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 : adn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4069 b2744 b3708 b3008 b3115 b1849 b2296 b2883 b2797 b3117 b1814 b4471 b0411 b4381 b2239 b3453 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b3927 b3825 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.750988 (mmol/gDw/h)
  Minimum Production Rate : 0.319069 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.303653
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.705948
  EX_pi_e : 0.724407
  EX_so4_e : 0.189114
  EX_k_e : 0.146588
  EX_fe2_e : 0.012062
  EX_mg2_e : 0.006515
  EX_cl_e : 0.003909
  EX_ca2_e : 0.003909
  EX_cu2_e : 0.000532
  EX_mn2_e : 0.000519
  EX_zn2_e : 0.000256
  EX_ni2_e : 0.000243
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.449871
  EX_co2_e : 25.108604
  EX_h_e : 8.932934
  EX_ac_e : 0.437215
  Auxiliary production reaction : 0.319069
  DM_mththf_c : 0.000336
  DM_5drib_c : 0.000169
  DM_4crsol_c : 0.000167

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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