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 : g3pg_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b3831 b4384 b3614 b0910 b3752 b4152 b2781 b3617 b1612 b1611 b4122 b1779 b1759 b3449 b0411 b4388 b4138 b4123 b0621 b2239 b0529 b3918 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.575567 (mmol/gDw/h)
  Minimum Production Rate : 0.303983 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.989477
  EX_o2_e : 276.375466
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.032404
  EX_pi_e : 0.859179
  EX_so4_e : 0.144939
  EX_k_e : 0.112347
  EX_mg2_e : 0.004993
  EX_cl_e : 0.002996
  EX_ca2_e : 0.002996
  EX_cu2_e : 0.000408
  EX_mn2_e : 0.000398
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000186
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990756
  EX_h2o_e : 545.537337
  EX_co2_e : 27.701806
  EX_acald_e : 1.408230
  EX_succ_e : 0.600197
  EX_ura_e : 0.408162
  EX_g3pg_e : 0.303983
  DM_5drib_c : 0.000130
  DM_4crsol_c : 0.000128

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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