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 : 2mppal_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (32 of 32: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YOL086C YDL168W YMR303C YGL256W YBR145W YBR068C YMR083W YMR318C YBR036C YDR046C YBR069C YKL192C YAL054C YCR010C YCL025C YKR039W YAR035W YER024W YPL262W YOR273C YLL028W YLR348C YKL141W YMR118C YML120C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.172110 (mmol/gDw/h)
  Minimum Production Rate : 0.153352 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 0.963208
  EX_pi_e : 0.034026
  EX_so4_e : 0.013304

Product: (mmol/gDw/h)
  EX_co2_e : 14.495011
  EX_btd_RR_e : 6.919310
  EX_h2o_e : 6.104054
  EX_glyc_e : 3.589927
  EX_h_e : 0.995046
  EX_2mppal_e : 0.153352
  EX_succ_e : 0.064643

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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