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 : air_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b4382 b1241 b0351 b4384 b3752 b0871 b2925 b2097 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0937 b1982 b3946 b0825 b4015 b0261 b0411 b2799 b3945 b1602 b1727 b0529 b2492 b0904 b3927 b1380 b2660 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.378616 (mmol/gDw/h)
  Minimum Production Rate : 0.021749 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.923209
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.156386
  EX_pi_e : 0.386964
  EX_so4_e : 0.095343
  EX_k_e : 0.073903
  EX_fe2_e : 0.006081
  EX_mg2_e : 0.003284
  EX_cl_e : 0.001971
  EX_ca2_e : 0.001971
  EX_cu2_e : 0.000268
  EX_mn2_e : 0.000262
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 43.008702
  EX_co2_e : 29.511678
  EX_h_e : 7.837361
  EX_pyr_e : 4.291120
  EX_etoh_e : 0.948779
  Auxiliary production reaction : 0.021749
  EX_ade_e : 0.000424
  DM_5drib_c : 0.000254
  DM_4crsol_c : 0.000084

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