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 (77 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2836 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2407 b1238 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b2210 b0261 b4381 b2406 b0112 b2868 b0114 b0509 b3125 b2366 b2492 b0904 b1533 b0508 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.446607 (mmol/gDw/h)
  Minimum Production Rate : 0.222730 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.296392
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.166777
  EX_pi_e : 1.098992
  EX_so4_e : 1.003387
  EX_tungs_e : 0.222730
  EX_k_e : 0.087175
  EX_fe2_e : 0.007173
  EX_mg2_e : 0.003874
  EX_ca2_e : 0.002325
  EX_cl_e : 0.002325
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.624236
  EX_co2_e : 28.025432
  EX_h_e : 8.253286
  EX_ac_e : 3.478691
  Auxiliary production reaction : 0.222730
  EX_ade_e : 0.000500
  DM_5drib_c : 0.000300
  EX_glyclt_e : 0.000299
  DM_4crsol_c : 0.000100

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.

Last updated: 09-Jul-2025
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