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 (58 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3553 b3399 b4382 b0586 b1241 b0351 b4069 b2502 b2744 b3708 b1479 b2297 b2458 b2926 b3617 b3236 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b4267 b1033 b0675 b2361 b1014 b0261 b3945 b0507 b4381 b2406 b0112 b0114 b0306 b1539 b3605 b2492 b0904 b1533 b2835 b1380 b0325 b0494 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.318961 (mmol/gDw/h)
  Minimum Production Rate : 0.635166 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.681508
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.026383
  EX_so4_e : 0.382916
  EX_pi_e : 0.307672
  EX_k_e : 0.062259
  EX_fe2_e : 0.005123
  EX_mg2_e : 0.002767
  EX_ca2_e : 0.001660
  EX_cl_e : 0.001660
  EX_cu2_e : 0.000226
  EX_mn2_e : 0.000220
  EX_zn2_e : 0.000109
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_h2o_e : 48.549963
  EX_co2_e : 34.423159
  EX_h_e : 5.899401
  EX_ac_e : 1.983304
  EX_trp__L_e : 0.635166
  EX_met__L_e : 0.302596
  DM_oxam_c : 0.008703
  DM_5drib_c : 0.000214
  EX_glyclt_e : 0.000213
  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