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 (78 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 64
  Gene deletion: b4467 b1478 b3399 b4382 b0238 b0125 b1241 b4069 b4384 b2744 b3708 b3752 b3115 b1849 b2296 b3844 b1004 b3713 b1109 b0046 b3124 b3236 b2883 b1638 b1779 b0120 b0937 b1982 b0477 b4139 b2797 b3117 b1814 b4471 b1623 b4014 b0261 b2976 b0411 b2799 b3945 b1602 b2913 b2406 b2789 b3127 b2975 b0114 b3603 b2366 b2492 b0904 b2954 b1533 b2835 b3029 b1380 b0494 b0514 b4141 b1798 b3662 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.467830 (mmol/gDw/h)
  Minimum Production Rate : 0.221829 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.473948
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.649657
  EX_pi_e : 0.451272
  EX_so4_e : 0.117809
  EX_k_e : 0.091317
  EX_mg2_e : 0.004058
  EX_fe2_e : 0.003861
  EX_fe3_e : 0.003653
  EX_cl_e : 0.002435
  EX_ca2_e : 0.002435
  EX_cu2_e : 0.000332
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.790499
  EX_co2_e : 37.507502
  EX_h_e : 5.171759
  EX_ac_e : 0.272364
  EX_trp__L_e : 0.221829
  EX_gly_e : 0.150856
  EX_ade_e : 0.000524
  DM_5drib_c : 0.000314
  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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