Table 2 Elementary modes for acetate-producing E. coli knockout strategiesa
From: Analysis of complex metabolic behavior through pathway decomposition
Knockouts (Number in brackets, Separated by semi-colons) | Mode | Weight | Overall conversion (Acetate production in bold) | Biomass (g/mmol Glc) | NGAM (mmol/mmol Glc) | Number of reactions |
|---|---|---|---|---|---|---|
(0) None | 1 | 2.92 | 1.000 Glc + 0.005 K + 0.315 NH4 + 0.028 Pi + 0.007 SO4 → 0.785 Ac + 1.661 CO2 + 0.766 EtOH + 1.073 H + 1.675 H2 + 0.010 Succ | 0.029 | 0.2 | 412 |
|  | 2 | 7.08 | 1.000 Glc + 0.297 H2O + 0.004 K + 0.222 NH4 + 0.020 Pi + 0.005 SO4 → 0.849 Ac + 1.762 CO2 + 0.835 EtOH + 1.051 H + 1.772 H2 + 0.007 Succ | 0.021 | 1.1 | 414 |
|  | Combined | 10.000 Glc + 2.101 H2O + 0.041 K + 0.002 Mg2 + 2.492 NH4 + 0.222 Pi + 0.058 SO4 → 8.301 Ac + 17.322 CO2 + 8.152 EtOH + 10.578 H + 17.434 H2 + 0.077 Succ | 0.23 | 8.4 | 415 | |
(1) frmA, adhE, adhP | 1 | 4.18 | 1.000 Glc + 0.667 H2O → 0.667 12PPD-R + 1.333 Ac + 1.333 CO2 + 1.333 H + 1.333 H2 | 0 | 2 | 38 |
|  | 2 | 5.82 | 1.000 Glc + 0.004 K + 0.228 NH4 + 0.020 Pi + 0.005 SO4 → 0.554 12PPD-R + 1.121 Ac + 1.201 CO2 + 1.330 H + 1.211 H2 + 0.007 Succ | 0.021 | 0.0045 | 414 |
|  | Combined | 10.000 Glc + 2.788 H2O + 0.022 K + 1.327 NH4 + 0.118 Pi + 0.031 SO4 → 6.011 12PPD-R + 12.101 Ac + 12.563 CO2 + 13.313 H + 12.623 H2 + 0.041 Succ | 0.12 | 8.4 | 418 | |
(2) mhpF, adhE; ydfG | 1 | 4.07 | 1.000 Glc + 0.750 H2O → 1.500 Ac + 1.500 CO2 + 0.750 EtOH + 1.500 H + 1.500 H2 | 0 | 2.1 | 54 |
|  | 2 | 5.93 | 1.000 Glc + 0.047 H2O + 0.004 K + 0.237 NH4 + 0.021 Pi + 0.005 SO4 → 1.296 Ac + 1.306 CO2 + 0.586 EtOH + 1.513 H + 1.353 H2 + 0.007 Succ | 0.022 | 0 | 417 |
|  | Combined | 10.000 Glc + 3.331 H2O + 0.023 K + 0.001 Mg2 + 1.406 NH4 + 0.125 Pi + 0.033 SO4 → 13.791 Ac + 13.848 CO2 + 6.529 EtOH + 15.075 H + 14.128 H2 + 0.044 Succ | 0.13 | 8.4 | 418 | |
(3) atpABCDEFGH; frmA, adhE, adhP; pgi | 1 | 2.82 | 1.000 Glc + 0.444 H2O + 0.167 SO4 → 0.444 12PPD-R + 1.556 Ac + 1.556 CO2 + 1.222 H + 1.556 H2 + 0.167 H2S | 0 | 1.3 | 59 |
|  | 2 | 7.18 | 1.000 Glc + 0.233 H2O + 0.001 K + 0.077 NH4 + 0.007 Pi + 0.159 SO4 → 0.408 12PPD-R + 1.495 Ac + 1.486 CO2 + 1.251 H + 1.501 H2 + 0.157 H2S + 0.002 Succ | 0.0071 | 0.64 | 418 |
|  | Combined | 10.000 Glc + 2.926 H2O + 0.009 K + 0.552 NH4 + 0.049 Pi + 1.609 SO4 → 4.181 12PPD-R + 15.118 Ac + 15.056 CO2 + 12.431 H + 15.166 H2 + 1.596 H2S + 0.017 Succ | 0.051 | 8.4 | 421 | |
(4) atpABCDEFGH; frmA, adhE, adhP; pgi; yahI, ybcF, yqeA | 1 | 2.91 | 1.000 Glc + 0.444 H2O + 0.167 SO4 → 0.444 12PPD-R + 1.556 Ac + 1.556 CO2 + 1.222 H + 1.556 H2 + 0.167 H2S | 0 | 1.3 | 59 |
|  | 2 | 7.09 | 1.000 Glc + 0.233 H2O + 0.001 K + 0.077 NH4 + 0.007 Pi + 0.159 SO4 → 0.408 12PPD-R + 1.495 Ac + 1.486 CO2 + 1.251 H + 1.501 H2 + 0.157 H2S + 0.002 Succ | 0.0071 | 0.64 | 416 |
|  | Combined | 10.000 Glc + 2.946 H2O + 0.009 K + 0.545 NH4 + 0.049 Pi + 1.609 SO4 → 4.185 12PPD-R + 15.124 Ac + 15.062 CO2 + 12.428 H + 15.171 H2 + 1.597 H2S + 0.017 Succ | 0.051 | 8.4 | 419 | |
(5) atpABCDEFGH; frmA, adhE, adhP; pgi; tnaA; yahI, ybcF, yqeA | 1 | 2.87 | 1.000 Glc + 0.444 H2O + 0.167 SO4 → 0.444 12PPD-R + 1.556 Ac + 1.556 CO2 + 1.222 H + 1.556 H2 + 0.167 H2S | 0 | 1.3 | 59 |
|  | 2 | 7.13 | 1.000 Glc + 0.235 H2O + 0.001 K + 0.076 NH4 + 0.007 Pi + 0.158 SO4 → 0.408 12PPD-R + 1.496 Ac + 1.486 CO2 + 1.252 H + 1.501 H2 + 0.157 H2S + 0.002 Succ | 0.0071 | 0.64 | 413 |
|  | Combined | 10.000 Glc + 2.949 H2O + 0.009 K + 0.544 NH4 + 0.049 Pi + 1.607 SO4 → 4.185 12PPD-R + 15.128 Ac + 15.057 CO2 + 12.435 H + 15.168 H2 + 1.595 H2S + 0.017 Succ | 0.05 | 8.4 | 417 | |
(6) atpABCDEFGH; galP; mhpF, adhE; pgi; pitAB; ydfG | 1 | 6.53 | 1.000 Glc + 0.762 H2O → 0.071 12PPD-R + 1.690 Ac + 1.357 CO2 + 0.524 EtOH + 1.690 H + 1.524 H2 | 0 | 1.3 | 77 |
|  | 2 | 3.47 | 1.000 Glc + 0.280 H2O + 0.003 K + 0.156 NH4 + 0.014 Pi + 0.004 SO4 → 0.114 12PPD-R + 1.404 Ac + 1.304 CO2 + 0.467 EtOH + 1.546 H + 1.388 H2 + 0.005 Succ | 0.014 | 0 | 424 |
|  | Combined | 10.000 Glc + 5.945 H2O + 0.009 K + 0.542 NH4 + 0.048 Pi + 0.013 SO4 → 0.863 12PPD-R + 15.908 Ac + 13.386 CO2 + 5.042 EtOH + 16.403 H + 14.766 H2 + 0.017 Succ | 0.05 | 8.4 | 427 | |
(8) (sapD or trkA or trkG), (sapD or trkA or trkH), kch, kup; atpABCDEFGH; galP; guaB; mhpF, adhE; pgi; pitAB; ydfG | 1 | 6.53 | 1.000 Glc + 0.762 H2O → 0.071 12PPD-R + 1.690 Ac + 1.357 CO2 + 0.524 EtOH + 1.690 H + 1.524 H2 | 0 | 1.3 | 77 |
|  | 2 | 3.47 | 1.000 Glc + 0.282 H2O + 0.003 K + 0.155 NH4 + 0.014 Pi + 0.004 SO4 → 0.114 12PPD-R + 1.406 Ac + 1.304 CO2 + 0.468 EtOH + 1.547 H + 1.389 H2 + 0.005 Succ | 0.014 | 0 | 424 |
|  | Combined | 10.000 Glc + 5.953 H2O + 0.009 K + 0.539 NH4 + 0.048 Pi + 0.013 SO4 → 0.861 12PPD-R + 15.915 Ac + 13.387 CO2 + 5.043 EtOH + 16.407 H + 14.769 H2 + 0.017 Succ | 0.05 | 8.4 | 427 | |