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 (63 of 63: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: YBR068C YMR083W YDR046C YBR069C YDR380W YDL080C YDR508C YKL192C YCR032W YCR010C YCL025C YML042W YKR039W YOR120W YIL111W YNL052W YOL059W YJR077C YMR267W YKL174C YJL121C YBR006W YML120C YOR377W YGR177C YOR184W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.180670 (mmol/gDw/h)
  Minimum Production Rate : 0.021910 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.098752
  EX_pi_e : 0.057628
  EX_o2_e : 0.020062
  EX_so4_e : 0.013966

Product: (mmol/gDw/h)
  EX_co2_e : 17.682594
  EX_etoh_e : 16.622154
  EX_h2o_e : 2.903880
  EX_h_e : 0.996458
  EX_ibutoh_e : 0.415494
  EX_glyc_e : 0.181669
  Auxiliary production reaction : 0.021910

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
Contact