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 (174 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: YBR069C YPL061W YML035C YFL053W YML070W YGR019W YKL106W YPL148C YNL141W YOL052C YCL025C YKR039W YLL043W YIL111W YNL052W YPL262W YIL155C YGR191W YLR231C YJR077C YHR208W YJL121C YPL092W YDL085W YMR145C YHR074W YOR155C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.164317 (mmol/gDw/h)
  Minimum Production Rate : 0.045480 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.980814
  EX_pi_e : 0.051316
  EX_o2_e : 0.018246
  EX_so4_e : 0.012702

Product: (mmol/gDw/h)
  EX_etoh_e : 17.115229
  EX_co2_e : 16.569995
  EX_h2o_e : 3.344240
  EX_h_e : 2.956519
  EX_succ_e : 0.544256
  EX_urea_e : 0.443087
  EX_ind3eth_e : 0.045480
  EX_arg__L_e : 0.020622
  EX_pap_e : 0.009415
  EX_for_e : 0.000850

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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