AraCyc includes a large number of pathways that have been created by PMN curators or have been imported from MetaCyc or other collaborator databases and added* to the database since the initial AraCyc 1.0 build:
- A. Top
- abscisic acid biosynthesis
- abscisic acid glucose ester biosynthesis
- acyl-ACP desaturation pathway
- acyl-ACP thioesterase pathway
- acyl carrier protein metabolism
- acetyl-CoA biosynthesis (from citrate)
- acetyl-CoA biosynthesis (from pyruvate)
- acyl-CoA synthetase pathway
- acyl-CoA thioesterase pathway
- adenosylmethionine biosynthesis
- aerobic respiration
- aerobic respiration -- alternative oxidase pathway
- ajugose biosynthesis II (galactinol-independent)
- alanine biosynthesis II
- adenosylmethionine biosynthesis
- allantoin degradation to glyoxylate II
- allantoin degradation to ureidoglycolate (ammonia producing)
- 4-aminobutyrate degradation I
- alpha-amyrin biosynthesis
- ammonia assimilation
- ammonium transport
- antheraxanthin and violaxanthin biosynthesis
- anthocyanin biosynthesis (pelargonidin-3-O-glucoside, cyanidin-3-O-glucoside)
- arabidiol biosynthesis
- arabidopsis flavonoid biosynthesis
- arginine biosynthesis
- arginine biosynthesis II
- arginine biosynthesis III
- aromatic amino acid biosynthesis (plants)
- ascorbate biosynthesis
- ascorbate biosynthesis II (L-gulose pathway)
- ascorbate biosynthesis III (VTC2 cycle)
- ascorbate biosynthesis IV (extended VTC2 cycle)
- ascorbate glutathione cycle
- asparagine biosynthesis I
- asparagine degradation I
- asparaginyl-tRNAasn biosynthesis via transamidation
- auxin biosynthesis
- B. Top
- baruol biosynthesis
- benzoate biosynthesis II
- beta-alanine biosynthesis I
- beta-alanine biosynthesis II
- beta-alanine biosynthesis III
- beta-carotene biosynthesis
- beta-caryophyllene biosynthesis
- biotin biosynthesis II
- branched-chain a-keto acid dehydrogenase complex
- brassinosteroid biosynthesis
- brassinosteroid biosynthesis II
- brassinosteroid biosynthesis III
- brassinosteroids inactivation
- C. Top
- CA1P biosynthesis
- camalexin biosynthesis
- carbon tetrachloride degradation
- cardiolipin biosynthesis
- carotene biosynthesis
- CDP-diacylglycerol biosynthesis I
- CDP-diacylglycerol biosynthesis II
- cellulose biosynthesis
- ceramide degradation
- chlorophyll biosynthesis
- chlorophyll biosynthesis I
- chlorophyll biosynthesis II
- chlorophyll cycle
- chlorophyll degradation
- cholesterol biosynthesis
- choline biosynthesis I
- choline biosynthesis II
- choline biosynthesis III
- 2,3-cis-flavanols biosynthesis
- cis-zeatin biosynthesis
- citrulline biosynthesis
- citrulline-nitric oxide cycle
- CMP-KDO biosynthesis I
- CMP-KDO biosynthesis II
- coniferin metabolism
- coumarin biosynthesis (via 2-coumarate)
- cutin biosynthesis
- cyanide degradation
- cyclopropane and cyclopropene fatty acid biosynthesis
- cytokinin biosynthesis
- cytokinins 7-N-glucoside biosynthesis
- cytokinins 9-N-glucoside biosynthesis
- cytokinins-O-glucoside biosynthesis
- cytokinins degradation
- D. Top
- delta-carotene biosynthesis
- 1,4-dihydroxy-2-naphthoate biosynthesis II (plants)
- dTDP-L-rhamnose biosynthesis
- E. Top
- Entner-Doudoroff pathway I
- ent-kaurene biosynthesis
- epicuticular wax biosynthesis(previously named 'wax biosynthesis')
- epoxysqualene biosynthesis
- esculetin biosynthesis
- ethanol degradation
- F. Top
- farnesene biosynthesis
- farnesylcysteine salvage pathway
- fatty acid β-oxidation I (saturated)
- fatty acid β-oxidation II (unsaturated, even number)
- fatty acid β-oxidation III (unsaturated, odd number)
- fatty acid biosynthesis - initial steps
- fatty acid oxidation pathway II
- fatty acid oxidation pathway III
- Fe(III)-reduction and Fe(II) transport
- ferulate and sinapate biosynthesis
- folate polyglutamylation I
- folate polyglutamylation II
- folate transformations
- formaldehyde oxidation (glutathione-dependent)
- free phenylpropanoid biosynthesis (previously named 'phenylpropanoid biosynthesis')
- G. Top
- galactose degradation I
- galactosylcyclitol biosynthesis
- gamma-glutamyl cycle (plant pathway)
- gibberellin biosynthesis (has been deleted and replaced)
- GA12 biosynthesis
- GDP-L-galactose biosynthesis (from GDP-D-mannose)
- GDP-glucose biosynthesis
- GDP-D-mannose biosynthesis
- geranylgeranyl diphosphate biosynthesis I (cytosolic)
- geranylgeranyl diphosphate biosynthesis II (plastidic)
- geranyl diphosphate biosynthesis
- gibberellin biosynthesis I
- gibberellin biosynthesis II
- gibberellin biosynthesis III
- gibberellin inactivation
- gibberellin inactivation II (methylation)
- gluconeogenesis
- glucosinolate biosynthesis from dihomomethionine
- glucosinolate biosynthesis from hexahomomethionine
- glucosinolate biosynthesis from homomethionine
- glucosinolate biosynthesis from pentahomomethionine
- glucosinolate biosynthesis from phenylalanine
- glucosinolate biosynthesis from tetrahomomethionine
- glucosinolate biosynthesis from trihomomethionine
- glucosinolate biosynthesis from tryptophan
- glucosinolate breakdown
- glutamate biosynthesis I
- glutamate biosynthesis II
- glutamate degradation I
- glutamate degradation II
- glutamine biosynthesis III
- glutaminyl-tRNAgln biosynthesis via transamidation
- glutathione degradation
- glutathione redox reactions
- glutathione redox reactions II
- glycerol degradation
- glycerol-3-phosphate shuttle
- glycine cleavage complex
- glycine betaine biosynthesis III (plants)
- glycolate and glyoxylate degradation
- glycolysis IV
- glycosylglycerate biosynthesis
- glycosylglyceride desaturation pathway
- glyoxylate cycle II
- H. Top
- heme biosynthesis
- homogalacturonan biosynthesis
- homogalacturonan degradation
- homomethionine biosynthesis
- hydroxycinnamic acid tyramine amides biosynthesis
- hydroxyjasmonate sulfate biosynthesis
- 4-hydroxyphenylpyruvate biosynthesis
- hypusine biosynthesis
- I. Top
- IAA biosynthesis II
- IAA biosynthesis III
- IAA conjugate biosynthesis
- IAA degradation IV
- indole glucosinolate breakdown (active in intact plant cell)
- Indole glucosinolate breakdown (insect chewing induced)
- indole-3-acetyl-amino acid biosynthesis
- myo-inositol biosynthesis
- inositol oxidation pathway
- J. Top
- jasmonic acid biosynthesis
- jasmonoyl-amino acid conjugates biosynthesis I
- K. Top
- kaempferol glucoside biosynthesis
- KDO transfer to lipid A
- L. Top
- lactose degradation
- 13-LOX and 13-HPL pathway
- leucodelphinidin biosynthesis
- leucopelargonidin and leucocyanidin biosynthesis
- linalool biosynthesis
- linoleate biosynthesis
- lipid-dependent phytate biosynthesis I
- lipid-dependent phytate biosynthesis II
- lipoate biosynthesis and incorporation
- lipid-independent phytate biosynthesis
- lupeol biosynthesis
- lutein biosynthesis
- luteolin biosynthesis
- lysine biosynthesis
- lysine biosynthesis I
- lysine degradation II
- M. Top
- mannitol biosynthesis
- mannitol degradation
- mannose degradation
- 2-O-alpha-mannosyl-D-glycerate degradation
- marneral biosynthesis
- melibiose degradation
- methionine biosynthesis
- methionine salvage pathway
- methyl indole-3-acetate interconversion
- methylquercetin biosynthesis
- molybdenum cofactor biosynthesis
- monolignol glucoside biosynthesis
- monoterpene biosynthesis
- N. Top
- NAD biosynthesis II (from tryptophan)
- NAD/NADH phosphorylation and dephosphorylation
- nicotianamine biosynthesis
- nitrate assimilation pathway
- nonaprenyl diphosphate biosynthesis
- 0. Top
- ornithine biosynthesis
- oxidative ethanol degradation
- oxidative ethanol degradation I
- oxidized GTP and dGTP detoxification
- P. Top
- palmitate biosynthesis
- pantothenate biosynthesis
- pelargonidin conjugates biosynthesis
- phaseic acid biosynthesis
- phenylalanine biosynthesis I
- phenylalanine degradation III
- phenylethanol biosynthesis
- phenylpropanoid biosynthesis (previously named 'lignin biosynthesis')
- phenylpropanoid ester biosynthesis
- phosphate acquisition *
- phosphatidylcholine biosynthesis I
- phosphatidylcholine biosynthesis II
- phosphatidylcholine biosynthesis III
- phosphatidylcholine biosynthesis IV
- phosphatidylethanolamine biosynthesis I
- phosphatidylethanolamine biosynthesis II
- phospholipid desaturation pathway
- photorespiration
- photosynthesis (light reaction)
- phylloquinone biosynthesis
- phytate degradation I
- phytate degradation II
- phytol biosynthesis
- phytyl-PP biosynthesis
- plant sterol biosynthesis II
- plastoquinone biosynthesis
- poly-hydroxy fatty acids biosynthesis
- polyisoprenoid biosynthesis
- proanthocyanidin biosynthesis from flavonols
- proline biosynthesis I
- proline biosynthesis II (from arginine)
- proline degradation
- purine degradation
- putrescine biosynthesis
- putrescine biosynthesis via N-carbamoylputrescine
- putrescine biosynthesis IV
- putrescine degradation IV
- pyridine nucleotide cycling (plants)
- pyridoxal 5'-phosphate biosynthesis II
- pyrimidine nucleotide metabolism (phosphotransfer and nucleotide modification)
- pyrimidine ribonucleosides degradation II
- pyrimidine salvage pathway
- pyruvate fermentation to ethanol
- pyruvate fermentation to lactate
- Q. Top
- quercetin glucoside biosynthesis
- quercetinsulphates biosynthesis
- R. Top
- RUBISCO shunt
- S. Top
- S-adenosyl-L-methionine cycle
- salicylate glucosides biosynthesis I
- salicylate glucosides biosynthesis II
- salicylate glucosides biosynthesis III
- salicylate glucosides biosynthesis IV
- salicylic acid biosynthesis
- salvage pathway of purine nucleosides
- scopoletin biosynthesis
- serine racemization
- side chain elongation cycle aliphatic glucosinolates (Arabidopsis)
- simple coumarins biosynthesis
- sinapate ester biosynthesis
- siroheme biosynthesis
- SMM cycle
- sorbitol degradation
- spermidine hydroxycinnamic acids conjugates biosynthesis
- spermine and spermidine degradation III
- sphingolipid biosynthesis
- sporopollenin precursor biosynthesis
- stachyose biosynthesis
- starch biosynthesis
- starch degradation
- stearate biosynthesis
- sterol biosynthesis
- suberin biosynthesis
- sucrose degradation to ethanol and lactate (anaerobic)
- sulfate activation for sulfonation
- sulfite oxidation
- sulfolipid biosynthesis
- T. Top
- TCA cycle
- TCA cycle variation I
- TCA cycle V
- tetrahydrofolate biosynthesis I
- thalianol and derivatives biosynthesis
- thiamine biosynthesis
- thioredoxin pathway
- thiosulfate disproportionation (rhodanese)
- thymine degradation
- TMTT biosynthesis
- trans-lycopene biosynthesis I (bacteria)(has been deleted and replaced)
- trans-lycopene biosynthesis II (plants)
- trans,trans-farnesyl diphosphate biosynthesis
- trans-zeatin biosynthesis
- trehalose degradation (high osmolarity)
- 2,4,6-trinitrotoluene degradation
- tyrosine biosynthesis II
- U. Top
- ubiquinone-9 biosynthesis
- UDP-D-apiose biosynthesis (from UDP-D-glucuronate)
- UDP-L-arabinose biosynthesis I
- UDP-L-arabinose biosynthesis II
- UDP-L-fucose biosynthesis I
- UDP-L-fucose biosynthesis II
- UDP-galactose biosynthesis
- UDP-galacturonate biosynthesis I
- UDP-galacturonate biosynthesis II
- UDP-glucose biosynthesis (from glucose 6-P)
- UDP-glucose biosynthesis (from sucrose)
- UDP-N-acetyl-D-glucosamine biosynthesis
- UDP-rhamnose biosynthesis
- UDP-xylose biosynthesis
- urate biosynthesis
- urate degradation to allantoin
- urea cycle
- urea degradation
- V. Top
- cis-vaccenate biosynthesis
- very long chain fatty acid biosynthesis
- vitamin E biosynthesis
- volatile benzenoid ester biosynthesis
- X. Top
- xanthophyll cycle
- xylan biosynthesis
- xylogalacturonan biosynthesis
- Z. Top
- zeaxanthin biosynthesis
- Superpathways. Top
- photosynthesis
- superpathway of acetyl-CoA biosynthesis
- superpathway of anthocyanin biosynthesis (from cyanidin and cyanidin 3-O-glucoside)
- superpathway of C28 brassinosteroid biosynthesis
- superpathway of choline biosynthesis
- superpathway of citrulline metabolism
- superpathway of fatty acid biosynthesis
- superpathway of flavones and derivatives biosynthesis
- superpathway of GA12 biosynthesis
- superpathway of gibberellin biosynthesis
- superpathway of isoleucine biosynthesis
- superpathway of KDO2-lipid A biosynthesis
- superpathway of lipid-dependent phytate biosynthesis
- superpathway of lysine, methionine and threonine biosynthesis
- superpathway of polyamine biosynthesis
- superpathway of proto- and siroheme biosynthesis
- superpathway of ribose and deoxyribose phosphate degradation
- UDP-sugars interconversion
* Note: Following their initial addition to the database, some of these pathways have later been deleted from AraCyc or given a new ID. These changes will result in a broken link. Efforts will be made to remove these in the future.
Return to the AraCyc Release Notes page
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