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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b1241 b0351 b4069 b4384 b2744 b3752 b2297 b2458 b2926 b1004 b3713 b1109 b0046 b3236 b2883 b1982 b3616 b3589 b0261 b0411 b1602 b4381 b2868 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b2660 b3662 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.367314 (mmol/gDw/h)
  Minimum Production Rate : 0.718389 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.543756
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.192708
  EX_pi_e : 0.354314
  EX_so4_e : 0.092497
  EX_k_e : 0.071697
  EX_mg2_e : 0.003186
  EX_fe2_e : 0.003031
  EX_fe3_e : 0.002868
  EX_ca2_e : 0.001912
  EX_cl_e : 0.001912
  EX_cu2_e : 0.000260
  EX_mn2_e : 0.000254
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 51.787688
  EX_co2_e : 33.243099
  EX_h_e : 7.817489
  Auxiliary production reaction : 0.718389
  EX_his__L_e : 0.689507
  EX_etoh_e : 0.323612
  EX_ac_e : 0.213845
  EX_ade_e : 0.000411
  DM_5drib_c : 0.000246
  DM_4crsol_c : 0.000082

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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