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 : g3pg_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3500 b4382 b4384 b2744 b3614 b0910 b4152 b2779 b2781 b2235 b1612 b1611 b4122 b1779 b1759 b4374 b0675 b4138 b4123 b0621 b2239 b3453 b2197 b2835 b3918 b0789 b1249 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.628500 (mmol/gDw/h)
  Minimum Production Rate : 0.078343 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.130043
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.679142
  EX_pi_e : 0.684598
  EX_so4_e : 0.158269
  EX_k_e : 0.122679
  EX_fe2_e : 0.010094
  EX_mg2_e : 0.005452
  EX_ca2_e : 0.003271
  EX_cl_e : 0.003271
  EX_cu2_e : 0.000446
  EX_mn2_e : 0.000434
  EX_zn2_e : 0.000214
  EX_ni2_e : 0.000203
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 47.541392
  EX_co2_e : 27.806967
  EX_h_e : 7.898750
  EX_succ_e : 0.655394
  EX_thymd_e : 0.253596
  EX_ura_e : 0.192104
  EX_g3pg_e : 0.078343
  DM_5drib_c : 0.000141
  DM_4crsol_c : 0.000140

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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