MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iMM904 [2].
Target metabolite : ind3eth_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (179 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: YMR083W YBR069C YPL061W YML035C YKL106W YKL192C YLR209C YNL141W YHR002W YCL025C YKR039W YOR120W YLL043W YBL045C YPL262W YOL059W YGR191W YHR208W YJR078W YML004C YHL016C YJL121C YLR348C YPL092W YLR017W YML120C YFR047C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.157943 (mmol/gDw/h)
  Minimum Production Rate : 0.109355 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.117815
  EX_pi_e : 0.049326
  EX_o2_e : 0.017538
  EX_so4_e : 0.012209

Product: (mmol/gDw/h)
  EX_co2_e : 17.194590
  EX_etoh_e : 16.474545
  EX_h2o_e : 3.607742
  EX_h_e : 1.793115
  EX_succ_e : 0.391865
  EX_2mbtoh_e : 0.261653
  EX_ind3eth_e : 0.109355
  EX_arg__L_e : 0.019822
  EX_pap_e : 0.009050
  EX_for_e : 0.000817

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

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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