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 (942 of 943: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: Rv1445c Rv3319 Rv0247c Rv2495c Rv2215 Rv0248c Rv2443 Rv2697c Rv2967c Rv3356c Rv2476c Rv1902c Rv2332 Rv1240 Rv1188 Rv1712 Rv0211 Rv3339c Rv0066c Rv3293 Rv0147 Rv0084 Rv2899c Rv0859 Rv3535c   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.025653 (mmol/gDw/h)
  Minimum Production Rate : 0.004624 (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_h2o_e : 0.641841
  EX_h_e : 0.486992
  EX_cit_e : 0.475193
  EX_nh4_e : 0.063398
  EX_pi_e : 0.037681
  EX_so4_e : 0.001655
  EX_fe3_e : 0.000038

Product: (mmol/gDw/h)
  EX_h2co3_e : 3.971269
  EX_lac__L_e : 1.028832
  EX_ppa_e : 0.841196
  EX_val__L_e : 0.653850
  EX_leu__L_e : 0.232616
  EX_pdima_e : 0.015555
  Auxiliary production reaction : 0.004625

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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