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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4467 b2836 b3399 b4382 b1241 b0351 b4069 b2502 b2744 b3708 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0675 b2361 b0261 b1602 b0153 b4381 b2406 b1727 b0114 b2366 b2492 b0904 b0591 b1533 b1380 b2660 b1771 b4141 b1798 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.368227 (mmol/gDw/h)
  Minimum Production Rate : 0.207041 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.024170
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.274785
  EX_pi_e : 0.769276
  EX_so4_e : 0.092727
  EX_k_e : 0.071875
  EX_fe2_e : 0.005914
  EX_mg2_e : 0.003194
  EX_ca2_e : 0.001917
  EX_cl_e : 0.001917
  EX_cu2_e : 0.000261
  EX_mn2_e : 0.000254
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 51.471436
  EX_co2_e : 34.345993
  EX_h_e : 6.481676
  EX_etoh_e : 0.850671
  EX_his__L_e : 0.668494
  EX_ac_e : 0.214377
  Auxiliary production reaction : 0.207041
  EX_ade_e : 0.010047
  DM_5drib_c : 0.000247
  DM_4crsol_c : 0.000082

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