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 : urdglyc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (9 of 23: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 10
  Gene deletion: PHATRDRAFT_22357 PHATRDRAFT_50742 PHATRDRAFT_859 PHATRDRAFT_41886 PHATRDRAFT_39681 PHATRDRAFT_52223 PHATRDRAFT_49073 PHATRDRAFT_10409 PHATRDRAFT_48886 PHATRDRAFT_23365   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.331393 (mmol/gDw/h)
  Minimum Production Rate : 0.069043 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_photon_e : 1000.000000
  EX_h2o_e : 54.675595
  EX_co2_e : 49.267118
  EX_no3_e : 1.760000
  EX_pi_e : 0.082287
  EX_so4_e : 0.058935
  EX_mg2_e : 0.005922

Product: (mmol/gDw/h)
  EX_o2_e : 57.435338
  SK_for_c : 14.440061
  EX_h_e : 12.598015
  EX_etoh_e : 9.439138
  DM_biomass_c : 0.331393
  Auxiliary production reaction : 0.069043

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.

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Last updated: 27-Sep-2023
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