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 (172 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: YBR208C YML035C YNL270C YEL063C YOR348C YCR032W YCR010C YNL141W YPL265W YJL060W YML042W YKR039W YOL020W YOR120W YLL043W YIL111W YNL052W YPL262W YBR263W YMR267W YHL016C YJL121C YBR176W YOR377W YGR177C YKL184W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.181426 (mmol/gDw/h)
  Minimum Production Rate : 0.098994 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.187080
  EX_pi_e : 0.067044
  EX_o2_e : 0.020146
  EX_so4_e : 0.014024

Product: (mmol/gDw/h)
  EX_co2_e : 17.214144
  EX_etoh_e : 16.501335
  EX_h2o_e : 3.641145
  EX_h_e : 1.470696
  EX_2hb_e : 0.239662
  EX_2mbtoh_e : 0.147971
  EX_ind3eth_e : 0.098994
  EX_succ_e : 0.088926
  EX_nadp_e : 0.010392

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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