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 : cdpea_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 69: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YBR068C YMR083W YDR046C YBR069C YGR087C YLR044C YLR134W YDR380W YOR348C YKL192C YBR291C YPL265W YCL025C YKR039W YOL020W YOL059W YIL053W YER062C YBR263W YMR020W YJR078W YJL121C YLR348C YPR069C YML120C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.125999 (mmol/gDw/h)
  Minimum Production Rate : 0.130082 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 1.275999
  EX_pi_e : 0.306726
  EX_so4_e : 0.009740

Product: (mmol/gDw/h)
  EX_h_e : 20.286930
  EX_h2o_e : 13.944304
  EX_succ_e : 6.736879
  EX_pyr_e : 6.020410
  EX_iamoh_e : 1.483641
  EX_2mbtoh_e : 0.292382
  Auxiliary production reaction : 0.130082
  EX_nadp_e : 0.007217

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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