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 (92 of 104: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: YDL168W YMR303C YBR068C YDR046C YBR069C YDR035W YGR087C YFL053W YML070W YLR044C YLR134W YDR380W YDL080C YKL192C YOL052C YHR002W YCL025C YKR039W YOL020W YOL059W YGR191W YBR166C YJR078W YJL121C YLR348C YML120C YHR074W YEL046C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.106788 (mmol/gDw/h)
  Minimum Production Rate : 0.121531 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 0.871846
  EX_pi_e : 0.276411
  EX_so4_e : 0.008255

Product: (mmol/gDw/h)
  EX_h_e : 21.933299
  EX_h2o_e : 13.567655
  EX_succ_e : 6.935176
  EX_3c3hmp_e : 3.309679
  EX_pyr_e : 0.626913
  EX_3mop_e : 0.247802
  Auxiliary production reaction : 0.121531
  EX_pap_e : 0.006119
  EX_gly_e : 0.000554
  EX_for_e : 0.000552

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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