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 : cdpea_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 69: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YDL168W YMR303C YBR068C YDR046C YBR069C YDR035W YGR087C YLR044C YLR134W YDR380W YDL080C YOR348C YKL192C YOL052C YPL265W YCL025C YKR039W YOL020W YOR120W YOL059W YBR263W YLR231C YJL121C YLR348C YML120C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.103562 (mmol/gDw/h)
  Minimum Production Rate : 0.106918 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 1.048779
  EX_pi_e : 0.252106
  EX_so4_e : 0.008005

Product: (mmol/gDw/h)
  EX_h_e : 22.347809
  EX_h2o_e : 13.718236
  EX_succ_e : 7.081965
  EX_3c3hmp_e : 3.331418
  EX_pyr_e : 0.629134
  EX_3mop_e : 0.240317
  Auxiliary production reaction : 0.106918
  EX_nadp_e : 0.005932

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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