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 : glyc__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (23 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2926 b2407 b3124 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b2406 b0112 b0452 b0114 b0755 b3612 b1539 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.467746 (mmol/gDw/h)
  Minimum Production Rate : 0.318306 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.844033
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.688442
  EX_pi_e : 0.451191
  EX_so4_e : 0.117788
  EX_k_e : 0.091301
  EX_fe2_e : 0.007512
  EX_mg2_e : 0.004058
  EX_ca2_e : 0.002435
  EX_cl_e : 0.002435
  EX_cu2_e : 0.000332
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 42.534957
  EX_co2_e : 27.000529
  EX_h_e : 7.857509
  EX_ac_e : 1.967718
  DM_oxam_c : 0.636823
  DM_5drib_c : 0.636614
  DM_4crsol_c : 0.636404
  EX_glyc__R_e : 0.318306

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