Arabidopsis Reactome: table of contents

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Topic	Authors	Released	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
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
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
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]
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]
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] - G1/S checkpoint - G2/M checkpoint - Mitotic Spindle checkpoint	Higgins, JA	2008-04-10 NEW	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
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	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	2008-04-10 NEW	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
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
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
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