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 : skm_h
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 40: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 24
  Gene deletion: PHATRDRAFT_draft870 PHATRDRAFT_23871 PHATRDRAFT_13987 PHATRDRAFT_draft877 PHATRDRAFT_27976 PHATRDRAFT_22913 PHATRDRAFT_55079 PHATRDRAFT_8828 PHATRDRAFT_draft1186 PHATRDRAFT_22404 PHATRDRAFT_8691 PHATRDRAFT_45239 PHATRDRAFT_1155 PHATRDRAFT_13232 PHATRDRAFT_28191 Phatr3_EG02361 PHATRDRAFT_42458 PHATRDRAFT_39711 PHATRDRAFT_48078 PHATRDRAFT_10306 PHATRDRAFT_43697 PHATRDRAFT_49505 PHATRDRAFT_draft18 PHATRDRAFT_44384   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.114036 (mmol/gDw/h)
  Minimum Production Rate : 1.551431 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_photon_e : 1000.000000
  EX_co2_e : 26.333922
  EX_h2o_e : 15.791879
  EX_no3_e : 1.760000
  EX_h_e : 0.260560
  EX_pi_e : 0.220000
  EX_so4_e : 0.020280
  EX_mg2_e : 0.002038

Product: (mmol/gDw/h)
  EX_o2_e : 32.064351
  Auxiliary production reaction : 1.551431
  DM_indole_c : 1.201882
  EX_etoh_e : 0.125148
  DM_biomass_c : 0.114036
  DM_minohp_c : 0.031947

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
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