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 : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (15 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4382 b4384 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b0030 b2407 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b2440 b2406 b2868 b0114 b1539 b2492 b0904 b1533 b3927 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.639303 (mmol/gDw/h)
  Minimum Production Rate : 0.063053 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.516537
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.347942
  EX_pi_e : 0.805834
  EX_so4_e : 0.224042
  EX_k_e : 0.124788
  EX_fe2_e : 0.010268
  EX_mg2_e : 0.005546
  EX_ca2_e : 0.003328
  EX_cl_e : 0.003328
  EX_cu2_e : 0.000453
  EX_mn2_e : 0.000442
  EX_zn2_e : 0.000218
  EX_ni2_e : 0.000206
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 46.950369
  EX_co2_e : 27.019771
  EX_h_e : 7.848490
  EX_pyr_e : 1.783007
  Auxiliary production reaction : 0.063053
  EX_ade_e : 0.000430
  DM_mththf_c : 0.000286
  DM_5drib_c : 0.000144
  DM_4crsol_c : 0.000143

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