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.'