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 (177 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: YPL061W YDL210W YMR009W YOR348C YKL106W YKL192C YCR032W YPL265W YJL060W YKR039W YOL020W YOR120W YDR272W YPL262W YIL155C YOR323C YDL198C YBR263W YBR166C YOR273C YLL028W YJL121C YBR006W YDL085W YMR145C YML120C YLR328W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.182132 (mmol/gDw/h)
  Minimum Production Rate : 0.002594 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.050359
  EX_pi_e : 0.036007
  EX_o2_e : 0.020695
  EX_so4_e : 0.014079

Product: (mmol/gDw/h)
  EX_co2_e : 17.181622
  EX_etoh_e : 16.701368
  EX_h2o_e : 2.056775
  EX_h_e : 1.103033
  EX_glyc_e : 0.824996
  EX_fum_e : 0.077898
  EX_his__L_e : 0.009491
  EX_ind3eth_e : 0.002594

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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