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 : adn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b2836 b1478 b4382 b1241 b4069 b4384 b3752 b2297 b2458 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b4139 b1623 b4015 b2799 b3945 b1602 b2406 b3915 b0529 b2492 b0904 b2954 b3029 b1380 b2660 b1517 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.468215 (mmol/gDw/h)
  Minimum Production Rate : 0.262924 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.262251
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.371299
  EX_pi_e : 0.451643
  EX_so4_e : 0.117906
  EX_k_e : 0.091392
  EX_fe3_e : 0.007520
  EX_mg2_e : 0.004062
  EX_ca2_e : 0.002437
  EX_cl_e : 0.002437
  EX_cu2_e : 0.000332
  EX_mn2_e : 0.000324
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.858503
  EX_co2_e : 37.605843
  EX_h_e : 5.897187
  EX_ac_e : 0.272588
  Auxiliary production reaction : 0.262924
  EX_glyclt_e : 0.000315
  EX_mththf_e : 0.000210
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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