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 : lys__L_m
List of minimal gene deletion strategies (Download)

Gene deletion strategy (4 of 4: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: YHR104W YBR068C YDR046C YBR069C YGR087C YLR044C YLR134W YDR380W YDL080C YDR508C YLR027C YCL050C YIL013C YOR011W YIL009W YOR317W YMR246W YCL025C YKR039W YOL020W YLL043W YOR323C YBR263W YOR375C YAL062W YHR208W YNL268W YJL121C YKR080W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.128362 (mmol/gDw/h)
  Minimum Production Rate : 0.004713 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 9.672669
  EX_o2_e : 2.000000
  EX_nh4_e : 0.735150
  EX_pi_e : 0.025377
  EX_so4_e : 0.017275

Product: (mmol/gDw/h)
  EX_h_e : 22.353135
  EX_h2o_e : 12.410797
  EX_succ_e : 7.542629
  EX_3c3hmp_e : 3.312411
  EX_met__L_e : 0.007353
  Auxiliary production reaction : 0.004713

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