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 : pendp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 52: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: YHR104W YOL086C YDL168W YMR303C YGL256W YBR145W YBR068C YDR046C YBR069C YGR087C YLR044C YLR134W YHR037W YLR027C YCL025C YKR039W YIL053W YER062C YMR250W YNL104C YLR348C YKL085W YCL064C YLR164W YDR178W YDL085W YMR145C YKL218C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.111134 (mmol/gDw/h)
  Minimum Production Rate : 0.238615 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.164818
  EX_o2_e : 2.000000
  EX_pi_e : 0.499202
  EX_so4_e : 0.008591

Product: (mmol/gDw/h)
  EX_h_e : 23.025626
  EX_h2o_e : 16.301825
  EX_succ_e : 9.018605
  EX_ala__L_e : 4.542863
  Auxiliary production reaction : 0.238615
  EX_ac_e : 0.125136
  EX_2mbtoh_e : 0.017394

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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