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 (51 of 52: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: YHR104W YOL086C YDL168W YMR303C YGL256W YBR145W YMR318C YBR036C YGR087C YLR044C YLR134W YLR027C YFL055W YLR089C YPL265W YCL025C YKR039W YLL043W YOR323C YDR536W YMR189W YMR250W YDL066W YHR208W YKL174C YLR348C YKL085W YLR164W YDR178W YDL085W YMR145C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.113900 (mmol/gDw/h)
  Minimum Production Rate : 0.187807 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.066727
  EX_o2_e : 2.000000
  EX_pi_e : 0.398133
  EX_so4_e : 0.008804

Product: (mmol/gDw/h)
  EX_h_e : 23.194290
  EX_h2o_e : 15.831973
  EX_succ_e : 9.082883
  EX_ala__L_e : 4.096389
  EX_ac_e : 0.380544
  Auxiliary production reaction : 0.187807
  EX_lys__L_e : 0.166452
  EX_iamoh_e : 0.166108

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
Contact