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 (44 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b1241 b0351 b4069 b2744 b3708 b2297 b2458 b2779 b2925 b2097 b3617 b3236 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b0261 b4381 b2406 b2868 b0114 b2366 b2492 b0904 b1533 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.350533 (mmol/gDw/h)
  Minimum Production Rate : 0.349905 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.440656
  EX_o2_e : 281.672098
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.535254
  EX_pi_e : 1.387840
  EX_so4_e : 0.088271
  EX_k_e : 0.068422
  EX_mg2_e : 0.003041
  EX_ca2_e : 0.001825
  EX_cl_e : 0.001825
  EX_cu2_e : 0.000249
  EX_mn2_e : 0.000242
  EX_zn2_e : 0.000120
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994370
  EX_h2o_e : 545.699198
  EX_co2_e : 31.546731
  EX_ac_e : 5.283043
  Auxiliary production reaction : 0.349905
  EX_glyc__R_e : 0.000117
  DM_5drib_c : 0.000079
  DM_4crsol_c : 0.000078

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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