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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b3708 b0512 b0871 b2925 b2097 b3236 b2690 b2797 b3117 b1814 b4471 b3616 b3589 b2210 b0675 b0261 b0822 b4381 b2406 b0511 b1727 b0114 b2366 b2492 b0904 b1533 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.467964 (mmol/gDw/h)
  Minimum Production Rate : 1.118194 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.434787
  EX_o2_e : 276.554825
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.193634
  EX_pi_e : 0.451401
  EX_so4_e : 0.117843
  EX_k_e : 0.091343
  EX_mg2_e : 0.004060
  EX_ca2_e : 0.002436
  EX_cl_e : 0.002436
  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_fe3_e : 999.992484
  EX_h2o_e : 543.709146
  EX_co2_e : 29.065208
  Auxiliary production reaction : 1.118194
  EX_acald_e : 0.804804
  EX_thym_e : 0.010737
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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