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 : amet_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b3708 b3752 b2297 b2458 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b0261 b0335 b2799 b3945 b1602 b0153 b2406 b2975 b3603 b0728 b2366 b2492 b0904 b0591 b1533 b3825 b1380 b0494 b2660 b3662 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.347802 (mmol/gDw/h)
  Minimum Production Rate : 0.447129 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.646204
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.440956
  EX_so4_e : 0.534713
  EX_pi_e : 0.335492
  EX_k_e : 0.067889
  EX_fe2_e : 0.005586
  EX_mg2_e : 0.003017
  EX_ca2_e : 0.001810
  EX_cl_e : 0.001810
  EX_cu2_e : 0.000247
  EX_mn2_e : 0.000240
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_h2o_e : 50.835722
  EX_co2_e : 35.387526
  EX_h_e : 6.352644
  EX_ac_e : 1.813564
  Auxiliary production reaction : 0.447129
  EX_ade_e : 0.000389
  DM_5drib_c : 0.000233
  DM_4crsol_c : 0.000078

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