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 : udpglcur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (943 of 943: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: Rv3319 Rv0247c Rv0843 Rv0462 Rv2495c Rv0248c Rv2443 Rv3356c Rv2476c Rv0753c Rv1902c Rv2332 Rv1240 Rv1188 Rv1121 Rv1447c Rv1712 Rv0694 Rv3293 Rv0147 Rv0084 Rv2899c Rv0859 Rv1475c Rv3535c   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.019697 (mmol/gDw/h)
  Minimum Production Rate : 0.003553 (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_h_e : 0.824629
  EX_nh4_e : 0.776615
  EX_o2_e : 0.641891
  EX_cit_e : 0.494424
  EX_pi_e : 0.028933
  EX_so4_e : 0.001270
  EX_fe3_e : 0.000030

Product: (mmol/gDw/h)
  EX_h2co3_e : 4.092603
  EX_val__L_e : 1.640760
  EX_ppa_e : 0.878064
  EX_h2o_e : 0.023778
  EX_ppdima_e : 0.011944
  Auxiliary production reaction : 0.003551

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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