Table 2

Native pathway identification in auxotrophic E. coli

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


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.

Carbonell et al. BMC Systems Biology 2011 5:122   doi:10.1186/1752-0509-5-122

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