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 : bmoco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (105 of 137: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b0238 b0125 b4069 b4384 b2744 b3708 b3008 b3752 b3115 b1849 b2296 b2883 b1982 b0477 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b2406 b2868 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3927 b3825 b0494 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.737919 (mmol/gDw/h)
  Minimum Production Rate : 0.072134 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.605029
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.055603
  EX_pi_e : 0.928203
  EX_so4_e : 0.474359
  EX_k_e : 0.144037
  EX_mobd_e : 0.072139
  EX_fe2_e : 0.011852
  EX_mg2_e : 0.006401
  EX_cl_e : 0.003841
  EX_ca2_e : 0.003841
  EX_cu2_e : 0.000523
  EX_mn2_e : 0.000510
  EX_zn2_e : 0.000252
  EX_ni2_e : 0.000238
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.774288
  EX_co2_e : 26.105730
  EX_h_e : 7.718968
  EX_ac_e : 0.718142
  Auxiliary production reaction : 0.072134
  EX_ade_e : 0.000826
  DM_5drib_c : 0.000495
  DM_4crsol_c : 0.000165

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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