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 : gdpmann_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b2836 b4382 b4069 b4384 b3708 b3752 b0871 b2297 b2458 b2925 b2097 b2407 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b3665 b0261 b2913 b2406 b0114 b2366 b0755 b3612 b0529 b2492 b0904 b1533 b3927 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.347972 (mmol/gDw/h)
  Minimum Production Rate : 0.147372 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.732846
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.496877
  EX_pi_e : 0.630400
  EX_so4_e : 0.087626
  EX_k_e : 0.067922
  EX_fe2_e : 0.005589
  EX_mg2_e : 0.003019
  EX_ca2_e : 0.001811
  EX_cl_e : 0.001811
  EX_cu2_e : 0.000247
  EX_mn2_e : 0.000240
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_h2o_e : 43.872316
  EX_co2_e : 27.448597
  EX_h_e : 9.011587
  EX_pyr_e : 5.167632
  EX_ac_e : 0.202585
  Auxiliary production reaction : 0.147372
  EX_ade_e : 0.000389
  DM_5drib_c : 0.000233
  DM_4crsol_c : 0.000078

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