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 : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b3708 b3115 b1849 b2296 b2779 b3617 b1238 b3124 b3962 b1982 b1200 b4139 b0104 b2797 b3117 b1814 b4471 b3946 b0825 b4267 b0595 b0675 b2361 b1415 b1014 b0261 b2799 b4381 b2406 b0112 b2789 b3127 b3915 b0452 b2868 b2975 b0114 b3603 b0509 b3125 b1539 b2492 b0904 b2954 b1533 b1380 b0514 b4266 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.320265 (mmol/gDw/h)
  Minimum Production Rate : 0.344053 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.985228
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.762712
  EX_so4_e : 0.694633
  EX_pi_e : 0.308929
  EX_k_e : 0.062513
  EX_fe3_e : 0.005144
  EX_mg2_e : 0.002778
  EX_ca2_e : 0.001667
  EX_cl_e : 0.001667
  EX_cu2_e : 0.000227
  EX_mn2_e : 0.000221
  EX_zn2_e : 0.000109
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_h2o_e : 47.814724
  EX_co2_e : 35.376020
  EX_h_e : 5.334246
  EX_ac_e : 2.310256
  EX_met__L_e : 0.613984
  EX_trp__L_e : 0.344053
  EX_ade_e : 0.000358
  DM_5drib_c : 0.000215
  EX_dxylnt_e : 0.000214
  DM_4crsol_c : 0.000071

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