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 : pail3p205n3_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 37: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: PHATRDRAFT_27726 PHATRDRAFT_34010 PHATRDRAFT_800 PHATRDRAFT_42015 PHATRDRAFT_54219 PHATRDRAFT_16571 PHATRDRAFT_12762 Phatr3_EG02232 PHATRDRAFT_55126 PHATRDRAFT_48983 PHATRDRAFT_22404 PHATRDRAFT_3046 PHATRDRAFT_34120 PHATRDRAFT_45017 PHATRDRAFT_14762 PHATRDRAFT_38509 PHATRDRAFT_54493 Phatr3_EG02042 PHATRDRAFT_36906 PHATRDRAFT_28797 PHATRDRAFT_44546 PHATRDRAFT_11273 PHATRDRAFT_1784 PHATRDRAFT_1358 PHATRDRAFT_51242 PHATRDRAFT_22117 PHATRDRAFT_49073 PHATRDRAFT_19901 PHATRDRAFT_31436 PHATRDRAFT_15777 PHATRDRAFT_32849 PHATRDRAFT_draft1517 PHATRDRAFT_28585 PHATRDRAFT_43697 PHATRDRAFT_45428 PHATRDRAFT_28181 PHATRDRAFT_12452 Phatr3_EG02611 PHATRDRAFT_8945 PHATRDRAFT_41686 PHATRDRAFT_23365   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.115932 (mmol/gDw/h)
  Minimum Production Rate : 0.001843 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_photon_e : 283.104993
  EX_co2_e : 23.521423
  EX_h2o_e : 16.250590
  EX_no3_e : 1.760000
  EX_pi_e : 0.032472
  EX_so4_e : 0.020617
  EX_mg2_e : 0.002072

Product: (mmol/gDw/h)
  EX_o2_e : 25.173037
  SK_for_c : 8.175643
  EX_h_e : 6.360944
  DM_indole_c : 1.192600
  DM_biomass_c : 0.115932
  EX_etoh_e : 0.103869
  Auxiliary production reaction : 0.001843

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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