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 (29 of 174: 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 YMR289W YOL052C YPL265W YCL025C YKR039W YOL020W YOR120W YOL059W YGR191W YLR231C YJL121C YLR348C YML120C YHR074W YDR402C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.137916 (mmol/gDw/h)
  Minimum Production Rate : 0.084854 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 1.065919
  EX_pi_e : 0.212780
  EX_so4_e : 0.010661

Product: (mmol/gDw/h)
  EX_h_e : 20.463424
  EX_h2o_e : 13.570719
  EX_succ_e : 6.712138
  EX_pyr_e : 6.135458
  EX_iamoh_e : 1.599033
  EX_2mbtoh_e : 0.189898
  Auxiliary production reaction : 0.084854
  EX_pap_e : 0.007903
  EX_for_e : 0.000713

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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