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 : 25aics_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b4467 b4269 b0493 b3588 b3003 b3011 b4384 b2744 b0871 b2779 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1982 b4139 b1623 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b4381 b2406 b3915 b2868 b1727 b4064 b4464 b2975 b0114 b3603 b0529 b2492 b0904 b2954 b3927 b3029 b1380 b2660 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.439180 (mmol/gDw/h)
  Minimum Production Rate : 0.338818 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.668343
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.100839
  EX_pi_e : 0.762454
  EX_so4_e : 0.110594
  EX_k_e : 0.085725
  EX_fe3_e : 0.007054
  EX_mg2_e : 0.003810
  EX_ca2_e : 0.002286
  EX_cl_e : 0.002286
  EX_cu2_e : 0.000311
  EX_mn2_e : 0.000303
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.915663
  EX_co2_e : 36.915026
  EX_h_e : 6.077783
  Auxiliary production reaction : 0.338818
  EX_etoh_e : 0.325286
  EX_ade_e : 0.000491
  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.

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Last updated: 21-Sep-2023
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