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 : udpg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 104: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YBR068C YMR083W YDR046C YBR069C YDR035W YGR087C YFL053W YML070W YLR044C YLR134W YDR380W YOR348C YKL192C YPL265W YJL060W YCL025C YKR039W YOL020W YOL059W YMR189W YJL121C YLR348C YBR176W YML120C YKL184W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.130886 (mmol/gDw/h)
  Minimum Production Rate : 0.135126 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 1.055229
  EX_pi_e : 0.318620
  EX_so4_e : 0.010117

Product: (mmol/gDw/h)
  EX_h_e : 19.815119
  EX_h2o_e : 13.749451
  EX_succ_e : 6.552770
  EX_pyr_e : 6.021202
  EX_iamoh_e : 1.463617
  EX_2mbtoh_e : 0.303720
  Auxiliary production reaction : 0.135126
  EX_nadp_e : 0.007497

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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