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 (35 of 37: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: PHATRDRAFT_27726 PHATRDRAFT_13987 PHATRDRAFT_draft877 PHATRDRAFT_34010 PHATRDRAFT_800 PHATRDRAFT_30145 PHATRDRAFT_16571 Phatr3_EG02232 PHATRDRAFT_3969 PHATRDRAFT_draft1186 PHATRDRAFT_13322 PHATRDRAFT_55126 PHATRDRAFT_22404 Phatr3_EG02269 PHATRDRAFT_34120 PHATRDRAFT_29016 PHATRDRAFT_13951 PHATRDRAFT_28191 PHATRDRAFT_41063 PHATRDRAFT_33839 PHATRDRAFT_54731 PHATRDRAFT_54493 Phatr3_EG02042 PHATRDRAFT_36906 PHATRDRAFT_20310 PHATRDRAFT_13005 PHATRDRAFT_50084 PHATRDRAFT_1784 PHATRDRAFT_1358 PHATRDRAFT_51242 PHATRDRAFT_22117 PHATRDRAFT_49073 PHATRDRAFT_39772 PHATRDRAFT_15777 PHATRDRAFT_43697 PHATRDRAFT_45428 PHATRDRAFT_49505 PHATRDRAFT_28181 PHATRDRAFT_12452 Phatr3_EG02611   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.115740 (mmol/gDw/h)
  Minimum Production Rate : 0.002002 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_photon_e : 321.589549
  EX_co2_e : 26.289731
  EX_h2o_e : 18.744952
  EX_no3_e : 1.760000
  EX_so4_e : 0.290046
  EX_pi_e : 0.032743
  EX_mg2_e : 0.002068

Product: (mmol/gDw/h)
  EX_o2_e : 28.044239
  SK_for_c : 9.590138
  EX_h_e : 7.236442
  DM_indole_c : 1.193541
  DM_dmsp_c : 0.269463
  DM_biomass_c : 0.115740
  EX_etoh_e : 0.104021
  Auxiliary production reaction : 0.002002

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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