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 (168 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YBR069C YPL061W YML035C YPL111W YNL270C YEL063C YPL148C YNL141W YOL052C YCL025C YKR039W YIL111W YNL052W YPL262W YIL053W YER062C YGR191W YJR078W YJL121C YPL092W YPL188W YJR049C YEL041W YOR155C YKL184W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.158404 (mmol/gDw/h)
  Minimum Production Rate : 0.239024 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.170908
  EX_pi_e : 0.049470
  EX_o2_e : 0.017589
  EX_so4_e : 0.012245

Product: (mmol/gDw/h)
  EX_co2_e : 17.295876
  EX_etoh_e : 16.916335
  EX_h2o_e : 3.995843
  EX_h_e : 1.430174
  EX_ind3eth_e : 0.239024
  EX_succ_e : 0.174067
  EX_pap_e : 0.009077
  EX_for_e : 0.000819

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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