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 (40 of 69: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: YBR068C YMR083W YDR046C YBR069C YPL061W YGR087C YLR044C YLR134W YDR380W YKL192C YLR209C YPL148C YNL141W YNR033W YCL025C YKR039W YOL020W YOR120W YOL059W YGR191W YLR231C YDR403W YJL121C YLR348C YPL092W YLR017W YML120C YFR047C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.128993 (mmol/gDw/h)
  Minimum Production Rate : 0.123176 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 1.252235
  EX_pi_e : 0.286637
  EX_so4_e : 0.009971

Product: (mmol/gDw/h)
  EX_h_e : 20.365728
  EX_h2o_e : 13.855141
  EX_succ_e : 6.796132
  EX_pyr_e : 5.963126
  EX_iamoh_e : 1.506558
  EX_2mbtoh_e : 0.265236
  Auxiliary production reaction : 0.123176
  EX_pap_e : 0.007391
  EX_gly_e : 0.000669
  EX_for_e : 0.000667

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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