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 (163 of 174: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: YDL168W YMR303C YBR068C YDR046C YBR069C YGR087C YFL053W YML070W YLR044C YLR134W YDR380W YDL080C YKL192C YPL148C YNR033W YOL052C YJL060W YCL025C YKR039W YOL020W YOL059W YGR191W YJL121C YLR348C YML120C YEL046C YBR180W YFR047C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.111606 (mmol/gDw/h)
  Minimum Production Rate : 0.106573 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 0.976876
  EX_pi_e : 0.248002
  EX_so4_e : 0.008627

Product: (mmol/gDw/h)
  EX_h_e : 22.491050
  EX_h2o_e : 13.613260
  EX_succ_e : 7.073141
  EX_3c3hmp_e : 3.371536
  EX_pyr_e : 0.564521
  EX_3mop_e : 0.229485
  Auxiliary production reaction : 0.106573
  EX_pap_e : 0.006395
  EX_gly_e : 0.000579
  EX_for_e : 0.000577

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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