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 : pant__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b1241 b0351 b4069 b0871 b3115 b1849 b2296 b2925 b2097 b3617 b2690 b0477 b0675 b0822 b2868 b1727 b0114 b0755 b3612 b2492 b0904 b0789 b1249 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.659177 (mmol/gDw/h)
  Minimum Production Rate : 0.135287 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.877878
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.119056
  EX_pi_e : 0.635846
  EX_so4_e : 0.165994
  EX_k_e : 0.128667
  EX_fe2_e : 0.010587
  EX_mg2_e : 0.005718
  EX_ca2_e : 0.003431
  EX_cl_e : 0.003431
  EX_cu2_e : 0.000467
  EX_mn2_e : 0.000455
  EX_zn2_e : 0.000225
  EX_ni2_e : 0.000213
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 42.826906
  EX_co2_e : 25.419862
  EX_h_e : 9.548182
  EX_ac_e : 3.356113
  Auxiliary production reaction : 0.135287
  DM_5drib_c : 0.000148
  DM_4crsol_c : 0.000147

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