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 : dhpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 115: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3553 b1241 b0351 b4069 b4384 b3115 b1849 b2296 b3617 b0030 b2407 b1982 b1033 b4014 b0261 b2976 b4381 b2406 b0112 b0114 b0509 b3125 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.364182 (mmol/gDw/h)
  Minimum Production Rate : 1.395889 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 983.551216
  EX_o2_e : 272.268327
  EX_nh4_e : 12.308872
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.351292
  EX_so4_e : 0.091708
  EX_k_e : 0.071086
  EX_mg2_e : 0.003159
  EX_ca2_e : 0.001896
  EX_cl_e : 0.001896
  EX_cu2_e : 0.000258
  EX_mn2_e : 0.000252
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994151
  EX_h2o_e : 550.807786
  EX_co2_e : 18.858641
  EX_ac_e : 1.928518
  EX_glyclt_e : 1.396133
  Auxiliary production reaction : 1.395889
  DM_oxam_c : 0.000408
  DM_5drib_c : 0.000244
  DM_4crsol_c : 0.000081

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