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 : udpgal_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (163 of 192: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: YBR068C YMR083W YDR046C YBR069C YGR087C YFL053W YML070W YLR044C YLR134W YDR380W YOR348C YKL192C YPL148C YNR033W YPL265W YCL025C YKR039W YOL020W YOL059W YIL145C YGR191W YLR231C YDR403W YJL121C YLR348C YML120C YLR328W YKL184W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.136414 (mmol/gDw/h)
  Minimum Production Rate : 0.083930 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 0.970376
  EX_pi_e : 0.210462
  EX_so4_e : 0.010545

Product: (mmol/gDw/h)
  EX_h_e : 20.123463
  EX_h2o_e : 13.469677
  EX_succ_e : 6.642239
  EX_pyr_e : 6.113000
  EX_iamoh_e : 1.582419
  EX_2mbtoh_e : 0.187829
  Auxiliary production reaction : 0.083930
  EX_pap_e : 0.007817
  EX_for_e : 0.000705

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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