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Table 2 Native pathway identification in auxotrophic E. coli

From: A retrosynthetic biology approach to metabolic pathway design for therapeutic production

Compound Total Native pathways % of natives in best 10 p-value
Alanine 19 7 60.00% 8.59e-08
Arginine 1 1 100.00% 4.65e-02
Asparagine 3 3 100.00% 8.42e-05
Aspartic acid 7 7 100.00% 6.91e-09
Cysteine 11 5 100.00% 1.32e-07
Glutamic acid 74 53 100.00% 6.41e-52
Glutamine 7 5 100.00% 1.41e-05
Glycine 31 16 80.00% 3.16e-08
Histidine 4 4 100.00% 4.85e-04
Isoleucine 1 1 100.00% 4.55e-02
Leucine 1 1 100.00% 4.54e-02
Lysine 1 1 100.00% 6.38e-02
Methionine 107 106 100.00% 1.08e-259
Phenylalanine 4 1 100.00% 6.38e-02
Proline 1 1 100.00% 2.17e-02
Serine 2 2 100.00% 1.11e-03
Threonine 1 1 100.00% 4.35e-02
Tryptophan 2 2 100.00% 1.89e-03
Tyrosine 2 1 100.00% 1.92e-02
Valine 1 1 100.00% 4.55e-02
Citrate 4 3 100.00% 5.71e-05
ATP 12 6 100.00% 6.73e-06
GTP 2 2 100.00% 2.08-03
ADP 316 204 100.00% 2.89e-169
GDP 283 171 100.00% < 1.0e-324
  1. Biosynthetic pathways for the 20 amino acids, citrate and ATP/ADP and GTP/GDP enumerated for E. coli strains where enzymes producing the compounds have been deleted. For each test, columns correspond to: total number of enumerated pathways; number of native pathways in the wild-type strain; percentage of native pathways in the top 10 best ranked pathways; and p-values for the number of genes in E. coli strains top ranked with respect to the total enzyme genes in the database.