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 1.1.99.1)

Glycine betaine biosynthesis II (Gram-positive bacteria)

Gram-positive bacteria, such as Bacillus subtilis, use an alcohol dehydrogenase (EC 1.1.1.1)

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.

Enterobacterial common antigen biosynthesis

Enterobacteriaceae

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

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

Ergosterol biosynthesis

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

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.

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.

Enterobactin biosynthesis

Enterobacteriaceae

Glycogen biosynthesis

Mammalian and yeast enzymes utilize UDP-D-glucose

Trehalose biosynthesis II

Saccharomyces cerevisiae - first EC number generalised

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

Bacteria

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

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

Methylcitrate cycle

Salmonella typhimurium and E.coli specific pathway

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.

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

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

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

Superpathway glycolysis+Entner Doudoroff

Subpathway no longer in RiceCyc

Superpathway glycolysis+TCA variation VIII

Subpathway no longer in RiceCyc