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 : sql_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 69: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YHR104W YOL086C YDL168W YMR303C YGL256W YBR145W YMR083W YMR318C YBR036C YGR087C YLR044C YLR134W YLR027C YLL043W YDR300C YMR250W YDL066W YHR208W YKL174C YLR348C YKL085W YKL148C YDR178W YDL085W YMR145C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.115839 (mmol/gDw/h)
  Minimum Production Rate : 0.095729 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.308555
  EX_o2_e : 2.000000
  EX_pi_e : 0.022901
  EX_so4_e : 0.008954

Product: (mmol/gDw/h)
  EX_h_e : 23.352229
  EX_h2o_e : 15.160389
  EX_succ_e : 9.639273
  EX_ala__L_e : 3.321696
  EX_3mbald_e : 0.685348
  EX_lys__L_e : 0.169286
  Auxiliary production reaction : 0.095729

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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