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 (173 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: YBR069C YML035C YPL111W YKL106W YCR032W YCR010C YNL141W YHR002W YCL025C YML042W YKR039W YBL045C YPL262W YIL053W YER062C YGR191W YHR208W YMR267W YJR078W YML004C YJL121C YPL092W YBR176W YFR047C YOR155C YOR377W YGR177C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.193206 (mmol/gDw/h)
  Minimum Production Rate : 0.034165 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.243529
  EX_pi_e : 0.060338
  EX_o2_e : 0.021454
  EX_so4_e : 0.014935

Product: (mmol/gDw/h)
  EX_co2_e : 17.473892
  EX_etoh_e : 17.267959
  EX_h2o_e : 2.959856
  EX_h_e : 1.382955
  EX_succ_e : 0.099661
  EX_ind3eth_e : 0.034165
  EX_for_e : 0.025246
  EX_spmd_e : 0.024247
  EX_pap_e : 0.011071

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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