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