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 : adn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4382 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2407 b1982 b2797 b3117 b1814 b4471 b2406 b2943 b2868 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3821 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.733051 (mmol/gDw/h)
  Minimum Production Rate : 0.310955 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.268651
  EX_o2_e : 275.155766
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.474126
  EX_pi_e : 0.707105
  EX_so4_e : 0.184597
  EX_k_e : 0.143086
  EX_mg2_e : 0.006359
  EX_ca2_e : 0.003816
  EX_cl_e : 0.003816
  EX_cu2_e : 0.000520
  EX_mn2_e : 0.000507
  EX_zn2_e : 0.000250
  EX_ni2_e : 0.000237
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988226
  EX_h2o_e : 548.721827
  EX_co2_e : 25.944434
  EX_ac_e : 0.426772
  Auxiliary production reaction : 0.310955
  EX_ade_e : 0.000493
  DM_mththf_c : 0.000328
  DM_5drib_c : 0.000165
  DM_4crsol_c : 0.000163

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.

Last updated: 21-Sep-2023
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