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 : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b3617 b2883 b1982 b2797 b3117 b1814 b4471 b1623 b0411 b4381 b2868 b0114 b2366 b2492 b0904 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.645010 (mmol/gDw/h)
  Minimum Production Rate : 0.632408 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.091992
  EX_nh4_e : 10.197778
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.519406
  EX_so4_e : 0.162426
  EX_k_e : 0.125901
  EX_fe2_e : 0.010360
  EX_mg2_e : 0.005595
  EX_cl_e : 0.003357
  EX_ca2_e : 0.003357
  EX_cu2_e : 0.000457
  EX_mn2_e : 0.000446
  EX_zn2_e : 0.000220
  EX_ni2_e : 0.000208
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 48.887050
  EX_co2_e : 22.844158
  EX_h_e : 10.028041
  EX_ac_e : 2.134524
  Auxiliary production reaction : 0.632408
  EX_hxan_e : 0.016877
  EX_ade_e : 0.000434
  DM_mththf_c : 0.000289
  DM_5drib_c : 0.000145
  DM_4crsol_c : 0.000144

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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