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 (165 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YBR069C YPL061W YKL106W YPL148C YBR085W YMR056C YBL030C YCL025C YKR039W YEL047C YOR120W YLL043W YMR189W YGR191W YHR208W YCR028C YMR267W YJR078W YJL121C YPL092W YPR069C YBR006W YPL188W YJR049C YEL041W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.177363 (mmol/gDw/h)
  Minimum Production Rate : 0.095268 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.184127
  EX_o2_e : 0.267251
  EX_pi_e : 0.055390
  EX_so4_e : 0.013710

Product: (mmol/gDw/h)
  EX_co2_e : 17.594922
  EX_etoh_e : 16.534797
  EX_h2o_e : 3.716281
  EX_h_e : 1.301122
  EX_2hb_e : 0.238759
  EX_ibutoh_e : 0.209324
  EX_ind3eth_e : 0.095268
  EX_orn_e : 0.022259
  EX_pap_e : 0.010163
  EX_gly_e : 0.000921
  EX_for_e : 0.000917

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.

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Last updated: 27-Sep-2023
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