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 : gsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4382 b0238 b0125 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2779 b3236 b2883 b0477 b3616 b3589 b2210 b0261 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.434476 (mmol/gDw/h)
  Minimum Production Rate : 0.555237 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.860729
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.469957
  EX_pi_e : 0.419098
  EX_so4_e : 0.109410
  EX_k_e : 0.084807
  EX_fe2_e : 0.006978
  EX_mg2_e : 0.003769
  EX_cl_e : 0.002261
  EX_ca2_e : 0.002261
  EX_cu2_e : 0.000308
  EX_mn2_e : 0.000300
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000140
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.705322
  EX_co2_e : 33.121467
  EX_h_e : 8.515510
  EX_ac_e : 1.745719
  Auxiliary production reaction : 0.555237
  EX_ade_e : 0.000292
  DM_5drib_c : 0.000098
  DM_4crsol_c : 0.000097

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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