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 : imacp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b1241 b0351 b3831 b4069 b3708 b3614 b0910 b3752 b2297 b2458 b2779 b3617 b2407 b2883 b2797 b3117 b1814 b4471 b4381 b2406 b0112 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.394167 (mmol/gDw/h)
  Minimum Production Rate : 1.109211 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.778422
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.618086
  EX_pi_e : 1.489428
  EX_so4_e : 0.099259
  EX_k_e : 0.076939
  EX_fe2_e : 0.006331
  EX_mg2_e : 0.003419
  EX_ca2_e : 0.002052
  EX_cl_e : 0.002052
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 52.414495
  EX_co2_e : 34.993632
  EX_h_e : 6.890247
  Auxiliary production reaction : 1.109211
  EX_ac_e : 0.907367
  EX_thym_e : 0.071345
  DM_mththf_c : 0.000177
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000088

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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