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 : cdp_n
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 174: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YDL168W YMR303C YBR068C YDR046C YBR069C YDR035W YGR087C YLR044C YLR134W YDR380W YDL080C YOR348C YKL192C YOL052C YPL265W YJL060W YCL025C YKR039W YOL020W YOR120W YOL059W YMR189W YJL121C YLR348C YML120C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.109315 (mmol/gDw/h)
  Minimum Production Rate : 0.128511 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 0.997312
  EX_pi_e : 0.278634
  EX_so4_e : 0.008450

Product: (mmol/gDw/h)
  EX_h_e : 22.431577
  EX_h2o_e : 13.694564
  EX_succ_e : 7.030968
  EX_3c3hmp_e : 3.360099
  EX_pyr_e : 0.595131
  EX_3mop_e : 0.247405
  Auxiliary production reaction : 0.128511

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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