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 : gsn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (23 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b4069 b4384 b3708 b3752 b2297 b2458 b2407 b1779 b1982 b2797 b3117 b1814 b4471 b0261 b0411 b4381 b2406 b0114 b2366 b0529 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.662030 (mmol/gDw/h)
  Minimum Production Rate : 0.280381 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.678771
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.551776
  EX_pi_e : 0.638598
  EX_so4_e : 0.166712
  EX_k_e : 0.129224
  EX_fe2_e : 0.010633
  EX_mg2_e : 0.005743
  EX_ca2_e : 0.003446
  EX_cl_e : 0.003446
  EX_cu2_e : 0.000469
  EX_mn2_e : 0.000457
  EX_zn2_e : 0.000226
  EX_ni2_e : 0.000214
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.817142
  EX_co2_e : 29.250563
  EX_h_e : 7.870328
  EX_ac_e : 0.385425
  EX_gsn_e : 0.280381
  DM_5drib_c : 0.000444
  DM_4crsol_c : 0.000148

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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