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 : sbzcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b2407 b3844 b0583 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b4374 b2361 b2291 b4014 b0261 b2976 b0411 b0507 b3709 b3161 b0112 b3915 b0452 b2975 b0114 b3603 b1539 b2492 b0904 b1533 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.390292 (mmol/gDw/h)
  Minimum Production Rate : 0.583607 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.420925
  EX_o2_e : 268.582949
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.300807
  EX_pi_e : 2.127298
  EX_so4_e : 0.681890
  EX_k_e : 0.076182
  EX_mg2_e : 0.003386
  EX_ca2_e : 0.002031
  EX_cl_e : 0.002031
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993732
  EX_h2o_e : 545.478500
  EX_co2_e : 20.000446
  EX_ac_e : 2.651345
  Auxiliary production reaction : 0.583607
  DM_oxam_c : 0.000437
  DM_5drib_c : 0.000262
  DM_4crsol_c : 0.000087

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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