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 (45 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3708 b3115 b1849 b2296 b2779 b2925 b2097 b3617 b2797 b3117 b1814 b4471 b3946 b0825 b4381 b2406 b2868 b0114 b1539 b2492 b0904 b1533 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.354533 (mmol/gDw/h)
  Minimum Production Rate : 0.347606 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.578055
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.598673
  EX_pi_e : 1.403834
  EX_so4_e : 0.089278
  EX_k_e : 0.069202
  EX_fe2_e : 0.005694
  EX_mg2_e : 0.003076
  EX_ca2_e : 0.001845
  EX_cl_e : 0.001845
  EX_cu2_e : 0.000251
  EX_mn2_e : 0.000245
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 45.767229
  EX_co2_e : 31.449702
  EX_h_e : 9.548411
  EX_ac_e : 5.228854
  Auxiliary production reaction : 0.353950
  DM_mththf_c : 0.000159
  EX_glyc__R_e : 0.000119
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000079

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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