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 (27 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2836 b3399 b0586 b4069 b2744 b3708 b3008 b3115 b1849 b2296 b0160 b3844 b1238 b3236 b1982 b2688 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b4381 b2406 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b0516 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.707878 (mmol/gDw/h)
  Minimum Production Rate : 0.446740 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.167714
  EX_o2_e : 273.437546
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.549557
  EX_pi_e : 0.682823
  EX_so4_e : 0.178258
  EX_k_e : 0.138173
  EX_mg2_e : 0.006141
  EX_ca2_e : 0.003685
  EX_cl_e : 0.003685
  EX_cu2_e : 0.000502
  EX_mn2_e : 0.000489
  EX_zn2_e : 0.000241
  EX_ni2_e : 0.000229
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988631
  EX_h2o_e : 547.456791
  EX_co2_e : 25.170194
  EX_trp__L_e : 0.446740
  EX_ac_e : 0.412117
  EX_alltn_e : 0.002764
  DM_5drib_c : 0.002446
  DM_4crsol_c : 0.002129

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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