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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b4382 b1241 b0351 b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b2779 b3617 b2407 b1982 b2688 b2797 b3117 b1814 b4471 b3946 b0825 b0261 b2913 b2239 b2406 b0112 b3453 b2868 b0114 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b2835 b2413 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.356996 (mmol/gDw/h)
  Minimum Production Rate : 0.245829 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.964473
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.349180
  EX_pi_e : 0.836019
  EX_so4_e : 0.089899
  EX_k_e : 0.069683
  EX_fe2_e : 0.005734
  EX_mg2_e : 0.003097
  EX_ca2_e : 0.001858
  EX_cl_e : 0.001858
  EX_cu2_e : 0.000253
  EX_mn2_e : 0.000247
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 44.407891
  EX_co2_e : 27.949132
  EX_h_e : 8.588904
  EX_pyr_e : 5.060858
  Auxiliary production reaction : 0.245829
  EX_ade_e : 0.000399
  DM_5drib_c : 0.000240
  DM_4crsol_c : 0.000080

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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