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 (42 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 18
  Gene deletion: YPL061W YFL053W YML070W YOR348C YKL106W YPL265W YKR039W YOL020W YEL047C YLL043W YIL111W YNL052W YIL145C YMR189W YLR231C YHR208W YJL121C YPR069C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.149752 (mmol/gDw/h)
  Minimum Production Rate : 0.289851 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.208407
  EX_pi_e : 0.046761
  EX_o2_e : 0.016628
  EX_so4_e : 0.011576

Product: (mmol/gDw/h)
  EX_co2_e : 17.247776
  EX_etoh_e : 15.744957
  EX_h2o_e : 4.854727
  EX_h_e : 1.401307
  EX_2mbtoh_e : 0.323149
  EX_2hb_e : 0.296482
  EX_ind3eth_e : 0.289851
  EX_orn_e : 0.018794
  EX_pap_e : 0.008578

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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