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 (189 of 192: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: YDL168W YMR303C YBR068C YDR046C YBR069C YDR035W YGR087C YLR044C YLR134W YDR380W YDL080C YOR348C YKL192C YPL148C YPL265W YCL025C YKR039W YOL020W YOR120W YOL059W YGR191W YLR231C YJL121C YLR348C YBR176W YML120C YBR180W YFR047C YKL184W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.109815 (mmol/gDw/h)
  Minimum Production Rate : 0.082077 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 0.810192
  EX_pi_e : 0.198449
  EX_so4_e : 0.008489

Product: (mmol/gDw/h)
  EX_h_e : 22.128738
  EX_h2o_e : 13.360300
  EX_succ_e : 6.910023
  EX_3c3hmp_e : 3.404806
  EX_pyr_e : 0.734421
  EX_3mop_e : 0.180230
  Auxiliary production reaction : 0.082077
  EX_pap_e : 0.006292
  EX_for_e : 0.000568

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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