+ + H2O -> L-histidine + NADH tRNA 6.1.1.21 : tRNAhis + L-histidine + ATP -> L-histidyl-tRNAhis + diphosphate + AMP # Val, Ile and Leu # valine - Val _2.2.1.6d : pyruvate -> 2-acetolactate 1.1.1.86a : 2,3-dihydroxy-isovalerate + NADP+ + H+ <-> 2-acetolactate + NADPH 4.2.1.9a : 2,3-dihydroxy-isovalerate -> 2-keto-isovalerate + H2O 2.6.1.42a : L-glutamate + 2-keto-isovalerate <-> L-valine + 2-ketoglutarate tRNA 6.1.1.9 : tRNAval + L-valine + ATP -> L-valyl-tRNAval + diphosphate + AMP # isoleucine - Ile _2.2.1.6e : pyruvate + 2-oxobutanoate -> 2-aceto-2-hydroxy-butyrate 1.1.1.86b : 2-aceto-2-hydroxy-butyrate + NADPH <-> 2,3-dihydroxy-3-methylvalerate + NADP+ + H+ 4.2.1.9b : 2,3-dihydroxy-3-methylvalerate -> 2-keto-3-methyl-valerate + H2O 2.6.1.42b : L-isoleucine + 2-ketoglutarate <-> L-glutamate + 2-keto-3-methyl-valerate tRNA 6.1.1.5 : tRNAile + L-isoleucine + ATP -> L-isoleucyl-tRNAile + diphosphate + AMP # leucine - Leu 2.3.3.13 : 2-keto-isovalerate + acetyl-CoA + H2O -> 2-isopropylmalate + coenzyme A 4.2.1.33a : 2-isopropylmalate <-> isopropylmaleate + H2O 4.2.1.33b : 3-isopropylmalate <-> isopropylmaleate + H2O 1.1.1.85 : 3-isopropylmalate + NAD+ + H+ -> 2-isopropyl-3-oxosuccinate + NADH RXN-7800 : 2-isopropyl-3-oxosuccinate <-> 2-ketoisocaproate + CO2 2.6.1.42c : L-glutamate + 2-ketoisocaproate -> L-leucine + 2-ketoglutarate tRNA 6.1.1.4 : L-leucine + tRNAleu + ATP -> L-leucyl-tRNAleu + diphosphate + AMP # methionine - Met # from homoserine to L-homocysteine # not pres ! would produce L-homocysteine ~~IMPORTANT, following 2 reactions not in sequence!!~~ ·2.3.1.31 : acetyl-CoA + homoserine <-> coenzyme A + O-acetyl-L-homoserine ·2.5.1.48 : O-acetyl-L-homoserine <-> L-homocysteine # - from L-homocysteine to Met 3.3.1.1 : S-adenosyl-L-homocysteine + H2O <-> L-homocysteine + adenosine 2.1.1.13 : L-homocysteine + 5-methyl-THF <-> L-methionine + tetrahydrofolate 2.5.1.6 : ATP + L-methionine + H2O -> phosphate O4P + diphosphate + S-adenosyl-L-methionine tRNA 2.1.2.9b : 10-formyl-tetrahydrofolate + L-methionyl-tRNAmet + H2O -> tetrahydrofolate + N-formyl-L-methionyl-tRNAfmet tRNA 6.1.1.10 : tRNAmet + L-methionine + ATP -> L-methionyl-tRNAmet + diphosphate + AMP # additional aa reactions 1.2.1.16 : succinate semialdehyde + NADP+ + H2O -> NADPH + succinate + H+ 2.4.2.28 : S-methyl-5'-thioadenosine + phosphate O4P -> adenine + 5-methylthioribose-1-phosphate 5.3.1.23 : 5-methylthioribose-1-phosphate -> 5-methylthioribulose-1-phosphate 3.5.2.10 : H2O + creatinine -> creatine 1.13.11.27 : 4-hydroxyphenylpyruvate + O2 -> CO2 + homogentisate # NUCLEIC ACIDS # Pyrimidine biosynthesis (C, T, U) 6.3.5.5 : 2 ATP + L-glutamine + HCO3- + H2O -> L-glutamate + 2 ADP + phosphate O4P + carbamoyl-phosphate 2.1.3.2 : L-aspartate + carbamoyl-phosphate -> N-carbamoyl-L-aspartate + phosphate O4P 3.5.2.3 : dihydroorotate + H2O <-> N-carbamoyl-L-aspartate 1.3.3.1 : O2 + dihydroorotate <-> H2O2 + orotate 2.4.2.10 : orotidine-5'-phosphate + diphosphate <-> 5-phosphoribosyl 1-pyrophosphate + orotate 4.1.1.23 : orotidine-5'-phosphate -> CO2 + UMP # - Uracil 3.1.3.5g : UMP + H2O <-> uridine + phosphate O4P 2.7.4.14a : ATP + UMP <-> ADP + UDP 2.4.2.9 : diphosphate + UMP <-> 5-phosphoribosyl 1-pyrophosphate + uracil 3.6.1.19e : H2O + UTP -> diphosphate + UMP 2.7.4.6e : UDP + ATP <-> UTP + ADP 3.5.4.13a : H2O + CTP -> ammonia H3N + UTP 6.3.4.2 : ATP + UTP + ammonia H3N -> ADP + phosphate O4P + CTP 2.7.4.6h : dUDP + ATP <-> dUTP + ADP 3.6.1.19f : H2O + dUTP -> diphosphate + dUMP 2.7.4.9b : ATP + dUMP <-> ADP + dUDP 1.17.4.1e : dUDP + thioredoxin + H2O <-> UDP + thioredoxin disulfide 2.1.1.148 : 5,10-methylene-THF + dUMP + FADH2 -> dTMP + tetrahydrofolate + FAD 2.7.7.8c : RNAn1 + phosphate O4P -> RNAn + UDP 2.7.7.6c : UTP + RNAn -> diphosphate + RNAn1 3.5.4.1a : H2O + cytosine -> ammonia H3N + uracil # - Cytosine 2.7.4.6f : CDP + ATP <-> CTP + ADP 2.7.4.14b : ATP + CMP <-> ADP + CDP 1.17.4.1d : dCDP + thioredoxin + H2O <-> CDP + thioredoxin disulfide 3.1.3.5h : CMP + H2O <-> cytidine + phosphate O4P 2.7.4.6g : dCDP + ATP <-> dCTP + ADP 2.7.4.14c : ATP + dCMP <-> ADP + dCDP 3.1.3.5i : dCMP + H2O <-> deoxycytidine + phosphate O4P 3.5.4.13b : H2O + dCTP -> ammonia H3N + dUTP 2.7.7.6d : CTP + RNAn -> diphosphate + RNAn1 2.7.7.8d : RNAn1 + phosphate O4P -> RNAn + CDP 2.7.7.7c : dCTP + DNAn <-> diphosphate + DNAn1 # - Thymine 3.1.3.5j : thymidine + H2O <-> dTMP + phosphate O4P 2.7.4.9a : ATP + dTMP <-> ADP + dTDP 2.7.4.6i : dTDP + ATP <-> dTTP + ADP 2.7.7.7d : dTTP + DNAn <-> diphosphate + DNAn1 _3.5.4.1b : H2O + thymine -> ammonia H3N + 5-methylcytosine # Purine metabolism (A, G) 2.7.6.1 : ATP + D-ribose-5-phosphate -> 5-phosphoribosyl 1-pyrophosphate + AMP 2.4.2.14 : 5-phosphoribosyl 1-pyrophosphate + L-glutamine + H2O -> 5-phospho-beta-D-ribosyl-amine + diphosphate + L-glutamate 6.3.4.13 : 5-phospho-beta-D-ribosyl-amine + ATP + glycine -> ADP + phosphate O4P + 5-phospho-ribosyl-glycineamide 2.1.2.2a : 10-formyl-tetrahydrofolate + 5-phospho-ribosyl-glycineamide <-> tetrahydrofolate + 5'-phosphoribosyl-N-formylglycineamide 6.3.5.3 : ATP + 5'-phosphoribosyl-N-formylglycineamide + L-glutamine + H2O -> L-glutamate + ADP + phosphate O4P + 5-phosphoribosyl-N-formylglycineamidine 6.3.3.1 : ATP + 5-phosphoribosyl-N-formylglycineamidine -> ADP + phosphate O4P + 5-aminoimidazole ribonucleotide 4.1.1.21 : 4-carboxyaminoimidazole ribonucleotide <-> 5-aminoimidazole ribonucleotide + CO2 6.3.2.6 : ATP + 4-carboxyaminoimidazole ribonucleotide + L-aspartate <-> ADP + phosphate O4P + 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole 4.3.2.2b : 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole <-> fumarate + aminoimidazole carboxamide ribonucleotide 2.1.2.3 : 10-formyl-tetrahydrofolate + aminoimidazole carboxamide ribonucleotide <-> tetrahydrofolate + phosphoribosyl-formamido-carboxamide 2.4.2.7c : aminoimidazole carboxamide ribonucleotide <-> 5-Amino-4-imidazolecarboxyamide # - Inosine 3.5.4.10 : inosine-5'-phosphate + H2O <-> phosphoribosyl-formamido-carboxamide 3.1.3.5c : inosine-5'-phosphate + H2O <-> inosine + phosphate O4P _2.7.4.3c : inosine-5'-phosphate + ITP <-> 2 IDP 3.6.1.19a : H2O + ITP -> diphosphate + inosine-5'-phosphate 3.6.1.19g : H2O + dITP -> diphosphate + dIMP _1.17.4.1b : dIDP + thioredoxin + H2O <-> IDP + thioredoxin disulfide 2.7.4.6j : IDP + ATP <-> ITP + ADP 2.7.4.6b : dIDP + ATP <-> dITP + ADP 1.1.1.205 : H2O + NAD+ + H+ + inosine-5'-phosphate <-> xanthosine-5-phosphate + NADH # - Xanthosine 3.1.3.5d : xanthosine-5-phosphate + H2O <-> xanthosine + phosphate O4P 3.6.1.19b : H2O + XTP -> diphosphate + xanthosine 6.3.5.2 : xanthosine-5-phosphate + H2O + L-glutamine + ATP -> L-glutamate + GMP + diphosphate + AMP # - Adenine 3.1.3.5a : AMP + H2O <-> adenosine + phosphate O4P 2.4.2.7a : AMP + diphosphate <-> 5-phosphoribosyl 1-pyrophosphate + adenine 2.7.4.3a : AMP + ATP <-> 2 ADP 3.6.1.15 : H2O + ATP -> phosphate O4P + ADP 2.7.4.6a : dADP + ATP <-> dATP + ADP 2.7.1.40b : dATP + pyruvate <-> dADP + phosphoenolpyruvate 1.17.4.1a : dADP + thioredoxin + H2O <-> ADP + thioredoxin disulfide 2.7.4.3b : dAMP + dATP <-> 2 dADP 3.1.3.5b : dAMP + H2O <-> 5'-deoxyadenosine + phosphate O4P 2.7.7.7a : dATP + DNAn <-> diphosphate + DNAn1 2.7.7.6a : ATP + RNAn -> diphosphate + RNAn1 2.7.7.8a : RNAn1 + phosphate O4P -> RNAn + ADP 2.4.2.-b : adenosine + phosphate O4P <-> ribose-1-phosphate + adenine # - Guanine 3.1.3.5e : GMP + H2O <-> guanosine + phosphate O4P 2.4.2.7b : GMP + diphosphate <-> 5-phosphoribosyl 1-pyrophosphate + guanine 2.7.4.8a : GMP + ATP <-> GDP + ADP 3.6.1.19c : H2O + GTP -> diphosphate + GMP 1.17.4.1c : dGDP + thioredoxin + H2O <-> GDP + thioredoxin disulfide 2.7.4.6c : GDP + ATP <-> GTP + ADP 2.7.1.40c : GTP + pyruvate <-> GDP + phosphoenolpyruvate 2.7.4.8b : dGMP + ATP <-> dGDP + ADP 2.7.4.6d : dGDP + ATP <-> dGTP + ADP 2.7.1.40d : dGTP + pyruvate <-> dGDP + phosphoenolpyruvate 3.1.3.5f : dGMP + H2O <-> deoxyguanosine + phosphate O4P 3.1.5.1 : H2O + dGTP -> diphosphate + deoxyguanosine 3.6.1.19d : H2O + dGTP -> diphosphate + dGMP 3.1.7.2 : guanosine 5'-diphosphate,3'-diphosphate + H2O <-> diphosphate + GDP 3.6.1.11 : H2O + guanosine 3'-diphosphate 5'-triphosphate <-> phosphate O4P + guanosine 5'-diphosphate,3'-diphosphate 2.7.7.6b : GTP + RNAn -> diphosphate + RNAn1 2.7.7.8b : RNAn1 + phosphate O4P -> RNAn + GDP 2.7.7.7b : dGTP + DNAn <-> diphosphate + DNAn1 # - ApppA production 2.7.7.4 : sulfate O4s + ATP -> adenosine 5'-phosphosulfate + diphosphate 2.7.1.25 : adenosine 5'-phosphosulfate + ATP -> phosphoadenosine-5'-phosphosulfate + ADP _2.7.7.53a : 2 adenosine 5'-phosphosulfate + ATP -> sulfite O3s + phosphate O4P + 5',5'''-diadenosine tetraphosphate + AMP 2.7.7.53b : ATP + ADP <-> phosphate O4P + 5',5'''-diadenosine tetraphosphate # - Purine cyclases 4.6.1.1 : ATP -> cyclic-AMP + diphosphate 4.6.1.2 : GTP -> cyclic-GMP + diphosphate # - from xanthine to Gly - mainly NOT PRESENT 4.1.1.-b : 4-amino-5-imidazole carboxylate <-> 4-aminoimidazole + CO2 # Folate biosynthesis 3.5.4.16 : GTP + H2O -> formate + 7,8-dihydroneopterin triphosphate 3.6.1.-a : 7,8-dihydroneopterin triphosphate + H2O <-> dihydroneopterin phosphate + diphosphate 3.6.1.-b : dihydroneopterin phosphate + H2O <-> 7,8-dihydro-D-neopterin + phosphate O4P 4.1.2.25 : 7,8-dihydro-D-neopterin <-> glycolaldehyde + 6-hydroxymethyl-7,8-dihydropterin 2.7.6.3 : 6-hydroxymethyl-7,8-dihydropterin + ATP -> (2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphate + AMP 2.5.1.15 : p-aminobenzoate + (2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphate -> 7,8-dihydropteroate + diphosphate 4.1.3.38 : 4-amino-4-deoxychorismate <-> p-aminobenzoate + pyruvate # not pres ! (would connect formate to folate biosynthesis) ~~IMPORTANT, following reaction not in sequence!!~~ ·6.3.4.3 : tetrahydrofolate + formate + ATP <-> ADP + phosphate O4P + 10-formyl-tetrahydrofolate # not pres ! (would connect 4.1.3.38 to aa production) ~~IMPORTANT, following reaction not in sequence!!~~ ·2.6.1.85 : L-glutamine + chorismate <-> L-glutamate + 4-amino-4-deoxychorismate 6.3.2.12 : L-glutamate + 7,8-dihydropteroate + ATP -> 7,8-dihydrofolate + phosphate O4P + ADP # not pres ! (would complete this pathway) ~~IMPORTANT, following reaction not in sequence!!~~ ·1.5.1.3 : NADP+ + H+ + tetrahydrofolate <-> NADPH + 7,8-dihydrofolate # - from tetrahydrofolate to a tetrahydrofolate polyglutamate 6.3.2.17a : tetrahydrofolate + L-glutamate + ATP <-> tetrahydrofolate-L-glutamate + ADP + phosphate O4P 6.3.2.17b : tetrahydrofolate-L-glutamate + L-glutamate + ATP <-> a tetrahydrofolate polyglutamate + ADP + phosphate O4P # - from 7,8-dihydropteroate to dihydrobiopterin 6.3.2.17c : L-glutamate + 7,8-dihydropteroate + ATP -> 7,8-dihydrofolate + phosphate O4P + ADP _4.2.3.12 : 7,8-dihydroneopterin triphosphate -> 6-pyruvoyl-5,6,7,8-tetrahydropterin + diphosphate _1.1.1.153 : tetrahydrobiopterin + 2 NADP+ -> 6-pyruvoyl-5,6,7,8-tetrahydropterin + 2 NADPH + H+ # - one carbon pool by folate 2.1.2.2b : H2O + 5,10-methenyltetrahydrofolate + 5-phospho-ribosyl-glycineamide -> tetrahydrofolate + 5'-phosphoribosyl-N-formylglycineamide _1.4.4.2 : H-protein-lipoyllysine + glycine -> H-Protein-S-aminomethyldihydrolipoyllysine + CO2 _2.1.2.10a : H-Protein-S-aminomethyldihydrolipoyllysine + tetrahydrofolate -> [H protein]-dihydrolipoyllysine C8H16NOS2R + 5,10-methylene-THF + ammonia H3N _1.8.1.4c : [H protein]-dihydrolipoyllysine C8H16NOS2R + NAD+ + H+ -> H-protein-lipoyllysine + NADH 1.5.1.5 : 5,10-methylene-THF + NADP+ + H+ <-> NADPH + 5,10-methenyltetrahydrofolate 3.5.1.10 : H2O + 10-formyl-tetrahydrofolate -> tetrahydrofolate + formate 3.5.4.9a : H2O + 5,10-methenyltetrahydrofolate <-> 10-formyl-tetrahydrofolate 6.3.3.2 : 5-formyl-tetrahydrofolate + ATP -> 5,10-methenyltetrahydrofolate + ADP + phosphate O4P 2.1.2.10b : 5,10-methenyltetrahydrofolate + H2O <-> 5-formyl-tetrahydrofolate # not pres ! (would complete this pathway, reaction 2.1.1.13 HAS TO CONSUME 5-methyl-THF) ~~IMPORTANT, following 2 reactions not in sequence!!~~ ·1.5.1.20a : 5-methyl-THF + NADP+ + H+ <-> 5,10-methylene-THF + NADPH ·1.5.1.20b : 5-methyl-THF + NAD+ + H+ <-> 5,10-methylene-THF + NADH 2.1.2.9a : 10-formyl-tetrahydrofolate + L-methionyl-tRNAfmet + H2O -> tetrahydrofolate + N-formyl-L-methionyl-tRNAfmet # Photosynthesis # in "SPECIAL" _lightII : photonII_extrac -> photonII # in "SPECIAL" _lightI : photonI_extrac -> photonI _PSII : 2 photonII + 2 H2O + 4 H+ + 2 PSII -> O2 + 4 H+_thylac + 2 PSII* _UQ : PSII* + UQ + 2 H+ -> PSII + UQH2 _citb6 : UQH2 + citb6f + 2 H+ -> UQ + citb6f* + 2 H+_thylac _1.10.99.1 : citb6f* + PC -> citb6f + PC* _PSI : photonI + PC* + PSI -> PC + PSI* _Fd : PSI* + Fd -> PSI + Fd* _FNR : Fd* + FNR -> Fd + FNR* _1.18.1.2 : FNR* + NADP+ + H+ -> FNR + NADPH _3.6.3.14 : 3 H+_thylac + phosphate O4P + ADP <-> 3 H+ + H2O + ATP 3.6.1.1 : H2O + diphosphate -> 2 phosphate O4P 2.7.4.1 : ATP + diphosphate -> ADP + PPPi _NADPH2 : NADPH -> NADPH2 _1.12.1.3 : NADPH2 + 2 H+ <-> H2 _cyclicPS : Fd* + UQ + 2 H+ -> Fd + UQH2 _NDH1 : NADPH + PC -> NADP+ + H+ + PC* # Oxidative phosphorylation CHECK REACTIONS AND STOICHIOMETRY _1.6.5.3 : NADH + UQ + 7 H+ -> NAD+ + UQH2 + 4 H+_thylac _1.6.99.3 : NADH + UQ + 7 H+ -> NAD+ + UQH2 + 4 H+_thylac _quinol oxidase : 2 UQH2 + O2 + 4 H+ -> 2 UQ + 4 H+_thylac + 2 H2O _cit c : citb6f* + cit c -> citb6f + cit c* _1.9.3.1 : 4 cit c* + O2 + 4 H+ -> 4 cit c + 4 H+_thylac + 2 H2O _PSIaltern : photonI + cit c* + PSI -> cit c + PSI* # Urea Cycle and metabolism of amino groups 2.3.1.35 : L-glutamate + N-acetyl-L-ornithine <-> N-acetyl-L-glutamate + L-ornithine 2.6.1.11 : N-acetyl-L-ornithine + 2-ketoglutarate <-> L-glutamate + N-acetyl-L-glutamate 5-semialdehyde _3.5.1.14 : N-acetyl-L-ornithine + H2O -> L-ornithine + acetate 1.2.1.38 : N-acetyl-L-glutamate 5-semialdehyde + NADP+ + H+ + phosphate O4P <-> N-acetylglutamyl-phosphate + NADPH 2.7.2.8 : N-acetyl-L-glutamate + ATP -> N-acetylglutamyl-phosphate + ADP 2.3.1.1 : L-glutamate + acetyl-CoA -> N-acetyl-L-glutamate + coenzyme A 3.5.1.5 : H2O + urea -> 2 ammonia H3N + CO2 4.2.1.1a : H2CO3 <-> H2O + CO2 _1.4.3.4 : O2 + H2O + N-acetylputrescine -> ammonia H3N + H2O2 + N4-acetylaminobutanal _1.2.1.3a : N4-acetylaminobutanal + NAD+ + H+ + H2O <-> N4-acetylaminobutanoate + NADH _1.2.1.3b : 4-aminobutanal + NAD+ + H+ + H2O <-> 4-aminobutanoate + NADH _3.5.1.4 : 4-Guanidinobutanamide + H2O -> 4-Guanidinobutanoate + ammonia H3N # Nitrogen metabolism 1.7.7.2 : nitrite NO2 + 2 thioredoxin disulfide + H2O <-> 2 thioredoxin + nitrate NO3 1.7.7.1 : ammonia H3N + 2 H2O + 6 thioredoxin disulfide <-> nitrite NO2 + 6 thioredoxin + 7 H+ 2.7.2.2a : ammonia H3N + CO2 + ATP -> carbamoyl-phosphate + ADP 4.2.1.104 : cyanate + HCO3- + H+ <-> carbamate + CO2 _2.7.2.2b : carbamate + ATP + H+ <-> carbamoyl-phosphate + ADP 1.7.99.7 : 2 nitric oxide + reduced acceptor -> nitrous oxide + acceptor + H2O # Nicotinate and nicotinamide metabolism (NAD biosynthesis) 1.4.3.- : O2 + L-aspartate -> H2O2 + iminoaspartate QUINOLINATE-SYNTHA-RXN : iminoaspartate + dihydroxy-acetone phosphate -> quinolinate + 2 H2O + phosphate O4P 2.4.2.19 : 5-phosphoribosyl 1-pyrophosphate + quinolinate -> CO2 + diphosphate + nicotinate nucleotide 3.1.3.5k : nicotinate nucleotide + H2O -> nicotinate D-ribonucleoside + phosphate O4P 2.7.7.1a : nicotinate nucleotide + ATP -> deamido-NAD + diphosphate 2.7.7.18a : ATP + nicotinate nucleotide -> diphosphate + deamido-NAD 6.3.5.1 : ATP + deamido-NAD + L-glutamine + H2O -> L-glutamate + AMP + diphosphate + NAD+ + H+ 2.7.7.1b : nicotinamide mononucleotide + ATP -> NAD+ + H+ + diphosphate 2.7.7.18b : ATP + nicotinamide mononucleotide -> diphosphate + NAD+ + H+ 3.1.3.5l : nicotinamide mononucleotide + H2O -> N-Ribosylnicotinamide + phosphate O4P 2.7.1.23 : NAD+ + ATP -> NADP+ + ADP 1.6.1.2 : NAD+ + NADPH <-> NADH + NADP+ # Ubiquinone biosynthesis (not complete, should be! -> forced to be complete) # - Ubiquinone branch # not pres ! would begin UQ branch ~~IMPORTANT, following 2 reactions not in sequence!!~~ ·4.1.3.40 : chorismate <-> 4-hydroxybenzoate + pyruvate ·octaprenylsyn : all-trans-geranyl-geranyl diphosphate -> all-trans-octaprenyl diphosphate 2.5.1.-c : all-trans-octaprenyl diphosphate + 4-hydroxybenzoate -> 3-octaprenyl-4-hydroxybenzoate + diphosphate 4.1.1.-a : 3-octaprenyl-4-hydroxybenzoate -> 2-octaprenylphenol + CO2 OCTAPRENYLPHENOL-HYDROX-RXN : 2 2-octaprenylphenol + O2 <-> 2 2-octaprenyl-6-hydroxyphenol # not pres ! would allow UQ biosynthesis ~~IMPORTANT, following reaction not in sequence!!~~ ·2.1.1.64b : S-adenosyl-L-methionine + 2-octaprenyl-6-hydroxyphenol <-> S-adenosyl-L-homocysteine + 2-octaprenyl-6-methoxyphenol 1.14.13.-a : 2-octaprenyl-6-methoxyphenol + O2 -> 2-octaprenyl-6-methoxy-1,4-benzoquinone + H2O 2.1.1.-c : 2-octaprenyl-6-methoxy-1,4-benzoquinone + S-adenosyl-L-methionine -> S-adenosyl-L-homocysteine + 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone 1.14.13.-b : 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone + O2 <-> 3-demethylubiquinone-8 + H2O # not pres ! would allow UQ biosynthesis ~~IMPORTANT, following reaction not in sequence!!~~ ·2.1.1.64a : S-adenosyl-L-methionine + 3-demethylubiquinone-8 <-> S-adenosyl-L-homocysteine + ubiquinone-8 _UQsyn : ubiquinone-8 -> UQ # - Phylloquinone/Menaquinone branch 5.4.4.2 : chorismate -> isochorismate 2.5.1.64 : 2-ketoglutarate + isochorismate -> 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate + pyruvate + CO2 4.2.1.113 : 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate -> o-succinylbenzoate + H2O 6.2.1.26 : ATP + o-succinylbenzoate + coenzyme A -> AMP + diphosphate + O-succinylbenzoyl-CoA 4.1.3.36 : O-succinylbenzoyl-CoA <-> coenzyme A + 1,4-dihydroxy-2-naphthoate 2.5.1.-a : all-trans-octaprenyl diphosphate + 1,4-dihydroxy-2-naphthoate -> demethylmenaquinone-8 + diphosphate + CO2 2.1.1.-a : demethylmenaquinone-8 + S-adenosyl-L-methionine -> S-adenosyl-L-homocysteine + menaquinone-8 2.5.1.-b : 1,4-dihydroxy-2-naphthoate + phytyl diphosphate -> demethylphylloquinone + CO2 + diphosphate 2.1.1.-b : demethylphylloquinone + S-adenosyl-L-methionine -> phylloquinone + S-adenosyl-L-homocysteine # Sulfur metabolism 1.8.4.8 : phosphoadenosine-5'-phosphosulfate + thioredoxin <-> sulfite O3s + adenosine-3',5'-bisphosphate + thioredoxin disulfide 1.8.7.1 : sulfite O3s + 6 Fd* + 6 H+ <-> hydrogen sulfide H2s + 6 Fd + 3 H2O ·1.13.11.8 : sulfite O3s -> S0 + O2 + H2O # Ethanol metabolism (part of Glycolysis) 6.2.1.1 : coenzyme A + acetate + ATP <-> acetyl-CoA + diphosphate + AMP 1.2.1.3c : acetaldehyde + NAD+ + H+ + H2O <-> NADH + acetate 1.1.1.1 : acetaldehyde + NADH -> ethanol + NAD+ + H+ 1.1.1.2 : NADPH + acetaldehyde -> NADP+ + H+ + ethanol 2.3.1.8 : phosphate O4P + acetyl-CoA <-> acetylphosphate + coenzyme A 2.7.2.1 : ATP + acetate <-> ADP + acetylphosphate # coenzyme A biosynthesis _1.1.1.86 : 2-acetolactate + NADPH -> 2,3-dihydroxy-3-methylbutanoate + NADP+ + H+ _4.2.1.9 : 2,3-dihydroxy-3-methylbutanoate -> 2-keto-isovalerate + H2O 2.1.2.11 : 5,10-methylene-THF + 2-keto-isovalerate + H2O -> tetrahydrofolate + 2-dehydropantoate 1.1.1.169 : R-pantoate + NADP+ + H+ <-> 2-dehydropantoate + NADPH 6.3.2.1 : beta-alanine + R-pantoate + ATP -> pantothenate + diphosphate + AMP _1.2.1.3d : beta-aminopropion aldehyde + NAD+ + H+ + H2O <-> NADH + beta-alanine 2.7.1.33 : pantothenate + ATP -> D-4'-phosphopantothenate + ADP 6.3.2.5 : D-4'-phosphopantothenate + L-cysteine + CTP -> R-4'-phosphopantothenoyl-L-cysteine + diphosphate + CMP 4.1.1.36 : R-4'-phosphopantothenoyl-L-cysteine -> pantetheine 4'-phosphate + CO2 _2.7.7.3 : ATP + pantetheine 4'-phosphate -> diphosphate + 3'-dephospho-CoA C21H35N7O13P2S _2.7.1.24 : ATP + 3'-dephospho-CoA C21H35N7O13P2S -> ADP + coenzyme A # Fatty acid biosynthesis _6.4.1.2 : ATP + acetyl-CoA + HCO3- + H+ -> ADP + phosphate O4P + malonyl-CoA 2.3.1.39 : malonyl-CoA + an [acyl-carrier protein] -> coenzyme A + a malonyl-ACP 2.3.1.41a : acetyl-CoA + an [acyl-carrier protein] -> an acetyl-ACP + coenzyme A + CO2 2.3.1.41b : an acetyl-ACP + a malonyl-ACP -> acetoacetyl-[acp] C4H5O2SR + CO2 1.1.1.100a : acetoacetyl-[acp] C4H5O2SR + NADP+ + H+ <-> (3R)-3-Hydroxybutanoyl-[acyl-carrier protein] C4H7O2SR + NADPH 4.2.1.-a : (3R)-3-Hydroxybutanoyl-[acyl-carrier protein] C4H7O2SR <-> but-2-enoyl-[acyl-carrier protein] C4H5OSR + H2O 1.3.1.9a : but-2-enoyl-[acyl-carrier protein] C4H5OSR + NAD+ + H+ <-> butyryl-[acyl-carrier protein] C4H7OSR + NADH 2.3.1.41c : butyryl-[acyl-carrier protein] C4H7OSR + a malonyl-ACP -> 3-oxohexanoyl-[acyl-carrier protein] C6H9O2SR + CO2 1.1.1.100b : 3-oxohexanoyl-[acyl-carrier protein] C6H9O2SR + NADP+ + H+ <-> (R)-3-Hydroxyhexanoyl-[acyl-carrier protein] C6H11O2SR + NADPH 4.2.1.-b : (R)-3-Hydroxyhexanoyl-[acyl-carrier protein] C6H11O2SR <-> trans-hex-2-enoyl-[acyl-carrier protein] C6H9OSR + H2O 1.3.1.9b : trans-hex-2-enoyl-[acyl-carrier protein] C6H9OSR + NAD+ + H+ <-> hexanoyl-[acyl-carrier protein] C6H11OSR + NADH 2.3.1.41d : hexanoyl-[acyl-carrier protein] C6H11OSR + a malonyl-ACP -> 3-oxooctanoyl-[acyl-carrier protein] C8H13O2SR + CO2 + an [acyl-carrier protein] 1.1.1.100c : 3-oxooctanoyl-[acyl-carrier protein] C8H13O2SR + NADP+ + H+ <-> (R)-3-Hydroxyoctanoyl-[acyl-carrier protein] C8H15O2SR + NADPH 4.2.1.-c : (R)-3-Hydroxyoctanoyl-[acyl-carrier protein] C8H15O2SR <-> trans-oct-2-enoyl-[acyl-carrier protein] C8H13OSR + H2O 1.3.1.9c : trans-oct-2-enoyl-[acyl-carrier protein] C8H13OSR + NAD+ + H+ <-> octanoyl-[acyl-carrier protein] C8H15OSR + NADH 2.3.1.41e : octanoyl-[acyl-carrier protein] C8H15OSR + a malonyl-ACP -> 3-oxodecanoyl-[acyl-carrier protein] C10H17O2SR + CO2 + an [acyl-carrier protein] 1.1.1.100d : 3-oxodecanoyl-[acyl-carrier protein] C10H17O2SR + NADP+ + H+ <-> (R)-3-Hydroxydecanoyl-[acyl-carrier protein] C10H19O2SR + NADPH 1.3.1.9d : trans-dec-2-enoyl-[acyl-carrier protein] C10H17OSR + NAD+ + H+ <-> decanoyl-[acyl-carrier protein] C10H19OSR + NADH 4.2.1.-d : (R)-3-Hydroxydecanoyl-[acyl-carrier protein] C10H19O2SR <-> trans-dec-2-enoyl-[acyl-carrier protein] C10H17OSR + H2O 2.3.1.41f : decanoyl-[acyl-carrier protein] C10H19OSR + a malonyl-ACP -> 3-oxododecanoyl-[acyl-carrier protein] C12H21O2SR + CO2 + an [acyl-carrier protein] 1.1.1.100e : 3-oxododecanoyl-[acyl-carrier protein] C12H21O2SR + NADP+ + H+ <-> (R)-3-Hydroxydodecanoyl-[acyl-carrier protein] C12H23O2SR + NADPH 4.2.1.-e : (R)-3-Hydroxydodecanoyl-[acyl-carrier protein] C12H23O2SR <-> trans-dodec-2-enoyl-[acyl-carrier protein] C12H21OSR + H2O 1.3.1.9e : trans-dodec-2-enoyl-[acyl-carrier protein] C12H21OSR + NAD+ + H+ <-> dodecanoyl-[acyl-carrier protein] C12H23OSR + NADH 2.3.1.41g : dodecanoyl-[acyl-carrier protein] C12H23OSR + a malonyl-ACP -> 3-oxotetradecanoyl-[acyl-carrier protein] C14H25O2SR + CO2 + an [acyl-carrier protein] 1.1.1.100f : 3-oxotetradecanoyl-[acyl-carrier protein] C14H25O2SR + NADP+ + H+ <-> (R)-3-Hydroxytetradecanoyl-[acyl-carrier protein] C14H27O2SR + NADPH 4.2.1.-f : (R)-3-Hydroxytetradecanoyl-[acyl-carrier protein] C14H27O2SR <-> trans-tetradec-2-enoyl-[acyl-carrier protein] C14H25OSR + H2O 1.3.1.9f : trans-tetradec-2-enoyl-[acyl-carrier protein] C14H25OSR + NAD+ + H+ <-> tetradecanoyl-[acyl-carrier protein] C14H27OSR + NADH 2.3.1.41h : tetradecanoyl-[acyl-carrier protein] C14H27OSR + a malonyl-ACP -> 3-oxohexadecanoyl-[acyl-carrier protein] C16H29O2SR + CO2 + an [acyl-carrier protein] 1.1.1.100g : 3-oxohexadecanoyl-[acyl-carrier protein] C16H29O2SR + NADP+ + H+ <-> (R)-3-Hydroxypalmitoyl-[acyl-carrier protein] C16H31O2SR + NADPH 4.2.1.-g : (R)-3-Hydroxypalmitoyl-[acyl-carrier protein] C16H31O2SR <-> trans-hexadec-2-enoyl-[acyl-carrier protein] C16H29OSR + H2O 1.3.1.9g : trans-hexadec-2-enoyl-[acyl-carrier protein] C16H29OSR + NAD+ + H+ <-> hexadecanoyl-[acyl-carrier protein] C16H31OSR + NADH 2.3.1.179i : hexadecanoyl-[acyl-carrier protein] C16H31OSR + a malonyl-ACP -> 3-oxooctadecanoyl-[acp] C18H33O2SR + CO2 + an [acyl-carrier protein] 1.1.1.100h : 3-oxooctadecanoyl-[acp] C18H33O2SR + NADP+ + H+ <-> 3-Hydroxyoctadecanoyl-[acp] C18H35O2SR + NADPH 4.2.1.-h : 3-Hydroxyoctadecanoyl-[acp] C18H35O2SR <-> trans-octadec-2-enoyl-[acp] C18H33OSR + H2O 1.3.1.9h : trans-octadec-2-enoyl-[acp] C18H33OSR + NAD+ + H+ <-> octadecanoyl-[acyl-carrier protein] C18H35OSR + NADH _1.14.19.1a : hexadecanoyl-[acyl-carrier protein] C16H31OSR + O2 + 2 H+ <-> (9Z)-hexadecanoyl-[acyl-carrier protein] C16H31OSR + H2O _1.14.19.1b : octadecanoyl-[acyl-carrier protein] C18H35OSR + O2 + 2 H+ <-> (9Z)-octadecanoyl-[acyl-carrier protein] C18H33OSR + H2O _1.14.19.-a : (9Z)-octadecanoyl-[acyl-carrier protein] C18H33OSR + NADPH + O2 <-> (9Z,12Z)-octadecadienoyl-[acyl-carrier protein] C18H31OSR + NADP+ + H+ + 2 H2O _1.14.19.-b : (9Z,12Z)-octadecadienoyl-[acyl-carrier protein] C18H31OSR + NADPH + O2 <-> (9Z,12Z,15Z)-octadecadienoyl-[acyl-carrier protein] C18H29OSR + NADP+ + H+ + 2 H2O _1.14.19.-c : (9Z)-octadecanoyl-[acyl-carrier protein] C18H33OSR + NADPH + O2 <-> (6Z,9Z)-octadecadienoyl-[acyl-carrier protein] C18H31OSR + NADP+ + H+ + 2 H2O _1.14.19.-d : (6Z,9Z)-octadecadienoyl-[acyl-carrier protein] C18H31OSR + NADPH + O2 <-> (6Z,9Z,12Z)-octadecadienoyl-[acyl-carrier protein] C18H29OSR + NADP+ + H+ + 2 H2O _1.14.19.-e : (6Z,9Z,12Z)-octadecadienoyl-[acyl-carrier protein] C18H29OSR + NADPH + O2 <-> (6Z,9Z,12Z,15Z)-octadecadienoyl-[acyl-carrier protein] C18H27OSR + NADP+ + H+ + 2 H2O # not pres ! would end ACP release and fatty acid formation ~~IMPORTANT, following 6 reactions not in sequence!!~~ ·3.1.2.14a : octanoyl-[acyl-carrier protein] C8H15OSR + H2O -> octanoic acid + an [acyl-carrier protein] ·3.1.2.14b : decanoyl-[acyl-carrier protein] C10H19OSR + H2O -> decanoic acid + an [acyl-carrier protein] ·3.1.2.14c : dodecanoyl-[acyl-carrier protein] C12H23OSR + H2O -> dodecanoic acid + an [acyl-carrier protein] ·3.1.2.14d : tetradecanoyl-[acyl-carrier protein] C14H27OSR + H2O -> tetradecanoic acid + an [acyl-carrier protein] ·3.1.2.14e : hexadecanoyl-[acyl-carrier protein] C16H31OSR + H2O -> hexadecanoic acid + an [acyl-carrier protein] ·3.1.2.14f : (9Z)-hexadecanoyl-[acyl-carrier protein] C16H31OSR + H2O -> (9Z)-hexadecanoic acid + an [acyl-carrier protein] ·3.1.2.14g : octadecanoyl-[acyl-carrier protein] C18H35OSR + H2O -> octadecanoic acid + an [acyl-carrier protein] ·3.1.2.14h : (9Z)-octadecanoyl-[acyl-carrier protein] C18H33OSR + H2O -> (9Z)-octadecanoic acid + an [acyl-carrier protein] ·3.1.2.14i : (9Z,12Z)-octadecadienoyl-[acyl-carrier protein] C18H31OSR + H2O -> (9Z,12Z)-octadecanoic acid + an [acyl-carrier protein] ·3.1.2.14j : (9Z,12Z,15Z)-octadecadienoyl-[acyl-carrier protein] C18H29OSR + H2O -> (9Z,12Z,15Z)-octadecanoic acid + an [acyl-carrier protein] ·3.1.2.14k : (6Z,9Z)-octadecadienoyl-[acyl-carrier protein] C18H31OSR + H2O -> (6Z,9Z)-octadecanoic acid + an [acyl-carrier protein] ·3.1.2.14l : (6Z,9Z,12Z)-octadecadienoyl-[acyl-carrier protein] C18H29OSR + H2O -> (6Z,9Z,12Z)-octadecanoic acid + an [acyl-carrier protein] ·3.1.2.14m : (6Z,9Z,12Z,15Z)-octadecadienoyl-[acyl-carrier protein] C18H27OSR + H2O -> (6Z,9Z,12Z,15Z)-octadecanoic acid + an [acyl-carrier protein] 2.3.1.179a : acetyl-CoA + acyl-carrier protein HSR -> an acetyl-ACP + CO2 2.3.1.179b : an acetyl-ACP + a malonyl-ACP -> acetoacetyl-[acp] C4H5O2SR + CO2 + an [acyl-carrier protein] 2.3.1.179c : butyryl-[acyl-carrier protein] C4H7OSR + a malonyl-ACP -> 3-oxohexanoyl-[acyl-carrier protein] C6H9O2SR + CO2 + an [acyl-carrier protein] 2.3.1.179d : hexanoyl-[acyl-carrier protein] C6H11OSR + a malonyl-ACP -> 3-oxooctanoyl-[acyl-carrier protein] C8H13O2SR + CO2 + an [acyl-carrier protein] 2.3.1.179e : octanoyl-[acyl-carrier protein] C8H15OSR + a malonyl-ACP -> 3-oxodecanoyl-[acyl-carrier protein] C10H17O2SR + CO2 + an [acyl-carrier protein] 2.3.1.179f : decanoyl-[acyl-carrier protein] C10H19OSR + a malonyl-ACP -> 3-oxododecanoyl-[acyl-carrier protein] C12H21O2SR + CO2 + an [acyl-carrier protein] 2.3.1.179g : dodecanoyl-[acyl-carrier protein] C12H23OSR + a malonyl-ACP -> 3-oxotetradecanoyl-[acyl-carrier protein] C14H25O2SR + CO2 + an [acyl-carrier protein] 2.3.1.179h : tetradecanoyl-[acyl-carrier protein] C14H27OSR + a malonyl-ACP -> 3-oxohexadecanoyl-[acyl-carrier protein] C16H29O2SR + CO2 + an [acyl-carrier protein] 2.3.1.180a : acetyl-CoA + acyl-carrier protein HSR -> an acetyl-ACP + CO2 2.3.1.180b : an acetyl-ACP + a malonyl-ACP -> acetoacetyl-[acp] C4H5O2SR + CO2 + an [acyl-carrier protein] 2.3.1.180c : butyryl-[acyl-carrier protein] C4H7OSR + a malonyl-ACP -> 3-oxohexanoyl-[acyl-carrier protein] C6H9O2SR + CO2 + an [acyl-carrier protein] 2.3.1.180d : hexanoyl-[acyl-carrier protein] C6H11OSR + a malonyl-ACP -> 3-oxooctanoyl-[acyl-carrier protein] C8H13O2SR + CO2 + an [acyl-carrier protein] 2.3.1.180e : octanoyl-[acyl-carrier protein] C8H15OSR + a malonyl-ACP -> 3-oxodecanoyl-[acyl-carrier protein] C10H17O2SR + CO2 + an [acyl-carrier protein] 2.3.1.180f : decanoyl-[acyl-carrier protein] C10H19OSR + a malonyl-ACP -> 3-oxododecanoyl-[acyl-carrier protein] C12H21O2SR + CO2 + an [acyl-carrier protein] 2.3.1.180g : dodecanoyl-[acyl-carrier protein] C12H23OSR + a malonyl-ACP -> 3-oxotetradecanoyl-[acyl-carrier protein] C14H25O2SR + CO2 + an [acyl-carrier protein] 2.3.1.180h : tetradecanoyl-[acyl-carrier protein] C14H27OSR + a malonyl-ACP -> 3-oxohexadecanoyl-[acyl-carrier protein] C16H29O2SR + CO2 + an [acyl-carrier protein] # Porphyrin and chlorophyll metabolism # - from glutamate-1-semialdehyde to uroporphyrinogen-III tRNA 1.2.1.70 : glutamate-1-semialdehyde + NADP+ + H+ + tRNAGlu <-> L-glutamyl-tRNAGlu + NADPH 5.4.3.8 : glutamate-1-semialdehyde -> 5-amino-levulinate 4.2.1.24 : 2 5-amino-levulinate -> 2 H2O + porphobilinogen 2.5.1.61 : H2O + 4 porphobilinogen -> 4 ammonia H3N + hydroxymethylbilane 4.2.1.75 : hydroxymethylbilane -> uroporphyrinogen-III + H2O _uroporphyrinogen-I : hydroxymethylbilane -> uroporphyrinogen-I + H2O _uroporphyrin-I : uroporphyrinogen-I -> uroporphyrin-I + 6 H+ 4.1.1.37b : uroporphyrinogen-III -> 4 CO2 + coproporphyrinogen I _coproporphyrin-I : coproporphyrinogen I -> coproporphyrin I + 6 H+ _uroporphyrin-III : uroporphyrinogen-III -> uroporphyrin-III + 6 H+ # - from uroporphyrinogen-III to protoporphyrinogen-IX 4.1.1.37a : uroporphyrinogen-III -> 4 CO2 + coproporphyrinogen III _1.3.3.3 : coproporphyrinogen III + O2 + 2 H+ -> protoporphyrinogen-IX + 2 CO2 + 2 H2O _1.3.99.22 : coproporphyrinogen III + 2 S-adenosyl-L-methionine -> protoporphyrinogen-IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine # not pres ! (would connect protoporphyrinogen-IX to protoporphyrin IX production) ~~IMPORTANT, following reaction not in sequence!!~~ ·1.3.3.4 : protoporphyrinogen-IX + O2 -> protoporphyrin IX + 3 H2O # - Heme production 4.99.1.1 : Fe2+ + protoporphyrin IX -> 2 H+ + protoheme IX 2.5.1.-d : protoheme IX + (E,E)-farnesyl diphosphate + H2O -> heme o + diphosphate _COX15 : heme o -> heme a _1.14.99.3 : 3 O2 + 3 thioredoxin + protoheme IX -> biliverdin + 3 H2O + 3 thioredoxin disulfide + CO + Fe2+ 1.3.7.5 : biliverdin + thioredoxin -> (3Z)-phycocyanobilin + thioredoxin disulfide 1.3.1.24a : biliverdin + NADPH -> NADP+ + H+ + bilirubin 1.3.1.24b : biliverdin + NADH -> NAD+ + H+ + bilirubin # - Chlorophyll pathway 6.6.1.1 : ATP + protoporphyrin IX + Mg2+ + H2O -> Mg-protoporphyrin + phosphate O4P + ADP + 2 H+ 2.1.1.11 : Mg-protoporphyrin + S-adenosyl-L-methionine -> S-adenosyl-L-homocysteine + Mg-protoporphyrin monomethyl ester Zn-Bacterio-chlorophyll-a : Mg-protoporphyrin monomethyl ester + Zn2+ -> Zn-Bacterio-chlorophyll a + Mg2+ 1.14.13.81a : Mg-protoporphyrin monomethyl ester + NADPH + O2 -> 131-hydroxy-magnesium-protoporphyrin IX 13-monomethyl ester + NADP+ + H+ + H2O 1.14.13.81b : 131-hydroxy-magnesium-protoporphyrin IX 13-monomethyl ester + NADPH + O2 -> 131-oxo-magnesium-protoporphyrin IX 13-monomethyl ester + NADP+ + H+ + 2 H2O 1.14.13.81c : 131-oxo-magnesium-protoporphyrin IX 13-monomethyl ester + NADPH + O2 -> divinyl protochlorophyllide a + NADP+ + H+ + 2 H2O 1.3.1.33a : divinyl protochlorophyllide a + NADPH -> NADP+ + H+ + divinylchlorophyllide a # not pres ! (would connect divinylchlorophyllide a to chlorophyllide a production) ~~IMPORTANT, following reaction not in sequence!!~~ ·1.3.1.75a : divinylchlorophyllide a + NADPH <-> chlorophyllide a + NADP+ + H+ # not pres ! (would connect divinyl protochlorophyllide a to monovinyl protochlorophyllide a production) ~~IMPORTANT, following reaction not in sequence!!~~ ·1.3.1.75b : divinyl protochlorophyllide a + NADPH <-> monovinyl protochlorophyllide a + NADP+ + H+ _BacChl : monovinyl protochlorophyllide a + phytyl diphosphate -> bacterio-chlorophylls _BacPheo : monovinyl protochlorophyllide a + phytyl diphosphate -> bacterio-pheophytins 1.3.1.33b : monovinyl protochlorophyllide a + NADPH -> NADP+ + H+ + chlorophyllide a _1.18.-.- : monovinyl protochlorophyllide a + ATP -> chlorophyllide a + ADP _dChla : divinyl protochlorophyllide a -> divinylchlorophyll a _Chla : divinylchlorophyll a -> chlorophyll a 2.5.1.62 : chlorophyllide a + phytyl diphosphate -> chlorophyll a + diphosphate _Chlb : chlorophyll a + H2O -> chlorophyll b + 4 H+ _Pheo : chlorophyll a -> pheophytins # - Cob(II)yrinate a,c diamide pathway 2.1.1.107a : S-adenosyl-L-methionine + uroporphyrinogen-III -> S-adenosyl-L-homocysteine + precorrin-1 2.1.1.107b : S-adenosyl-L-methionine + precorrin-1 -> S-adenosyl-L-homocysteine + precorrin-2 # - Cobalt pathway 4.99.1.3 : precorrin-2 + Co2+ <-> cobalt-precorrin-2 + 2 H+ 2.1.1.151 : S-adenosyl-L-methionine + cobalt-precorrin-2 <-> S-adenosyl-L-homocysteine + cobalt-precorrin-3 2.1.1.131a : cobalt-precorrin-3 + S-adenosyl-L-methionine <-> cobalt-precorrin-4 + S-adenosyl-L-homocysteine 2.1.1.133a : S-adenosyl-L-methionine + cobalt-precorrin-4 <-> S-adenosyl-L-homocysteine + cobalt-precorrin-5A RXN-8763 : cobalt-precorrin-5A + H2O <-> cobalt-precorrin-5B + acetaldehyde RXN-8764 : cobalt-precorrin-5B + S-adenosyl-L-methionine -> cobalt-precorrin-6A + S-adenosyl-L-homocysteine _1.3.1.54a : cobalt-precorrin-6A + NADPH <-> cobalt-precorrin-6B + NADP+ + H+ RXN-8766 : cobalt-precorrin-6B + S-adenosyl-L-methionine -> cobalt-precorrin-7 + S-adenosyl-L-homocysteine RXN-8767 : cobalt-precorrin-7 + S-adenosyl-L-methionine -> cobalt-precorrin-8x + S-adenosyl-L-homocysteine + CO2 RXN-8768 : cobalt-precorrin-8x <-> cobyrinate _6.3.1.- : cobyrinate + 2 L-glutamine + 2 ATP + 2 H2O <-> cob(II)yrinate a,c-diamide + 2 L-glutamate + 2 ADP + 2 phosphate O4P # - Non-Cobalt pathway 2.1.1.131b : precorrin-3B + S-adenosyl-L-methionine -> precorrin-4 + S-adenosyl-L-homocysteine 2.1.1.133b : S-adenosyl-L-methionine + precorrin-4 -> S-adenosyl-L-homocysteine + precorrin-5 1.3.1.54b : precorrin-6B + NADP+ + H+ -> precorrin-6A + NADPH 5.4.1.2 : precorrin-8x -> hydrogenobyrinate 6.6.1.2 : hydrogenobyrinate a,c-diamide + Co2+ + ATP + H2O -> cob(II)yrinate a,c-diamide + ADP + phosphate O4P + 2 H+ # - coenzyme B12 pathway # not pres ! (would connect cob(II)yrinate a,c-diamide to cob(I)yrinate a,c-diamide production) ~~IMPORTANT, following reaction not in sequence!!~~ ·1.16.8.1 : 2 cob(II)yrinate a,c-diamide + FMN -> 2 cob(I)yrinate a,c-diamide + FMNH2 2.5.1.17a : cob(I)yrinate a,c-diamide + ATP -> adenosyl-cobyrinate a,c-diamide + PPPi 6.3.5.10 : adenosyl-cobyrinate a,c-diamide + 4 L-glutamine + 4 ATP + 4 H2O -> 4 L-glutamate + adenosyl-cobyrate + 4 ADP + 4 phosphate O4P 6.3.1.10a : ATP + adenosyl-cobyrate + (R)-1-amino-2-propanol O-2-phosphate -> ADP + phosphate O4P + adenosylcobinamide RXN-8626 : L-threonine + ATP <-> L-threonine O-3-phosphate + ADP 4.1.1.81 : L-threonine O-3-phosphate -> (R)-1-amino-2-propanol O-2-phosphate + CO2 6.3.1.10b : ATP + adenosyl-cobyrate + (R)-1-Aminopropan-2-ol -> ADP + phosphate O4P + adenosylcobinamide 2.5.1.17b : cobinamide + ATP -> adenosylcobinamide + PPPi 2.7.1.156 : adenosylcobinamide + ATP -> adenosyl-cobinamide phosphate + ADP 2.7.7.62 : adenosyl-cobinamide phosphate + GTP -> adenosylcobinamide-GDP + diphosphate 2.7.8.26 : adenosylcobinamide-GDP + alpha-ribazole -> coenzyme B12 + GMP # Riboflavin metabolism 3.5.4.25 : 3 H2O + GTP -> diphosphate + 2,5-diamino-6-(ribosylamino)-4-(3H)-pyrimidinone 5'-phosphate + formate 3.5.4.26 : H2O + 2,5-diamino-6-(ribosylamino)-4-(3H)-pyrimidinone 5'-phosphate -> 5-amino-6-(5'-phosphoribosylamino)uracil + ammonia H3N 1.1.1.193 : 5-amino-6-(5'-phosphoribosylamino)uracil + NADPH -> 5-amino-6-(5'-phosphoribitylamino)uracil + NADP+ + H+ RIBOPHOSPHAT-RXN : 5-amino-6-(5'-phosphoribitylamino)uracil + H2O <-> 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione + phosphate O4P LUMAZINESYN-RXN : 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione + 3,4-dihydroxy-2-butanone-4-P -> 6,7-dimethyl-8-(1-D-ribityl)lumazine + phosphate O4P + 2 H2O DIOHBUTANONEPSYN-RXN : D-ribulose-5-phosphate -> 3,4-dihydroxy-2-butanone-4-P + formate 2.5.1.9 : 2 6,7-dimethyl-8-(1-D-ribityl)lumazine -> 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione + riboflavin _lumazine : 6,7-dimethyl-8-(1-D-ribityl)lumazine + UQ -> 7-Hydroxy-6-methyl-8-ribityl lumazine + UQH2 2.7.1.26 : riboflavin + ATP -> FMN + ADP 2.7.7.2 : FMN + ATP -> FAD + diphosphate _benzimidazole : 2 riboflavin + 2 CO2 -> 4 dimethylbenzimidazole + 3 O2 # not pres ! would end producing alpha-ribazole ~~IMPORTANT, following 3 reactions not in sequence!!~~ ·2.4.2.21 : nicotinate nucleotide + dimethylbenzimidazole <-> nicotinate + alpha-ribazole-5'-P ·3.1.3.73 : H2O + alpha-ribazole-5'-P <-> alpha-ribazole + phosphate O4P ·2.4.2.1 : nicotinate + ribose-1-phosphate <-> nicotinate D-ribonucleoside + phosphate O4P ·2.7.1.1 : nicotinate D-ribonucleoside + ATP -> nicotinate nucleotide + ADP # REDOX compounds _1.8.1.9 : thioredoxin disulfide + NADPH <-> thioredoxin + NADP+ + H+ _Thiored : thioredoxin disulfide + 2 Fd* + 2 H+ <-> 2 Fd + thioredoxin _FMNH2 : FMNH2 + thioredoxin disulfide -> FMN + thioredoxin 1.11.1.6 : 2 H2O2 -> 2 H2O + O2 # Pyruvate metabolism 1.1.1.38 : NAD+ + H+ + malate -> NADH + CO2 + pyruvate 4.1.1.31 : phosphoenolpyruvate + H2O + CO2 -> phosphate O4P + oxaloacetate 1.2.4.1 : pyruvate + lipoate acetyltransferase N6-(lipoyl)lysine <-> lipoate acetyltransferase N6-(S-acetyldihydrolipoyl)lysine + CO2 2.3.1.12 : acetyl-CoA + lipoate acetyltransferase N6-(dihydrolipoyl)lysine <-> coenzyme A + lipoate acetyltransferase N6-(S-acetyldihydrolipoyl)lysine 1.8.1.4a : lipoate acetyltransferase N6-(dihydrolipoyl)lysine + NAD+ + H+ -> lipoate acetyltransferase N6-(lipoyl)lysine + NADH 4.2.3.3 : dihydroxy-acetone phosphate -> methylglyoxal + phosphate O4P 4.4.1.5 : S-lactoyl-glutathione <-> methylglyoxal + glutathione 3.1.2.6 : S-lactoyl-glutathione + H2O -> glutathione + D-lactate 1.1.1.28 : NAD+ + H+ + D-lactate -> NADH + pyruvate 2.3.1.9 : 2 acetyl-CoA <-> acetoacetyl-CoA + coenzyme A # Glutathione metabolism 3.4.11.2a : cysteinylglycine + H2O -> L-cysteine + glycine 3.4.11.2b : R-S-cysteinylglycine + H2O -> R-S-cysteine + glycine 6.3.2.3 : glycine + L-gamma-glutamylcysteine + ATP -> glutathione + phosphate O4P + ADP _2.3.2.2a : glutathione -> L-glutamate + cysteinylglycine _2.3.2.2b : L-alanine + glutathione -> (5-L-glutamyl)-L-alanine + cysteinylglycine _2.3.2.2c : L-aspartate + glutathione -> (5-L-glutamyl)-L-aspartate + cysteinylglycine _2.3.2.2d : L-arginine + glutathione -> (5-L-glutamyl)-L-arginine + cysteinylglycine _2.3.2.2e : L-asparagine + glutathione -> (5-L-glutamyl)-L-asparagine + cysteinylglycine _2.3.2.2f : L-lysine + glutathione -> (5-L-glutamyl)-L-lysine + cysteinylglycine _2.3.2.2g : L-threonine + glutathione -> (5-L-glutamyl)-L-threonine + cysteinylglycine _2.3.2.2h : L-serine + glutathione -> (5-L-glutamyl)-L-serine + cysteinylglycine _2.3.2.2i : L-cysteine + glutathione -> (5-L-glutamyl)-L-cysteine + cysteinylglycine _2.3.2.2j : L-glutamate + glutathione -> (5-L-glutamyl)-L-glutamate + cysteinylglycine _2.3.2.2k : L-glutamine + glutathione -> (5-L-glutamyl)-L-glutamine + cysteinylglycine _2.3.2.2l : L-proline + glutathione -> (5-L-glutamyl)-L-proline + cysteinylglycine _2.3.2.2m : L-tryptophan + glutathione -> (5-L-glutamyl)-L-tryptophan + cysteinylglycine _2.3.2.2n : L-phenylalanine + glutathione -> (5-L-glutamyl)-L-phenylalanine + cysteinylglycine _2.3.2.2o : L-tyrosine + glutathione -> (5-L-glutamyl)-L-tyrosine + cysteinylglycine _2.3.2.2p : L-histidine + glutathione -> (5-L-glutamyl)-L-histidine + cysteinylglycine _2.3.2.2q : L-valine + glutathione -> (5-L-glutamyl)-L-valine + cysteinylglycine _2.3.2.2r : L-isoleucine + glutathione -> (5-L-glutamyl)-L-isoleucine + cysteinylglycine _2.3.2.2s : L-leucine + glutathione -> (5-L-glutamyl)-L-leucine + cysteinylglycine _2.3.2.2t : L-methionine + glutathione -> (5-L-glutamyl)-L-methionine + cysteinylglycine 3.5.2.9 : 5-oxoproline + 2 H2O + ATP -> L-glutamate + phosphate O4P + ADP _2.5.1.18 : glutathione -> R-S-glutathione _2.3.2.2u : R-S-glutathione + H2O -> R-S-cysteinylglycine + L-glutamate 1.11.1.9 : H2O2 + 2 glutathione -> glutathione disulfide + 2 H2O # not pres ! would close g-glutamyl cycle ~~IMPORTANT, following 20 reactions not in sequence!!~~ ·6.3.2.2 : ATP + L-glutamate + L-cysteine -> ADP + diphosphate + L-gamma-glutamylcysteine ·2.3.2.4a : (5-L-glutamyl)-L-alanine -> L-alanine + 5-oxoproline ·2.3.2.4b : (5-L-glutamyl)-L-aspartate -> L-aspartate + 5-oxoproline ·2.3.2.4c : (5-L-glutamyl)-L-arginine -> L-arginine + 5-oxoproline ·2.3.2.4d : (5-L-glutamyl)-L-asparagine -> L-asparagine + 5-oxoproline ·2.3.2.4e : (5-L-glutamyl)-L-lysine -> L-lysine + 5-oxoproline ·2.3.2.4f : (5-L-glutamyl)-L-threonine -> L-threonine + 5-oxoproline ·2.3.2.4g : (5-L-glutamyl)-L-serine -> L-serine + 5-oxoproline ·2.3.2.4h : (5-L-glutamyl)-L-cysteine -> L-cysteine + 5-oxoproline ·2.3.2.4i : (5-L-glutamyl)-L-glutamate -> L-glutamate + 5-oxoproline ·2.3.2.4j : (5-L-glutamyl)-L-glutamine -> L-glutamine + 5-oxoproline ·2.3.2.4k : (5-L-glutamyl)-L-proline -> L-proline + 5-oxoproline ·2.3.2.4l : (5-L-glutamyl)-L-tryptophan -> L-tryptophan + 5-oxoproline ·2.3.2.4m : (5-L-glutamyl)-L-phenylalanine -> L-phenylalanine + 5-oxoproline ·2.3.2.4n : (5-L-glutamyl)-L-tyrosine -> L-tyrosine + 5-oxoproline ·2.3.2.4o : (5-L-glutamyl)-L-histidine -> L-histidine + 5-oxoproline ·2.3.2.4p : (5-L-glutamyl)-L-valine -> L-valine + 5-oxoproline ·2.3.2.4q : (5-L-glutamyl)-L-isoleucine -> L-isoleucine + 5-oxoproline ·2.3.2.4r : (5-L-glutamyl)-L-leucine -> L-leucine + 5-oxoproline ·2.3.2.4s : (5-L-glutamyl)-L-methionine -> L-methionine + 5-oxoproline # Fructose and mannose metabolism 4.1.2.13c : fructose-1-phosphate <-> dihydroxy-acetone phosphate + glyceraldehyde 2.7.1.4 : fructose + ATP <-> fructose-6-phosphate + ADP 5.3.1.8 : D-mannose-6-phosphate <-> fructose-6-phosphate 5.4.2.8 : alpha-D-mannose 1-phosphate <-> D-mannose-6-phosphate 2.7.7.22 : alpha-D-mannose 1-phosphate + GDP -> GDP-D-mannose + phosphate O4P 2.7.7.13 : alpha-D-mannose 1-phosphate + GTP -> GDP-D-mannose + diphosphate 4.2.1.47 : GDP-D-mannose -> H2O + GDP-4-dehydro-6-deoxy-D-mannose 1.1.1.271 : NADP+ + H+ + GDP-L-fucose <-> NADPH + GDP-4-dehydro-6-deoxy-D-mannose # Aminosugars metabolism 2.6.1.16 : fructose-6-phosphate + L-glutamine <-> L-glutamate + D-glucosamine-6-phosphate 5.4.2.10 : D-glucosamine-6-phosphate -> D-glucosamine 1-phosphate 2.3.1.157 : D-glucosamine 1-phosphate + acetyl-CoA -> N-acetyl-glucosamine-1-phosphate + coenzyme A 2.7.7.23 : N-acetyl-glucosamine-1-phosphate + UTP <-> UDP-N-acetyl-D-glucosamine + diphosphate 2.5.1.7 : UDP-N-acetyl-D-glucosamine + phosphoenolpyruvate <-> UDP-GlcNAc-enolpyruvate + phosphate O4P _1.1.1.158 : NADP+ + H+ + UDP-N-acetylmuramate <-> NADPH + UDP-GlcNAc-enolpyruvate _5.1.3.8 : N-acetyl-D-glucosamine <-> N-acetyl-D-mannosamine _5.1.3.14a : N-acetyl-D-mannosamine + UTP <-> UDP-N-acetyl-D-glucosamine + diphosphate _5.1.3.14b : UDP-N-acetyl-D-mannosamine <-> UDP-N-acetyl-D-glucosamine # Peptidoglycan biosynthesis 6.3.2.8 : L-alanine + UDP-N-acetylmuramate + ATP -> UDP-N-acetylmuramoyl-L-alanine + phosphate O4P + ADP 6.3.2.9 : UDP-N-acetylmuramoyl-L-alanine + D-glutamate + ATP -> UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + phosphate O4P + ADP 6.3.2.13 : UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + meso-diaminopimelate + ATP -> UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate + phosphate O4P + ADP 6.3.2.10a : UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate + D-alanyl-D-alanine + ATP -> UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate- D-alanyl-D-alanine + phosphate O4P + ADP 2.7.8.13a : UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate- D-alanyl-D-alanine + undecaprenyl phosphate -> undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP 2.4.1.227a : undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UDP-N-acetyl-D-glucosamine -> undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UDP _6.3.1.2b : undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + ATP + ammonia H3N -> undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + ADP + phosphate O4P 6.3.2.10b : UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine + D-alanyl-D-alanine + ATP -> UDPMurAc(oyl-L-Ala-D-gamma-Glu-L-Lys-D-Ala-D-Ala) + phosphate O4P + ADP 2.7.8.13b : UDPMurAc(oyl-L-Ala-D-gamma-Glu-L-Lys-D-Ala-D-Ala) + undecaprenyl phosphate -> MurAc(oyl-L-Ala-D-gamma-Glu-L-Lys-D-Ala-D-Ala)-diphospho-undecaprenol + UMP 2.4.1.227b : MurAc(oyl-L-Ala-D-gamma-Glu-L-Lys-D-Ala-D-Ala)-diphospho-undecaprenol + UDP-N-acetyl-D-glucosamine -> undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine + UDP _6.3.1.2c : undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine + ATP + ammonia H3N -> undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-isoglutaminyl-L-lysyl-D-alanyl-D-alanine + ADP + phosphate O4P 6.3.2.10c : UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine + D-alanyl-D-alanine + ATP -> UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine + phosphate O4P + ADP 2.7.8.13c : UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine + undecaprenyl phosphate -> undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine + UMP 2.4.1.227c : undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine + UDP-N-acetyl-D-glucosamine -> undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine + UDP _6.3.1.2d : undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine + ATP + ammonia H3N -> undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-L-lysyl-D-alanyl-D-alanine + ADP + phosphate O4P # not pres ! would complete peptidoglycan biosynthesis ~~IMPORTANT, following 3 reactions not in sequence!!~~ ·2.3.2.10a : undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + glycyl-tRNAgly <-> undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-(glycyl)5-D-alanyl-D-alanine + tRNAgly ·2.3.2.10b : undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-isoglutaminyl-L-lysyl-D-alanyl-D-alanine + glycyl-tRNAgly <-> undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-isoglutaminyl-L-lysyl-(glycyl)5-D-alanyl-D-alanine + tRNAgly ·2.3.2.10c : undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-L-lysyl-D-alanyl-D-alanine + glycyl-tRNAgly <-> undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-L-lysyl-(glycyl)5-D-alanyl-D-alanine + tRNAgly 6.3.2.4 : 2 D-alanine + ATP -> D-alanyl-D-alanine + phosphate O4P + ADP 3.6.1.27 : undecaprenyl diphosphate + H2O -> undecaprenyl phosphate + phosphate O4P _peptidoglycan_syna : undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-(glycyl)5-D-alanyl-D-alanine -> peptidoglycan + undecaprenyl diphosphate _peptidoglycan_synb : undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-isoglutaminyl-L-lysyl-(glycyl)5-D-alanyl-D-alanine -> peptidoglycan + undecaprenyl diphosphate _peptidoglycan_sync : undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-L-lysyl-(glycyl)5-D-alanyl-D-alanine -> peptidoglycan + undecaprenyl diphosphate 3.4.16.4 : D-alanyl-D-alanine + H2O <-> 2 D-alanine # additional glycan biosynthesis 2.3.1.129 : (R)-3-hydroxymyristoyl-ACP + UDP-N-acetyl-D-glucosamine -> UDP-3-O-(3-hydroxymyristoyl)-N-acetylglucosamine + an [acyl-carrier protein] # Starch and sucrose metabolism 2.4.1.14 : fructose-6-phosphate + UDP-D-glucose -> sucrose-6-phosphate + UDP _5.4.2.6 : beta-D-glucose 1-phosphate <-> beta-D-glucose 6-phosphate 2.4.1.25 : maltotriose + maltose -> maltotetraose + beta-D-glucose _2.4.1.1 : a glycogen_n1 + phosphate O4P -> a glycogen_n + alpha-D-glucose 1-phosphate 2.7.7.27 : alpha-D-glucose 1-phosphate + ATP -> ADP-D-glucose + diphosphate _a-glucansyn : 2 ADP-D-glucose -> a 1,4-alpha-D-glucan_n _2.4.1.21a : ADP-D-glucose + a 1,4-alpha-D-glucan_n -> ADP + a 1,4-alpha-D-glucan_n1 _glycsyn : 2 ADP-D-glucose + a 1,4-alpha-D-glucan_n1 -> a glycogen_n _2.4.1.21b : ADP-D-glucose + a glycogen_n -> ADP + a glycogen_n1 _2.4.1.18 : a glycogen_n1 + a 1,4-alpha-D-glucan_n <-> a glycogen_n + a 1,4-alpha-D-glucan_n1 5.4.2.2 : alpha-D-glucose 1-phosphate <-> alpha-D-glucose 6-phosphate 4.2.1.45 : CDP-D-glucose -> H2O + CDP-4-dehydro-6-deoxy-D-glucose _cellulosedeg : cellulose <-> 1,4-beta-D-glucan_n1 _3.2.1.4 : 1,4-beta-D-glucan_n1 + H2O <-> 1,4-beta-D-glucan_n + cellobiose _3.2.1.21a : cellobiose <-> beta-D-glucose _3.2.1.21b : 1,4-beta-D-glucan_n <-> beta-D-glucose _2.4.1.213 : ADP-D-glucose + sn-glycerol-3-phosphate <-> 2-(beta-D-glucosyl)-sn-glycerol-3-phosphate + ADP 3.1.3.69 : H2O + 2-(beta-D-glucosyl)-sn-glycerol-3-phosphate -> phosphate O4P + 2-(beta-D-glucosyl)-sn-glycerol # Biosynthesis of steroids # - NON-Mevalonate pathway - produces Isopentenyl-PP 2.2.1.7 : pyruvate + D-glyceraldehyde-3-phosphate -> 1-deoxy-D-xylulose 5-phosphate + CO2 1.1.1.267 : 2-C-methyl-D-erythritol-4-phosphate + NADP+ + H+ <-> 1-deoxy-D-xylulose 5-phosphate + NADPH 2.7.7.60 : 2-C-methyl-D-erythritol-4-phosphate + CTP -> 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + diphosphate 2.7.1.148 : 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + ATP -> 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + ADP 4.6.1.12 : 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol -> 2-C-methyl-D-erythritol-2,4-cyclodiphosphate + CMP 1.17.7.1 : 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate + H2O + a protein disulfide <-> 2-C-methyl-D-erythritol-2,4-cyclodiphosphate + a protein dithiol 1.17.1.2a : 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate + NADPH -> isopentenyl diphosphate + NADP+ + H+ + H2O 1.17.1.2b : isopentenyl diphosphate + NADP+ + H+ + H2O -> (E)-4-hydroxy-3-methylbut 2-en-1-yl diphosphate + NADPH # - Isopentenyl-PP to Squalene 5.3.3.2 : isopentenyl diphosphate -> dimethylallyl diphosphate 2.5.1.29a : isopentenyl diphosphate + (E,E)-farnesyl diphosphate -> all-trans-geranyl-geranyl diphosphate + diphosphate _2.5.1.29b : dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate _2.5.1.29c : geranyl diphosphate + isopentenyl diphosphate -> (E,E)-farnesyl diphosphate + diphosphate _UbiQ : a ubiquinone + a menaquinone <-> all-trans-geranyl-geranyl diphosphate + isopentenyl diphosphate _2.5.1.21a : (E,E)-farnesyl diphosphate -> diphosphate + presqualene diphosphate _2.5.1.21b : presqualene diphosphate + NADPH -> squalene + diphosphate + NADP+ + H+ # - Vit E production _1.3.1.2 : all-trans-geranyl-geranyl diphosphate + 3 H+ + 3 NADPH -> phytyl diphosphate + 3 NADP+ _HPT : phytyl diphosphate + homogentisate -> 2-methyl-6-phytylquinol + diphosphate + CO2 _PhytQnol : 2-methyl-6-phytylquinol + S-adenosyl-L-methionine -> 2,3-dimethyl-5-phytylquinol + S-adenosyl-L-homocysteine _VTE1a : 2,3-dimethyl-5-phytylquinol -> gamma-tocopherol _VTE1b : 2-methyl-6-phytylquinol -> delta-tocopherol _GTMTa : gamma-tocopherol + S-adenosyl-L-methionine -> alpha-tocopherol + S-adenosyl-L-homocysteine _GTMTb : delta-tocopherol + S-adenosyl-L-methionine -> beta-tocopherol + S-adenosyl-L-homocysteine _VitE : beta-tocopherol -> alpha-tocopherol # Lipoic acid metabolism _2.3.1.181a : octanoyl-[acyl-carrier protein] C8H15OSR + a protein -> a protein-N-6-octanoyl-lysine + an [acyl-carrier protein] _2.8.1.8a : a protein-N-6-octanoyl-lysine + 2 S0 + 2 S-adenosyl-L-methionine -> a protein-N-6-lipoyl-lysine + 2 L-methionine + 2 5'-deoxyadenosine _2.8.1.8b : octanoyl-[acyl-carrier protein] C8H15OSR + 2 S0 + 2 S-adenosyl-L-methionine -> lipoyl-[acyl carrier protein] C8H13OS3R + 2 L-methionine + 2 5'-deoxyadenosine _2.3.1.181b : lipoyl-[acyl carrier protein] C8H13OS3R + a protein -> a protein-N-6-lipoyl-lysine + an [acyl-carrier protein] _2.7.7.63a : ATP + lipoate -> diphosphate + lipoyl-AMP ·transp_lipoate : lipoate_extrac -> lipoate _2.7.7.63b : lipoyl-AMP + a protein -> a protein-N-6-lipoyl-lysine + AMP # Carotenoid biosynthesis _2.5.1.32 : 2 all-trans-geranyl-geranyl diphosphate -> phytoene + diphosphate _CrtP1 : phytoene + thioredoxin <-> phytofluene + thioredoxin disulfide _CrtP2 : phytofluene + thioredoxin <-> zeta-carotene + thioredoxin disulfide 1.14.99.30a : zeta-carotene + O2 + thioredoxin disulfide -> neurosporene + 2 H2O + thioredoxin 1.14.99.30b : O2 + thioredoxin disulfide + neurosporene -> 2 H2O + thioredoxin + trans-lycopene _crtHa : zeta-carotene + O2 + thioredoxin disulfide -> neurosporene + 2 H2O + thioredoxin _crtHb : O2 + thioredoxin disulfide + neurosporene -> 2 H2O + thioredoxin + trans-lycopene # not pres ! would end producing carotene ~~IMPORTANT, following 2 reactions not in sequence!!~~ ·CrtLa : trans-lycopene -> gamma-carotene ·CrtLb : gamma-carotene -> beta-carotene _CrtRa : beta-carotene -> beta-cryptoxanthin _CrtRb : beta-cryptoxanthin -> zeaxanthin _CrtOa : beta-carotene -> echinenone _CrtOb : echinenone -> canthaxanthin _CrtRc : echinenone -> 3-hydroxyechinenone _CrtRd : 3-hydroxyechinenone -> adonixanthin _CrtRe : canthaxanthin -> phoenicoxanthin _CrtRf : phoenicoxanthin -> astaxanthin _gCar : gamma-carotene <-> (2'S)-deoxymyxol 2'-(2,4-di-O-methyl-alpha-L-fucoside) _CrtRg : (2'S)-deoxymyxol 2'-(2,4-di-O-methyl-alpha-L-fucoside) <-> (3R,2'S)-myxol 2'-(2,4-di-O-methyl-alpha-L-fucoside) # Nucleotide sugars metabolism - present? necessary? 5.1.3.2a : UDP-D-glucose <-> UDP-galactose 1.1.1.22 : UDP-D-glucose + H2O + 2 NAD+ + H+ -> UDP-D-glucuronate + 2 NADH 2.7.7.24 : alpha-D-glucose 1-phosphate + dTTP -> dTDP-D-glucose + diphosphate 5.1.3.2b : dTDP-D-glucose <-> dTDP-D-galactose 2.7.7.33 : alpha-D-glucose 1-phosphate + CTP -> CDP-D-glucose + diphosphate 4.2.1.46 : dTDP-D-glucose -> H2O + dTDP-4-dehydro-6-deoxy-D-glucose 5.1.3.13a : dTDP-4-dehydro-6-deoxy-D-glucose -> dTDP-4-dehydro-6-deoxy-L-mannose 5.1.3.13b : dTDP-4-dehydro-6-deoxy-D-glucose + GTP -> GDP-4-dehydro-6-deoxy-L-mannose + dTDP + phosphate O4P 1.1.1.133a : NADP+ + H+ + dTDP-alpha-L-rhamnose <-> NADPH + dTDP-4-dehydro-6-deoxy-L-mannose 1.1.1.133b : NADP+ + H+ + GDP-6-deoxy-L-mannose <-> NADPH + GDP-4-dehydro-6-deoxy-L-mannose # Propanoate metabolism - present? _1.2.1.3e : 2-propyn-1-al + NAD+ + H+ + H2O -> NADH + propynoate # Butanoate metabolism - present? # Thiamine metabolism - present? PYRIMSYN1-RXN : 5-aminoimidazole ribonucleotide <-> hydroxymethylpyrimidine phosphate 2.5.1.3 : 4-methyl-5-(beta-hydroxyethyl)thiazole phosphate + 4-amino-5-hydroxymethyl-2-methylpyrimidine-pyrophosphate -> thiamine-phosphate + diphosphate 2.7.1.49 : ATP + hydroxymethylpyrimidine <-> ADP + hydroxymethylpyrimidine phosphate 2.7.4.7 : hydroxymethylpyrimidine phosphate + ATP <-> 4-amino-5-hydroxymethyl-2-methylpyrimidine-pyrophosphate + ADP 2.7.4.16 : thiamine-phosphate + ATP -> thiamine diphosphate + ADP # Biotin metabolism - present? 2.3.1.47 : pimeloyl-CoA + L-alanine -> CO2 + coenzyme A + 7-keto-8-aminopelargonate 6.3.3.3 : CO2 + 7,8-diaminopelargonate + ATP -> dethiobiotin + phosphate O4P + ADP 2.8.1.6 : dethiobiotin + 2 S-adenosyl-L-methionine + hydrogen sulfide H2s -> biotin + 2 5'-deoxyadenosine + 2 L-methionine 6.3.4.15 : BCCP + biotin + ATP -> diphosphate + AMP + biotin-BCCP (monomer) RXN-7101 : 2 biotin-BCCP (monomer) <-> a biotin-BCCP (dimer) 2.1.1.142 : cycloartenol + S-adenosyl-L-methionine -> (24R)-24-methylcycloarta-25-en-3-beta-ol + S-adenosyl-L-homocysteine # Penicillin and cephalosporin biosynthesis - mostly not present _3.5.2.6 : H2O + penicillin -> penicilloic acid _3.5.1.11 : penicillin + H2O -> 6-aminopenicillanate C8H12N2O3S + acetate # Terpenoid biosynthesis - mostly not present _2.5.1.31a : (E,E)-farnesyl diphosphate + isopentenyl diphosphate <-> all-trans-geranyl-geranyl diphosphate + diphosphate _2.5.1.31b : all-trans-geranyl-geranyl diphosphate + 7 isopentenyl diphosphate <-> di-trans,poly-cis-Undecaprenyl diphosphate + 7 diphosphate # Vitamin B6 metabolism - present? 1.4.3.5a : O2 + pyridoxine-5'-phosphate -> H2O2 + pyridoxal 5'-phosphate 1.4.3.5b : O2 + H2O + pyridoxamine 5'-phosphate -> ammonia H3N + H2O2 + pyridoxal 5'-phosphate 1.4.3.5c : O2 + pyridoxine <-> H2O2 + pyridoxal 1.4.3.5d : O2 + H2O + pyridoxamine <-> ammonia H3N + H2O2 + pyridoxal 2.6.99.2 : 1-deoxy-D-xylulose 5-phosphate + 1-amino-propan-2-one-3-phosphate -> pyridoxine-5'-phosphate + phosphate O4P + 2 H2O _1.1.1.262 : O-phospho-4-hydroxy-L-threonine + NAD+ + H+ -> NADH + (2S)-2-amino-3-oxo-4-phosphonooxybutanoate RXN-8447 : (2S)-2-amino-3-oxo-4-phosphonooxybutanoate + H+ <-> 1-amino-propan-2-one-3-phosphate + CO2 4.2.3.1b : O-phospho-4-hydroxy-L-threonine + H2O -> phosphate O4P + 4-hydroxy-L-threonine _VitB6 : O-phospho-4-hydroxy-L-threonine -> pyridoxine # Glycerophospholipid metabolism & Inositol phosphate metabolism - mostly not present 1.1.5.3 : sn-glycerol-3-phosphate + a ubiquinone -> dihydroxy-acetone phosphate + a ubiquinol 2.3.1.51 : a fatty acyl CoA C22H35N7O17RP3s + a 2-lysophosphatidate -> an L-phosphatidate + coenzyme A 2.7.7.41 : CTP + an L-phosphatidate -> a CDP-diacylglycerol C14H19N3O15R1R2P2 + diphosphate 2.7.1.107 : ATP + a 1,2-diacylglycerol -> an L-phosphatidate + ADP 2.7.8.5 : a CDP-diacylglycerol C14H19N3O15R1R2P2 + sn-glycerol-3-phosphate -> an L-1-phosphatidylglycerol-phosphate + CMP 3.1.3.25 : D-myo-inositol (3)-monophosphate + H2O -> myo-inositol + phosphate O4P # reactions with cognate genes !!! 3.1.4.- : 1-(1-Alkenyl)-sn-glycero-3-phosphoethanolamine + H2O <-> 1-(1-Alkenyl)-sn-glycerol + Ethanolamine phosphate 4.-.-.- : dTDP-(3R)-amino-3,6-dideoxy-D-glucose <-> dTDP-3-amino-4,6-deoxy-3,4-dehydroglucose + H2O 6.3.4.- : formate + ATP + 1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide <-> ADP + phosphate O4P + 1-(5'-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide 4.2.-.- : N-Acetylmuramic acid 6-phosphate + H2O <-> N-Acetyl-D-glucosamine 6-phosphate + (R)-Lactate ### # BIOMASS out of amino acids, nucleic acids, lipids and antenna proteins Alabm : L-alanine -> Ala Aspbm : L-aspartate -> Asp Argbm : L-arginine -> Arg Asnbm : L-asparagine -> Asn Lysbm : L-lysine -> Lys Thrbm : L-threonine -> Thr Serbm : L-serine -> Ser Cysbm : L-cysteine -> Cys Glybm : glycine -> Gly Glubm : L-glutamate -> Glu Glnbm : L-glutamine -> Gln Probm : L-proline -> Pro Trpbm : L-tryptophan -> Trp Phebm : L-phenylalanine -> Phe Tyrbm : L-tyrosine -> Tyr Hisbm : L-histidine -> His Valbm : L-valine -> Val Ilebm : L-isoleucine -> Ile Leubm : L-leucine -> Leu Metbm : L-methionine -> Met dATP : dATP -> dATPbm dGTP : dGTP -> dGTPbm dTTP : dTTP -> dTTPbm dUTP : dUTP -> dUTPbm dCTP : dCTP -> dCTPbm AMP : AMP -> AMPbm UMP : UMP -> UMPbm CMP : CMP -> CMPbm GMP : GMP -> GMPbm 8C-lipidbm : octanoic acid -> 8C-lipidbm 10C-lipidbm : decanoic acid -> 10C-lipidbm 12C-lipidbm : dodecanoic acid -> 12C-lipidbm 14C-lipidbm : tetradecanoic acid -> 14C-lipidbm 16C-lipidbm : hexadecanoic acid -> 16C-lipidbm 18C-lipidbm : octadecanoic acid -> 18C-lipidbm (9Z)16C-lipidbm : (9Z)-hexadecanoic acid -> (9Z)16C-lipidbm (9Z)18C-lipidbm : (9Z)-octadecanoic acid -> (9Z)18C-lipidbm (9Z,12Z)18C-lipidbm : (9Z,12Z)-octadecanoic acid -> (9Z,12Z)18C-lipidbm (9Z,12Z,15Z)18C-lipidbm : (9Z,12Z,15Z)-octadecanoic acid -> (9Z,12Z,15Z)18C-lipidbm (6Z,9Z)18C-lipidbm : (6Z,9Z)-octadecanoic acid -> (6Z,9Z)18C-lipidbm (6Z,9Z,12Z)18C-lipidbm : (6Z,9Z,12Z)-octadecanoic acid -> (6Z,9Z,12Z)18C-lipidbm (6Z,9Z,12Z,15Z)18C-lipidbm : (6Z,9Z,12Z,15Z)-octadecanoic acid -> (6Z,9Z,12Z,15Z)18C-lipidbm hemebm : heme a -> hemebm PhCybibm : (3Z)-phycocyanobilin -> PhCybibm Bilibm : bilirubin -> Bilibm BacChlabm : Zn-Bacterio-chlorophyll a -> BacChlabm BacChlsbm : bacterio-chlorophylls -> BacChlsbm BacPheobm : bacterio-pheophytins -> BacPheobm Chlabm : chlorophyll a -> Chlabm Chlbbm : chlorophyll b -> Chlbbm Pheobm : pheophytins -> Pheobm CobIIbm : cob(II)yrinate a,c-diamide -> CobIIbm B12bm : coenzyme B12 -> B12bm Carotenebm : trans-lycopene -> Lycopbm PepGlycbm : peptidoglycan -> PepGlycbm Glycbm : a glycogen_n1 -> Glycbm Squalbm : squalene -> Squalbm aTphbm : alpha-tocopherol -> aTphbm PLipLysbm : a protein-N-6-lipoyl-lysine -> PLipLysbm Cxntbm : canthaxanthin -> Cxntbm 3hxcbm : 3-hydroxyechinenone -> 3hxcbm Adnxbm : adonixanthin -> Adnxbm Astxbm : astaxanthin -> Astxbm ATPbm : ATP -> ATPbm ADPbm : ADP -> ADPbm Biomass : 0.499149 Ala + 0.28742 Arg + 0.234232 Asp + 0.234232 Asn + 0.088988 Cys + 0.255712 Gln + 0.255712 Glu + 0.595297 Gly + 0.092056 His + 0.282306 Ile + 0.437778 Leu + 0.333448 Lys + 0.149336 Met + 0.180021 Phe + 0.214798 Pro + 0.209684 Ser + 0.246506 Thr + 0.055234 Trp + 0.133993 Tyr + 0.411184 Val + 0.024150597 dATPbm + 0.024150597 dTTPbm + 0.021729829 dGTPbm + 0.021729829 dCTPbm + 0.140389293 AMPbm + 0.140389293 UMPbm + 0.123745851 GMPbm + 0.123745851 CMPbm + 0.206837179 16C-lipidbm + 0.015734119 (9Z)16C-lipidbm + 0.003517764 18C-lipidbm + 0.031885959 (9Z)18C-lipidbm + 0.035683674 (9Z,12Z)18C-lipidbm + 0.017971092 (9Z,12Z,15Z)18C-lipidbm + 0.050319059 (6Z,9Z,12Z)18C-lipidbm + 0.014481787 (6Z,9Z,12Z,15Z)18C-lipidbm + 0.027281834 Chlabm + 0.00820225 Lycopbm + 0.014506173 Glycbm + 59.28 ATP -> BM + 59.28 ADP + 59.305000 phosphate O4P _Growth : BM -> BM_out ### # SPECIAL # - heterotrophic growth TRANS-RXN59G-152 : beta-D-glucose_extrac + H+_extrac -> beta-D-glucose + H+ CO2out : CO2 -> CO2_extrac # - autotrophic growth _lightII : photonII_extrac -> photonII _lightI : photonI_extrac -> photonI 4.1.1.39 : D-ribulose-1,5-bisphosphate + CO2 + H2O -> 2 3-phosphoglycerate + 2 H+ CO2in : CO2_extrac <-> CO2 4.2.1.1b : CO2 + H2O <-> HCO3- + H+ _H2CO3transport : H2CO3_extrac <-> H2CO3 _H2CO3desprot : H2CO3 <-> HCO3- # maintenance NADHmain : NADH -> NAD+ + H+ NADPHmain : NADPH -> NADP+ + H+ # - transport Phosphate TRANS-RXN59G-90 : phosphate O4P_extrac + H+_extrac -> phosphate O4P + H+ Phosphate TRANS-RXN59G-100 : phosphate O4P_extrac + ATP + H2O -> ADP + 2 phosphate O4P Phosphate TRANS-RXN59G-108 : phosphate O4P_extrac + ATP + H2O -> ADP + 2 phosphate O4P _Phosphate_out : phosphate O4P -> phosphate O4P_extrac H2O : H2O_extrac <-> H2O PROTONS : H+_extrac <-> H+ urea TRANS-RXN59G-410 : urea_extrac + ATP + H2O -> urea + ADP + phosphate O4P sulfate TRANS-RXN59G-407 : sulfate O4S_extrac <-> sulfate O4s sulfate TRANS-RXN59G-713 : sulfate O4S_extrac + ATP + H2O -> sulfate O4s + ADP + phosphate O4P nitrate TRANS-RXN59G-237 : nitrate NO3_extrac + ATP + H2O -> nitrate NO3 + ADP + phosphate O4P ammonia TRANS-RXN59G-0 : NH4+_extrac + methylamine_extrac -> NH4+ + methylamine ammonia TRANS-RXN59G-178 : NH4+_extrac + H+_extrac <-> NH4+ + H+ _ammonia : ammonia H3N <-> NH4+ iron TRANS-RXN59G-711 : Fe2+_extrac -> Fe2+ magnesium TRANS-RXN59G-340 : Mg2+_extrac + ATP + H2O -> Mg2+ + ADP + phosphate O4P magnesium TRANS-RXN59G-53 : Mg2+_extrac <-> Mg2+ zinc TRANS-RXN59G-813 : Zn2+_extrac + ATP + H2O -> Zn2+ + ADP + phosphate O4P zinc TRANS-RXN59G-228 : Zn2+ <-> Zn2+_extrac cobalt TRANS-RXN59G-71 : Co2+_extrac + ATP + H2O -> Co2+ + ADP + phosphate O4P _COtransp : CO_extrac <-> CO _H2O2transp : H2O2_extrac <-> H2O2 _O2in : O2_extrac -> O2 _O2out : O2 -> O2_extrac potassium 3.6.3.12 : K+_extrac + ATP + H2O -> K+ + ADP + phosphate O4P potassium TRANS-RXN59G-35 : K+_extrac -> K+ chloride TRANS-RXN59G-171 : chloride_extrac -> chloride sodium TRANS-RXN59G-47 : Na+_extrac + H+ -> Na+ + H+_extrac calcium TRANS-RXN59G-708 : Ca2+_extrac + H+ -> Ca2+ + H+_extrac manganese _Mn transport : Mn2+_extrac + ATP + H2O -> Mn2+ + ADP + phosphate O4P _H2 : H2 -> H2_extrac _an [acyl-carrier protein] : an [acyl-carrier protein]_extrac <-> an [acyl-carrier protein] _a protein : Ala + Asp + Arg + Asn + Lys + Thr + Ser + Cys + Gly + Glu + Gln + Pro + Trp + Phe + Tyr + His + Val + Ile + Leu + Met <-> a protein _a protein disulfide R1Protein2R2R3S2 : a protein + 2 hydrogen sulfide H2s <-> a protein disulfide _a protein dithiol H2R1Protein2R2R3S2 : a protein disulfide <-> a protein dithiol + H2O _RNAout : RNAn1 -> RNAn1_out _DNAout : DNAn1 -> DNAn1_out _glycout : a glycogen_n1 -> a glycogen_n1_out _PPPi : 2 PPPi + H2O -> 3 diphosphate _glycolaldehyde : glycolaldehyde -> glycolaldehyde_extrac -CONSTRAINTS # all units should be mmol/g DW·h # carbon input (3,4 mmole/g.h) normalized: input flux/number C % # - heterotrophic # -- 3,4 mmole/g.h --> 3.4/6 = 0.566666667 TRANS-RXN59G-152 [0, 0.567] CO2out [0, 98] CO2in [0, 0] 4.2.1.1b [-10, 10] _H2CO3transport [0, 0] # following for dark heterotrophic: #_lightI [0, 0] #_lightII [0, 0] #_Thiored [-1, 1] #4.1.1.39 [0, 0] # no dark heterotrophic _Thiored [0, 100] # - autotrophic # -- for a doubling time of 8 hours, a 0.09 specific growth is needed, # -- values resulting from the inverse optimization of light uptake: _lightI [0, 0.8] _lightII [0, 0.8] CO2in [0, 1.7] _H2CO3transport [0, 1.7] 4.2.1.1b [-10, 10] TRANS-RXN59G-152 [0, 0] _Thiored [0, 100] % # - mixotrophic _lightI [0, 0.8] _lightII [0, 0.8] TRANS-RXN59G-152 [0.01, 0.567] CO2in [0, 1.7] _H2CO3transport [0, 1.7] 4.2.1.1b [-10, 10] _Thiored [0, 100] ### NADHmain [0.5, 1000] NADPHmain [0.50, 1000] _1.8.1.9 [0, 100] 1.4.1.4 [-100, 0] _1.1.1.3a [0, 100] _1.5.1.2a1 [-100, 0] 1.6.1.2 [0, 100] _1.3.1.26a [-100, 0] ·1.5.1.20a [-100, 0] ·1.3.1.75b [0, 100] _1.1.1.3a [0, 100] 1.1.1.49 [-100, 0] 1.2.1.41 [-100, 0] 1.1.1.86a [-100, 0] 1.1.1.86b [0, 100] # - transport _Phosphate_out [0, 100] H2O [-500, 500] urea TRANS-RXN59G-410 [0, 0] sulfate TRANS-RXN59G-407 [-104, 104] sulfate TRANS-RXN59G-713 [0, 105] nitrate TRANS-RXN59G-237 [0, 160] ammonia TRANS-RXN59G-0 [0, 116] ammonia TRANS-RXN59G-178 [-1000, 1000] _COtransp [-10, 10] _H2O2transp [-100, 100] # shut down transport for Glu and Gln transport TRANS-RXN59G-639 [0, 0] transport TRANS-RXN59G-245 [0, 0] -EXTERNAL METABOLITES BM_out photonII_extrac photonI_extrac O2_extrac H2O2_extrac urea_extrac H2CO3_extrac glycolaldehyde_extrac an [acyl-carrier protein]_extrac Fe2+_extrac Mg2+_extrac Zn2+_extrac Co2+_extrac CO_extrac tRNAala tRNAasp tRNAarg tRNAasn tRNAlys tRNAthr tRNAser tRNAcys tRNAgly tRNAGlu tRNApro tRNAtrp tRNAphe tRNAtyr tRNAhis tRNAval tRNAile tRNAleu tRNAmet DNAn RNAn RNAn1_out DNAn1_out a glycogen_n1_out lipoate_extrac methylamine_extrac L-glutamate_extrac L-glutamine_extrac nitrate NO3_extrac sulfate O4S_extrac NH4+_extrac phosphate O4P_extrac CO2_extrac beta-D-glucose_extrac H2O_extrac H+_extrac K+_extrac chloride_extrac Na+_extrac Ca2+_extrac Mn2+_extrac H2_extrac -OBJ _Growth 1 1 -DESIGNOBJ _Growth 1 1