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 : 1pyr5c_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 45: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 10
  Gene deletion: PHATR_10581 PHATRDRAFT_14792 PHATRDRAFT_42015 PHATRDRAFT_55192 PHATRDRAFT_31599 PHATRDRAFT_28191 PHATRDRAFT_859 PHATRDRAFT_35240 Phatr3_EG02247 PHATRDRAFT_16649   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.222292 (mmol/gDw/h)
  Minimum Production Rate : 0.672052 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_photon_e : 1000.000000
  EX_co2_e : 17.477147
  EX_h2o_e : 13.397149
  EX_no3_e : 1.760000
  EX_h_e : 0.291301
  EX_so4_e : 0.118052
  EX_pi_e : 0.055197
  EX_mg2_e : 0.003973

Product: (mmol/gDw/h)
  EX_o2_e : 22.954731
  EX_lac__D_e : 1.055034
  Auxiliary production reaction : 0.672052
  DM_biomass_c : 0.222292
  DM_dmsp_c : 0.078519

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