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 : cdp_n
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 174: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YBR068C YMR083W YDR046C YBR069C YDR035W YGR087C YLR044C YLR134W YDR380W YOR348C YKL192C YPL265W YJL060W YCL025C YKR039W YOL020W YOL059W YIL053W YER062C YBR263W YKL174C YJL121C YLR348C YBR176W YML120C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.133308 (mmol/gDw/h)
  Minimum Production Rate : 0.156717 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 1.216204
  EX_pi_e : 0.339789
  EX_so4_e : 0.010305

Product: (mmol/gDw/h)
  EX_h_e : 20.364371
  EX_h2o_e : 13.915638
  EX_succ_e : 6.667430
  EX_pyr_e : 6.045501
  EX_iamoh_e : 1.496687
  EX_2mbtoh_e : 0.301705
  Auxiliary production reaction : 0.156717

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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