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 : no2_h
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 36: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: PHATRDRAFT_10257 PHATRDRAFT_draft870 PHATRDRAFT_10073 PHATRDRAFT_34010 PHATRDRAFT_54082 PHATRDRAFT_800 PHATRDRAFT_14792 PHATRDRAFT_12902 PHATRDRAFT_55192 Phatr3_EG02232 PHATRDRAFT_draft1186 PHATRDRAFT_55086 PHATRDRAFT_55126 PHATRDRAFT_49372 PHATRDRAFT_46664 PHATRDRAFT_50097 PHATRDRAFT_54731 Phatr3_EG02042 PHATRDRAFT_36906 PHATRDRAFT_20310 PHATRDRAFT_19482 PHATRDRAFT_13005 PHATRDRAFT_50084 Phatr3_EG01947 PHATRDRAFT_draft462 PHATRDRAFT_46692 PHATRDRAFT_17265 Phatr3_EG02569 PHATRDRAFT_21970 PHATRDRAFT_39772 PHATRDRAFT_51970 PHATRDRAFT_43697   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.356322 (mmol/gDw/h)
  Minimum Production Rate : 0.016078 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_photon_e : 1000.000000
  EX_co2_e : 20.816513
  EX_h2o_e : 16.425363
  EX_no3_e : 1.760000
  EX_pi_e : 0.220000
  EX_so4_e : 0.063368
  EX_mg2_e : 0.006368

Product: (mmol/gDw/h)
  EX_o2_e : 25.193120
  SK_for_c : 3.759181
  EX_h_e : 1.852805
  DM_biomass_c : 0.356322
  DM_minohp_c : 0.021920
  Auxiliary production reaction : 0.016078

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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