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 (42 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 b0907 b1759 b3449 b4374 b4161 b0675 b2361 b2291 b4138 b4123 b0621 b2239 b3918 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.616134 (mmol/gDw/h)
  Minimum Production Rate : 0.325408 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.776771
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.528052
  EX_pi_e : 0.919734
  EX_so4_e : 0.155155
  EX_k_e : 0.120265
  EX_fe2_e : 0.009896
  EX_mg2_e : 0.005345
  EX_ca2_e : 0.003207
  EX_cl_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_h2o_e : 47.537914
  EX_co2_e : 28.440376
  EX_h_e : 7.494733
  EX_succ_e : 0.642499
  EX_ura_e : 0.436930
  EX_g3pg_e : 0.325408
  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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