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 (181 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: YMR083W YBR069C YEL063C YPL148C YAL054C YCR032W YCR010C YGR088W YCL025C YKR039W YAR035W YER024W YIL111W YNL052W YIL155C YIL053W YER062C YGR191W YJR077C YJR078W YJL121C YPL092W YLR164W YDR178W YFR047C YOR377W YGR177C YKL184W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.174991 (mmol/gDw/h)
  Minimum Production Rate : 0.075977 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.413300
  EX_pi_e : 0.054650
  EX_so4_e : 0.013527
  EX_o2_e : 0.009754

Product: (mmol/gDw/h)
  EX_co2_e : 17.553761
  EX_etoh_e : 16.396509
  EX_h2o_e : 3.842944
  EX_h_e : 1.276870
  EX_2mbtoh_e : 0.392708
  EX_arg__L_e : 0.076964
  EX_ind3eth_e : 0.075977
  EX_succ_e : 0.019354
  EX_pap_e : 0.010027
  EX_for_e : 0.000905

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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