Metabolic pathways - Reference pathway
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Reference pathway
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Category title
KEGG module
Energy metabolism
Carbon fixation
M00165
Reductive pentose phosphate cycle (Calvin cycle)
M00166
Reductive pentose phosphate cycle, ribulose-5P => glyceraldehyde-3P
M00167
Reductive pentose phosphate cycle, glyceraldehyde-3P => ribulose-5P
M00168
CAM (Crassulacean acid metabolism), dark
M00169
CAM (Crassulacean acid metabolism), light
M00172
C4-dicarboxylic acid cycle, NADP - malic enzyme type
M00171
C4-dicarboxylic acid cycle, NAD - malic enzyme type
M00170
C4-dicarboxylic acid cycle, phosphoenolpyruvate carboxykinase type
M00173
Reductive citrate cycle (Arnon-Buchanan cycle)
M00579
Phosphate acetyltransferase-acetate kinase pathway, acetyl-CoA => acetate
Nitrogen metabolism
M00175
Nitrogen fixation, nitrogen => ammonia
Methane metabolism
M00567
Methanogenesis, CO2 => methane
M00174
Methane oxidation, methanotroph, methane => formaldehyde
Sulfur metabolism
M00176
Assimilatory sulfate reduction, sulfate => H2S
M00596
Dissimilatory sulfate reduction, sulfate => H2S
M00595
Thiosulfate oxidation by SOX complex, thiosulfate => sulfate
Carbohydrate and lipid metabolism
Central carbohydrate metabolism
M00001
Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate
M00002
Glycolysis, core module involving three-carbon compounds
M00003
Gluconeogenesis, oxaloacetate => fructose-6P
M00307
Pyruvate oxidation, pyruvate => acetyl-CoA
M00009
Citrate cycle (TCA cycle, Krebs cycle)
M00010
Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate
M00011
Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate
M00004
Pentose phosphate pathway (Pentose phosphate cycle)
M00006
Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P
M00007
Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P
M00580
Pentose phosphate pathway, archaea, fructose 6P => ribose 5P
M00005
PRPP biosynthesis, ribose 5P => PRPP
M00008
Entner-Doudoroff pathway, glucose-6P => glyceraldehyde-3P + pyruvate
M00308
Semi-phosphorylative Entner-Doudoroff pathway, gluconate => glycerate-3P
M00633
Semi-phosphorylative Entner-Doudoroff pathway, gluconate/galactonate => glycerate-3P
M00309
Non-phosphorylative Entner-Doudoroff pathway, gluconate/galactonate => glycerate
Other carbohydrate metabolism
M00012
Glyoxylate cycle
M00532
Photorespiration
M00013
Malonate semialdehyde pathway, propanoyl-CoA => acetyl-CoA
M00741
Propanoyl-CoA metabolism, propanoyl-CoA => succinyl-CoA
M00632
Galactose degradation, Leloir pathway, galactose => alpha-D-glucose-1P
M00552
D-galactonate degradation, De Ley-Doudoroff pathway, D-galactonate => glycerate-3P
M00014
Glucuronate pathway (uronate pathway)
M00630
D-Galacturonate degradation (fungi)
M00631
D-Galacturonate degradation (bacteria)
M00061
D-Glucuronate degradation
M00081
Pectin degradation
M00854
Glycogen biosynthesis, glucose-1P => glycogen/starch
M00855
Glycogen degradation, glycogen => glucose-6P
M00565
Trehalose biosynthesis, D-glucose 1P => trehalose
M00549
Nucleotide sugar biosynthesis, glucose => UDP-glucose
M00554
Nucleotide sugar biosynthesis, galactose => UDP-galactose
M00761
Undecaprenylphosphate alpha-L-Ara4N biosynthesis, UDP-GlcA => undecaprenyl phosphate alpha-L-Ara4N
Fatty acid metabolism
M00082
Fatty acid biosynthesis, initiation
M00083
Fatty acid biosynthesis, elongation
M00085
Fatty acid biosynthesis, elongation, mitochondria
M00415
Fatty acid biosynthesis, elongation, endoplasmic reticulum
M00113
Jasmonic acid biosynthesis
M00086
beta-Oxidation, acyl-CoA synthesis
M00087
beta-Oxidation
M00088
Ketone body biosynthesis, acetyl-CoA => acetoacetate/3-hydroxybutyrate/acetone
Lipid metabolism
M00089
Triacylglycerol biosynthesis
M00098
Acylglycerol degradation
M00090
Phosphatidylcholine (PC) biosynthesis, choline => PC
M00091
Phosphatidylcholine (PC) biosynthesis, PE => PC
M00092
Phosphatidylethanolamine (PE) biosynthesis, ethanolamine => PE
M00093
Phosphatidylethanolamine (PE) biosynthesis, PA => PS => PE
M00130
Inositol phosphate metabolism, PI=> PIP2 => Ins(1,4,5)P3 => Ins(1,3,4,5)P4
M00131
Inositol phosphate metabolism, Ins(1,3,4,5)P4 => Ins(1,3,4)P3 => myo-inositol
M00132
Inositol phosphate metabolism, Ins(1,3,4)P3 => phytate
M00094
Ceramide biosynthesis
M00066
Lactosylceramide biosynthesis
M00067
Cerebroside and sulfatide biosynthesis
M00099
Sphingosine biosynthesis
M00100
Sphingosine degradation
Lipopolysaccharide metabolism
M00060
Lipopolysaccharide biosynthesis, KDO2-lipid A
M00063
CMP-KDO biosynthesis
M00064
ADP-L-glycero-D-manno-heptose biosynthesis
M00080
Lipopolysaccharide biosynthesis, inner core => outer core => O-antigen
Glycan metabolism
M00055
N-glycan precursor biosynthesis
M00072
N-glycosylation by oligosaccharyltransferase
M00073
N-glycan precursor trimming
M00074
N-glycan biosynthesis, high-mannose type
M00075
N-glycan biosynthesis, complex type
M00056
O-glycan biosynthesis, mucin type core
M00070
Glycosphingolipid biosynthesis, lacto-series, LacCer => Lc4Cer
M00071
Glycosphingolipid biosynthesis, neolacto-series, LacCer => nLc4Cer
M00068
Glycosphingolipid biosynthesis, globo-series, LacCer => Gb4Cer
M00069
Glycosphingolipid biosynthesis, ganglio series, LacCer => GT3
M00065
GPI-anchor biosynthesis, core oligosaccharide
Glycosaminoglycan metabolism
M00057
Glycosaminoglycan biosynthesis, linkage tetrasaccharide
M00058
Glycosaminoglycan biosynthesis, chondroitin sulfate backbone
M00059
Glycosaminoglycan biosynthesis, heparan sulfate backbone
M00076
Dermatan sulfate degradation
M00077
Chondroitin sulfate degradation
M00078
Heparan sulfate degradation
M00079
Keratan sulfate degradation
Terpenoid backbone biosynthesis
M00095
C5 isoprenoid biosynthesis, mevalonate pathway
M00096
C5 isoprenoid biosynthesis, non-mevalonate pathway
M00364
C10-C20 isoprenoid biosynthesis, bacteria
M00365
C10-C20 isoprenoid biosynthesis, archaea
M00366
C10-C20 isoprenoid biosynthesis, plants
M00367
C10-C20 isoprenoid biosynthesis, non-plant eukaryotes
Sterol biosynthesis
M00101
Cholesterol biosynthesis, squalene 2,3-epoxide => cholesterol
M00102
Ergocalciferol biosynthesis
M00103
Cholecalciferol biosynthesis
M00104
Bile acid biosynthesis, cholesterol => cholate/chenodeoxycholate
M00106
Conjugated bile acid biosynthesis, cholate => taurocholate/glycocholate
M00862
beta-Oxidation, peroxisome, tri/dihydroxycholestanoyl-CoA => choloyl/chenodeoxycholoyl-CoA
M00107
Steroid hormone biosynthesis, cholesterol => prognenolone => progesterone
M00108
C21-Steroid hormone biosynthesis, progesterone => corticosterone/aldosterone
M00109
C21-Steroid hormone biosynthesis, progesterone => cortisol/cortisone
M00110
C19/C18-Steroid hormone biosynthesis, pregnenolone => androstenedione => estrone
Other terpenoid biosynthesis
M00097
beta-Carotene biosynthesis, GGAP => beta-carotene
M00372
Abscisic acid biosynthesis, beta-carotene => abscisic acid
Nucleotide and amino acid metabolism
Purine metabolism
M00048
Inosine monophosphate biosynthesis, PRPP + glutamine => IMP
M00049
Adenine ribonucleotide biosynthesis, IMP => ADP,ATP
M00050
Guanine ribonucleotide biosynthesis IMP => GDP,GTP
M00546
Purine degradation, xanthine => urea
Pyrimidine metabolism
M00051
Uridine monophosphate biosynthesis, glutamine (+ PRPP) => UMP
M00052
Pyrimidine ribonucleotide biosynthesis, UMP => UDP/UTP,CDP/CTP
M00053
Pyrimidine deoxyribonuleotide biosynthesis, CDP/CTP => dCDP/dCTP,dTDP/dTTP
M00046
Pyrimidine degradation, uracil => beta-alanine, thymine => 3-aminoisobutanoate
Serine and threonine metabolism
M00020
Serine biosynthesis, glycerate-3P => serine
M00018
Threonine biosynthesis, aspartate => homoserine => threonine
M00555
Betaine biosynthesis, choline => betaine
Cysteine and methionine metabolism
M00021
Cysteine biosynthesis, serine => cysteine
M00338
Cysteine biosynthesis, homocysteine + serine => cysteine
M00609
Cysteine biosynthesis, methionine => cysteine
M00017
Methionine biosynthesis, apartate => homoserine => methionine
M00034
Methionine salvage pathway
M00035
Methionine degradation
Branched-chain amino acid metabolism
M00019
Valine/isoleucine biosynthesis, pyruvate => valine / 2-oxobutanoate => isoleucine
M00535
Isoleucine biosynthesis, pyruvate => 2-oxobutanoate
M00570
Isoleucine biosynthesis, threonine => 2-oxobutanoate => isoleucine
M00432
Leucine biosynthesis, 2-oxoisovalerate => 2-oxoisocaproate
M00036
Leucine degradation, leucine => acetoacetate + acetyl-CoA
Lysine metabolism
M00016
Lysine biosynthesis, succinyl-DAP pathway, aspartate => lysine
M00525
Lysine biosynthesis, acetyl-DAP pathway, aspartate => lysine
M00526
Lysine biosynthesis, DAP dehydrogenase pathway, aspartate => lysine
M00030
Lysine biosynthesis, AAA pathway, 2-oxoglutarate => 2-aminoadipate => lysine
M00433
Lysine biosynthesis, 2-oxoglutarate => 2-oxoadipate
M00031
Lysine biosynthesis, mediated by LysW, 2-aminoadipate => lysine
M00032
Lysine degradation, lysine => saccharopine => acetoacetyl-CoA
Arginine and proline metabolism
M00015
Proline biosynthesis, glutamate => proline
M00028
Ornithine biosynthesis, glutamate => ornithine
M00763
Ornithine biosynthesis, mediated by LysW, glutamate => ornithine
M00844
Arginine biosynthesis, ornithine => arginine
M00845
Arginine biosynthesis, glutamate => acetylcitrulline => arginine
M00029
Urea cycle
Histidine metabolism
M00026
Histidine biosynthesis, PRPP => histidine
M00045
Histidine degradation, histidine => N-formiminoglutamate => glutamate
Aromatic amino acid metabolism
M00022
Shikimate pathway, phosphoenolpyruvate + erythrose-4P => chorismate
M00023
Tryptophan biosynthesis, chorismate => tryptophan
M00024
Phenylalanine biosynthesis, chorismate => phenylalanine
M00025
Tyrosine biosynthesis, chorismate => tyrosine
M00040
Tyrosine biosynthesis, prephanate => pretyrosine => tyrosine
M00042
Catecholamine biosynthesis, tyrosine => dopamine => noradrenaline => adrenaline
M00043
Thyroid hormone biosynthesis, tyrosine => triiodothyronine/thyroxine
M00044
Tyrosine degradation, tyrosine => homogentisate
M00350
Capsaicin biosynthesis, L-Phenylalanine => Capsaicin
M00037
Melatonin biosynthesis, tryptophan => serotonin => melatonin
M00038
Tryptophan metabolism, tryptophan => kynurenine => 2-aminomuconate
Other amino acid metabolism
M00033
Ectoine biosynthesis, aspartate => ectoine
M00027
GABA (gamma-Aminobutyrate) shunt
M00047
Creatine pathway
Cofactor and vitamin biosynthesis
M00127
Thiamine biosynthesis, AIR => thiamine-P/thiamine-2P
M00125
Riboflavin biosynthesis, GTP => riboflavin/FMN/FAD
M00124
Pyridoxal biosynthesis, erythrose-4P => pyridoxal-5P
M00115
NAD biosynthesis, aspartate => NAD
M00119
Pantothenate biosynthesis, valine/L-aspartate => pantothenate
M00120
Coenzyme A biosynthesis, pantothenate => CoA
M00572
Pimeloyl-ACP biosynthesis, BioC-BioH pathway, malonyl-ACP => pimeloyl-ACP
M00123
Biotin biosynthesis, pimeloyl-ACP/CoA => biotin
M00573
Biotin biosynthesis, BioI pathway, long-chain-acyl-ACP => pimeloyl-ACP => biotin
M00577
Biotin biosynthesis, BioW pathway, pimelate => pimeloyl-CoA => biotin
M00126
Tetrahydrofolate biosynthesis, GTP => THF
M00840
Tetrahydrofolate biosynthesis, mediated by ribA and trpF, GTP => THF
M00841
Tetrahydrofolate biosynthesis, mediated by PTPS, GTP => THF
M00842
Tetrahydrobiopterin biosynthesis, GTP => BH4
M00843
L-threo-Tetrahydrobiopterin biosynthesis, GTP => L-threo-BH4
M00121
Heme biosynthesis, glutamate => heme
M00846
Siroheme biosynthesis, glutamate => siroheme
M00129
Ascorbate biosynthesis, animals, glucose-1P => ascorbate
M00114
Ascorbate biosynthesis, plants, glucose-6P => ascorbate
M00550
Ascorbate degradation, ascorbate => D-xylulose-5P
M00112
Tocopherol/tocotorienol biosynthesis
M00122
Cobalamin biosynthesis, cobinamide => cobalamin
M00117
Ubiquinone biosynthesis, prokaryotes, chorismate => ubiquinone
M00128
Ubiquinone biosynthesis, eukaryotes, 4-hydroxybenzoate => ubiquinone
M00116
Menaquinone biosynthesis, chorismate => menaquinone
M00118
Glutathione biosynthesis, glutamate => glutathione
M00140
C1-unit interconversion, prokaryotes
M00141
C1-unit interconversion, eukaryotes
Polyamine biosynthesis
M00133
Polyamine biosynthesis, arginine => agmatine => putrescine => spermidine
M00134
Polyamine biosynthesis, arginine => ornithine => putrescine
M00135
GABA biosynthesis, eukaryotes, putrescine => GABA
M00136
GABA biosynthesis, prokaryotes, putrescine => GABA
Secondary metabolism
Aromatics degradation
M00537
Xylene degradation, xylene => methylbenzoate
M00551
Benzoate degradation, benzoate => catechol / methylbenzoate => methylcatechol
M00568
Catechol ortho-cleavage, catechol => 3-oxoadipate
M00569
Catechol meta-cleavage, catechol => acetyl-CoA / 4-methylcatechol => propanoyl-CoA
M00544
Carbazole degradation, carbazole => 2-oxopent-4-enoate + anthranilate
M00418
Toluene degradation, anaerobic, toluene => benzoyl-CoA
M00541
Benzoyl-CoA degradation, benzoyl-CoA => 3-hydroxypimeloyl-CoA
M00534
Naphthalene degradation, naphthalene => salicylate
M00624
Terephthalate degradation, terephthalate => 3,4-dihydroxybenzoate
M00623
Phthalate degradation, phthalate => protocatechuate
Biosynthesis of secondary metabolites
M00039
Monolignol biosynthesis, phenylalanine / tyrosine => monolignol
M00137
Flavanone biosynthesis, phenylalanine => naringenin
M00138
Flavonoid biosynthesis, naringenin => pelargonidin
M00661
Paspaline biosynthesis, geranylgeranyl-PP + indoleglycerol phosphate => paspaline