MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iNJ661 [2].
Target metabolite : nh4_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 183: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 8
  Gene deletion: Rv3010c Rv2476c Rv3777 Rv1188 Rv0694 Rv1311 Rv3150 Rv1475c   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.013164 (mmol/gDw/h)
  Minimum Production Rate : 0.033891 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_glyc_e : 1.000000
  EX_o2_e : 1.000000
  EX_glu__L_e : 0.277198
  EX_glc__D_e : 0.019512
  EX_pi_e : 0.014590
  EX_so4_e : 0.000849
  EX_fe3_e : 0.000020

Product: (mmol/gDw/h)
  EX_h2o_e : 1.293137
  EX_h_e : 1.158813
  EX_mal__L_e : 0.732439
  EX_h2co3_e : 0.252208
  EX_h2_e : 0.227045
  EX_val__L_e : 0.157258
  EX_nh4_e : 0.033891

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

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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