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 : bwco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2744 b3708 b2297 b2458 b2926 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b1033 b0675 b2361 b0261 b1701 b1805 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b2366 b2492 b0904 b1533 b1380 b4141 b1798 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.421862 (mmol/gDw/h)
  Minimum Production Rate : 0.091196 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.616011
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.926365
  EX_pi_e : 0.680517
  EX_so4_e : 0.471016
  EX_tungs_e : 0.091196
  EX_k_e : 0.082344
  EX_fe3_e : 0.006777
  EX_mg2_e : 0.003660
  EX_ca2_e : 0.002196
  EX_cl_e : 0.002196
  EX_cu2_e : 0.000299
  EX_mn2_e : 0.000292
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.579825
  EX_co2_e : 37.425687
  EX_h_e : 5.418788
  EX_ac_e : 1.259830
  Auxiliary production reaction : 0.091196
  EX_ade_e : 0.000472
  DM_5drib_c : 0.000283
  DM_4crsol_c : 0.000094

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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