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 (184 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: YBR069C YPL061W YKL106W YCL050C YKL192C YEL071W YDL174C YDL178W YPL148C YCR010C YCL025C YKR039W YIL155C YIL053W YER062C YGR191W YLR231C YHR208W YOR273C YLL028W YJL121C YLR146C YLR164W YDR178W YDL085W YMR145C YML120C YHR074W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.150928 (mmol/gDw/h)
  Minimum Production Rate : 0.244374 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.189103
  EX_pi_e : 0.047135
  EX_o2_e : 0.026620
  EX_so4_e : 0.011667

Product: (mmol/gDw/h)
  EX_co2_e : 17.668205
  EX_etoh_e : 17.122158
  EX_h2o_e : 3.925612
  EX_h_e : 1.122590
  EX_ind3eth_e : 0.244374
  EX_spmd_e : 0.018941
  EX_pap_e : 0.008648

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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