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 : glyc_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4467 b1241 b0351 b4069 b3926 b2297 b2458 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b1602 b4381 b3915 b0529 b2492 b0904 b1380 b2660 b1771 b1518 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.467853 (mmol/gDw/h)
  Minimum Production Rate : 0.324151 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.421285
  EX_o2_e : 283.031144
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.052776
  EX_pi_e : 0.451294
  EX_so4_e : 0.117815
  EX_k_e : 0.091322
  EX_mg2_e : 0.004059
  EX_cl_e : 0.002435
  EX_ca2_e : 0.002435
  EX_cu2_e : 0.000332
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992486
  EX_h2o_e : 545.670309
  EX_co2_e : 35.155174
  EX_glyc_e : 1.424155
  EX_etoh_e : 0.411665
  EX_ac_e : 0.272378
  DM_mththf_c : 0.000210
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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