Table 3

The entire set of pathways in HumanCyc, grouped by classes using the MetaCyc pathway classification hierarchy

Class
Subclass
Pathway
EcoCyc
AraCyc

Biosynthesis
Polyamines
Betaine biosynthesis
*
*


Betaine biosynthesis II




Spermine biosynthesis

*


Polyamine biosynthesis II




Ornithine spermine biosynthesis

*


Polyamine biosynthesis
*
*


UDP-N-acetylgalactosamine biosynthesis

*


UDP-N-acetylglucosamine biosynthesis
*


Nucleotides
De novo biosynthesis of purine nucleotides
*



Purine and pyrimidine metabolism




Purine biosynthesis 2




De novo biosynthesis of pyrimidine ribonucleotides
*



Salvage pathways of pyrimidine ribonucleotides
*



De novo biosynthesis of pyrimidine deoxyribonucleotides
*



Salvage pathways of pyrimidine deoxyribonucleotides
*


Fatty acids and lipids
Fatty acid elongation - saturated
*
*


Fatty acid biosynthesis - initial steps
*
*


Phospholipid biosynthesis
*
*


Phospholipid biosynthesis II




Mevalonate pathway

*


Triacylglycerol biosynthesis

*

Cofactors, prosthetic groups, electron carriers
Heme biosynthesis II




NAD biosynthesis II




NAD biosynthesis III




NAD phosphorylation and dephosphorylation
*



Pyridine nucleotide biosynthesis
*
*


Pyridine nucleotide cycling
*



Glutathione-glutaredoxin redox reactions
*



Glutathione biosynthesis
*
*


Thioredoxin pathway
*
*


Pantothenate and coenzyme A biosynthesis
*
*


Pyridoxal 5'-phosphate salvage pathway
*
*


FormylTHF biosynthesis
*
*


Polyisoprenoid biosynthesis
*
*


Methyl-donor molecule biosynthesis
*


Cell structures
Colanic acid building blocks biosynthesis
*
*


GDP-mannose metabolism
*
*


Mannosyl-chito-dolichol biosynthesis

*


UDP-N-acetylglucosamine biosynthesis
*


Carbohydrates
GDP-D-rhamnose biosynthesis




Gluconeogenesis
*
*


Mannosyl-chito-dolichol biosynthesis

*


Trehalose degradation - low osmolarity
*
*

Aminoacyl-tRNAs
tRNA charging pathway
*
*

Amino acid biosynthesis
Alanine biosynthesis II

*


Arginine biosynthesis 4

*


Citrulline biosynthesis




Asparagine biosynthesis I




Aspartate biosynthesis II




Cysteine biosynthesis II




Glutamate biosynthesis II

*


Glutamine biosynthesis II




Glycine cleavage
*



Glycine biosynthesis I
*
*


Methionine salvage pathway




Proline biosynthesis I
*
*


Serine biosynthesis
*
*


Tyrosine biosynthesis II







Degradation
Sugars and polysaccharides
Lactose degradation 4

*


Lactose degradation 2

*


Sucrose degradation III




Galactose metabolism
*
*


Glucose 1-phosphate metabolism
*
*


Glycogen degradation
*
*


Mannose degradation
*



Non-phosphorylated glucose degradation

*


UDP-glucose conversion

*


Ribose degradation
*
*


Trehalose degradation - low osmolarity
*
*

Sugar derivatives
Lactate oxidation




Mannitol degradation
*



Sorbitol degradation
*



Glucosamine catabolism
*


Other degradation
Removal of superoxide radicals
*
*


Methylglyoxal degradation



Nucleosides and nucleotides
(Deoxy)ribose phosphate metabolism
*
*


Periplasmic NAD degradation



Fatty acids
Fatty acid oxidation pathway
*
*


Triacylglycerol degradation

*


Lipases pathway

*

Carboxylates, other
Propionate metabolism - methylmalonyl pathway
*



2-Oxobutyrate degradation




Acetate degradation
*
*


Pyruvate metabolism




N-acetylneuraminate degradation



C1 compounds
Carbon monoxide dehydrogenase pathway

*


Serine-isocitrate lyase pathway

*

Amino acids, amines
Alanine degradation 3

*


Arginine degradation III




Arginase degradation pathway




Arginine proline degradation

*


Asparagine degradation 1

*


Aspartate degradation 1




Malate/aspartate shuttle pathway




L-cysteine degradation IV

*


L-cysteine degradation VI




Cysteine degradation I




Glutamate degradation I

*


Glutamate degradation IV




Glutamate degradation VII

*


Glutamine degradation 1




Glutamine degradation II




Glycine degradation II




Glycine degradation I




Histidine degradation III




Histidine degradation I




Homocysteine degradation I




Isoleucine degradation I

*


Isoleucine degradation III




Leucine degradation II




Leucine degradation I

*


Lysine degradation I

*


Methionine degradation 1

*


4-Hydroxyproline degradation

*


S-adenosylhomocysteine degradation




Phenylalanine degradation I




Proline degradation III




Proline degradation II




L-serine degradation
*
*


Threonine degradation 2




Tryptophan degradation I




Tryptophan degradation III

*


Tryptophan kynurenine degradation




Tyrosine degradation




Valine degradation I

*

Alcohols
Aerobic glycerol degradation II

*


Glycerol metabolism
*
*


Glycerol degradation I
*



Ethanol degradation
*


Amines and polyamines, other
Citrulline degradation




N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminic acid dissimilation
*
*


Glucosamine catabolism
*






Energy metabolism

Glycolysis 3

*


Glycolysis
*
*


Glycolysis 2




Glyceraldehyde 3-phosphate degradation

*


Non-oxidative branch of the pentose phosphate pathway
*
*


Oxidative branch of the pentose phosphate pathway
*
*


Aerobic respiration - electron donors reaction list
*



Pyruvate dehydrogenase
*
*


TCA cycle - aerobic respiration
*
*


Entner-Doudoroff pathway
*


More detailed subclasses were not included for brevity. An asterisk in one of the last two columns means that the pathway is also present in the EcoCyc (E. coli) and/or AraCyc (A. thaliana) databases, respectively. Note that pathway names are derived from the MetaCyc database, which explains why HumanCyc contains a pathway called 'Heme Biosynthesis II' but not 'Heme Biosynthesis I.'

Romero et al. Genome Biology 2004 6:R2   doi:10.1186/gb-2004-6-1-r2