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 (187 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: YBR069C YML035C YNL270C YEL063C YGR019W YCR032W YCR010C YNL141W YER170W YOL052C YHR002W YJL060W YCL025C YML042W YKR039W YOR120W YLL043W YBL045C YPL262W YIL155C YOR323C YGR191W YJR077C YBR166C YML004C YKL174C YJL121C YPL092W YDL085W YMR145C YHR074W YOR155C YOR377W YGR177C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.170668 (mmol/gDw/h)
  Minimum Production Rate : 0.005888 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.520146
  EX_pi_e : 0.053299
  EX_o2_e : 0.018951
  EX_so4_e : 0.013193

Product: (mmol/gDw/h)
  EX_etoh_e : 17.465788
  EX_co2_e : 17.166522
  EX_h2o_e : 2.748618
  EX_h_e : 2.101945
  EX_succ_e : 0.338773
  EX_urea_e : 0.255114
  EX_pap_e : 0.009779
  EX_ind3eth_e : 0.005888
  EX_for_e : 0.000882

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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