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

Model : iML1515 [2].
Target metabolite : air_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b3399 b4069 b2502 b2744 b3708 b3008 b3115 b1849 b2296 b2926 b1238 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b4381 b0114 b1539 b2492 b0904 b1533 b3927 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.473970 (mmol/gDw/h)
  Minimum Production Rate : 0.301102 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.873480
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.022144
  EX_pi_e : 0.758296
  EX_so4_e : 0.119355
  EX_k_e : 0.092516
  EX_fe2_e : 0.007612
  EX_mg2_e : 0.004112
  EX_ca2_e : 0.002467
  EX_cl_e : 0.002467
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000328
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.207904
  EX_co2_e : 37.583946
  EX_h_e : 5.534273
  Auxiliary production reaction : 0.301102
  EX_ac_e : 0.275939
  DM_5drib_c : 0.000318
  DM_4crsol_c : 0.000106

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] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[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: 21-Sep-2023
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