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 : cdigmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b3617 b2883 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b0411 b4381 b2406 b0114 b2366 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.601252 (mmol/gDw/h)
  Minimum Production Rate : 0.441927 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.281176
  EX_nh4_e : 10.912739
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.463825
  EX_so4_e : 0.151407
  EX_k_e : 0.117360
  EX_fe2_e : 0.009657
  EX_mg2_e : 0.005216
  EX_ca2_e : 0.003130
  EX_cl_e : 0.003130
  EX_cu2_e : 0.000426
  EX_mn2_e : 0.000415
  EX_zn2_e : 0.000205
  EX_ni2_e : 0.000194
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 49.280332
  EX_co2_e : 21.912831
  EX_h_e : 11.344291
  EX_ac_e : 2.284333
  Auxiliary production reaction : 0.441927
  DM_5drib_c : 0.000403
  DM_4crsol_c : 0.000134

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