MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : bmoco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (103 of 137: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2925 b2097 b1850 b3617 b2407 b3844 b3124 b1982 b2797 b3117 b1814 b4471 b3665 b0261 b0507 b2406 b0112 b0452 b0114 b2366 b0755 b3612 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.453765 (mmol/gDw/h)
  Minimum Production Rate : 0.018582 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.902978
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.297581
  EX_pi_e : 0.493450
  EX_so4_e : 0.188593
  EX_k_e : 0.088572
  EX_mobd_e : 0.018585
  EX_fe2_e : 0.007288
  EX_mg2_e : 0.003936
  EX_ca2_e : 0.002362
  EX_cl_e : 0.002362
  EX_cu2_e : 0.000322
  EX_mn2_e : 0.000314
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 46.134435
  EX_co2_e : 25.228284
  EX_h_e : 9.839544
  EX_ac_e : 1.872751
  EX_ade_e : 0.623646
  DM_5drib_c : 0.623443
  EX_glyclt_e : 0.623442
  DM_4crsol_c : 0.623239
  Auxiliary production reaction : 0.018582

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.

Last updated: 21-Sep-2023
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