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 : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b2836 b3553 b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b1033 b0261 b2799 b3945 b1602 b0153 b2406 b1727 b0114 b0584 b0509 b3125 b2366 b2492 b0904 b1533 b1380 b2660 b4141 b1798 b3662 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.358833 (mmol/gDw/h)
  Minimum Production Rate : 0.351913 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.520789
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.746264
  EX_pi_e : 0.346132
  EX_so4_e : 0.090361
  EX_k_e : 0.070042
  EX_fe2_e : 0.005763
  EX_mg2_e : 0.003113
  EX_ca2_e : 0.001868
  EX_cl_e : 0.001868
  EX_cu2_e : 0.000254
  EX_mn2_e : 0.000248
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 50.365394
  EX_co2_e : 34.709490
  EX_h_e : 6.376907
  EX_etoh_e : 0.969733
  EX_his__L_e : 0.721822
  EX_trp__L_e : 0.351913
  EX_ac_e : 0.208907
  EX_hxan_e : 0.000402
  DM_5drib_c : 0.000241
  DM_4crsol_c : 0.000080

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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