MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iLB1027_lipid [2].
Target metabolite : 3odd5811coa_m
List of minimal gene deletion strategies (Download)

Gene deletion strategy (16 of 21: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 6
  Gene deletion: PHATRDRAFT_20183 PHATRDRAFT_36256 PHATRDRAFT_20310 PHATRDRAFT_18064 PHATRDRAFT_20445 PHATRDRAFT_23365   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.271706 (mmol/gDw/h)
  Minimum Production Rate : 0.050844 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_photon_e : 1000.000000
  EX_co2_e : 29.296183
  EX_h2o_e : 25.059906
  EX_no3_e : 1.760000
  EX_pi_e : 0.220000
  EX_so4_e : 0.099165
  EX_mg2_e : 0.004856

Product: (mmol/gDw/h)
  EX_o2_e : 27.890399
  SK_for_c : 14.367595
  EX_h_e : 12.313361
  DM_biomass_c : 0.271706
  DM_fald_m : 0.096626
  Auxiliary production reaction : 0.050844
  SK_5mthglu_c : 0.008255

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

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: 27-Sep-2023
Contact