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 : thymd_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b0474 b2518 b1241 b0351 b3831 b4069 b3752 b4152 b3115 b1849 b2296 b2926 b2781 b1612 b1611 b4122 b1759 b3616 b3589 b4161 b0411 b4138 b4123 b0621 b2913 b4381 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.597370 (mmol/gDw/h)
  Minimum Production Rate : 0.315498 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.067240
  EX_o2_e : 276.073345
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.298791
  EX_pi_e : 0.576227
  EX_so4_e : 0.150430
  EX_k_e : 0.116602
  EX_mg2_e : 0.005182
  EX_ca2_e : 0.003109
  EX_cl_e : 0.003109
  EX_cu2_e : 0.000424
  EX_mn2_e : 0.000413
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990406
  EX_h2o_e : 545.545776
  EX_co2_e : 26.719139
  EX_ac_e : 1.341181
  EX_succ_e : 0.622932
  EX_thymd_e : 0.315498
  EX_ura_e : 0.108126
  DM_5drib_c : 0.000134
  DM_4crsol_c : 0.000133

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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