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 : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b2297 b2458 b2925 b2097 b2926 b3617 b0030 b2407 b1238 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0596 b0261 b4381 b2406 b0112 b2975 b0114 b3603 b0509 b3125 b1539 b2492 b0904 b1533 b3821 b0508 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.411843 (mmol/gDw/h)
  Minimum Production Rate : 1.232391 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.339336
  EX_o2_e : 273.232438
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.913114
  EX_pi_e : 0.397266
  EX_so4_e : 0.103710
  EX_k_e : 0.080389
  EX_mg2_e : 0.003573
  EX_ca2_e : 0.002144
  EX_cl_e : 0.002144
  EX_cu2_e : 0.000292
  EX_mn2_e : 0.000285
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993385
  EX_h2o_e : 545.460812
  EX_co2_e : 24.728431
  EX_ac_e : 2.403891
  EX_trp__L_e : 1.232391
  DM_oxam_c : 0.000461
  DM_5drib_c : 0.000276
  EX_dxylnt_e : 0.000276
  DM_4crsol_c : 0.000092

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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