MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : e_coli_core [2].
Target metabolite : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 9
  Gene deletion: b1241 b0351 b1849 b3115 b2296 b0474 b0727 b4014 b2976   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.690395 (mmol/gDw/h)
  Minimum Production Rate : 4.711922 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.041939
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.764584
  EX_pi_e : 2.539755

Product: (mmol/gDw/h)
  EX_h2o_e : 26.225176
  EX_h_e : 18.561239
  EX_co2_e : 16.484143
  EX_pyr_e : 4.711922

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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