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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 23: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: PHATRDRAFT_26934 PHATRDRAFT_20342 PHATRDRAFT_27726 PHATRDRAFT_800 PHATRDRAFT_12902 PHATRDRAFT_55192 PHATRDRAFT_26290 PHATRDRAFT_55126 PHATRDRAFT_22404 PHATRDRAFT_3046 PHATRDRAFT_40430 PHATRDRAFT_draft1572 PHATRDRAFT_28191 PHATRDRAFT_29702 Phatr3_EG02361 PHATRDRAFT_41063 PHATRDRAFT_33839 PHATRDRAFT_36641 PHATRDRAFT_46880 PHATRDRAFT_37658 PHATRDRAFT_34976 PHATRDRAFT_859 PHATRDRAFT_39914 PHATRDRAFT_48307 PHATRDRAFT_13005 PHATRDRAFT_50084 Phatr3_EG02569 PHATRDRAFT_21970 PHATRDRAFT_43697 PHATRDRAFT_45428 PHATRDRAFT_12452 Phatr3_EG02611   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.111722 (mmol/gDw/h)
  Minimum Production Rate : 0.095885 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_photon_e : 358.430331
  EX_co2_e : 31.380786
  EX_h2o_e : 24.415149
  EX_no3_e : 1.760000
  EX_so4_e : 0.059332
  EX_pi_e : 0.027741
  EX_mg2_e : 0.001997

Product: (mmol/gDw/h)
  EX_o2_e : 28.812684
  SK_for_c : 16.466488
  EX_h_e : 14.576626
  DM_indole_c : 1.021439
  DM_biomass_c : 0.111722
  Auxiliary production reaction : 0.095885
  EX_etoh_e : 0.091898
  DM_dmsp_c : 0.039463

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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