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 (169 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: YBR069C YPL061W YKL106W YAL054C YBR085W YMR056C YBL030C YOL052C YHR002W YCL025C YKR039W YEL047C YIL053W YER062C YMR189W YGR191W YLR231C YJR077C YHR208W YJL121C YLR348C YPL092W YBR006W YPL188W YJR049C YEL041W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.179057 (mmol/gDw/h)
  Minimum Production Rate : 0.083662 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.182921
  EX_o2_e : 0.282320
  EX_pi_e : 0.055920
  EX_so4_e : 0.013841

Product: (mmol/gDw/h)
  EX_co2_e : 17.634530
  EX_etoh_e : 16.583053
  EX_h2o_e : 3.657907
  EX_h_e : 1.276002
  EX_2hb_e : 0.216007
  EX_ibutoh_e : 0.211323
  EX_ind3eth_e : 0.083662
  EX_orn_e : 0.022472
  EX_pap_e : 0.010260
  EX_gly_e : 0.000929
  EX_for_e : 0.000926

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.

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Last updated: 27-Sep-2023
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