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 (44 of 52: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YHR104W YBR068C YDR046C YBR069C YGR087C YLR044C YLR134W YDR380W YDL080C YDR508C YLR027C YCL025C YKR039W YIL053W YER062C YOR323C YBR263W YDL171C YLR348C YKL085W YLR164W YDR178W YDL085W YMR145C YKL184W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.112305 (mmol/gDw/h)
  Minimum Production Rate : 0.014408 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.923584
  EX_o2_e : 2.000000
  EX_pi_e : 0.458364
  EX_so4_e : 0.008681

Product: (mmol/gDw/h)
  EX_h_e : 23.015542
  EX_h2o_e : 16.123975
  EX_succ_e : 8.971962
  EX_ala__L_e : 4.073451
  EX_4abut_e : 0.221622
  Auxiliary production reaction : 0.218081
  EX_3c3hmp_e : 0.214850
  EX_etoh_e : 0.006433

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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