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 (186 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: YNL270C YEL063C YOR348C YPL148C YCR032W YCR010C YBR085W YMR056C YBL030C YLR089C YPL265W YJL060W YML042W YKR039W YOL020W YEL047C YIL053W YER062C YMR189W YMR250W YHR208W YMR267W YJL121C YPL188W YJR049C YEL041W YOR377W YGR177C YKL184W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.191631 (mmol/gDw/h)
  Minimum Production Rate : 0.049307 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.176643
  EX_o2_e : 0.139963
  EX_pi_e : 0.059839
  EX_so4_e : 0.014813

Product: (mmol/gDw/h)
  EX_co2_e : 17.442119
  EX_etoh_e : 16.979783
  EX_h2o_e : 3.187430
  EX_h_e : 1.345116
  EX_2hb_e : 0.276972
  EX_ind3eth_e : 0.049307
  EX_pap_e : 0.010977

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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