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 (18 of 174: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 24
  Gene deletion: YBR068C YMR083W YDR046C YBR069C YDR035W YGR087C YLR044C YLR134W YDR380W YOR348C YKL192C YOL052C YPL265W YCL025C YKR039W YOL020W YOR120W YOL059W YGR191W YLR231C YJL121C YLR348C YML120C YHR074W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.135203 (mmol/gDw/h)
  Minimum Production Rate : 0.101052 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 1.098552
  EX_pi_e : 0.244329
  EX_so4_e : 0.010451

Product: (mmol/gDw/h)
  EX_h_e : 20.408781
  EX_h2o_e : 13.664891
  EX_succ_e : 6.648135
  EX_pyr_e : 6.190862
  EX_iamoh_e : 1.575653
  EX_2mbtoh_e : 0.221897
  Auxiliary production reaction : 0.101052
  EX_pap_e : 0.007747
  EX_for_e : 0.000699

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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