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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b3617 b0160 b2407 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b2835 b0494   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.540105 (mmol/gDw/h)
  Minimum Production Rate : 1.616201 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 21.259792
  EX_nh4_e : 10.681694
  EX_glc__D_e : 10.000000
  EX_pi_e : 5.369590
  EX_so4_e : 0.136009
  EX_k_e : 0.105425
  EX_fe2_e : 0.008675
  EX_mg2_e : 0.004685
  EX_ca2_e : 0.002811
  EX_cl_e : 0.002811
  EX_cu2_e : 0.000383
  EX_mn2_e : 0.000373
  EX_zn2_e : 0.000184
  EX_ni2_e : 0.000174
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.221002
  EX_co2_e : 20.796308
  EX_h_e : 7.822824
  Auxiliary production reaction : 1.616201
  EX_ac_e : 1.243919
  DM_5drib_c : 0.000362
  DM_4crsol_c : 0.000120

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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