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Table 2 Components of minimal pathway maps, experimentally-derived and computationally-derived essential pathway maps for E. coli and B. subtilis, and components of pathway maps for B. aphidicola APS

From: An evaluation of minimal cellular functions to sustain a bacterial cell

Classification1

 

Pathway map2

E. coli

B. subtilis

General

Minor

 

MPM3

%4

Exp5

Com6

Par7

MPM3

%4

Exp5

Com6

Metabolism

Carbohydrate

Glycolysis/Gluconeogenesis

OS

59.5

X

X

X

OS

85.1

X

X

  

Citrate cycle (TCA cycle)

OS

51.4

X

X

X

OS

28.2

X

X

  

Pentose phosphate pathway

OS

100.0

X

X

X

OS

100.0

X

X

  

Pentose and glucuronate interconversions

 

62.2

    

63.4

  
  

Fructose and mannose metabolism

 

16.2

  

X

 

43.7

X

X

  

Galactose metabolism

 

16.2

 

X

  

24.9

  
  

Ascorbate and aldarate metabolism

 

21.6

    

10.1

  
  

Starch and sucrose metabolism

 

32.4

  

X

 

18.0

 

X

  

Aminosugars metabolism

C

 

X

X

X

C

 

X

X

  

Nucleotide sugars metabolism

      

10.3

  
  

Pyruvate metabolism

 

64.9

X

X

X

 

31.2

X

X

  

Glyoxylate and dicarboxylate metabolism

OS

91.9

  

X

OS

92.9

 

X

  

Propanoate metabolism

OS

94.6

X

X

X

 

92.5

X

X

  

C5-Branched dibasic acid metabolism

OS

100.0

 

X

  

98.3

  
  

Butanoate metabolism

 

35.1

  

X

 

30.3

 

X

 

Energy

Oxidative phosphorylation

   

X

X

   

X

  

Carbon fixation

OS

83.8

X

X

X

 

74.8

X

X

  

Reductive carboxylate cycle (CO2 fixation)

 

56.8

 

X

  

45.9

 

X

  

Methane metabolism

 

86.5

  

X

 

67.9

 

X

  

Nitrogen metabolism

OS

97.3

   

OS

99.9

 

X

  

Sulfur metabolism

OS

100.0

  

X

OS

99.2

 

X

 

Lipid

Fatty acid biosynthesis

C

 

X

X

X

C

 

X

X

  

Fatty acid elongation in mitochondria

 

24.3

    

4.9

  
  

Fatty acid metabolism

OS

59.5

    

13.7

  
  

Synthesis and degradation of ketone bodies

      

5.2

  
  

Biosynthesis of steroids

 

5.4

X

X

X

C

 

X

 
  

Glycerolipid metabolism

 

21.6

X

  

OS

100.0

  
  

Glycerophospholipid metabolism

OS

100.0

X

X

 

C

 

X

 
 

Nucleotide

Purine metabolism

C

 

X

X

X

C

 

X

X

  

Pyrimidine metabolism

C

 

X

X

X

C

 

X

X

 

Amino Acid

Urea cycle and metabolism of amino groups

C

  

X

X

C

   
  

Glutamate metabolism

C

 

X

X

X

C

 

X

X

  

Alanine and aspartate metabolism

OS

100.0

X

X

X

C

 

X

X

  

Glycine, serine and threonine metabolism

OS

100.0

X

X

X

OS

99.8

X

X

  

Methionine metabolism

OS

97.3

X

X

X

OS

98.3

X

X

  

Cysteine metabolism

 

40.5

 

X

X

 

71.8

  
  

Valine, leucine and isoleucine degradation

OS

100.0

  

X

OS

99.3

 

X

  

Valine, leucine and isoleucine biosynthesis

C

 

X

X

X

C

 

X

X

  

Lysine biosynthesis

C

 

X

X

X

C

 

X

X

  

Lysine degradation

 

54.1

  

X

 

33.2

  
  

Arginine and proline metabolism

OS

89.2

X

X

X

C

 

X

 
  

Histidine metabolism

C

  

X

X

C

   
  

Tyrosine metabolism

 

13.5

    

13.9

  
  

Phenylalanine metabolism

 

67.6

    

12.5

  
  

Tryptophan metabolism

 

24.3

  

X

 

21.0

 

X

  

Phenylalanine, tyrosine and tryptophan biosynthesis

C

 

X

X

X

C

 

X

X

 

Other Amino Acids

beta-Alanine metabolism

OS

100.0

  

X

 

76.8

  
  

Taurine and hypotaurine metabolism

 

5.4

  

X

 

25.7

 

X

  

Selenoamino acid metabolism

 

48.6

X

X

X

 

32.0

X

X

  

Cyanoamino acid metabolism

 

75.7

   

OS

96.8

 

X

  

D-Glutamine and D-glutamate metabolism

OS

67.6

X

X

X

OS

57.9

X

 
  

D-Alanine metabolism

 

62.2

    

28.3

X

X

  

Glutathione metabolism

OS

100.0

  

X

OS

60.8

 

X

 

Glycan

Lipopolysaccharide biosynthesis

 

2.7

X

 

X

    
  

Peptidoglycan biosynthesis

C

 

X

X

X

C

 

X

 
  

Polyunsaturated fatty acid biosynthesis

 

70.3

    

36.3

  
 

Cofactors and Vitamins

Ubiquinone biosynthesis

 

24.3

    

6.1

X

 
  

One carbon pool by folate

C

 

X

X

X

C

 

X

X

  

Thiamine metabolism

 

8.1

 

X

X

 

29.7

X

 
  

Riboflavin metabolism

C

 

X

 

X

C

   
  

Vitamin B6 metabolism

 

27.0

  

X

 

22.7

 

X

  

Nicotinate and nicotinamide metabolism

OS

100.0

X

 

X

OS

100.0

X

 
  

Pantothenate and CoA biosynthesis

C

 

X

X

X

C

 

X

X

  

Biotin metabolism

OS

100.0

  

X

OS

98.1

  
  

Folate biosynthesis

 

35.1

X

X

X

C

   
  

Porphyrin and chlorophyll metabolism

C

 

X

X

X

C

   
 

Polyketides, Nonribosomal Peptides

Biosynthesis of siderophore group nonribosomal peptides

 

27.0

    

6.8

  
 

Secondary Metabolites

Terpenoid biosynthesis

  

X

 

X

OS

97.7

  
  

Alkaloid biosynthesis I

 

16.2

    

4.2

  
  

Alkaloid biosynthesis II

 

51.4

       
  

Novobiocin biosynthesis

 

27.0

    

4.5

  
  

Streptomycin biosynthesis

 

5.4

    

26.8

  
 

Xenobiotics

Caprolactam degradation

 

10.8

       
  

Biphenyl degradation

 

27.0

       
  

Toluene and xylene degradation

 

18.9

       
  

3-Chloroacrylic acid degradation

      

3.7

  
  

Styrene degradation

 

18.9

       
  

1,4-Dichlorobenzene degradation

 

27.0

       
  

Ethylbenzene degradation

 

27.0

       
  

Fluorene degradation

 

27.0

       
  

Carbazole degradation

 

16.2

       
  

Benzoate degradation via CoA ligation

 

18.9

    

15.8

  
  

Benzoate degradation via hydroxylation

 

24.3

       

Genetic Information Processing

Transcription

RNA polymerase

C

 

X

X

X

C

 

X

X

 

Translation

Aminoacyl-tRNA biosynthesis

C

 

X

X

X

C

 

X

X

  

Ribosome

C

 

X

X

X

C

 

X

X

 

Folding, Sorting, Degradation

Protein export

C

 

X

X

X

C

 

X

X

 

Replication and Repair

DNA polymerase

C

 

X

X

X

C

 

X

X

Environmental Information Processing

Membrane Transport

ABC transporters - General

  

X

X

X

  

X

X

  

Phosphotransferase system (PTS)

    

X

   

X

 

Signal Transduction

Two-component system - General

   

X

X

  

X

X

Cellular Processes

Cell Motility

Bacterial chemotaxis - General

    

X

   

X

  

Flagellar assembly

    

X

   

X

  1. 1KEGG classification (General/Minor) for each pathway map. Minor classifications are denoted as the abbreviations of ''official'' KEGG classifications, e.g, Energy (''Energy metabolism'' in KEGG).
  2. 2Only the pathway maps referred to in this work are listed.
  3. 3The components of the minimal pathway maps. C: the conserved pathway maps, OS: the organism-specific pathway maps.
  4. 4The percentage of appearance of organism-specific maps in the 54 autonomous pathway maps20* of E. coli (or 3,391 autonomous pathway maps25* of B. subtilis). Only the pathway maps appeared at least once are shown.
  5. 5The experimentally-derived essential pathway maps.
  6. 6The computationally-derived essential pathway maps.
  7. 7The pathway maps for Buchnera aphidicola APS.
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BMC Systems Biology

ISSN: 1752-0509

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