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 (183 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: YBR069C YML035C YKL106W YLR209C YPL148C YAL054C YCR032W YCR010C YNL141W YCL025C YML042W YKR039W YBL045C YPL262W YIL053W YER062C YGR191W YHR208W YJR078W YML004C YHL016C YKL174C YJL121C YPL092W YBR176W YHR074W YOR377W YGR177C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.175082 (mmol/gDw/h)
  Minimum Production Rate : 0.088137 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.162085
  EX_pi_e : 0.054678
  EX_o2_e : 0.019441
  EX_so4_e : 0.013534

Product: (mmol/gDw/h)
  EX_co2_e : 17.570272
  EX_etoh_e : 17.350578
  EX_h2o_e : 3.097804
  EX_h_e : 1.213535
  EX_ind3eth_e : 0.088137
  EX_succ_e : 0.085824
  EX_orn_e : 0.021973
  EX_pap_e : 0.010032
  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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