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 : pe120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (89 of 104: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3831 b3614 b0910 b3752 b4152 b2781 b3844 b1612 b1611 b4122 b0907 b1759 b3449 b4138 b4123 b0621 b4381 b2239 b2406 b0452 b2197 b3918 b0789 b1249 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.504161 (mmol/gDw/h)
  Minimum Production Rate : 0.206787 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 998.819252
  EX_h_e : 992.678471
  EX_o2_e : 276.511644
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.366734
  EX_pi_e : 0.752587
  EX_so4_e : 0.126958
  EX_k_e : 0.098409
  EX_mg2_e : 0.004374
  EX_ca2_e : 0.002624
  EX_cl_e : 0.002624
  EX_cu2_e : 0.000357
  EX_mn2_e : 0.000348
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 998.811155
  EX_h2o_e : 545.072533
  EX_co2_e : 29.419734
  EX_succ_e : 0.525735
  EX_ura_e : 0.357525
  Auxiliary production reaction : 0.206787
  EX_g3pg_e : 0.059483
  DM_5drib_c : 0.000113
  DM_4crsol_c : 0.000112

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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