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 : 3c3hmp_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (4 of 18: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 9
  Gene deletion: YGR087C YLR044C YLR134W YDR380W YDL080C YDR148C YOR375C YAL062W YLR348C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.135054 (mmol/gDw/h)
  Minimum Production Rate : 3.160638 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 1.105535
  EX_pi_e : 0.026700
  EX_so4_e : 0.010440

Product: (mmol/gDw/h)
  EX_h_e : 22.517238
  EX_h2o_e : 13.174814
  EX_succ_e : 7.113208
  EX_3c3hmp_e : 3.160638
  EX_pyr_e : 0.939779
  EX_val__L_e : 0.349711
  EX_for_e : 0.000698

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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