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 : 12ppd__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b3942 b1732 b1241 b0351 b3926 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b3844 b1004 b3713 b1109 b0046 b2463 b1302 b2662 b3946 b2210 b0825 b4015 b0726 b1602 b1380 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.559001 (mmol/gDw/h)
  Minimum Production Rate : 1.718000 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.339792
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.037158
  EX_pi_e : 0.539215
  EX_so4_e : 0.140768
  EX_k_e : 0.109113
  EX_fe2_e : 0.008978
  EX_mg2_e : 0.004849
  EX_ca2_e : 0.002910
  EX_cl_e : 0.002910
  EX_cu2_e : 0.000396
  EX_mn2_e : 0.000386
  EX_zn2_e : 0.000191
  EX_ni2_e : 0.000181
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 44.294370
  EX_co2_e : 31.250711
  EX_h_e : 5.461762
  EX_12ppd__R_e : 1.718000
  EX_ac_e : 0.325442
  DM_5drib_c : 0.000126
  DM_4crsol_c : 0.000125

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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