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 (65 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b2297 b2458 b2779 b2407 b3844 b1004 b3713 b1109 b0046 b3124 b3236 b0207 b3012 b0937 b1602 b2913 b2492 b0904 b1781 b3001 b1380 b0325 b0514 b1771 b1511 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.496571 (mmol/gDw/h)
  Minimum Production Rate : 0.440279 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.140238
  EX_o2_e : 286.215948
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.362921
  EX_pi_e : 0.478995
  EX_so4_e : 0.125046
  EX_k_e : 0.096927
  EX_mg2_e : 0.004308
  EX_ca2_e : 0.002585
  EX_cl_e : 0.002585
  EX_cu2_e : 0.000352
  EX_mn2_e : 0.000343
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992025
  EX_h2o_e : 550.386705
  EX_co2_e : 37.717913
  EX_12ppd__S_e : 0.440279
  EX_ac_e : 0.289097
  DM_mththf_c : 0.000222
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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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