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__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b2836 b1478 b1241 b0351 b4069 b3115 b1849 b2296 b3617 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b4139 b1623 b3665 b4015 b3945 b1602 b4381 b3915 b3654 b3714 b3664 b2492 b0904 b2954 b3029 b1380 b2660 b1511 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.481134 (mmol/gDw/h)
  Minimum Production Rate : 0.327859 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.749385
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.196208
  EX_pi_e : 0.464105
  EX_so4_e : 0.121159
  EX_k_e : 0.093914
  EX_fe3_e : 0.007727
  EX_mg2_e : 0.004174
  EX_ca2_e : 0.002504
  EX_cl_e : 0.002504
  EX_cu2_e : 0.000341
  EX_mn2_e : 0.000332
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.479626
  EX_co2_e : 37.105926
  EX_h_e : 5.509117
  EX_ac_e : 1.080537
  EX_12ppd__S_e : 0.327859
  DM_mththf_c : 0.000216
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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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