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 : ade_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (121 of 133: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b0469 b0474 b2518 b1241 b0351 b4069 b3708 b2297 b2458 b2925 b2097 b2407 b1779 b0477 b2797 b3117 b1814 b4471 b3616 b3589 b3946 b0825 b4381 b2868 b4064 b4464 b0114 b2366 b2492 b0904 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.354691 (mmol/gDw/h)
  Minimum Production Rate : 0.354134 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.928986
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.601300
  EX_pi_e : 0.342137
  EX_so4_e : 0.089318
  EX_k_e : 0.069233
  EX_fe2_e : 0.005697
  EX_mg2_e : 0.003077
  EX_ca2_e : 0.001846
  EX_cl_e : 0.001846
  EX_cu2_e : 0.000251
  EX_mn2_e : 0.000245
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 44.708311
  EX_co2_e : 31.800568
  EX_h_e : 10.964878
  EX_ac_e : 5.935168
  EX_ade_e : 0.354134
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000079

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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