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 (47 of 52: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: YHR104W YBR068C YDR046C YBR069C YGR087C YLR044C YLR134W YDR380W YDL080C YDR508C YLR027C YOL064C YCL025C YKR039W YIL053W YER062C YMR189W YDR300C YDL171C YHR208W YLR348C YKL085W YLR164W YDR178W YLR017W YDL085W YMR145C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.107863 (mmol/gDw/h)
  Minimum Production Rate : 0.002266 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 8.934139
  EX_nh4_e : 2.480437
  EX_o2_e : 2.000000
  EX_pi_e : 0.038217
  EX_so4_e : 0.008338

Product: (mmol/gDw/h)
  EX_h_e : 21.009539
  EX_h2o_e : 12.602567
  EX_succ_e : 7.695322
  EX_3c3hmp_e : 1.680391
  EX_4abut_e : 1.527907
  EX_lys__L_e : 0.158988
  EX_pap_e : 0.006181
  Auxiliary production reaction : 0.002266

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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