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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3752 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2407 b3236 b1982 b3616 b3589 b3946 b2210 b0825 b0261 b0411 b2913 b4381 b0114 b0529 b2492 b0904 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.398494 (mmol/gDw/h)
  Minimum Production Rate : 1.527406 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.281699
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.358957
  EX_pi_e : 3.439201
  EX_so4_e : 0.100349
  EX_k_e : 0.077783
  EX_fe2_e : 0.006400
  EX_mg2_e : 0.003457
  EX_ca2_e : 0.002074
  EX_cl_e : 0.002074
  EX_cu2_e : 0.000283
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 48.722617
  EX_co2_e : 25.228856
  EX_h_e : 7.147752
  Auxiliary production reaction : 1.527406
  EX_ac_e : 1.207431
  EX_pyr_e : 0.750503
  DM_oxam_c : 0.000446
  DM_5drib_c : 0.000267
  DM_4crsol_c : 0.000089

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