Arabidopsis Reactome: table of contents

Find

Topic	Authors	Revised	Reviewers
(deoxy)ribose phosphate degradation (AraCyc) [Arabidopsis thaliana] - D-ribose-5-phosphate + D-xylulose-5-phosphate <=> D-sedoheptulose-7-phosphate + D-glyceraldehyde-3-phosphate - H2O + cytidine <=> NH3 + uridine - H2O + deoxycytidine <=> NH3 + deoxyuridine
1,1,1-Trichloro -2,2-bis (4-chlorophenyl) ethane (DDT) degradation (KEGG) [Arabidopsis thaliana]
1- and 2-Methylnaphthalene degradation (KEGG) [Arabidopsis thaliana]
abscisic acid biosynthesis (AraCyc) [Arabidopsis thaliana] - neoxanthin + O2 <=> xanthoxin + C25-allenic-apo-aldehyde
acrylonitrile degradation (AraCyc) [Arabidopsis thaliana] - acrylonitrile + H2O <=> acrylamide
adenosylmethionine biosynthesis (AraCyc) [Arabidopsis thaliana] - ATP + L-methionine + H2O <=> phosphate + pyrophosphate + S-adenosyl-L-methionine
aerobic respiration (AraCyc) [Arabidopsis thaliana] - O2 + 4 ferrocytochrome c <=> 2 H2O + 4 ferricytochrome c - 2 ferricytochrome c + a ubiquinol <=> 2 ferrocytochrome c + a ubiquinone - a ubiquinone + NADH <=> a ubiquinol + NAD+ - a ubiquinone + succinate <=> a ubiquinol + fumarate
Alanine and aspartate metabolism (KEGG) [Arabidopsis thaliana]
alanine biosynthesis (AraCyc) [Arabidopsis thaliana] - alpha-ketoglutarate + L-alanine <=> L-glutamate + pyruvate
alanine degradation (AraCyc) [Arabidopsis thaliana] - alpha-ketoglutarate + L-alanine <=> L-glutamate + pyruvate
aldoxime degradation (AraCyc) [Arabidopsis thaliana] - 3-cyanopyridine + H2O <=> nicotinamide
Alkaloid biosynthesis I (KEGG) [Arabidopsis thaliana]
Alkaloid biosynthesis II (KEGG) [Arabidopsis thaliana]
Aminophosphonate metabolism (KEGG) [Arabidopsis thaliana]
Aminosugars metabolism (KEGG) [Arabidopsis thaliana]
ammonia assimilation cycle (AraCyc) [Arabidopsis thaliana] - NH3 + L-glutamate + ATP <=> ADP + phosphate + L-glutamine - 2 reduced ferredoxin + alpha-ketoglutarate + L-glutamine <=> 2 oxidized ferredoxin + 2 L-glutamate
Androgen and estrogen metabolism (KEGG) [Arabidopsis thaliana]
anthocyanin biosynthesis (AraCyc) [Arabidopsis thaliana] - dihydrokaempferol + O2 <=> dihydroquercetin + H2O - pelargonidin + UDP-D-glucose <=> pelargonidin-3-glucoside + UDP - leucopelargonidin + alpha-ketoglutarate + O2 <=> pelargonidin + succinate + CO2 + 2 H2O - NADPH + dihydrokaempferol <=> leucopelargonidin + NADP+ - dihydroquercetin + NADPH <=> leucocyanidin + NADP+ - leucocyanidin + alpha-ketoglutarate + O2 <=> cyanidin + succinate + CO2 + 2 H2O
Arachidonic acid metabolism (KEGG) [Arabidopsis thaliana]
Arginine and proline metabolism (KEGG) [Arabidopsis thaliana]
arginine biosynthesis (AraCyc) [Arabidopsis thaliana] - N-acetyl-L-glutamate + ATP <=> N-acetylglutamyl-phosphate + ADP - L-glutamate + acetyl-CoA <=> N-acetyl-L-glutamate + coenzyme A - H2O + HCO3- + L-glutamine + 2 ATP + H+ <=> carbamoyl-phosphate + L-glutamate + phosphate + 2 ADP - L-ornithine + carbamoyl-phosphate <=> citrulline + phosphate
arginine biosynthesis II (acetyl cycle) (AraCyc) [Arabidopsis thaliana] - N-acetyl-L-glutamate + ATP <=> N-acetylglutamyl-phosphate + ADP - L-glutamate + acetyl-CoA <=> N-acetyl-L-glutamate + coenzyme A - H2O + HCO3- + L-glutamine + 2 ATP + H+ <=> carbamoyl-phosphate + L-glutamate + phosphate + 2 ADP - L-ornithine + carbamoyl-phosphate <=> citrulline + phosphate
arginine biosynthesis III (AraCyc) [Arabidopsis thaliana] - L-ornithine + carbamoyl-phosphate <=> citrulline + phosphate - L-glutamate + ATP + NADPH <=> ADP + L-glutamate gamma-semialdehyde + NADP+ + phosphate
arginine degradation I (AraCyc) [Arabidopsis thaliana] - L-arginine <=> CO2 + agmatine - succinate semialdehyde + NADP+ + H2O <=> NADPH + succinate - alpha-ketoglutarate + 4-aminobutyrate <=> L-glutamate + succinate semialdehyde
arginine degradation II (AraCyc) [Arabidopsis thaliana] - H2O + L-arginine <=> urea + L-ornithine - L-delta1-pyrroline-5-carboxylate + NAD(P)H + H+ <=> L-proline + NAD(P)+
Ascorbate and aldarate metabolism (KEGG) [Arabidopsis thaliana]
ascorbate biosynthesis (AraCyc) [Arabidopsis thaliana] - mannose-6-phosphate <=> D-fructose-6-phosphate - beta-D-glucose-6-phosphate <=> D-fructose-6-phosphate
ascorbate glutathione cycle (AraCyc) [Arabidopsis thaliana] - L-dehydro-ascorbate + 2 glutathione <=> glutathione disulfide + L-ascorbate - L-ascorbate + O2 <=> monodehydroascorbate + 2 H2O - glutathione disulfide + NADPH + H+ <=> 2 glutathione + NADP+ - 2 L-ascorbate + H2O2 <=> 2 monodehydroascorbate + 2 H2O
asparagine biosynthesis (AraCyc) [Arabidopsis thaliana] - oxaloacetate + L-glutamate <=> L-aspartate + alpha-ketoglutarate
asparagine degradation I (AraCyc) [Arabidopsis thaliana] - L-asparagine + H2O <=> NH3 + L-aspartate
aspartate biosynthesis and degradation (AraCyc) [Arabidopsis thaliana] - oxaloacetate + L-glutamate <=> L-aspartate + alpha-ketoglutarate
Benzoate degradation via CoA ligation (KEGG) [Arabidopsis thaliana]
Benzoate degradation via hydroxylation (KEGG) [Arabidopsis thaliana]
beta-alanine biosynthesis I (AraCyc) [Arabidopsis thaliana] - H2O + acceptor + spermidine <=> reduced acceptor + 4-amino-butyraldehyde + 1,3-diaminopropane
beta-alanine biosynthesis II (AraCyc) [Arabidopsis thaliana] - 3-hydroxypropionyl-CoA + H2O <=> 3-hydroxy-propionate + coenzyme A - acrylyl-CoA + H2O <=> 3-hydroxypropionyl-CoA - FAD + propionyl-CoA <=> FADH2 + acrylyl-CoA
beta-alanine biosynthesis III (AraCyc) [Arabidopsis thaliana]
beta-Alanine metabolism (KEGG) [Arabidopsis thaliana]
beta-D-glucuronide degradation (AraCyc) [Arabidopsis thaliana] - H2O + beta-D-glucuronide <=> glucuronate + an alcohol
Bile acid biosynthesis (KEGG) [Arabidopsis thaliana]
biosynthesis of proto- and siroheme (AraCyc) [Arabidopsis thaliana] - glutamate-1-semialdehyde <=> 5-amino-levulinate - H2O + 4 porphobilinogen <=> 4 NH3 + hydroxymethylbilane - protoheme + trans, trans-farnesyl diphosphate + H2O <=> heme O + pyrophosphate - uroporphyrinogen-III <=> 4 CO2 + coproporphyrinogen III - L-glutamyl-tRNAglt + NADPH <=> glutamate-1-semialdehyde + NADP+ + tRNAglt - NAD(P)+ + coproporphyrinogen III <=> protoporphyrinogen + NAD(P)H + 2 CO2 - tRNAglt + L-glutamate + ATP <=> L-glutamyl-tRNAglt + pyrophosphate + AMP - 1.5 O2 + protoporphyrinogen <=> 3 H2O + protoporphyrin IX - uroporphyrinogen-III + 2 S-adenosyl-L-methionine <=> 2 S-adenosyl-homocysteine + dihydrosirohydrochlorin - 2 5-amino-levulinate <=> 2 H2O + porphobilinogen - coproporphyrinogen III + 2 O2 <=> protoporphyrinogen + 2 CO2 + 2 H2O2 - Fe2+ + protoporphyrin IX <=> 2 H+ + protoheme
Biosynthesis of steroids (KEGG) [Arabidopsis thaliana]
biotin biosynthesis II (AraCyc) [Arabidopsis thaliana] - S-adenosyl-L-methionine + 8-amino-7-oxononanoate <=> S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate - L-alanine + 6-carboxyhexanoyl-CoA <=> CO2 + coenzyme A + 8-amino-7-oxononanoate
Biotin metabolism (KEGG) [Arabidopsis thaliana]
Blood group glycolipid biosynthesis-lactoseries (KEGG) [Arabidopsis thaliana]
brassinosteroid biosynthesis I (AraCyc) [Arabidopsis thaliana] - 6-deoxocathasterone + O2 <=> 6-deoxoteasterone + H2O - campest-4-en-3-one + NADPH <=> 5alpha-campestan-3-one + NADP+ - cathasterone + O2 + reduced acceptor <=> teasterone + H2O + acceptor - campestanol + O2 + reduced acceptor <=> (6alpha)-hydroxycampestanol + H2O + acceptor - 6-oxocampestanol + O2 + reduced acceptor <=> cathasterone + H2O + acceptor - typhasterol + O2 + reduced acceptor <=> castasterone + H2O + acceptor
brassinosteroid biosynthesis II (AraCyc) [Arabidopsis thaliana] - 6-deoxocathasterone + O2 <=> 6-deoxoteasterone + H2O - campest-4-en-3-one + NADPH <=> 5alpha-campestan-3-one + NADP+ - 22alpha-hydroxy-campest-4-en-3-one + NADPH <=> 22alpha-hydroxy-5alpha-campestan-3-one + NADP+ - campesterol + O2 + reduced acceptor <=> (22alpha)-hydroxy-campesterol + H2O + acceptor
brassinosteroid biosynthesis III (AraCyc) [Arabidopsis thaliana] - campest-4-en-3-one + NADPH <=> 5alpha-campestan-3-one + NADP+
Butanoate metabolism (KEGG) [Arabidopsis thaliana]
C21-Steroid hormone metabolism (KEGG) [Arabidopsis thaliana]
Calvin cycle (AraCyc) [Arabidopsis thaliana] - D-erythrose-4-phosphate + D-xylulose-5-phosphate <=> D-fructose-6-phosphate + D-glyceraldehyde-3-phosphate - H2O + CO2 + D-ribulose-1,5-bisphosphate <=> 2 3-phosphoglycerate - fructose-1,6-bisphosphate + H2O <=> D-fructose-6-phosphate + phosphate - D-ribulose-5-phosphate <=> D-xylulose-5-phosphate - D-ribulose-5-phosphate + ATP <=> D-ribulose-1,5-bisphosphate + ADP - D-ribose-5-phosphate <=> D-ribulose-5-phosphate - fructose-1,6-bisphosphate <=> dihydroxy-acetone-phosphate + D-glyceraldehyde-3-phosphate - D-ribose-5-phosphate + D-xylulose-5-phosphate <=> D-sedoheptulose-7-phosphate + D-glyceraldehyde-3-phosphate - D-glyceraldehyde-3-phosphate <=> dihydroxy-acetone-phosphate - 3-phosphoglycerate + ATP <=> 1,3-diphosphateglycerate + ADP
camalexin biosynthesis (AraCyc) [Arabidopsis thaliana]
Caprolactam degradation (KEGG) [Arabidopsis thaliana]
Carbon fixation (KEGG) [Arabidopsis thaliana]
carbon monoxide dehydrogenase pathway (AraCyc) [Arabidopsis thaliana] - NADPH + CO2 <=> NADP+ + formate - 5-methyl-THF + [Co-E] <=> tetrahydrofolate + [Co-E-CH3] - reduced acceptor + CO2 <=> acceptor + H2O + CO
carnitine degradation (AraCyc) [Arabidopsis thaliana] - coenzyme A + L-carnitine <=> L-carnitinyl-CoA + H2O - D-carnitinyl-CoA <=> L-carnitinyl-CoA - reduced acceptor + crotonobetainyl-CoA <=> acceptor + gamma-butyrobetainyl-CoA
carotenoid biosynthesis (AraCyc) [Arabidopsis thaliana] - beta-carotene + 2 H2O <=> zeaxanthin
Cell Cycle Checkpoints [Arabidopsis thaliana] - G2/M checkpoint - Mitotic Spindle checkpoint	Higgins, JA	2008-01-22 NEW	Doonan, JH
Cell Cycle, Mitotic [Arabidopsis thaliana] - G1/G0 Transition - G0/G1 Transition - G1 Phase - G1/S Transition - S Phase - G2 Phase - G2/M Transition - M Phase - Cytokinesis - M/G1 Transition	Tsesmetzis, N, Higgins JA, , Higgins, JA		Doonan, JH
cellulose biosynthesis (AraCyc) [Arabidopsis thaliana] - (1-4-beta-D-glucan)(m+n) + H2O <=> (1-4-beta-D-glucan)(m) + (1-4-beta-D-glucan)(n) - UDP-D-glucose + (1,4-beta-D-glucosyl)(n) <=> UDP + (1,4-beta-D-glucosyl)(n+1)
chlorophyll a biosynthesis I (AraCyc) [Arabidopsis thaliana]
chlorophyll a biosynthesis II (AraCyc) [Arabidopsis thaliana] - chlorophyllide a + geranylgeranyl-PP <=> geranylgeranyl-chlorophyll a + pyrophosphate
chlorophyll cycle (AraCyc) [Arabidopsis thaliana] - chlorophyllide b + phytyl pyrophosphate <=> chlorophyll b + pyrophosphate
chlorophyllide a biosynthesis (AraCyc) [Arabidopsis thaliana] - monovinyl protochlorophyllide a + NADPH <=> NADP+ + chlorophyllide a - glutamate-1-semialdehyde <=> 5-amino-levulinate - H2O + 4 porphobilinogen <=> 4 NH3 + hydroxymethylbilane - uroporphyrinogen-III <=> 4 CO2 + coproporphyrinogen III - L-glutamyl-tRNAglt + NADPH <=> glutamate-1-semialdehyde + NADP+ + tRNAglt - 1.5 O2 + protoporphyrinogen <=> 3 H2O + protoporphyrin IX - tRNAglt + L-glutamate + ATP <=> L-glutamyl-tRNAglt + pyrophosphate + AMP - 2 5-amino-levulinate <=> 2 H2O + porphobilinogen - coproporphyrinogen III + 2 O2 <=> protoporphyrinogen + 2 CO2 + 2 H2O2 - ATP + protoporphyrin IX + Mg2+ + H2O <=> Mg-protoporphyrin + H+ + phosphate + ADP
choline biosynthesis I (AraCyc) [Arabidopsis thaliana] - N-methylethanolamine phosphate + S-adenosyl-L-methionine <=> N-dimethylethanolamine phosphate + S-adenosyl-homocysteine - phosphoryl-ethanolamine + S-adenosyl-L-methionine <=> S-adenosyl-homocysteine + N-methylethanolamine phosphate - N-dimethylethanolamine phosphate + S-adenosyl-L-methionine <=> phosphoryl-choline + S-adenosyl-homocysteine
choline biosynthesis II (AraCyc) [Arabidopsis thaliana]
choline biosynthesis III (AraCyc) [Arabidopsis thaliana] - 1,2-diacylglycerol + CDP-choline <=> a phosphatidylcholine + CMP - phosphoryl-choline + CTP <=> CDP-choline + pyrophosphate - a phosphatidylcholine + H2O <=> L-phosphatidate + choline
chorismate biosynthesis (AraCyc) [Arabidopsis thaliana] - shikimate + ATP <=> shikimate-3-phosphate + ADP - shikimate-3-phosphate + phosphoenolpyruvate <=> 5-enolpyruvyl-shikimate-3-phosphate + phosphate
Circadian Cycle [Arabidopsis thaliana] - Entrainment of the Clock by Light - Entrainment of Clock by Temperature - Circadian oscillator	Higgins, JA, Laurie, DA		Millar, AJ
cis-zeatin biosynthesis (AraCyc) [Arabidopsis thaliana] - a tRNA + dimethylallyl-pyrophosphate <=> prenyl-tRNA + pyrophosphate
Citrate cycle (TCA cycle) (KEGG) [Arabidopsis thaliana]
citrulline degradation (AraCyc) [Arabidopsis thaliana] - L-ornithine + carbamoyl-phosphate <=> citrulline + phosphate
coenzyme A biosynthesis (AraCyc) [Arabidopsis thaliana] - pantothenate + ATP <=> D-4'-phosphopantothenate + ADP
colanic acid building blocks biosynthesis (AraCyc) [Arabidopsis thaliana] - UDP-D-glucose <=> UDP-galactose - GDP-mannose <=> H2O + GDP-4-dehydro-6-deoxy-D-mannose - H2O + 2 NAD+ + UDP-D-glucose <=> 2 NADH + UDP-D-glucuronate - GDP-4-dehydro-6-deoxy-D-mannose <=> GDP-4-dehydro-6-L-deoxygalactose - alpha-D-galactose + ATP <=> alpha-D-galactose-1-phosphate + ADP - GDP-4-dehydro-6-L-deoxygalactose + NADPH <=> guanosine diphosphate fucose + NADP+ - mannose-6-phosphate <=> D-fructose-6-phosphate - alpha-D-glucose-1-phosphate + UTP <=> UDP-D-glucose + pyrophosphate
coniferin metabolism (AraCyc) [Arabidopsis thaliana] - coniferyl alcohol + UDP-D-glucose <=> coniferin + UDP
cutin biosynthesis (AraCyc) [Arabidopsis thaliana] - palmitate + NADPH + O2 <=> 16-hydroxypalmitate + NADP+ + H2O - oleate + 2 NADPH + O2 <=> 18-hydroxyoleate + 2 NADP+ + H2O
cyanate degradation (AraCyc) [Arabidopsis thaliana] - H2O + CO2 <=> H2CO3
Cyanoamino acid metabolism (KEGG) [Arabidopsis thaliana]
cyclopropane and cyclopropene fatty acid biosynthesis (AraCyc) [Arabidopsis thaliana]
cysteine biosynthesis (AraCyc) [Arabidopsis thaliana] - O-acetyl-L-serine + H2S <=> L-cysteine + acetate - L-serine + acetyl-CoA <=> O-acetyl-L-serine + coenzyme A
Cysteine metabolism (KEGG) [Arabidopsis thaliana]
cytokinins 7-N-glucoside biosynthesis (AraCyc) [Arabidopsis thaliana] - trans-zeatin + UDP-D-glucose <=> trans-zeatin-7-N-glucoside + UDP - isopentenyladenine + UDP-D-glucose <=> isopentenyladenine-7-N-glucoside + UDP - trans-zeatin-O-glucoside + UDP-D-glucose <=> trans-zeatin-O-glucoside-7-N-glucoside + UDP - cis-zeatin + UDP-D-glucose <=> cis-zeatin-7-N-glucoside + UDP - dihydrozeatin + UDP-D-glucose <=> dihydrozeatin-7-N-dihydrozeatin + UDP - kinetin + UDP-D-glucose <=> kinetin-7-N-glucoside + UDP - benzyladenine + UDP-D-glucose <=> benzyladenine-7-N-glucoside + UDP
cytokinins 9-N-glucoside biosynthesis (AraCyc) [Arabidopsis thaliana] - cis-zeatin + UDP-D-glucose <=> cis-zeatin-9-N-glucoside + UDP - dihydrozeatin + UDP-D-glucose <=> dihydrozeatin-9-N-glucoside + UDP - trans-zeatin + UDP-D-glucose <=> trans-zeatin-9-N-glucoside + UDP - benzyladenine + UDP-D-glucose <=> benzyladenine-9-N-glucoside + UDP - isopentenyladenine + UDP-D-glucose <=> isopentenyladenine-9-N-glucoside + UDP - kinetin + UDP-D-glucose <=> kinetin-9-N-glucoside + UDP
cytokinins degradation (AraCyc) [Arabidopsis thaliana] - isopentenyl adenosine + H2O + FAD <=> adenosine + 3-methyl-2-butenal + FADH2 - trans-zeatin + H2O + FAD <=> adenine + 3-methyl-4-trans-hydroxy-2-butenal + FADH2 - isopentenyladenine + FAD + H2O <=> 3-methyl-2-butenal + adenine + FADH2 - trans-zeatin riboside + H2O + FAD <=> adenosine + 3-methyl-4-trans-hydroxy-2-butenal + FADH2 - cis-zeatin + H2O + FAD <=> 3-methyl-4-cis-hydroxy-2-butenal + adenine + FADH2
cytokinins-O-glucoside biosynthesis (AraCyc) [Arabidopsis thaliana] - cis-zeatin + UDP-D-glucose <=> cis-zeatin-O-glucoside + UDP - dihydrozeatin-9-N-glucoside + UDP-D-glucose <=> dihydrozeatin-9-N-glucoside-O-glucoside + UDP - trans-zeatin + UDP-D-glucose <=> trans-zeatin-O-glucoside + UDP - dihydrozeatin + UDP-D-glucose <=> dihydrozeatin-O-glucoside + UDP
de novo biosynthesis of purine nucleotides I (AraCyc) [Arabidopsis thaliana] - ATP + phosphoribosyl-carboxy-aminoimidazole + L-aspartate <=> ADP + phosphate + 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole - GDP + ATP <=> GTP + ADP - xanthosine-5-phosphate + H2O + L-glutamine + ATP <=> L-glutamate + GMP + pyrophosphate + AMP - AMP + ATP <=> ADP + ADP - Reduced Thioredoxin + GDP <=> Oxidized Thioredoxin + dGDP + H2O - dADP + ATP <=> dATP + ADP - N10-formyl-THF + 5-phospho-ribosyl-glycineamide <=> tetrahydrofolate + 5'-phosphoribosyl-N-formylglycineamide - GMP + ATP <=> GDP + ADP - dGDP + ATP <=> dGTP + ADP - adenylo-succinate <=> fumarate + AMP - L-glutamine + PRPP + H2O <=> 5-phospho-beta-D-ribosyl-amine + pyrophosphate + L-glutamate - H2O + NAD+ + IMP <=> xanthosine-5-phosphate + NADH - 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole <=> fumarate + AICAR - Reduced Thioredoxin + ADP <=> Oxidized Thioredoxin + dADP + H2O - L-aspartate + IMP + GTP <=> adenylo-succinate + phosphate + GDP
de novo biosynthesis of purine nucleotides II (AraCyc) [Arabidopsis thaliana] - ATP + phosphoribosyl-carboxy-aminoimidazole + L-aspartate <=> ADP + phosphate + 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole - L-glutamine + PRPP + H2O <=> 5-phospho-beta-D-ribosyl-amine + pyrophosphate + L-glutamate - adenylo-succinate <=> fumarate + AMP - xanthosine-5-phosphate + H2O + L-glutamine + ATP <=> L-glutamate + GMP + pyrophosphate + AMP - 5-aminoimidazole ribonucleotide + ATP + CO2 + H2O <=> phosphate + phosphoribosyl-carboxy-aminoimidazole + ADP - H2O + NAD+ + IMP <=> xanthosine-5-phosphate + NADH - 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole <=> fumarate + AICAR - L-aspartate + IMP + GTP <=> adenylo-succinate + phosphate + GDP - N10-formyl-THF + 5-phospho-ribosyl-glycineamide <=> tetrahydrofolate + 5'-phosphoribosyl-N-formylglycineamide
de novo biosynthesis of pyrimidine deoxyribonucleotides (AraCyc) [Arabidopsis thaliana] - Reduced Thioredoxin + UDP <=> Oxidized Thioredoxin + dUDP + H2O - dCDP + ATP <=> dCTP + ADP - dUDP + ATP <=> dUTP + ADP - dTDP + ATP <=> dTTP + ADP - dTMP + ATP <=> dTDP + ADP - 5,10-methylene-THF + dUMP <=> dTMP + 7,8-dihydrofolate - Reduced Thioredoxin + CDP <=> Oxidized Thioredoxin + dCDP + H2O
de novo biosynthesis of pyrimidine ribonucleotides (AraCyc) [Arabidopsis thaliana] - ATP + UMP <=> ADP + UDP - PRPP + orotate <=> orotidine-5'-phosphate + pyrophosphate - CTP + ADP <=> CDP + ATP - orotidine-5'-phosphate <=> CO2 + UMP - O2 + dihydroorotate <=> H2O2 + orotate - UDP + ATP <=> UTP + ADP - H2O + HCO3- + L-glutamine + 2 ATP + H+ <=> carbamoyl-phosphate + L-glutamate + phosphate + 2 ADP - L-glutamine + H2O + UTP + ATP <=> CTP + phosphate + ADP + L-glutamate
Diterpenoid biosynthesis (KEGG) [Arabidopsis thaliana]
DNA Replication [Arabidopsis thaliana] - Synthesis of DNA	Tsesmetzis, N, Higgins JA, , Higgins, JA		Doonan, JH
dolichyl-diphosphooligosaccharide biosynthesis (AraCyc) [Arabidopsis thaliana] - (mannosyl)6-(N-acetylglucosaminyl)2-diphosphodolichol + dolichyl beta-D-mannosyl phosphate <=> (mannosyl)7-(N-acetylglucosaminyl)2-diphosphodolichol + dolichyl-phosphate - (mannosyl)2-(N-acetylglucosaminyl)2-diphosphodolichol + GDP-mannose <=> (mannosyl)3-(N-acetylglucosaminyl)2-diphosphodolichol + GDP - dolichyl-phosphate + UDP-N-acetyl-D-glucosamine <=> N-acetylglucosaminyl-diphosphodolichol + UMP
dTDP-L-rhamnose biosynthesis (AraCyc) [Arabidopsis thaliana] - dTDP-D-glucose <=> H2O + dTDP-4-dehydro-6-deoxy-D-glucose
Endoreduplication and Alternative cell cycles [Arabidopsis thaliana] - Endoreduplication - Coenocytic / Syncytial cell cycle - Meiosis	Higgins, JA, Tsesmetzis, N, Higgins JA,	2008-01-22 NEW	Doonan, JH
ent-kaurene biosynthesis (AraCyc) [Arabidopsis thaliana] - delta3-isopentenyl-PP + trans, trans-farnesyl diphosphate <=> geranylgeranyl-PP + pyrophosphate
epicuticular wax biosynthesis (AraCyc) [Arabidopsis thaliana] - fatty-acyl-CoA + malonyl-CoA <=> very-long-chain-fatty-acyl-CoA + CO2
Ethylbenzene degradation (KEGG) [Arabidopsis thaliana]
ethylene biosynthesis from methionine (AraCyc) [Arabidopsis thaliana] - ATP + L-methionine + H2O <=> phosphate + pyrophosphate + S-adenosyl-L-methionine - S-adenosyl-L-methionine <=> 5'-methylthioadenosine + 1-aminocyclopropane-1-carboxylate
fatty acid alpha-oxidation (AraCyc) [Arabidopsis thaliana]
fatty acid beta-oxidation (AraCyc) [Arabidopsis thaliana] - H2O + trans-delta2-enoyl-CoA <=> L-3-hydroxyacyl-CoA - coenzyme A + a fatty acid + ATP <=> acyl-CoA + pyrophosphate + AMP - coenzyme A + beta-ketoacyl-CoA <=> acyl-CoA + acetyl-CoA - acyl-CoA + FAD <=> FADH2 + delta2-enoyl-CoA
Fatty acid biosynthesis (KEGG) [Arabidopsis thaliana]
fatty acid biosynthesis - initial steps (AraCyc) [Arabidopsis thaliana] - HCO3- + H+ + acetyl-CoA + ATP <=> malonyl-CoA + phosphate + ADP
fatty acid elongation -- saturated (AraCyc) [Arabidopsis thaliana] - acyl-ACP + malonyl-ACP <=> acyl carrier protein + beta-ketoacyl-ACP + CO2
Fatty acid metabolism (KEGG) [Arabidopsis thaliana]
fatty acid omega-oxidation (AraCyc) [Arabidopsis thaliana] - a fatty alcohol + O2 <=> a fatty aldehyde + H2O2 - a omega-hydroxy fatty acid + O2 <=> a omega-oxo fatty acid + H2O2
flavonoid biosynthesis (AraCyc) [Arabidopsis thaliana] - naringenin chalcone <=> naringenin - coenzyme A + 4-coumarate + ATP <=> coumaroyl-CoA + pyrophosphate + AMP - naringenin + O2 + alpha-ketoglutarate <=> CO2 + succinate + dihydrokaempferol - coumaroyl-CoA + 3 malonyl-CoA <=> naringenin chalcone + 3 CO2 + 4 coenzyme A
Flavonoid biosynthesis (KEGG) [Arabidopsis thaliana]
flavonol biosynthesis (AraCyc) [Arabidopsis thaliana] - dihydrokaempferol + O2 <=> dihydroquercetin + H2O - dihydrokaempferol + alpha-ketoglutarate + O2 <=> kaempferol + succinate + CO2 + H2O - dihydroquercetin + alpha-ketoglutarate + O2 <=> quercetin + succinate + CO2 + H2O - quercetin + UDP-D-glucose <=> quercetin-3-glucoside + UDP - kaempferol + UDP-D-glucose <=> kaempferol-3-glucoside + UDP
Flowering Time [Arabidopsis thaliana] - Photoperiod pathway - Autonomous Pathway repression of FLC - Vernalization Pathway silencing of FLC - FLC Upregulation to Repress Flowering - Gibberellin Pathway - Modulation of brassinosteroid-regulated gene expression by ELF6 and REF6 - Flowering switch regulator - Flowering Switch	Higgins, JA, Laurie, DA		Laurie, DA, Wigge, PA, Millar, AJ
Fluorene degradation (KEGG) [Arabidopsis thaliana]
Folate biosynthesis (KEGG) [Arabidopsis thaliana]
formylTHF biosynthesis (AraCyc) [Arabidopsis thaliana] - 5,10-methylene-THF + glycine + H2O <=> L-serine + tetrahydrofolate - 5,10-methylene-THF + dUMP <=> dTMP + 7,8-dihydrofolate - 5,10-methylene-THF + NAD(P)H + H+ <=> 5-methyl-THF + NAD(P)+ - H2O + N10-formyl-THF <=> tetrahydrofolate + formate - 10-formyl-H4PteGlun + L-glutamate + ATP <=> 10-formyl-H4PteGlu(n+1) + ADP + phosphate - glycine + tetrahydrofolate + NAD+ <=> NH3 + 5,10-methylene-THF + CO2 + NADH - NADPH + 7,8-dihydrofolate <=> NADP+ + tetrahydrofolate
formylTHF biosynthesis I (AraCyc) [Arabidopsis thaliana] - L-glutamate + H4PteGlu(n) + ATP <=> H4PteGlu(n+1) + phosphate + ADP - 5,10-methylene-THF + glycine + H2O <=> L-serine + tetrahydrofolate - 5,10-methylene-THF + dUMP <=> dTMP + 7,8-dihydrofolate - 5,10-methylene-THF + NAD(P)H + H+ <=> 5-methyl-THF + NAD(P)+ - 5-methyl-THF + homocysteine <=> tetrahydrofolate + L-methionine - 10-formyl-H4PteGlun + L-glutamate + ATP <=> 10-formyl-H4PteGlu(n+1) + ADP + phosphate - glycine + tetrahydrofolate + NAD+ <=> NH3 + 5,10-methylene-THF + CO2 + NADH - NADPH + 7,8-dihydrofolate <=> NADP+ + tetrahydrofolate
Fructose and mannose metabolism (KEGG) [Arabidopsis thaliana]
GA12 biosynthesis (AraCyc) [Arabidopsis thaliana] - GA12-aldehyde + NADPH + O2 <=> GA12 + NADP+ + H2O - ent-kaurenoate + O2 + NADPH <=> ent-7-alpha-hydroxykaurenoate + H2O + NADP+ - ent-7-alpha-hydroxykaurenoate + NADPH + H+ + O2 <=> GA12-aldehyde + NADP+ + 2 H2O
galactose degradation I (AraCyc) [Arabidopsis thaliana] - UDP-D-glucose <=> UDP-galactose - fructose + UDP-D-glucose <=> sucrose + UDP - H2O + 2 NAD+ + UDP-D-glucose <=> 2 NADH + UDP-D-glucuronate - alpha-D-galactose + ATP <=> alpha-D-galactose-1-phosphate + ADP - alpha-D-glucose-1-phosphate + UTP <=> UDP-D-glucose + pyrophosphate
galactose degradation II (AraCyc) [Arabidopsis thaliana] - UDP-D-glucose <=> UDP-galactose - beta-D-galactose <=> alpha-D-galactose - alpha-D-galactose + ATP <=> alpha-D-galactose-1-phosphate + ADP - alpha-D-glucose-1-phosphate + UTP <=> UDP-D-glucose + pyrophosphate
Galactose metabolism (KEGG) [Arabidopsis thaliana]
gamma-Hexachlorocyclohexane degradation (KEGG) [Arabidopsis thaliana]
Ganglioside biosynthesis (KEGG) [Arabidopsis thaliana]
GDP-D-rhamnose biosynthesis (AraCyc) [Arabidopsis thaliana] - GDP-mannose <=> H2O + GDP-4-dehydro-6-deoxy-D-mannose - mannose-6-phosphate <=> D-fructose-6-phosphate
GDP-L-fucose biosynthesis I (from GDP-D-mannose) (AraCyc) [Arabidopsis thaliana] - GDP-mannose <=> H2O + GDP-4-dehydro-6-deoxy-D-mannose
GDP-L-fucose biosynthesis II (from L-fucose) (AraCyc) [Arabidopsis thaliana]
gibberellin biosynthesis I (non C-3, non C-13 hydroxylation) (AraCyc) [Arabidopsis thaliana] - GA25 + alpha-ketoglutarate + O2 <=> GA13 + succinate + CO2 - GA24 + alpha-ketoglutarate + O2 <=> GA9 + succinate + 2 CO2 - GA24 + alpha-ketoglutarate + O2 <=> GA36 + succinate + CO2 - GA15 + O2 + alpha-ketoglutarate <=> GA24 + H2O + CO2 + succinate - GA24 + alpha-ketoglutarate + O2 <=> GA25 + succinate + CO2 - GA12 + alpha-ketoglutarate + O2 <=> GA15 + succinate + CO2 - GA9 + alpha-ketoglutarate + O2 <=> GA4 + succinate + CO2
gibberellin biosynthesis II (early C-3 hydroxylation) (AraCyc) [Arabidopsis thaliana] - GA14 + O2 + alpha-ketoglutarate <=> GA37 + CO2 + succinate - GA37 + alpha-ketoglutarate + O2 <=> GA36 + succinate + CO2 + H2O - GA36 + O2 + alpha-ketoglutarate <=> GA4 + succinate + 2 CO2 - GA12 + alpha-ketoglutarate + O2 <=> GA14 + succinate + CO2 - GA15 + alpha-ketoglutarate + O2 <=> GA37 + succinate + CO2
gibberellin biosynthesis III (early C-13 hydroxylation) (AraCyc) [Arabidopsis thaliana] - GA19 + alpha-ketoglutarate + O2 <=> GA17 + succinate + CO2 - GA20 + alpha-ketoglutarate + O2 <=> GA1 + succinate + CO2 - GA44 + alpha-ketoglutarate + O2 <=> GA38 + succinate + CO2 - GA53 + alpha-ketoglutarate + O2 <=> GA44 + CO2 + succinate - GA44 + alpha-ketoglutarate + O2 <=> GA19 + succinate + CO2 - GA19 + alpha-ketoglutarate + O2 <=> GA20 + succinate + 2 CO2
gibberellin inactivation (AraCyc) [Arabidopsis thaliana] - GA51 + alpha-ketoglutarate + O2 <=> GA51-catabolite + succinate + CO2 + H2O - GA29 + alpha-ketoglutarate + O2 <=> GA29-catabolite + succinate + CO2 + H2O - GA9 + alpha-ketoglutarate + O2 <=> GA51 + succinate + CO2 - GA1 + alpha-ketoglutarate + O2 <=> GA8 + succinate + CO2 - GA4 + alpha-ketoglutarate + O2 <=> GA34 + succinate + CO2 - GA12 + alpha-ketoglutarate + O2 <=> GA110 + succinate + CO2 - GA8 + alpha-ketoglutarate + O2 <=> GA8-catabolite + succinate + CO2 + H2O - GA20 + alpha-ketoglutarate + O2 <=> GA29 + succinate + CO2 - GA34 + alpha-ketoglutarate + O2 <=> GA34-catabolite + succinate + CO2 + H2O - GA53 + alpha-ketoglutarate + O2 <=> GA97 + succinate + CO2 - GA44 + alpha-ketoglutarate + O2 <=> GA98 + succinate + CO2
Globoside metabolism (KEGG) [Arabidopsis thaliana]
gluconeogenesis (AraCyc) [Arabidopsis thaliana] - H2O + pyruvate + ATP <=> phosphate + phosphoenolpyruvate + AMP - fructose-1,6-bisphosphate + H2O <=> D-fructose-6-phosphate + phosphate - 3-phosphoglycerate <=> 2-phosphoglycerate - D-glyceraldehyde-3-phosphate + phosphate + NAD+ <=> 1,3-diphosphateglycerate + NADH - phosphate + oxaloacetate <=> phosphoenolpyruvate + H2O + CO2 - oxaloacetate + ATP <=> CO2 + phosphoenolpyruvate + ADP - 2-phosphoglycerate <=> phosphoenolpyruvate + H2O - 3-phosphoglycerate + ATP <=> 1,3-diphosphateglycerate + ADP - malate + NAD+ <=> oxaloacetate + NADH - beta-D-glucose-6-phosphate <=> D-fructose-6-phosphate - fructose-1,6-bisphosphate <=> dihydroxy-acetone-phosphate + D-glyceraldehyde-3-phosphate
glucosinolate biosynthesis from homomethionine (AraCyc) [Arabidopsis thaliana] - 3-methylthiopropyl-desulfoglucosinolate + PAPS <=> 3-methylthiopropyl-glucosinolate + adenosine 3',5'-bisphosphate - homomethionine + NADPH + O2 <=> 4-methylthiobutanaldoxime + NADP+ + H2O + CO2 - 4-methylthiobutylhydroximate + UDP-D-glucose <=> 3-methylthiopropyl-desulfoglucosinolate + UDP
glucosinolate biosynthesis from phenylalanine (AraCyc) [Arabidopsis thaliana] - phenylacetothiohydroximate + UDP-D-glucose <=> benzyl-desulfoglucosinolate + UDP - L-phenylalanine + NADPH + O2 <=> phenylacetaldoxime + NADP+ + H2O + CO2 - phenylacetaldoxime + NADPH + O2 + L-cysteine <=> phenylacetothiohydroximate + NADP+ + H2O + pyruvate + NH3 - benzyl-desulfoglucosinolate + PAPS <=> benzyl-glucosinolate + adenosine 3',5'-bisphosphate
glucosinolate biosynthesis from tryptophan (AraCyc) [Arabidopsis thaliana] - indolylmethyl-desulfoglucosinolate + PAPS <=> indolylmethyl-glucosinolate + adenosine 3',5'-bisphosphate - indolylmethylthiohydroximate + UDP-D-glucose <=> indolylmethyl-desulfoglucosinolate + UDP - L-tryptophan + NADPH + O2 <=> indole-3-acetaldoxime + CO2 + NADP+ + H2O
glutamate biosynthesis I (AraCyc) [Arabidopsis thaliana] - 2 reduced ferredoxin + alpha-ketoglutarate + L-glutamine <=> 2 oxidized ferredoxin + 2 L-glutamate
glutamate biosynthesis II (AraCyc) [Arabidopsis thaliana]
glutamate degradation I (AraCyc) [Arabidopsis thaliana] - H2O + NAD+ + L-glutamate <=> NH3 + NADH + alpha-ketoglutarate
glutamate degradation II (AraCyc) [Arabidopsis thaliana] - 4-aminobutyrate + pyruvate <=> succinate semialdehyde + L-alanine - L-glutamate <=> CO2 + 4-aminobutyrate - succinate semialdehyde + NAD(P)H <=> 4-hydroxybutyrate + NAD(P)+ - alpha-ketoglutarate + 4-aminobutyrate <=> L-glutamate + succinate semialdehyde
Glutamate metabolism (KEGG) [Arabidopsis thaliana]
glutamine biosynthesis (AraCyc) [Arabidopsis thaliana] - NH3 + L-glutamate + ATP <=> ADP + phosphate + L-glutamine
glutathione biosynthesis (AraCyc) [Arabidopsis thaliana]
Glutathione metabolism (KEGG) [Arabidopsis thaliana]
glyceraldehyde 3-phosphate degradation (AraCyc) [Arabidopsis thaliana] - H2O + pyruvate + ATP <=> phosphate + phosphoenolpyruvate + AMP - 3-phosphoglycerate <=> 2-phosphoglycerate - D-glyceraldehyde-3-phosphate + phosphate + NAD+ <=> 1,3-diphosphateglycerate + NADH - 2-phosphoglycerate <=> phosphoenolpyruvate + H2O - 3-phosphoglycerate + ATP <=> 1,3-diphosphateglycerate + ADP
glycerol degradation (AraCyc) [Arabidopsis thaliana] - glycerol + ATP <=> glycerol-3-phosphate + ADP
Glycerolipid metabolism (KEGG) [Arabidopsis thaliana]
Glycerophospholipid metabolism (KEGG) [Arabidopsis thaliana]
glycine biosynthesis (AraCyc) [Arabidopsis thaliana] - 3-phospho-serine + H2O <=> L-serine + phosphate - 5,10-methylene-THF + glycine + H2O <=> L-serine + tetrahydrofolate
glycine degradation (AraCyc) [Arabidopsis thaliana] - S-aminomethyldihydrolipoyl-GcvH-protein + tetrahydrofolate <=> NH3 + dihydrolipoyl-GcvH-protein + 5,10-methylene-THF - H-protein-(lipoyl)lysine + glycine <=> CO2 + S-aminomethyldihydrolipoyl-GcvH-protein
Glycine, serine and threonine metabolism (KEGG) [Arabidopsis thaliana]
glycolipid biosynthesis (AraCyc) [Arabidopsis thaliana] - 1,2-diacylglycerol + UDP-galactose <=> mono-beta-D-galactosyldiacylglycerol + UDP
glycolipid desaturation pathway (AraCyc) [Arabidopsis thaliana] - 1-18:2-2-16:2-monogalactosyldiacylglycerol <=> 1-18:3-2-16:3-monogalactosyldiacylglycerol - 1-18:1-2-16:0-monogalactosyldiacylglycerol <=> 1-18:1-2-16:1-monogalactosyldiacylglycerol - 1-18:1-2-16:1-monogalactosyldiacylglycerol <=> 1-18:2-2-16:2-monogalactosyldiacylglycerol
Glycolysis / Gluconeogenesis (KEGG) [Arabidopsis thaliana]
glycolysis I (AraCyc) [Arabidopsis thaliana] - 3-phosphoglycerate <=> 2-phosphoglycerate - D-glyceraldehyde-3-phosphate + phosphate + NAD+ <=> 1,3-diphosphateglycerate + NADH - ATP + D-fructose-6-phosphate <=> fructose-1,6-bisphosphate + ADP + H+ - 2-phosphoglycerate <=> phosphoenolpyruvate + H2O - D-glyceraldehyde-3-phosphate <=> dihydroxy-acetone-phosphate - 3-phosphoglycerate + ATP <=> 1,3-diphosphateglycerate + ADP - phosphoenolpyruvate + ADP + H+ <=> pyruvate + ATP - beta-D-glucose-6-phosphate <=> D-fructose-6-phosphate - fructose-1,6-bisphosphate <=> dihydroxy-acetone-phosphate + D-glyceraldehyde-3-phosphate
glycolysis II (AraCyc) [Arabidopsis thaliana] - 3-phosphoglycerate <=> 2-phosphoglycerate - D-glyceraldehyde-3-phosphate + phosphate + NAD+ <=> 1,3-diphosphateglycerate + NADH - ATP + D-fructose-6-phosphate <=> fructose-1,6-bisphosphate + ADP + H+ - 2-phosphoglycerate <=> phosphoenolpyruvate + H2O - D-glyceraldehyde-3-phosphate <=> dihydroxy-acetone-phosphate - 3-phosphoglycerate + ATP <=> 1,3-diphosphateglycerate + ADP - phosphoenolpyruvate + ADP + H+ <=> pyruvate + ATP - beta-D-glucose-6-phosphate <=> D-fructose-6-phosphate - fructose-1,6-bisphosphate <=> dihydroxy-acetone-phosphate + D-glyceraldehyde-3-phosphate
Glycosphingolipid metabolism (KEGG) [Arabidopsis thaliana]
Glyoxylate and dicarboxylate metabolism (KEGG) [Arabidopsis thaliana]
glyoxylate cycle (AraCyc) [Arabidopsis thaliana] - oxaloacetate + acetyl-CoA + H2O <=> citrate + coenzyme A - malate + NAD+ <=> oxaloacetate + NADH - citrate <=> cis-aconitate + H2O
histidine biosynthesis (AraCyc) [Arabidopsis thaliana] - phosphoribulosylformimino-AICAR-P + L-glutamine <=> D-erythro-imidazole-glycerol-phosphate + AICAR + L-glutamate - D-erythro-imidazole-glycerol-phosphate <=> imidazole acetol-phosphate + H2O - imidazole acetol-phosphate + L-glutamate <=> L-histidinol-phosphate + alpha-ketoglutarate
Histidine metabolism (KEGG) [Arabidopsis thaliana]
homocysteine and cysteine interconversion (AraCyc) [Arabidopsis thaliana] - O-acetyl-L-homoserine + L-cysteine <=> cystathionine + acetate - homocysteine + L-serine <=> H2O + cystathionine - cystathionine + H2O <=> NH3 + pyruvate + homocysteine
homogalacturonan degradation (AraCyc) [Arabidopsis thaliana]
homomethionine biosynthesis (AraCyc) [Arabidopsis thaliana] - 2-oxo-4-methylthiobutanoic acid + acetyl-CoA + H2O <=> 2-(2'-methylthio)ethylmalic-acid + coenzyme A
homoserine biosynthesis (AraCyc) [Arabidopsis thaliana] - NADPH + L-aspartate-semialdehyde <=> NADP+ + homoserine - NADPH + L-aspartyl-4-phosphate <=> NADP+ + phosphate + L-aspartate-semialdehyde - L-aspartate + ATP <=> L-aspartyl-4-phosphate + ADP
IAA biosynthesis I (AraCyc) [Arabidopsis thaliana] - 3-indoleacetonitrile + 2 H2O <=> NH3 + indole-3-acetate - L-tryptophan + NADPH + O2 <=> indole-3-acetaldoxime + CO2 + NADP+ + H2O
IAA biosynthesis II (AraCyc) [Arabidopsis thaliana] - indole-3-acetyl-ala + H2O <=> indole-3-acetate + L-alanine - indole-3-acetyl-leu + H2O <=> indole-3-acetate + L-leucine
IAA conjugate biosynthesis (AraCyc) [Arabidopsis thaliana]
Indole and ipecac alkaloid biosynthesis (KEGG) [Arabidopsis thaliana]
Inositol metabolism (KEGG) [Arabidopsis thaliana]
inositol oxidation pathway (AraCyc) [Arabidopsis thaliana] - O2 + myo-inositol -> H2O + glucuronate
Inositol phosphate metabolism (KEGG) [Arabidopsis thaliana]
isoleucine biosynthesis (AraCyc) [Arabidopsis thaliana] - 2-keto-3-methyl-valerate + L-glutamate <=> L-isoleucine + alpha-ketoglutarate - pyruvate + 2-oxobutanoate <=> 2-aceto-2-hydroxy-butyrate + CO2
isoleucine degradation (AraCyc) [Arabidopsis thaliana] - 2-keto-3-methyl-valerate + L-glutamate <=> L-isoleucine + alpha-ketoglutarate - tiglyl-CoA + H2O <=> 2-methyl-3-hydroxybutyryl-CoA - 2-methylaceto-acetyl-CoA + coenzyme A <=> propionyl-CoA + acetyl-CoA
isopentenyl diphosphate biosynthesis -- mevalonate-independent (AraCyc) [Arabidopsis thaliana] - pyruvate + D-glyceraldehyde-3-phosphate <=> 1-deoxy-D-xylulose 5-phosphate + CO2 - 2-C-methyl-D-erythritol-4-phosphate + CTP <=> 4-diphosphocytidyl-2-C-methylerythritol + pyrophosphate
jasmonic acid biosynthesis (AraCyc) [Arabidopsis thaliana] - a phosphatidylcholine + H2O <=> linolenate + a lysophosphatidylcholine - O2 + linolenate <=> 13(S)-hydroperoxylinolenate - NADPH + 12-oxo-cis-10,15-phytodienoate <=> NADP+ + 3-oxo-2-(cis-2'-pentenyl)-cyclopentane-1-octanoate - 12,13(S)-epoxylinolenate <=> 12-oxo-cis-10,15-phytodienoate
leucine biosynthesis (AraCyc) [Arabidopsis thaliana] - 3-carboxy-3-hydroxy-isocaproate <=> 2-D-threo-hydroxy-3-carboxy-isocaproate - 2-keto-isovalerate + acetyl-CoA + H2O <=> 3-carboxy-3-hydroxy-isocaproate + coenzyme A - 2-keto-4-methyl-pentanoate + L-glutamate <=> L-leucine + alpha-ketoglutarate - 2-D-threo-hydroxy-3-carboxy-isocaproate + NAD+ <=> 2-keto-4-methyl-pentanoate + NADH + CO2
leucine degradation (AraCyc) [Arabidopsis thaliana] - HCO3- + 3-methylcrotonyl-CoA + ATP <=> phosphate + trans-3-methylglutaconyl-CoA + ADP - 2-keto-4-methyl-pentanoate + L-glutamate <=> L-leucine + alpha-ketoglutarate
lignin biosynthesis (AraCyc) [Arabidopsis thaliana] - coumaroyl-CoA + NADPH <=> coumaraldehyde + NADP+ + coenzyme A - 5-hydroxy-coniferaldehyde + S-adenosyl-L-methionine <=> S-adenosyl-homocysteine + sinapaldehyde - sinapaldehyde + NADPH <=> sinapyl-alcohol + NADP+ - feruloyl-CoA + NADPH <=> coniferyl aldehyde + NADP+ + coenzyme A - caffeoyl-CoA + S-adenosyl-L-methionine <=> S-adenosyl-homocysteine + feruloyl-CoA - coenzyme A + 4-coumarate + ATP <=> coumaroyl-CoA + pyrophosphate + AMP - coniferyl aldehyde + NADPH <=> coniferyl alcohol + NADP+ - coumaraldehyde + NADPH <=> coumaryl-alcohol + NADP+
Limonene and pinene degradation (KEGG) [Arabidopsis thaliana]
lipases pathway (AraCyc) [Arabidopsis thaliana] - a phosphatidylcholine + H2O <=> 1-acylglycerophosphocholine + a carboxylate - phosphatidyl-myo-inositol 4,5-biphosphate + H2O <=> 1,2-diacylglycerol + inositol 1,4,5-trisphosphate - a phosphatidylcholine + H2O <=> L-phosphatidate + choline
lipid-A-precursor biosynthesis (AraCyc) [Arabidopsis thaliana] - UDP-3-O-(3-hydroxymyristoyl)glucosamine + (R)-3-hydroxymyristoyl-ACP <=> UDP-2,3-bis(3-hydroxymyristoyl)glucosamine + acyl carrier protein - UDP-3-O-(3-hydroxymyristoyl)-N-acetylglucosamine + H2O <=> UDP-3-O-(3-hydroxymyristoyl)glucosamine + acetate
lipid-dependent phytate biosynthesis I (via Ins(1,4,5)P3) (AraCyc) [Arabidopsis thaliana] - D-myo-inositol (1,4,5,6)-tetrakisphosphate + ATP <=> D-myo-inositol (1,2,4,5,6)-pentakisphosphate + ADP - D-myo-inositol (1,3,4,5,6)-pentakisphosphate + ATP <=> phytate + ADP - inositol 1,4,5-trisphosphate + ATP <=> D-myo-inositol (1,4,5,6)-tetrakisphosphate + ADP - D-myo-inositol (1,4,5,6)-tetrakisphosphate + ATP <=> D-myo-inositol (1,3,4,5,6)-pentakisphosphate + ADP
lipid-dependent phytate biosynthesis II (via Ins(1,3,4)P3) (AraCyc) [Arabidopsis thaliana] - D-myo-inositol (1,3,4,6)-tetrakisphosphate + ATP <=> D-myo-inositol (1,2,3,4,6)-pentakisphosphate + ADP - D-myo-inositol (1,3,4,6)-tetrakisphosphate + ATP <=> D-myo-inositol (1,3,4,5,6)-pentakisphosphate + ADP - D-myo-inositol (1,3,4,5,6)-pentakisphosphate + ATP <=> phytate + ADP - D-myo-inositol (1,2,3,4,6)-pentakisphosphate + ATP <=> phytate + ADP - 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ATP <=> D-myo-inositol (1,3,4,5,6)-pentakisphosphate + ADP
lipid-independent phytate biosynthesis (AraCyc) [Arabidopsis thaliana] - D-myo-inositol (1,3,4,5,6)-pentakisphosphate + ATP <=> phytate + ADP
Lipopolysaccharide biosynthesis (KEGG) [Arabidopsis thaliana]
lipoxygenase pathway (AraCyc) [Arabidopsis thaliana] - O2 + linolenate <=> 13(S)-hydroperoxylinolenate - 12,13(S)-epoxylinolenate <=> 12-oxo-cis-10,15-phytodienoate
lupeol biosynthesis (AraCyc) [Arabidopsis thaliana]
luteolin biosynthesis (AraCyc) [Arabidopsis thaliana] - apigenin + NADPH + O2 <=> luteolin + NADP+ + H2O - naringenin + NADPH + O2 <=> eriodictyol + NADP+ + H2O
lysine biosynthesis (AraCyc) [Arabidopsis thaliana] - pyruvate + L-aspartate-semialdehyde <=> 2 H2O + L-2,3-dihydrodipicolinate - H2O + N-succinyl-L,L-2,6-diaminopimelate <=> L,L-diaminopimelate + succinate - L-2,3-dihydrodipicolinate + NAD(P)H + H+ <=> L-2,3,4,5-tetrahydrodipicolinate + NAD(P)+ - meso-diaminopimelate <=> CO2 + L-lysine - NADPH + L-aspartyl-4-phosphate <=> NADP+ + phosphate + L-aspartate-semialdehyde - L-aspartate + ATP <=> L-aspartyl-4-phosphate + ADP
Lysine biosynthesis (KEGG) [Arabidopsis thaliana]
Lysine degradation (KEGG) [Arabidopsis thaliana]
lysine degradation I (AraCyc) [Arabidopsis thaliana] - L-lysine <=> CO2 + cadaverine
lysine degradation II (AraCyc) [Arabidopsis thaliana] - 2 acetyl-CoA <=> acetoacetyl-CoA + coenzyme A
mannitol biosynthesis (AraCyc) [Arabidopsis thaliana] - mannose-6-phosphate <=> D-fructose-6-phosphate - NADPH + mannose-6-phosphate <=> NADP+ + mannitol-1-phosphate
mannitol degradation (AraCyc) [Arabidopsis thaliana] - mannose-6-phosphate <=> D-fructose-6-phosphate - NAD+ + mannitol <=> NADH + mannose
menaquinone biosynthesis (AraCyc) [Arabidopsis thaliana] - alpha-ketoglutarate + thiamin diphosphate <=> succinate-semialdehyde-thiamine PPi + CO2 - chorismate <=> isochorismate - O-succinylbenzoyl-CoA <=> coenzyme A + 1,4-dihydroxy-2-naphthoate - ATP + O-succinylbenzoate + coenzyme A <=> AMP + pyrophosphate + O-succinylbenzoyl-CoA
Metabolism of xenobiotics by cytochrome P450 (KEGG) [Arabidopsis thaliana]
Methane metabolism (KEGG) [Arabidopsis thaliana]
methionine biosynthesis (AraCyc) [Arabidopsis thaliana] - homocysteine + S-adenosyl-L-methionine <=> S-adenosyl-homocysteine + L-methionine - cystathionine + H2O <=> NH3 + pyruvate + homocysteine - 5-methyltetrahydropteroyltri-L-glutamate + homocysteine <=> tetrahydropteroyltri-L-glutamate + L-methionine - homoserine + ATP <=> O-phospho-L-homoserine + ADP - L-cysteine + O-phospho-L-homoserine <=> cystathionine + phosphate - S-Methyl-L-methionine + homocysteine <=> 2 L-methionine
methionine degradation I (AraCyc) [Arabidopsis thaliana] - homocysteine + L-serine <=> H2O + cystathionine - ATP + L-methionine + H2O <=> phosphate + pyrophosphate + S-adenosyl-L-methionine - S-adenosyl-homocysteine + H2O <=> homocysteine + adenosine
methionine degradation II (AraCyc) [Arabidopsis thaliana] - L-methionine + H2O <=> NH3 + 2-oxobutanoate + methanethiol
Methionine metabolism (KEGG) [Arabidopsis thaliana]
methionine salvage pathway (AraCyc) [Arabidopsis thaliana] - ATP + L-methionine + H2O <=> phosphate + pyrophosphate + S-adenosyl-L-methionine - 2-oxo-4-methylthiobutanoic acid + an amino acid <=> L-methionine + keto acid - S-adenosyl-L-methionine <=> 5'-methylthioadenosine + 1-aminocyclopropane-1-carboxylate
methylglyoxal degradation (AraCyc) [Arabidopsis thaliana] - S-lactoyl-glutathione + H2O <=> glutathione + D-lactate - methylglyoxal + glutathione <=> S-lactoyl-glutathione
mevalonate pathway (AraCyc) [Arabidopsis thaliana] - dimethylallyl-pyrophosphate + delta3-isopentenyl-PP <=> pyrophosphate + geranyl-PP - delta3-isopentenyl-PP <=> dimethylallyl-pyrophosphate - mevalonate-5P + ATP <=> mevalonate-5-PP + ADP - 2 acetyl-CoA <=> acetoacetyl-CoA + coenzyme A - geranyl-PP + delta3-isopentenyl-PP <=> pyrophosphate + trans, trans-farnesyl diphosphate - 2 NADPH + 3-hydroxy-3-methyl-glutaryl-CoA <=> 2 NADP+ + coenzyme A + mevalonate - mevalonate-5-PP + ATP <=> phosphate + CO2 + delta3-isopentenyl-PP + ADP
monolignol glucosides biosynthesis (AraCyc) [Arabidopsis thaliana] - sinapyl-alcohol + UDP-D-glucose <=> syringin + UDP
monoterpene biosynthesis (AraCyc) [Arabidopsis thaliana] - geranyl-PP <=> limonene + pyrophosphate - geranyl-PP <=> myrcene + pyrophosphate + myrcene - geranyl-PP <=> (E)-beta-ocimene + pyrophosphate
Monoterpenoid biosynthesis (KEGG) [Arabidopsis thaliana]
N-Glycan biosynthesis (KEGG) [Arabidopsis thaliana]
NAD biosynthesis I (from aspartate) (AraCyc) [Arabidopsis thaliana] - PRPP + quinolinate <=> CO2 + pyrophosphate + nicotinate nucleotide
NAD biosynthesis II (from tryptophan) (AraCyc) [Arabidopsis thaliana] - PRPP + quinolinate <=> CO2 + pyrophosphate + nicotinate nucleotide
NAD/NADH phosphorylation and dephosphorylation (AraCyc) [Arabidopsis thaliana] - NAD+ + ATP <=> NADP+ + ADP - ubiquinol-8 + NAD+ <=> ubiquinone-8 + NADH
Nicotinate and nicotinamide metabolism (KEGG) [Arabidopsis thaliana]
nitrate assimilation pathway (AraCyc) [Arabidopsis thaliana] - NH3 + L-glutamate + ATP <=> ADP + phosphate + L-glutamine - NO3- + NADH <=> NO2- + H2O + NAD+
Nitrobenzene degradation (KEGG) [Arabidopsis thaliana]
Nitrogen metabolism (KEGG) [Arabidopsis thaliana]
non-oxidative branch of the pentose phosphate pathway (AraCyc) [Arabidopsis thaliana] - D-erythrose-4-phosphate + D-xylulose-5-phosphate <=> D-fructose-6-phosphate + D-glyceraldehyde-3-phosphate - D-ribulose-5-phosphate <=> D-xylulose-5-phosphate - D-glyceraldehyde-3-phosphate + D-sedoheptulose-7-phosphate <=> D-fructose-6-phosphate + D-erythrose-4-phosphate - D-ribose-5-phosphate <=> D-ribulose-5-phosphate - D-ribose-5-phosphate + D-xylulose-5-phosphate <=> D-sedoheptulose-7-phosphate + D-glyceraldehyde-3-phosphate
Novobiocin biosynthesis (KEGG) [Arabidopsis thaliana]
Nucleotide Sugar Metabolism [Arabidopsis thaliana] - UDP-sugar metabolism - GDP-sugar metabolism
Nucleotide sugars metabolism (KEGG) [Arabidopsis thaliana]
One carbon pool by folate (KEGG) [Arabidopsis thaliana]
oxidative branch of the pentose phosphate pathway (AraCyc) [Arabidopsis thaliana] - 6-phospho-D-gluconate + NAD(P)+ <=> D-ribulose-5-phosphate + CO2 + NAD(P)H - beta-D-glucose-6-phosphate + NAD(P)+ <=> D-glucono-delta-lactone-6-phosphate + NAD(P)H - D-glucono-delta-lactone-6-phosphate + H2O <=> 6-phospho-D-gluconate
Oxidative phosphorylation (KEGG) [Arabidopsis thaliana]
Pantothenate and CoA biosynthesis (KEGG) [Arabidopsis thaliana]
pantothenate biosynthesis (AraCyc) [Arabidopsis thaliana] - 2-keto-isovalerate + L-glutamate <=> L-valine + alpha-ketoglutarate - 2-dehydropantoate + NADPH <=> L-pantoate + NADP+ - H2O + 2-keto-isovalerate + 5,10-methylene-THF <=> 2-dehydropantoate + tetrahydrofolate
Pentose and glucuronate interconversions (KEGG) [Arabidopsis thaliana]
Pentose phosphate pathway (KEGG) [Arabidopsis thaliana]
Peptidoglycan biosynthesis (KEGG) [Arabidopsis thaliana]
phenylalanine biosynthesis I (AraCyc) [Arabidopsis thaliana] - chorismate <=> prephenate
phenylalanine biosynthesis II (AraCyc) [Arabidopsis thaliana] - phenylpyruvate + L-glutamate <=> L-phenylalanine + alpha-ketoglutarate - prephenate <=> phenylpyruvate + H2O + CO2 - chorismate <=> prephenate
phenylalanine degradation (AraCyc) [Arabidopsis thaliana] - malate + NAD+ <=> oxaloacetate + NADH - oxaloacetate + GTP <=> CO2 + phosphoenolpyruvate + GDP - p-hydroxyphenylpyruvate + O2 <=> CO2 + homogentisate - fumarate + H2O <=> malate - L-tyrosine + alpha-ketoglutarate <=> L-glutamate + p-hydroxyphenylpyruvate
Phenylalanine metabolism (KEGG) [Arabidopsis thaliana]
Phenylalanine, tyrosine and tryptophan biosynthesis (KEGG) [Arabidopsis thaliana]
phenylpropanoid biosynthesis (AraCyc) [Arabidopsis thaliana] - caffeate + S-adenosyl-L-methionine <=> S-adenosyl-homocysteine + ferulate - 4-coumarate + NADPH + O2 <=> H2O + caffeate + NADP+ - ferulate + NADPH + O2 <=> 5-hydroxy-ferulic-acid + H2O + NADP+ - 5-hydroxy-ferulic-acid + S-adenosyl-L-methionine <=> sinapate + S-adenosyl-homocysteine
phenylpropanoid biosynthesis, initial reactions (AraCyc) [Arabidopsis thaliana] - L-phenylalanine <=> NH3 + trans-cinnamate
Phosphatidylinositol signaling system (KEGG) [Arabidopsis thaliana]
phospholipid biosynthesis (AraCyc) [Arabidopsis thaliana] - CDP-diacylglycerol + glycerol-3-phosphate <=> L-1-phosphatidylglycerol-phosphate + CMP - 1,2-diacylglycerol + CDP-choline <=> a phosphatidylcholine + CMP - L-1-phosphatidylserine <=> L-1-phosphatidyl-ethanolamine + CO2 - CTP + L-phosphatidate <=> CDP-diacylglycerol + pyrophosphate - 1,2-diacylglycerol + CDP-ethanolamine <=> L-1-phosphatidyl-ethanolamine + CMP - CDP-diacylglycerol + myo-inositol <=> L-1-phosphatidyl-inositol + CMP - H2O + L-phosphatidate <=> phosphate + 1,2-diacylglycerol
phospholipid desaturation pathway (AraCyc) [Arabidopsis thaliana] - 1-18:1-2-16:0-sn-glycerol-3-phosphate <=> 1-18:1-2-trans-16:1-sn-glycerol-3-phosphate - 1-18:2-2-trans-16:1-sn-glycerol-3-phosphate <=> 1-18:3-2-trans-16:1-sn-glycerol-3-phosphate - 1-18:1-2-18:1-sn-glycerol-3-phosphocholine <=> 1-18:2-2-18:2-sn-glycerol-3-phosphocholine - 1-18:2-2-18:2-sn-glycerol-3-phosphocholine <=> 1-18:3-2-18:3-sn-glycerol-phosphocholine - 1-18:1-2-trans-16:1-sn-glycerol-3-phosphate <=> 1-18:2-2-trans-16:1-sn-glycerol-3-phosphate
photorespiration (AraCyc) [Arabidopsis thaliana] - 5,10-methylene-THF + glycine + H2O <=> L-serine + tetrahydrofolate - NADH + hydroxypyruvate <=> NAD+ + glycerate - glycolate + O2 <=> glyoxylate + H2O2 - D-ribulose-1,5-bisphosphate + O2 <=> 2-phosphoglycolate + 3-phosphoglycerate + 2 H+ - H2O + 2-phosphoglycolate <=> glycolate + phosphate - glycine + tetrahydrofolate + NAD+ <=> NH3 + 5,10-methylene-THF + CO2 + NADH - L-glutamate + glyoxylate <=> alpha-ketoglutarate + glycine
photosynthesis, light reaction (AraCyc) [Arabidopsis thaliana] - 2 NAD(P)+ + 2 H+ + 4 e- <=> 2 NAD(P)H - 2 H2O <=> 4 H+ + 4 e- + O2
phylloquinone biosynthesis (AraCyc) [Arabidopsis thaliana] - ATP + O-succinylbenzoate + coenzyme A <=> 4-(2'-carboxyphenyl)-4-oxobutyryl-CoA + AMP + pyrophosphate - 4-(2'-carboxyphenyl)-4-oxobutyryl-CoA <=> coenzyme A + 1,4-dihydroxy-2-naphthoate - chorismate <=> isochorismate
phytate degradation I (AraCyc) [Arabidopsis thaliana]
phytate degradation II (AraCyc) [Arabidopsis thaliana]
PIF related growth response to light [Arabidopsis thaliana] - Shade avoidance and response to light - Interaction between photomorphogensis and the circadian clock - Seedling deetiolation - PIF inhibition by Interaction with DELLAs	Higgins, JA		Franklin, KA
plastoquinone biosynthesis (AraCyc) [Arabidopsis thaliana] - p-hydroxyphenylpyruvate + O2 <=> CO2 + homogentisate - 2-methyl-6-solanyl-1,4-benzoquinone + S-adenosyl-L-methionine <=> plastoquinone-9 + S-adenosyl-homocysteine
polyamine biosynthesis I (AraCyc) [Arabidopsis thaliana] - putrescine + S-adenosylmethioninamine <=> spermidine + 5'-methylthioadenosine - L-arginine <=> CO2 + agmatine - S-adenosyl-L-methionine <=> CO2 + S-adenosylmethioninamine - H2O + agmatine <=> urea + putrescine
polyamine biosynthesis II (AraCyc) [Arabidopsis thaliana] - putrescine + S-adenosylmethioninamine <=> spermidine + 5'-methylthioadenosine - L-arginine <=> CO2 + agmatine - H2O + agmatine <=> urea + putrescine
polyamine biosynthesis III (AraCyc) [Arabidopsis thaliana] - putrescine + S-adenosylmethioninamine <=> spermidine + 5'-methylthioadenosine - L-arginine <=> CO2 + agmatine - S-adenosyl-L-methionine <=> CO2 + S-adenosylmethioninamine
polyisoprenoid biosynthesis (AraCyc) [Arabidopsis thaliana] - cis,trans-polyisoprenyln-PP + delta3-isopentenyl-PP <=> pyrophosphate + cis,trans-polyisoprenyln+1-PP - dimethylallyl-pyrophosphate + delta3-isopentenyl-PP <=> pyrophosphate + geranyl-PP - delta3-isopentenyl-PP <=> dimethylallyl-pyrophosphate - trans-polyisoprenyln-PP + delta3-isopentenyl-PP <=> trans-polyisoprenyln+1-PP + pyrophosphate - geranyl-PP + delta3-isopentenyl-PP <=> pyrophosphate + trans, trans-farnesyl diphosphate
Porphyrin and chlorophyll metabolism (KEGG) [Arabidopsis thaliana]
ppGpp biosynthesis (AraCyc) [Arabidopsis thaliana] - GTP + ATP <=> guanosine 3'-diphosphate 5'-triphosphate + AMP
proline biosynthesis (AraCyc) [Arabidopsis thaliana] - L-delta1-pyrroline-5-carboxylate + NAD(P)H + H+ <=> L-proline + NAD(P)+ - L-glutamate + ATP + NADPH <=> ADP + L-glutamate gamma-semialdehyde + NADP+ + phosphate
proline degradation (AraCyc) [Arabidopsis thaliana]
Propanoate metabolism (KEGG) [Arabidopsis thaliana]
Prostaglandin and leukotriene metabolism (KEGG) [Arabidopsis thaliana]
PRPP biosynthesis (AraCyc) [Arabidopsis thaliana] - ATP + D-ribose-5-phosphate <=> PRPP + AMP
purine degradation (AraCyc) [Arabidopsis thaliana] - H2O + NAD+ + xanthine <=> NADH + urate - urate + O2 <=> allantoin + CO2 + H2O2 - hypoxanthine + NAD+ + H2O <=> xanthine + NADH + H+ - H2O + NAD+ + IMP <=> xanthosine-5-phosphate + NADH
Purine metabolism (KEGG) [Arabidopsis thaliana]
pyridine nucleotide cycling (AraCyc) [Arabidopsis thaliana] - nicotinate + H2O + PRPP + ATP <=> nicotinate nucleotide + pyrophosphate + phosphate + ADP
pyridoxal 5'-phosphate salvage pathway (AraCyc) [Arabidopsis thaliana] - O2 + pyridoxine-5'-phosphate <=> H2O2 + pyridoxal 5'-phosphate - O2 + H2O + pyridoxamine 5'-phosphate <=> NH3 + H2O2 + pyridoxal 5'-phosphate - ATP + pyridoxine <=> ADP + pyridoxine-5'-phosphate
Pyrimidine metabolism (KEGG) [Arabidopsis thaliana]
Pyruvate metabolism (KEGG) [Arabidopsis thaliana]
Reductive carboxylate cycle (CO2 fixation) (KEGG) [Arabidopsis thaliana]
removal of superoxide radicals (AraCyc) [Arabidopsis thaliana] - 2 H2O2 <=> 2 H2O + O2 - 2 O2- + 2 H+ <=> H2O2 + O2
riboflavin and FMN and FAD biosynthesis (AraCyc) [Arabidopsis thaliana] - 3 H2O + GTP <=> pyrophosphate + 2,5-diamino-6-(ribosylamino)-4-(3H)-pyrimidinone 5'-phosphate + formate - riboflavin + ATP <=> FMN + ADP - D-ribulose-5-phosphate <=> 3,4-dihydroxy-2-butanone-4-P + formate
Riboflavin metabolism (KEGG) [Arabidopsis thaliana]
ribose degradation (AraCyc) [Arabidopsis thaliana] - D-ribose + ATP <=> D-ribose-5-phosphate + ADP - D-ribose-5-phosphate <=> D-ribulose-5-phosphate - D-ribose-5-phosphate + D-xylulose-5-phosphate <=> D-sedoheptulose-7-phosphate + D-glyceraldehyde-3-phosphate
salicylic acid biosynthesis (AraCyc) [Arabidopsis thaliana] - trans-cinnamate + coenzyme A <=> (E)-cinnamoyl-CoA + H2O - benzoate + NADPH + O2 <=> salicylate + NADP+ + H2O - L-phenylalanine <=> NH3 + trans-cinnamate - chorismate <=> isochorismate
salvage pathways of purine nucleosides (AraCyc) [Arabidopsis thaliana] - adenosine + ATP <=> AMP + ADP - hypoxanthine + NAD+ + H2O <=> xanthine + NADH + H+ - guanine + PRPP <=> pyrophosphate + GMP - PRPP + adenine <=> AMP + pyrophosphate - H2O + NAD+ + IMP <=> xanthosine-5-phosphate + NADH
SAM cycle (AraCyc) [Arabidopsis thaliana] - S-adenosyl-L-methionine + methyl acceptor <=> S-adenosyl-homocysteine + N-methylated acceptor - ATP + L-methionine + H2O <=> phosphate + pyrophosphate + S-adenosyl-L-methionine - S-adenosyl-homocysteine + H2O <=> homocysteine + adenosine - 5-methyl-THF + homocysteine <=> tetrahydrofolate + L-methionine
Selenoamino acid metabolism (KEGG) [Arabidopsis thaliana]
serine biosynthesis (AraCyc) [Arabidopsis thaliana] - 3-phospho-serine + H2O <=> L-serine + phosphate - 3-phosphoglycerate + NAD+ <=> 3-phospho-hydroxypyruvate + NADH
sinapate ester biosynthesis (AraCyc) [Arabidopsis thaliana]
spermine biosynthesis I (AraCyc) [Arabidopsis thaliana] - putrescine + S-adenosylmethioninamine <=> spermidine + 5'-methylthioadenosine - L-arginine <=> CO2 + agmatine - H2O + agmatine <=> urea + putrescine
spermine biosynthesis II (AraCyc) [Arabidopsis thaliana] - putrescine + S-adenosylmethioninamine <=> spermidine + 5'-methylthioadenosine
Starch and sucrose metabolism (KEGG) [Arabidopsis thaliana]
starch biosynthesis (AraCyc) [Arabidopsis thaliana] - 1,4-alpha-D-glucan <=> Starch - alpha-D-glucose-1-phosphate <=> alpha-D-glucose-6-phosphate - beta-D-glucose-6-phosphate <=> D-fructose-6-phosphate - alpha-D-glucose-1-phosphate + ATP <=> ADP-D-glucose + pyrophosphate
starch degradation (AraCyc) [Arabidopsis thaliana] - Long-linear-glucans <=> Short-glucans - Long-linear-glucans <=> maltose - Starch <=> Large-branched-glucans
Starch degradation in leaves [Arabidopsis thaliana] - Partial phosphorylation of starch granules - Branched and Linear glucans are released from starch granules - The alpha-1,6 linkages of branched glucans are hydrolysed to produce linear glucans - Linear glucans are converted to Maltose and Maltotriose - Export of maltose to the cytosol by maltose transporter (MEX1) - Metabolism of Maltose in the Cytosol - Maltotriose is converted to beta-D-Glucose - Export of beta-D-Glucose to the cytosol by glucose transporter - D-Gluc in converted to D-gluc 6P via a hexokinase - HYPOTHETICAL: Linear glucans are converted to triose phosphate. - HYPOTHETICAL: Export of triose phosphate to the cytosol by triose phosphate transporter - HYPOTHETICAL: Triose phosphate is converted back to hexose phosphate [cytosol]
sterol biosynthesis (AraCyc) [Arabidopsis thaliana] - 24-ethylidenelophenol <=> avenasterol - cycloartenol + S-adenosyl-L-methionine <=> 24-methylenecycloartenol + S-adenosyl-homocysteine - 2 trans, trans-farnesyl diphosphate <=> presqualene diphosphate + pyrophosphate - 24-methylenecycloartenol + S-adenosyl-homocysteine <=> cycloeucalenol + S-adenosyl-L-methionine - 24-methylenelophenol + S-adenosyl-homocysteine <=> episterol + S-adenosyl-L-methionine - presqualene diphosphate + NAD(P)H <=> squalene + NAD(P)+ + pyrophosphate - (S)-2,3-Epoxysqualene <=> cycloartenol - 24-methylenelophenol + S-adenosyl-L-methionine <=> 24-ethylidenelophenol + S-adenosyl-homocysteine - O2 + reduced acceptor + squalene <=> (S)-2,3-Epoxysqualene + H2O + acceptor
Stilbene, coumarine and lignin biosynthesis (KEGG) [Arabidopsis thaliana]
Streptomycin biosynthesis (KEGG) [Arabidopsis thaliana]
Styrene degradation (KEGG) [Arabidopsis thaliana]
suberin biosynthesis (AraCyc) [Arabidopsis thaliana] - caffeate + coenzyme A + ATP <=> caffeoyl-CoA + AMP + pyrophosphate - caffeoyl-CoA + S-adenosyl-L-methionine <=> S-adenosyl-homocysteine + feruloyl-CoA - L-phenylalanine <=> NH3 + trans-cinnamate - caffeate + S-adenosyl-L-methionine <=> S-adenosyl-homocysteine + ferulate - 4-coumarate + NADPH + O2 <=> H2O + caffeate + NADP+ - ferulate + coenzyme A + ATP <=> feruloyl-CoA + AMP + pyrophosphate - oleate + 2 NADPH + O2 <=> 18-hydroxyoleate + 2 NADP+ + H2O
Sucrose Biosynthesis [Arabidopsis thaliana] - alpha-D-Glucose 1-phosphate + UTP <=> UDP-D-Glucose + pyrophosphate - UDP-D-Glucose + Fructose => Sucrose + UDP - Sucrose 6-phosphate + H2O => Sucrose + phosphate - UDP-D-Glucose + D-Fructose 6-phosphate => Sucrose 6-phosphate + UDP
sucrose biosynthesis (AraCyc) [Arabidopsis thaliana] - fructose + UDP-D-glucose <=> sucrose + UDP - D-fructose-6-phosphate + UDP-D-glucose <=> sucrose-6'-phosphate + UDP - alpha-D-glucose-1-phosphate + UTP <=> UDP-D-glucose + pyrophosphate - H2O + sucrose-6'-phosphate <=> sucrose + phosphate
sucrose degradation (AraCyc) [Arabidopsis thaliana] - alpha-D-glucose-1-phosphate <=> alpha-D-glucose-6-phosphate - beta-D-glucose-6-phosphate <=> D-fructose-6-phosphate - fructose + UDP-D-glucose <=> sucrose + UDP - alpha-D-glucose-1-phosphate + UTP <=> UDP-D-glucose + pyrophosphate
sucrose degradation to ethanol and lactate (anaerobic) (AraCyc) [Arabidopsis thaliana] - 3-phosphoglycerate <=> 2-phosphoglycerate - ATP + D-fructose-6-phosphate <=> fructose-1,6-bisphosphate + ADP + H+ - D-glyceraldehyde-3-phosphate + phosphate + NAD+ <=> 1,3-diphosphateglycerate + NADH - fructose + UDP-D-glucose <=> sucrose + UDP - 2-phosphoglycerate <=> phosphoenolpyruvate + H2O - 3-phosphoglycerate + ATP <=> 1,3-diphosphateglycerate + ADP - D-glyceraldehyde-3-phosphate <=> dihydroxy-acetone-phosphate - alpha-D-glucose-1-phosphate <=> alpha-D-glucose-6-phosphate - acetaldehyde + NADH <=> ethanol + NAD+ - phosphoenolpyruvate + ADP + H+ <=> pyruvate + ATP - fructose-1,6-bisphosphate <=> dihydroxy-acetone-phosphate + D-glyceraldehyde-3-phosphate - alpha-D-glucose-6-phosphate <=> D-fructose-6-phosphate - NADH + pyruvate <=> NAD+ + lactate - alpha-D-glucose-1-phosphate + UTP <=> UDP-D-glucose + pyrophosphate
sulfate assimilation (AraCyc) [Arabidopsis thaliana] - reduced acceptor + APS <=> AMP + acceptor + SO3-2 - cystathionine + H2O <=> NH3 + pyruvate + homocysteine - SO42- + ATP <=> APS + pyrophosphate - 5-methyltetrahydropteroyltri-L-glutamate + homocysteine <=> tetrahydropteroyltri-L-glutamate + L-methionine - O-acetyl-L-serine + H2S <=> L-cysteine + acetate - L-serine + acetyl-CoA <=> O-acetyl-L-serine + coenzyme A - L-cysteine + O-phospho-L-homoserine <=> cystathionine + phosphate
sulfolipid biosynthesis (AraCyc) [Arabidopsis thaliana]
Sulfur metabolism (KEGG) [Arabidopsis thaliana]
sulfur oxidation (AraCyc) [Arabidopsis thaliana]
superpathway of gluconate degradation (AraCyc) [Arabidopsis thaliana] - 6-phospho-D-gluconate + NAD(P)+ <=> D-ribulose-5-phosphate + CO2 + NAD(P)H - D-ribose-5-phosphate <=> D-ribulose-5-phosphate
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass (AraCyc) [Arabidopsis thaliana]
superpathway of glyoxylate cycle (AraCyc) [Arabidopsis thaliana] - malate + NAD+ <=> oxaloacetate + NADH - malate <=> oxaloacetate - oxaloacetate + ATP <=> CO2 + phosphoenolpyruvate + ADP - fumarate + H2O <=> malate - a ubiquinone + succinate <=> a ubiquinol + fumarate
Synthesis and degradation of ketone bodies (KEGG) [Arabidopsis thaliana]
Taurine and hypotaurine metabolism (KEGG) [Arabidopsis thaliana]
TCA cycle -- aerobic respiration (AraCyc) [Arabidopsis thaliana] - oxaloacetate + acetyl-CoA + H2O <=> citrate + coenzyme A - malate + NAD+ <=> oxaloacetate + NADH - citrate <=> cis-aconitate + H2O - fumarate + H2O <=> malate - acceptor + malate <=> reduced acceptor + oxaloacetate - isocitrate + NADP+ <=> NADPH + alpha-ketoglutarate + CO2 - a ubiquinone + succinate <=> a ubiquinol + fumarate
TCA cycle variation I (AraCyc) [Arabidopsis thaliana] - oxaloacetate + acetyl-CoA + H2O <=> citrate + coenzyme A - malate + NAD+ <=> oxaloacetate + NADH - citrate <=> cis-aconitate + H2O - succinate + FAD <=> fumarate + FADH2 - fumarate + H2O <=> malate - isocitrate + NADP+ <=> NADPH + alpha-ketoglutarate + CO2
Terpenoid biosynthesis (KEGG) [Arabidopsis thaliana]
tetrahydrofolate biosynthesis I (AraCyc) [Arabidopsis thaliana] - tetrahydrofolate + L-glutamate + ATP <=> THF-L-glutamate + ADP + phosphate - p-aminobenzoate + 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate <=> 7,8-dihydropteroate + pyrophosphate - dihydro-neo-pterin <=> glycolaldehyde + 6-hydroxymethyl-dehydropterin - NADPH + 7,8-dihydrofolate <=> NADP+ + tetrahydrofolate
tetrahydrofolate biosynthesis II (AraCyc) [Arabidopsis thaliana] - L-glutamate + H4PteGlu(n) + ATP <=> H4PteGlu(n+1) + phosphate + ADP - p-aminobenzoate + 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate <=> 7,8-dihydropteroate + pyrophosphate - dihydro-neo-pterin <=> glycolaldehyde + 6-hydroxymethyl-dehydropterin - NADPH + 7,8-dihydrofolate <=> NADP+ + tetrahydrofolate
thiamin biosynthesis (AraCyc) [Arabidopsis thaliana] - pyruvate + D-glyceraldehyde-3-phosphate <=> 1-deoxy-D-xylulose 5-phosphate + CO2
Thiamine metabolism (KEGG) [Arabidopsis thaliana]
threonine biosynthesis from homoserine (AraCyc) [Arabidopsis thaliana] - homoserine + ATP <=> O-phospho-L-homoserine + ADP - O-phospho-L-homoserine + H2O <=> phosphate + L-threonine
threonine degradation (AraCyc) [Arabidopsis thaliana] - L-threonine + NAD+ <=> 2-amino-3-oxobutanoate + NADH - S-lactoyl-glutathione + H2O <=> glutathione + D-lactate - methylglyoxal + glutathione <=> S-lactoyl-glutathione
trans-zeatin biosynthesis (AraCyc) [Arabidopsis thaliana] - isopentenyladenosine-5'-diphosphate + NADPH + H2O <=> trans-zeatin riboside diphosphate + NADP+ - isopentenyladenosine-5'-monophosphate + NADPH + H2O <=> trans-zeatin riboside monophosphate + NADP+ - isopentenyladenosine-5'-triphosphate + NADPH + H2O <=> trans-zeatin riboside triphosphate + NADP+ - dimethylallyl-pyrophosphate + AMP <=> isopentenyladenosine-5'-monophosphate + pyrophosphate - dimethylallyl-pyrophosphate + ATP <=> isopentenyladenosine-5'-triphosphate + pyrophosphate - dimethylallyl-pyrophosphate + ADP <=> isopentenyladenosine-5'-diphosphate + pyrophosphate
trehalose biosynthesis (AraCyc) [Arabidopsis thaliana] - trehalose 6-phosphate + H2O <=> trehalose + phosphate - UDP-D-glucose + alpha-D-glucose-6-phosphate <=> UDP + trehalose 6-phosphate
triacylglycerol biosynthesis (AraCyc) [Arabidopsis thaliana] - H2O + L-phosphatidate <=> phosphate + 1,2-diacylglycerol
triacylglycerol degradation (AraCyc) [Arabidopsis thaliana] - H2O + triacylglycerol <=> a fatty acid + 1,2-diacylglycerol
tRNA charging pathway (AraCyc) [Arabidopsis thaliana] - tRNAasn + L-asparagine + ATP <=> L-asparaginyl-tRNAasn + pyrophosphate + AMP - tRNAhis + L-histidine + ATP <=> L-histidyl-tRNAhis + pyrophosphate + AMP - tRNAval + L-valine + ATP <=> L-valyl-tRNAval + pyrophosphate + AMP - L-proline + tRNApro + ATP <=> L-prolyl-tRNApro + pyrophosphate + AMP - tRNAglt + L-glutamate + ATP <=> L-glutamyl-tRNAglt + pyrophosphate + AMP - tRNAala + L-alanine + ATP <=> L-alanyl-tRNAala + pyrophosphate + AMP - tRNAser + L-serine + ATP <=> L-seryl-tRNAser + pyrophosphate + AMP - tRNAphe + L-phenylalanine + ATP <=> L-phenylalanyl-tRNAphe + pyrophosphate + AMP - tRNAile + L-isoleucine + ATP <=> L-isoleucyl-tRNAile + pyrophosphate + AMP - tRNAcys + L-cysteine + ATP <=> L-cysteinyl-tRNAcys + pyrophosphate + AMP - tRNAasp + L-aspartate + ATP <=> L-aspartyl-tRNAasp + pyrophosphate + AMP - tRNAmet + L-methionine + ATP <=> L-methionyl-tRNAmet + pyrophosphate + AMP - tRNAarg + L-arginine + ATP <=> L-arginyl-tRNAarg + pyrophosphate + AMP - L-leucine + tRNAleu + ATP <=> L-leucyl-tRNAleu + pyrophosphate + AMP - tRNAthr + L-threonine + ATP <=> L-threonyl-tRNAthr + pyrophosphate + AMP - tRNAtrp + L-tryptophan + ATP <=> L-tryptophanyl-tRNAtrp + pyrophosphate + AMP - tRNAlys + L-lysine + ATP <=> L-lysyl-tRNAlys + pyrophosphate + AMP - tRNAgly + glycine + ATP <=> glycyl-tRNAgly + pyrophosphate + AMP - L-tyrosine + tRNAtyr + ATP <=> L-tyrosyl-tRNAtyr + pyrophosphate + AMP
tryptophan biosynthesis (AraCyc) [Arabidopsis thaliana] - N-(5'-phosphoribosyl)-anthranilate <=> 1-(o-carboxyphenylamino)-1'-deoxyribulose-5'-phosphate - 1-(o-carboxyphenylamino)-1'-deoxyribulose-5'-phosphate <=> indole-3-glycerol-phosphate + CO2 + H2O - anthranilate + PRPP <=> N-(5'-phosphoribosyl)-anthranilate + pyrophosphate - chorismate + L-glutamine <=> anthranilate + pyruvate + L-glutamate
tryptophan degradation (AraCyc) [Arabidopsis thaliana] - 2 acetyl-CoA <=> acetoacetyl-CoA + coenzyme A
Tryptophan metabolism (KEGG) [Arabidopsis thaliana]
tyrosine biosynthesis I (AraCyc) [Arabidopsis thaliana] - chorismate <=> prephenate
tyrosine biosynthesis II (AraCyc) [Arabidopsis thaliana] - NAD+ + L-arogenate <=> L-tyrosine + CO2 + NADH - L-arogenate + NADP+ <=> L-tyrosine + NADPH + CO2 - chorismate <=> prephenate
tyrosine degradation (AraCyc) [Arabidopsis thaliana] - p-hydroxyphenylpyruvate + O2 <=> CO2 + homogentisate - L-tyrosine + alpha-ketoglutarate <=> L-glutamate + p-hydroxyphenylpyruvate
Tyrosine metabolism (KEGG) [Arabidopsis thaliana]
Ubiquinone biosynthesis (KEGG) [Arabidopsis thaliana]
UDP-D-galacturonate biosynthesis I (from UDP-D-glucuronate) (AraCyc) [Arabidopsis thaliana]
UDP-D-galacturonate biosynthesis II (from D-galacturonate) (AraCyc) [Arabidopsis thaliana]
UDP-D-xylose biosynthesis (AraCyc) [Arabidopsis thaliana] - UDP-D-glucuronate <=> UDP-D-xylose + CO2 - H2O + 2 NAD+ + UDP-D-glucose <=> 2 NADH + UDP-D-glucuronate
UDP-glucose conversion (AraCyc) [Arabidopsis thaliana] - UDP-D-glucose <=> UDP-galactose - H2O + pyrophosphate <=> 2 phosphate - alpha-D-glucose-1-phosphate + UTP <=> UDP-D-glucose + pyrophosphate
UDP-L-arabinose biosynthesis I (from UDP-xylose) (AraCyc) [Arabidopsis thaliana]
UDP-L-arabinose biosynthesis II (from L-arabinose) (AraCyc) [Arabidopsis thaliana]
UDP-L-rhamnose biosynthesis (AraCyc) [Arabidopsis thaliana]
UDP-N-acetyl-D-glucosamine biosynthesis (AraCyc) [Arabidopsis thaliana] - N-acetyl-glucosamine-1-phosphate + UTP <=> UDP-N-acetyl-D-glucosamine + pyrophosphate - D-fructose-6-phosphate + L-glutamine <=> D-glucosamine-6-phosphate + L-glutamate
Urea cycle and metabolism of amino groups (KEGG) [Arabidopsis thaliana]
ureide biosynthesis (AraCyc) [Arabidopsis thaliana] - H2O + NAD+ + xanthine <=> NADH + urate - urate + H2O2 <=> allantoin + CO2 - H2O + NAD+ + IMP <=> xanthosine-5-phosphate + NADH
ureide degradation (AraCyc) [Arabidopsis thaliana] - H2O + urea <=> 2 NH3 + CO2
valine biosynthesis (AraCyc) [Arabidopsis thaliana] - 2-keto-isovalerate + L-glutamate <=> L-valine + alpha-ketoglutarate - 2 pyruvate <=> 2-acetolactate + CO2
valine degradation (AraCyc) [Arabidopsis thaliana] - 2-keto-isovalerate + L-glutamate <=> L-valine + alpha-ketoglutarate - methacrylyl-CoA + H2O <=> 3-hydroxy-isobutyryl-CoA - NAD+ + 3-hydroxy-isobutyrate <=> NADH + methylmalonate-semialdehyde - H2O + 3-hydroxy-isobutyryl-CoA <=> 3-hydroxy-isobutyrate + coenzyme A
Valine, leucine and isoleucine biosynthesis (KEGG) [Arabidopsis thaliana]
Valine, leucine and isoleucine degradation (KEGG) [Arabidopsis thaliana]
very long chain fatty acid biosynthesis (AraCyc) [Arabidopsis thaliana] - 3-hydroxyacyl-CoA <=> trans-delta2-enoyl-CoA + H2O - fatty-acyl-CoA + malonyl-CoA <=> beta-ketoacyl-CoA + CO2 + coenzyme A
Vitamin B6 metabolism (KEGG) [Arabidopsis thaliana]
vitamin E biosynthesis (AraCyc) [Arabidopsis thaliana] - p-hydroxyphenylpyruvate + O2 <=> CO2 + homogentisate - 2-methyl-6-phytyl-1,4-benzoquinone + S-adenosyl-L-methionine <=> 2,3-dimethyl-6-phytyl-1,4-benzoquinone + S-adenosyl-homocysteine
volatile benzenoid ester biosynthesis (AraCyc) [Arabidopsis thaliana]
xanthophyll cycle (AraCyc) [Arabidopsis thaliana]
xylose degradation (AraCyc) [Arabidopsis thaliana] - xylulose + ATP <=> D-xylulose-5-phosphate + ADP

© 2007 John Innes Centre. All rights reserved.
Date: 2010-07-29 19:02:30	help@arabidopsisreactome.org