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 : udpgal_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (446 of 448: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: Rv3319 Rv0247c Rv3303c Rv0843 Rv0462 Rv0248c Rv2443 Rv1908c Rv3356c Rv0069c Rv2476c Rv0753c Rv2674 Rv0137c Rv1902c Rv1188 Rv1098c Rv2920c Rv3293 Rv0147 Rv2780 Rv0084 Rv2899c Rv0859 Rv1077 Rv3535c   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.021700 (mmol/gDw/h)
  Minimum Production Rate : 0.003913 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glyc_e : 1.000000
  EX_glu__L_e : 1.000000
  EX_glc__D_e : 1.000000
  EX_o2_e : 1.000000
  EX_cit_e : 0.200321
  EX_h2o_e : 0.197177
  EX_pi_e : 0.031875
  EX_so4_e : 0.001400
  EX_fe3_e : 0.000033

Product: (mmol/gDw/h)
  EX_h2co3_e : 3.320813
  EX_lac__L_e : 0.925107
  EX_ppa_e : 0.865662
  EX_val__L_e : 0.796698
  EX_h_e : 0.190260
  EX_ile__L_e : 0.053630
  EX_pdima_e : 0.013159
  Auxiliary production reaction : 0.003913

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.

Last updated: 27-Sep-2023
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