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 (25 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2744 b3614 b0910 b4152 b2781 b1612 b1611 b4122 b1759 b3449 b4374 b0675 b2361 b2291 b4138 b4123 b0621 b2913 b2239 b0529 b2197 b3918 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.690672 (mmol/gDw/h)
  Minimum Production Rate : 0.364775 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.587476
  EX_o2_e : 273.875697
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.438780
  EX_pi_e : 1.031002
  EX_so4_e : 0.173925
  EX_k_e : 0.134814
  EX_mg2_e : 0.005992
  EX_ca2_e : 0.003595
  EX_cl_e : 0.003595
  EX_cu2_e : 0.000490
  EX_mn2_e : 0.000477
  EX_zn2_e : 0.000236
  EX_ni2_e : 0.000223
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988907
  EX_h2o_e : 546.024729
  EX_co2_e : 24.622357
  EX_succ_e : 0.720228
  EX_ura_e : 0.489789
  EX_g3pg_e : 0.364775
  DM_5drib_c : 0.000155
  DM_4crsol_c : 0.000154

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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