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 (32 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b2744 b4152 b2779 b2781 b1612 b1611 b4122 b1759 b3449 b4374 b4161 b0675 b4388 b4138 b4123 b0621 b4381 b2239 b2406 b3918 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.616137 (mmol/gDw/h)
  Minimum Production Rate : 0.325409 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.495337
  EX_o2_e : 277.774152
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.528086
  EX_pi_e : 0.919738
  EX_so4_e : 0.155155
  EX_k_e : 0.120266
  EX_mg2_e : 0.005345
  EX_cl_e : 0.003207
  EX_ca2_e : 0.003207
  EX_cu2_e : 0.000437
  EX_mn2_e : 0.000426
  EX_zn2_e : 0.000210
  EX_ni2_e : 0.000199
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990104
  EX_h2o_e : 547.532910
  EX_co2_e : 28.440234
  EX_succ_e : 0.642502
  EX_ura_e : 0.436932
  EX_g3pg_e : 0.325409
  DM_5drib_c : 0.000139
  DM_4crsol_c : 0.000137

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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