Table 1

Different phenotypes of E. coli B REL606 and E. coli K-12 MG1655 and modifications of the corresponding reactions

PMa

Predictionb

Carbon source

B/K-12

B/K-12

Responsible reactionc

Modification


L-Arabinose

-/++

-/+

ARAI

Deletion

Succinic acid

+/++

-/+

EX_succ(e)

Turned off

L-Aspartic acid

+/++

-/+

EX_asp_L(e)

Turned off

L-Fucose

-/++

-/+

FUCtpp

Deletion

D-Malic acid

-/++

-/+

EX_mal_D(e), MALDt2_2pp

Turned off

L-Malic acid

+/++

-/+

EX_mal_L(e)

Turned off

p-Hydroxyphenyl acetic acid

++/-

+/-

4H3M, 34DH23OR, 5C2HMSO, 5C2HMDI, 5O3E125TC, HPAI, HPAP, HPAtex, EX_4hpa(e)

Addition

N-Acetyl-D-galactosamine

++/-

+/-

ACGALptspp, ACGAL6PI

Addition

D-Arabinose

++/-

+/-

ARABDI, RBK_D1, DARBtex, EX_arab-D(e)

Addition

N-Acetyl-L-glutamic acid

++/-

+/-

NACGLUtmp

Addition


The different phenotypes of E. coli B REL606 and E. coli K-12 MG1655 were determined from PM tests and modification of the corresponding reactions were verified by in silico complementation tests. Experimental and in silico cell growth on carbon sources are fully listed in Table S5 in Additional file 1. aThe experimental phenotypes are classified into no growth ('-'), low growth ('+'), or high growth ('++') based on growth area. See footnotes of Table S5 in Additional file 1 for details. bIn silico prediction of cell growth on each carbon source was performed by flux balance analysis: no growth ('-'), growth ('+'). cThe metabolic reactions and their associated genes are provided in Table S4 in Additional file 1.

Yoon et al. Genome Biology 2012 13:R37   doi:10.1186/gb-2012-13-5-r37

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