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 : ps160_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1054 b2836 b4382 b3846 b2341 b3831 b4384 b3614 b0910 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b4138 b4123 b0621 b2406 b2197 b3918 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.560373 (mmol/gDw/h)
  Minimum Production Rate : 0.295958 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 17.374892
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.142713
  EX_pi_e : 0.836497
  EX_so4_e : 0.141113
  EX_k_e : 0.109381
  EX_fe2_e : 0.009000
  EX_mg2_e : 0.004861
  EX_cl_e : 0.002917
  EX_ca2_e : 0.002917
  EX_cu2_e : 0.000397
  EX_mn2_e : 0.000387
  EX_zn2_e : 0.000191
  EX_ni2_e : 0.000181
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 40.378918
  EX_co2_e : 21.825896
  EX_h_e : 7.112410
  EX_succ_e : 0.584352
  EX_ura_e : 0.397387
  Auxiliary production reaction : 0.295958
  DM_5drib_c : 0.000126
  DM_4crsol_c : 0.000125

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
Contact