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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.