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 : fmnh2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 63: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 15
  Gene deletion: YMR083W YPL061W YFL053W YML070W YKL192C YBL045C YIL155C YJR077C YBR166C YML004C YKL174C YJL121C YBR006W YML120C YOR184W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.182437 (mmol/gDw/h)
  Minimum Production Rate : 0.001335 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.026343
  EX_pi_e : 0.037403
  EX_o2_e : 0.020258
  EX_so4_e : 0.014102

Product: (mmol/gDw/h)
  EX_co2_e : 15.247006
  EX_etoh_e : 13.905628
  EX_h2o_e : 4.137070
  EX_h_e : 4.114994
  EX_succ_e : 1.595973
  EX_ibutoh_e : 0.994498
  Auxiliary production reaction : 0.001335

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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