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 : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2836 b3942 b1732 b4069 b2744 b3708 b3115 b1849 b2296 b2925 b2097 b2926 b3236 b2883 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b4381 b2868 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b3927 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.392119 (mmol/gDw/h)
  Minimum Production Rate : 0.117055 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.167993
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.872747
  EX_pi_e : 0.729406
  EX_so4_e : 0.098743
  EX_k_e : 0.076539
  EX_fe2_e : 0.006298
  EX_mg2_e : 0.003402
  EX_ca2_e : 0.002041
  EX_cl_e : 0.002041
  EX_cu2_e : 0.000278
  EX_mn2_e : 0.000271
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 44.784623
  EX_co2_e : 32.685834
  EX_h_e : 9.004450
  EX_ac_e : 4.997719
  Auxiliary production reaction : 0.117055
  EX_ade_e : 0.010524
  DM_mththf_c : 0.000176
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000087

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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