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 : ins_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (95 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b1241 b0351 b4384 b2744 b3708 b3752 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b3617 b2883 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b3449 b0261 b3945 b4381 b2868 b4064 b4464 b0114 b0529 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 : 0.355423 (mmol/gDw/h)
  Minimum Production Rate : 0.081820 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.312961
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.167019
  EX_pi_e : 0.342844
  EX_so4_e : 0.089503
  EX_k_e : 0.069376
  EX_fe2_e : 0.005708
  EX_mg2_e : 0.003083
  EX_ca2_e : 0.001850
  EX_cl_e : 0.001850
  EX_cu2_e : 0.000252
  EX_mn2_e : 0.000246
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 43.817798
  EX_co2_e : 28.121131
  EX_h_e : 9.084573
  EX_pyr_e : 5.490325
  EX_ins_e : 0.081820
  EX_ade_e : 0.000239
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000079

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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