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 : ind3eth_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (167 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YPL061W YFL053W YML070W YOR348C YKL106W YER170W YBR291C YHR002W YPL265W YKR039W YOL020W YEL047C YLL043W YBR192W YMR189W YLR231C YMR250W YJR077C YHR208W YJL121C YLR348C YPL188W YJR049C YEL041W YKL184W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.178145 (mmol/gDw/h)
  Minimum Production Rate : 0.017610 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.215448
  EX_o2_e : 0.294416
  EX_pi_e : 0.055628
  EX_so4_e : 0.013771

Product: (mmol/gDw/h)
  EX_co2_e : 17.662148
  EX_etoh_e : 16.923780
  EX_h2o_e : 3.147038
  EX_h_e : 1.805687
  EX_2hb_e : 0.187843
  EX_pnto__R_e : 0.105123
  EX_orn_e : 0.022357
  EX_ind3eth_e : 0.017610
  EX_pap_e : 0.010204

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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