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 : cdp12dgr1619Z160_h
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: PHATRDRAFT_10257 PHATRDRAFT_draft870 PHATRDRAFT_10073 PHATRDRAFT_23871 PHATRDRAFT_54082 PHATRDRAFT_800 PHATRDRAFT_12902 PHATRDRAFT_30145 PHATRDRAFT_21988 Phatr3_EG02232 PHATRDRAFT_49372 PHATRDRAFT_34120 PHATRDRAFT_45239 PHATRDRAFT_32747 PHATRDRAFT_25308 PHATRDRAFT_31906 PHATRDRAFT_47090 PHATRDRAFT_42458 PHATRDRAFT_50097 PHATRDRAFT_50971 PHATRDRAFT_46133 PHATRDRAFT_20310 PHATRDRAFT_44546 PHATRDRAFT_11273 Phatr3_EG02569 PHATRDRAFT_21970 PHATRDRAFT_32849 PHATRDRAFT_draft1517 PHATRDRAFT_28585   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.354698 (mmol/gDw/h)
  Minimum Production Rate : 0.008008 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_photon_e : 283.507149
  EX_co2_e : 24.617795
  EX_h2o_e : 20.180215
  EX_no3_e : 1.760000
  EX_so4_e : 0.188369
  EX_pi_e : 0.104090
  EX_mg2_e : 0.006339

Product: (mmol/gDw/h)
  EX_o2_e : 27.966345
  SK_for_c : 6.790309
  EX_h_e : 4.602001
  DM_biomass_c : 0.354698
  DM_dmsp_c : 0.125289
  Auxiliary production reaction : 0.008008

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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