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 (68 of 69: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: YBR068C YMR083W YDR046C YBR069C YML035C YJL070C YBR284W YGR087C YLR044C YLR134W YDR380W YKL192C YLR209C YMR289W YOL052C YHR002W YCL025C YKR039W YOL020W YOR120W YOL059W YGR191W YJR078W YJL121C YLR348C YPL092W YML120C YPL188W YJR049C YEL041W YEL046C YDR402C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.128903 (mmol/gDw/h)
  Minimum Production Rate : 0.120679 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 1.253769
  EX_pi_e : 0.281615
  EX_so4_e : 0.009964

Product: (mmol/gDw/h)
  EX_h_e : 20.378322
  EX_h2o_e : 13.851431
  EX_succ_e : 6.799385
  EX_pyr_e : 5.960138
  EX_iamoh_e : 1.508711
  EX_2mbtoh_e : 0.265050
  Auxiliary production reaction : 0.120679
  EX_pap_e : 0.007386
  EX_gly_e : 0.003079
  EX_hxan_e : 0.002410
  EX_for_e : 0.000666

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
Contact