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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.'
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Genome Biology

ISSN: 1474-760X

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