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 : dmlz_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (161 of 163: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: YPL061W YDR035W YML035C YFL053W YML070W YNL270C YEL063C YOR348C YNL141W YER170W YLR089C YPL265W YKR039W YOL020W YLL043W YBR192W YPL262W YMR189W YLR231C YJR077C YHR208W YKL174C YJL121C YLR348C YPL188W YJR049C YEL041W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.189112 (mmol/gDw/h)
  Minimum Production Rate : 0.024777 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.335511
  EX_o2_e : 0.190985
  EX_pi_e : 0.108605
  EX_so4_e : 0.014618

Product: (mmol/gDw/h)
  EX_co2_e : 17.163317
  EX_etoh_e : 16.562317
  EX_h2o_e : 3.543173
  EX_h_e : 1.762612
  EX_2hb_e : 0.200127
  EX_ibutoh_e : 0.192044
  EX_succ_e : 0.167023
  EX_pap_e : 0.035609
  Auxiliary production reaction : 0.024777

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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