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 (49 of 52: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: YHR104W YDR368W YOL086C YDL168W YMR303C YGL256W YBR145W YBR068C YMR083W YMR318C YBR036C YDR046C YBR069C YGR087C YLR044C YLR134W YCL025C YKR039W YLL043W YNL104C YKL174C 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 : 0.111512 (mmol/gDw/h)
  Minimum Production Rate : 0.243174 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.204967
  EX_o2_e : 2.000000
  EX_pi_e : 0.508394
  EX_so4_e : 0.008620

Product: (mmol/gDw/h)
  EX_h_e : 22.983657
  EX_h2o_e : 16.393862
  EX_succ_e : 9.023351
  EX_ala__L_e : 4.580895
  Auxiliary production reaction : 0.243174
  EX_ac_e : 0.038299

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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