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 (182 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: YBR069C YML035C YFL053W YML070W YPL111W YKL106W YPL148C YCR032W YCR010C YNL141W YER170W YJL060W YCL025C YML042W YKR039W YLL043W YIL111W YNL052W YPL262W YGR191W YHR208W YJL121C YPL092W YBR176W YHR074W YOR155C YOR377W YGR177C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.192645 (mmol/gDw/h)
  Minimum Production Rate : 0.034065 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.239921
  EX_pi_e : 0.060163
  EX_o2_e : 0.021391
  EX_so4_e : 0.014891

Product: (mmol/gDw/h)
  EX_co2_e : 17.481223
  EX_etoh_e : 17.275887
  EX_h2o_e : 2.951267
  EX_h_e : 1.378941
  EX_succ_e : 0.099372
  EX_ind3eth_e : 0.034065
  EX_for_e : 0.025173
  EX_spmd_e : 0.024177
  EX_pap_e : 0.011039

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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