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 : pep_h
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: PHATRDRAFT_20342 PHATRDRAFT_22993 PHATRDRAFT_41423 PHATRDRAFT_draft825 PHATRDRAFT_draft870 PHATRDRAFT_23871 PHATRDRAFT_13987 PHATRDRAFT_draft877 PHATRDRAFT_54082 PHATRDRAFT_42015 PHATRDRAFT_12031 PHATRDRAFT_44906 Phatr3_EG02232 PHATRDRAFT_8828 PHATRDRAFT_55126 Phatr3_EG00092 Phatr3_EG02209 PHATRDRAFT_14284 PHATRDRAFT_draft1023 PHATRDRAFT_draft1645 PHATRDRAFT_46664 PHATRDRAFT_50742 PHATRDRAFT_14202 Phatr3_EG02361 PHATRDRAFT_7164 PHATRDRAFT_573 PHATRDRAFT_50076 PHATRDRAFT_35594 PHATRDRAFT_46706 PHATRDRAFT_39711 PHATRDRAFT_50971 PHATRDRAFT_48078 Phatr3_EG02359 PHATRDRAFT_44806 PHATRDRAFT_44968 PHATRDRAFT_45377 PHATRDRAFT_1784 PHATRDRAFT_draft462 PHATRDRAFT_46692 PHATRDRAFT_17265 PHATRDRAFT_52223 PHATRDRAFT_draft1628 PHATRDRAFT_1358 PHATRDRAFT_42245 PHATRDRAFT_43697 PHATRDRAFT_32823 PHATRDRAFT_49505 PHATRDRAFT_23830   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.063419 (mmol/gDw/h)
  Minimum Production Rate : 0.204252 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_photon_e : 1000.000000
  EX_co2_e : 3.804002
  EX_h2o_e : 2.637353
  EX_no3_e : 1.760000
  EX_pi_e : 0.220000
  EX_h_e : 0.045042
  EX_so4_e : 0.011279
  EX_mg2_e : 0.001133

Product: (mmol/gDw/h)
  EX_o2_e : 4.768942
  DM_no3_c : 1.449610
  Auxiliary production reaction : 0.204252
  EX_glyclt_e : 0.088717
  DM_biomass_c : 0.063419
  SK_for_c : 0.001292

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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