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 (175 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: YPL061W YML035C YOR348C YKL106W YNL141W YOL052C YPL265W YJL060W YKR039W YOL020W YOR120W YLL043W YBL045C YPL262W YIL155C YMR189W YJR077C YHR208W YMR267W YML004C YJL121C YBR006W YDL085W YMR145C YPL188W YJR049C YEL041W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.161816 (mmol/gDw/h)
  Minimum Production Rate : 0.078819 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.850271
  EX_pi_e : 0.050529
  EX_o2_e : 0.017968
  EX_so4_e : 0.012508

Product: (mmol/gDw/h)
  EX_etoh_e : 16.806078
  EX_co2_e : 16.521813
  EX_h2o_e : 3.548527
  EX_h_e : 2.876656
  EX_succ_e : 0.468763
  EX_urea_e : 0.369142
  EX_2hb_e : 0.200784
  EX_ind3eth_e : 0.078819
  EX_arg__L_e : 0.020308
  EX_pap_e : 0.009269

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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