Skip to main content

Table 3 The entire set of pathways in HumanCyc, grouped by classes using the MetaCyc pathway classification hierarchy

From: Computational prediction of human metabolic pathways from the complete human genome

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 *  
  1. 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.'