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 : thmnp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2779 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b3449 b0261 b0507 b2406 b0112 b2975 b0114 b3603 b2366 b2492 b0904 b1533 b0494 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.440773 (mmol/gDw/h)
  Minimum Production Rate : 1.318961 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.064806
  EX_nh4_e : 11.355611
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.425172
  EX_so4_e : 0.110996
  EX_k_e : 0.086036
  EX_fe2_e : 0.007079
  EX_mg2_e : 0.003824
  EX_cl_e : 0.002294
  EX_ca2_e : 0.002294
  EX_cu2_e : 0.000313
  EX_mn2_e : 0.000305
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.878098
  EX_co2_e : 25.366862
  EX_h_e : 12.980194
  EX_ac_e : 2.334403
  Auxiliary production reaction : 1.318961
  DM_oxam_c : 0.000493
  DM_5drib_c : 0.000296
  DM_4crsol_c : 0.000098

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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