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 (74 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b3399 b0238 b0125 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b3124 b2883 b1779 b3962 b1982 b0477 b4139 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b4374 b0675 b2361 b2291 b1415 b1014 b0261 b0411 b0822 b1701 b1805 b0112 b2975 b0114 b3603 b0509 b3125 b2366 b2492 b0904 b3035 b1533 b1380 b0325 b2413 b0508 b0514 b0515 b4266 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.318657 (mmol/gDw/h)
  Minimum Production Rate : 0.343813 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.117347
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.740244
  EX_so4_e : 0.689973
  EX_pi_e : 0.307378
  EX_k_e : 0.062200
  EX_fe2_e : 0.005118
  EX_mg2_e : 0.002764
  EX_ca2_e : 0.001659
  EX_cl_e : 0.001659
  EX_cu2_e : 0.000226
  EX_mn2_e : 0.000220
  EX_zn2_e : 0.000109
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_h2o_e : 47.879782
  EX_co2_e : 35.492489
  EX_h_e : 5.304649
  EX_ac_e : 2.297169
  EX_met__L_e : 0.609729
  EX_trp__L_e : 0.343813
  EX_alltn_e : 0.000357
  DM_5drib_c : 0.000214
  EX_dxylnt_e : 0.000213
  DM_4crsol_c : 0.000071

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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