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 : 6hmhptpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4382 b0474 b2518 b1241 b0351 b4069 b2502 b4384 b2744 b3752 b2297 b2458 b2781 b0099 b3124 b2883 b1982 b3616 b3589 b1623 b0261 b2406 b0112 b2789 b3127 b2868 b4064 b4464 b2975 b0114 b3603 b0529 b2492 b0904 b2954 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.440227 (mmol/gDw/h)
  Minimum Production Rate : 1.687366 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.358050
  EX_nh4_e : 13.193705
  EX_glc__D_e : 10.000000
  EX_pi_e : 3.799377
  EX_so4_e : 0.110858
  EX_k_e : 0.085929
  EX_fe2_e : 0.007070
  EX_mg2_e : 0.003819
  EX_ca2_e : 0.002291
  EX_cl_e : 0.002291
  EX_cu2_e : 0.000312
  EX_mn2_e : 0.000304
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.956446
  EX_co2_e : 22.077955
  EX_h_e : 14.815782
  EX_ac_e : 4.018875
  Auxiliary production reaction : 1.687366
  EX_ade_e : 0.000493
  DM_5drib_c : 0.000295
  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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