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 (80 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3399 b2066 b1241 b0351 b4069 b2502 b2744 b3708 b0910 b2297 b2458 b2779 b1850 b3617 b1238 b1982 b2797 b3117 b1814 b4471 b2498 b0675 b2361 b0261 b0335 b0507 b4381 b2406 b0112 b0452 b2868 b0114 b0728 b2366 b2492 b0904 b1533 b1380   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.412666 (mmol/gDw/h)
  Minimum Production Rate : 0.002353 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.597468
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.518031
  EX_pi_e : 0.405120
  EX_so4_e : 0.113331
  EX_k_e : 0.080550
  EX_fe2_e : 0.006628
  EX_mg2_e : 0.003580
  EX_tungs_e : 0.002353
  EX_ca2_e : 0.002148
  EX_cl_e : 0.002148
  EX_cu2_e : 0.000293
  EX_mn2_e : 0.000285
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 45.646581
  EX_co2_e : 25.643828
  EX_h_e : 9.238716
  EX_ac_e : 1.694984
  EX_hxan_e : 0.719145
  DM_5drib_c : 0.718960
  EX_glyclt_e : 0.718960
  DM_4crsol_c : 0.718776
  EX_ura_e : 0.074694
  Auxiliary production reaction : 0.002353

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 (2023).
[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: 09-Jul-2025
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