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 (11 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2407 b1238 b0593 b1982 b2797 b3117 b1814 b4471 b2265 b0261 b0507 b4381 b2406 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b3821 b3447 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.713938 (mmol/gDw/h)
  Minimum Production Rate : 0.450651 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.122343
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.618535
  EX_pi_e : 0.688669
  EX_so4_e : 0.179784
  EX_k_e : 0.139356
  EX_fe2_e : 0.011467
  EX_mg2_e : 0.006193
  EX_ca2_e : 0.003716
  EX_cl_e : 0.003716
  EX_cu2_e : 0.000506
  EX_mn2_e : 0.000493
  EX_zn2_e : 0.000243
  EX_ni2_e : 0.000231
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.355472
  EX_co2_e : 24.871679
  EX_h_e : 7.884456
  EX_trp__L_e : 0.453633
  EX_ac_e : 0.415645
  DM_oxam_c : 0.000799
  DM_5drib_c : 0.000479
  DM_4crsol_c : 0.000159

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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