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 (185 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: YBR069C YML035C YPL111W YNL270C YEL063C YLR209C YCR032W YCR010C YNL141W YHR002W YCL025C YKR039W YAR035W YER024W YOR120W YLL043W YIL111W YNL052W YPL262W YGR191W YLR231C YMR020W YMR267W YKL174C YJL121C YPL092W YFR047C YOR377W YGR177C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.173378 (mmol/gDw/h)
  Minimum Production Rate : 0.109038 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.129014
  EX_pi_e : 0.054146
  EX_o2_e : 0.019252
  EX_so4_e : 0.013402

Product: (mmol/gDw/h)
  EX_co2_e : 17.572165
  EX_etoh_e : 17.332851
  EX_h2o_e : 3.176444
  EX_h_e : 1.201722
  EX_ind3eth_e : 0.109038
  EX_succ_e : 0.084988
  EX_pap_e : 0.009935
  EX_for_e : 0.000896

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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