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 : ind3eth_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (176 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: YMR083W YBR069C YPL061W YEL063C YKL192C YCR010C YHR002W YCL025C YKR039W YDR272W YBL045C YIL155C YIL145C YIL053W YER062C YBR263W YGR191W YLR231C YJR077C YOR273C YLL028W YJL121C YDL085W YMR145C YML120C YHR074W YKL184W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.140622 (mmol/gDw/h)
  Minimum Production Rate : 0.194547 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.402181
  EX_pi_e : 0.043916
  EX_o2_e : 0.015615
  EX_so4_e : 0.010870

Product: (mmol/gDw/h)
  EX_co2_e : 17.675971
  EX_etoh_e : 16.074590
  EX_h2o_e : 4.522008
  EX_h_e : 1.228381
  EX_2mbtoh_e : 0.504588
  EX_ind3eth_e : 0.194547
  EX_arg__L_e : 0.094908
  EX_pap_e : 0.008058
  EX_gly_e : 0.000730
  EX_for_e : 0.000727

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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