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 : 5aizc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4382 b4069 b4384 b3708 b3752 b0871 b2297 b2458 b2779 b2925 b2097 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b0261 b0822 b2406 b2789 b3127 b2868 b1727 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3821 b1380 b4042 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.557773 (mmol/gDw/h)
  Minimum Production Rate : 0.354407 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.852241
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.090245
  EX_pi_e : 0.892438
  EX_so4_e : 0.140458
  EX_k_e : 0.108873
  EX_fe2_e : 0.008958
  EX_mg2_e : 0.004839
  EX_ca2_e : 0.002903
  EX_cl_e : 0.002903
  EX_cu2_e : 0.000395
  EX_mn2_e : 0.000385
  EX_zn2_e : 0.000190
  EX_ni2_e : 0.000180
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.089075
  EX_co2_e : 26.146251
  EX_h_e : 9.242599
  EX_pyr_e : 2.372080
  Auxiliary production reaction : 0.354407
  EX_ac_e : 0.324728
  EX_ade_e : 0.000624
  DM_5drib_c : 0.000374
  DM_4crsol_c : 0.000124

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