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The table below lists the pathways that have been modified in RiceCyc - Current version 2.0.3

chorismate biosynthesis
tryptophan biosynthesis
phenylpropanoid biosynthesis, initial reactions
phenylpropanoid biosynthesis
flavonoid biosynthesis
flavonol biosynthesis PWY-3101
leucine biosynthesis LEUSYN-PWY

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The table below lists the pathways that were modified in RiceCyc - version 2.0.1

glycolysis IV (plant cytosol)
Jasmonic acid biosynthesis
Phospholipid biosynthesis II
Starch degradation
Sucrose degradation III
geranylgeranyldiphosphate biosynthesis II (plastidic) PWY-5121
ent-kaurene biosynthesis PWY-5032
trans-zeatin biosynthesis PWY-2681

The table below lists the pathways that were added to RiceCyc - version 2.0.1

Momilactone Biosynthesis pathway
Oryzalexin S Biosynthesis Pathway
Phytocassane Biosynthesis Pathway
Oryzalexin A-F Biosynthesis Pathway PWY4KF-2307
9-LOX and 9-HPL pathway
13-LOX and 13-HPL pathway
Argenine biosynthesis I
Cardiolipin biosynthesis
Chlorophyll a biosynthesis I
Chlorophyll Cycle (update)
Cutin biosynthesis
GDP-L-fucose biosynthesis I (from GDP-D-mannose)
Inositol oxidation pathway
Homomethionine biosynthesis
NAD/NADH phosphorylation and dephosphorylation
Phylloquinone biosynthesis
Plastoquinone biosynthesis
Putrescine biosynthesis I
Pyridine nucleotide cycling (plants)
S-methylmethionine cycle
Stachyose biosynthesis
Tetrapyrrole biosynthesis
UDP-D-galacturonate biosynthesis I (from UDP-D-glucuronate)
UDP-D-xylose biosynthesis
UDP-L-arabinose biosynthesis I (from UDP-xylose)
UDP-L-arabinose biosynthesis II (from L-arabinose)
The table below lists the pathways that were deleted in RiceCyc - version 2.0.1

Reason for deletion
Biosynthesis - Amines and Polyamines

Choline-O-sulfate degradation
Microbial transformation of sulfur in the soil
Glycine betaine biosynthesis I (Gram-negative bacteria)
Gram-negative bacteria such as E. coli, Pseudomonas aeruginosa, and Synorhizobium meliloti utilize a choline dehydrogenase (EC
Glycine betaine biosynthesis II (Gram-positive bacteria)
Gram-positive bacteria, such as Bacillus subtilis, use an alcohol dehydrogenase (EC
Biosynthesis - Amino acids

Interconversion of arginine, ornithine and proline
Clostridium sticklandii, specific
Lysine biosynthesis V
prokaryote specific: the pathway continues in a path similar to bacterial arginine biosynthesis
Methionine biosynthesis III
bacteria, yeast and fungi can directly assimilate inorganic sulfur for the biosynthesis of sulfur-containing amino acids.
Biosynthesis - Cell structures

Enterobacterial common antigen biosynthesis
Peptidoglycan biosynthesis
Peptidoglycan is found on the outside of the cytoplasmic membrane of almost all eubacteria, and is unique to these organisms.
UDP-N-acetyl-D-glucosamine biosynthesis
Pathway needs to be rebuilt
Biosynthesis - Cofactors, Prosthetic Groups, Electron Carriers

Cobalamin biosynthesis II (aerobic pathway)
The biosynthesis of coenzyme B12 is intricate and involved, and is confined to some bacteria and archaea
Mycothiol biosynthesis
Mycobacterium smegmatis
Biosynthesis - Fatty Acids and Lipids

Ergosterol biosynthesis
The ergosterol biosynthesis pathway is required for generation of a major constituent of the fungal plasma membrane
Biosynthesis - Hormones

Catecholamine biosynthesis
The catecholamines (norepinephrine, epinephrine and dopamine) are synthesized in the central nervous system (CNS), sympathetic nerves and in the chromaffin cells of the adrenal medulla.
gibberellin biosynthesis IV (<i>Gibberella fujikuroi</i>)
Non-existent in Rice
Biosynthesis - Secondary Metabolites

Iisoflavonoid biosynthesis I
Isoflavonoids are restrictively distributed in the plant kingdom, being mostly biosynthesized in plants of the subfamily Papilionoideae of the Leguminosae.
Isoflavonoid biosynthesis II
Isoflavonoids are restrictively distributed in the plant kingdom, being mostly biosynthesized in plants of the subfamily Papilionoideae of the Leguminosae
(S)-reticuline biosynthesis
Restricted to Papaveraceae, Berberidaceae, and Ranunculaceae
berberine biosynthesis
Restricted to Papaveraceae, Berberidaceae, and Ranunculaceae
Chlorophyll biosynthesis
Updated/Replaced by Chlorophyll  a biosynthesis
Chlorophyll biosynthesis 1
Updated/Replaced by Chlorophyll  a biosynthesis
Chlorophyll cycle1
Updated/Replaced by Chlorophyll cycle
geranylgeranyldiphosphate biosynthesis I (cytosolic)
Non-exitent in Rice
Biosynthesis - Siderophores

Enterobactin biosynthesis
Biosynthesis - Sugars and Polysaccharides

Glycogen biosynthesis
Mammalian and yeast enzymes utilize UDP-D-glucose
Trehalose biosynthesis II
Saccharomyces cerevisiae - first EC number generalised
Degradation/Utilization/Assimilation - Amines and Polyamines

γ-butyrobetaine degradation
Pseudomonas species are able to grow on γ-butyrobetaine as their sole source of carbon and nitrogen.
Choline-O-sulfate degradation
Microbial transformation of sulfur in the soil
Superpathway of ornithine degradation
Degradation/Utilization/Assimilation - Amino Acids

Glutamate degradation VIII
Specific to Acidominococcaceae, Anaeromusa acidaminophila and Barkera propionica
Superpathway of arginine, putrescine, and 4-aminobutyrate degradation
Contains E.Coli specific sub pathways
Degradation/Utilization/Assimilation - C1 Compounds

Formaldehyde assimilation I (serine pathway)
Methanotrophic bacteria
Formaldehyde assimilation II (RuMP Cycle)
Methanotrophic bacteria
Formaldehyde oxidation I
Methanotrophic bacteria
Formaldehyde oxidation IV (thiol-independent)
Methanotrophic bacteria
Degradation/Utilization/Assimilation - Carboxylates

Methylcitrate cycle
Salmonella typhimurium and E.coli specific pathway
Degradation/Utilization/Assimilation - Other

Cyanide degradation
Chromobacterium violaceum specific pathway
D-camphor degradation
Camphor is a white, crystalline solid monoterpene ketone with a characteristic pungent odor and taste, which is naturally produced by the camphor tree
Octane oxidation
Pseudomonas putida PGo1 (formerly known as P. oleovorans) can utilize alkanes as a sole source of carbon and energy.
Thiocyanate degradation I
Microorganisms can use thiocyanate as a source of nitrogen, sulfur, carbon, or energy.
Degradation/Utilization/Assimilation - Aromatic Compounds

m-cresol degradation
Phenolic compounds commonly found in fuel processing activities such as coal gasification, and the fractionation of coal, tar, and petroleum.
p-cymene degradation
Thyme oil - pathway in rice only contains one out of ten reactions
Desulfonation of 2-aminobenzenesulfonate, benzenesulfonate and 4-toluenesulfonate
gram negative Bacteria; Alcaligenaceae
Phenylethylamine degradation
Superpathway of parathion degradation
Toluene degradation I (via benzoate)
Pseudomonas putida
Toluene degradation VI (anaerobic)
Urate degradation
Urate degradation may occur as a defence mechanism in plants, but this pathway is specific to Pseudomonas Species
Degradation/Utilization/Assimilation - Sugars and Polysaccharides

Entner-Doudoroff pathway II (non-phosphorylative)
The classical Entner-Doudoroff (ED) pathway of bacteria (and some eukaryotes)
Entner-Doudoroff pathway III (semi-phosphorylative)
Found in halophilic archaea (and some bacteria), in which 2-keto-3-deoxygluconate (KDG) is phosphorylated to KDPG by KDG kinase, rather than the general conversion of glucose into glucose 6-phosphate
Glycogen degradation
Pathway specific for E.Coli
Lactose degradation II
Agrobacterium tumefaciens specific
Lactose degradation III
Escherichia coli, Sinorhizobium meliloti, Rhizobium meliloti specific pathway
Xylose degradation
D-xylose, which can serve as a total source of carbon and energy for E. coli
Generation of precursor metabolites and energy

C4 photosynthetic carbon assimilation cycle
Rice not C4
Colanic acid building blocks biosynthesis
Escherichia coli specific pathway
Entner-Doudoroff pathway I
Escherichia coli specific pathway
Glucose fermentation to lactate II
This pathway is used by Bifidobacterium bifidum for glucose breakdown.
Glycolysis II
This glycolytic pathway in the archaeon Pyrococcus furiosus is a variant of the relatively well conserved glycolytic pathway in bacteria and eukaryotes
Glucose heterofermentation to lactate I
Microbial photosynthesis
Purine fermentation to acetate and CO2
Clostridium specific pathway
TCA cycle variation II
Helicobacter pylori specific pathway
TCA cycle variation IV
Not supported by Metacyc
TCA cycle variation VIII
Not supported by Metacyc
Pyruvate fermentation to propionate

Superpathway glycolysis+Entner Doudoroff
Subpathway no longer in RiceCyc
Superpathway glycolysis+TCA variation VIII
Subpathway no longer in RiceCyc

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