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 : pep_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (15 of 26: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 7
  Gene deletion: b1611 b4122 b1612 b3236 b0767 b1676 b1854   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.572635 (mmol/gDw/h)
  Minimum Production Rate : 0.069003 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 15.148038
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.122466
  EX_pi_e : 2.175556

Product: (mmol/gDw/h)
  EX_h2o_e : 22.891820
  EX_h_e : 22.783867
  EX_co2_e : 12.968610
  EX_succ_e : 5.613899
  Auxiliary production reaction : 0.069003

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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