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 (38 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4382 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2779 b2407 b2797 b3117 b1814 b4471 b3665 b0452 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b3927 b2835 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.675776 (mmol/gDw/h)
  Minimum Production Rate : 0.215295 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.417308
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.374795
  EX_pi_e : 1.297741
  EX_so4_e : 0.170174
  EX_k_e : 0.131907
  EX_fe2_e : 0.010854
  EX_mg2_e : 0.005862
  EX_cl_e : 0.003517
  EX_ca2_e : 0.003517
  EX_cu2_e : 0.000479
  EX_mn2_e : 0.000467
  EX_zn2_e : 0.000230
  EX_ni2_e : 0.000218
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 50.180688
  EX_co2_e : 29.321191
  EX_h_e : 7.248609
  EX_ac_e : 0.393427
  Auxiliary production reaction : 0.215295
  DM_mththf_c : 0.000303
  DM_5drib_c : 0.000152
  DM_4crsol_c : 0.000151

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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