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 : utp_h
List of minimal gene deletion strategies (Download)

Gene deletion strategy (14 of 26: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 24
  Gene deletion: PHATRDRAFT_800 PHATRDRAFT_14792 PHATRDRAFT_55192 PHATRDRAFT_draft1186 PHATRDRAFT_55086 PHATRDRAFT_55126 PHATRDRAFT_45017 PHATRDRAFT_14762 PHATRDRAFT_46664 Phatr3_EG02361 PHATRDRAFT_7164 PHATRDRAFT_47090 PHATRDRAFT_1341 PHATRDRAFT_draft462 PHATRDRAFT_46692 PHATRDRAFT_17265 PHATRDRAFT_23723 PHATRDRAFT_21970 PHATRDRAFT_22117 PHATRDRAFT_15777 PHATRDRAFT_32849 PHATRDRAFT_draft1517 PHATRDRAFT_28585 PHATRDRAFT_45428   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.108753 (mmol/gDw/h)
  Minimum Production Rate : 0.064332 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_photon_e : 1000.000000
  EX_co2_e : 7.095441
  EX_h2o_e : 5.440435
  EX_no3_e : 1.760000
  EX_pi_e : 0.220000
  EX_so4_e : 0.019341
  EX_mg2_e : 0.001944

Product: (mmol/gDw/h)
  EX_o2_e : 8.678797
  SK_for_c : 1.159738
  DM_no3_c : 1.099074
  EX_h_e : 0.320566
  DM_biomass_c : 0.108753
  EX_etoh_e : 0.095397
  Auxiliary production reaction : 0.064332

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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