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