MetNetComp Database [1] / Core Genes A set of core genes for simulation-based growth-coupled production. You can also see minimal gene deletions.

Model : e_coli_core [2].
Target metabolite : e4p_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 45
  Remaining genes: s0001 b0118 b0720 b0979 b0978 b2779 b2097 b0904 b2416 b2415 b1779 b2417 b1621 b3870 b3213 b3212 b1136 b2281 b2277 b2280 b2286 b2287 b2284 b2276 b2282 b2279 b2283 b2285 b2288 b2278 b1603 b1602 b1723 b0902 b0903 b4025 b2926 b0755 b2987 b3956 b1854 b4301 b4090 b2935 b3919   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.153333 (mmol/gDw/h)
  Minimum Production Rate : 0.082294 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 8.698742
  EX_nh4_e : 0.836093
  EX_pi_e : 0.646359
  EX_co2_e : 0.273960

Product: (mmol/gDw/h)
  EX_h_e : 21.375793
  EX_h2o_e : 18.485119
  EX_pyr_e : 17.559848
  EX_for_e : 0.740091
  Auxiliary production reaction : 0.082294

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Orth, J. D., Fleming, R. M., Palsson, B. Ø. (2010). Reconstruction and use of microbial metabolic networks: the core Escherichia coli metabolic model as an educational guide. EcoSal plus, 4(1).
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 27-Sep-2023
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