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 (139 of 174: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: YDL168W YMR303C YBR068C YDR046C YBR069C YPL061W YGR087C YLR044C YLR134W YDR380W YDL080C YKL192C YBR291C YHR002W YJL060W YCL025C YKR039W YOL020W YOR120W YOL059W YGR191W YBR166C YJL121C YLR348C YLR017W YML120C YLR328W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.108841 (mmol/gDw/h)
  Minimum Production Rate : 0.123868 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 1.265044
  EX_pi_e : 0.281726
  EX_so4_e : 0.008413

Product: (mmol/gDw/h)
  EX_h_e : 22.577248
  EX_h2o_e : 13.469098
  EX_succ_e : 7.038570
  EX_3c3hmp_e : 3.484623
  EX_pyr_e : 0.450750
  EX_gly_e : 0.253131
  EX_etoh_e : 0.252566
  Auxiliary production reaction : 0.123868
  EX_pap_e : 0.006237
  EX_for_e : 0.000563

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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