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 (164 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YPL061W YOR348C YKL106W YBR085W YMR056C YBL030C YER170W YHR002W YPL265W YJL060W YKR039W YOL020W YEL047C YOR120W YLL043W YMR189W YMR250W YJR077C YHR208W YJL121C YLR348C YPR069C YPL188W YJR049C YEL041W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.179895 (mmol/gDw/h)
  Minimum Production Rate : 0.004911 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.214516
  EX_o2_e : 0.310180
  EX_pi_e : 0.056174
  EX_so4_e : 0.013906

Product: (mmol/gDw/h)
  EX_co2_e : 17.703541
  EX_etoh_e : 16.977227
  EX_h2o_e : 3.081415
  EX_h_e : 1.784809
  EX_2hb_e : 0.163945
  EX_pnto__R_e : 0.106156
  EX_orn_e : 0.022577
  EX_pap_e : 0.010304
  EX_ind3eth_e : 0.004911

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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