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 (166 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YFL053W YML070W YEL063C YOR348C YKL106W YAL054C YCR032W YCR010C YPL265W YML042W YKR039W YOL020W YEL047C YLL043W YBL045C YBR263W YLR231C YJR077C YMR020W YML004C YKL174C YJL121C YLR348C YOR377W YGR177C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.164214 (mmol/gDw/h)
  Minimum Production Rate : 0.123348 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.171831
  EX_pi_e : 0.051277
  EX_o2_e : 0.018234
  EX_so4_e : 0.012694

Product: (mmol/gDw/h)
  EX_co2_e : 17.320164
  EX_etoh_e : 16.822940
  EX_h2o_e : 3.422054
  EX_h_e : 1.478391
  EX_2hb_e : 0.420145
  EX_ind3eth_e : 0.123348
  EX_arg__L_e : 0.020609
  EX_pap_e : 0.009406

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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