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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3553 b1478 b1241 b4069 b3115 b1849 b2296 b2779 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b1033 b4015 b0411 b2799 b1602 b2913 b2223 b4381 b3915 b3654 b3714 b3664 b4064 b4464 b0529 b2492 b0904 b1781 b3001 b1380 b0325 b1771 b1511 b3546 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.464164 (mmol/gDw/h)
  Minimum Production Rate : 0.344955 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.654673
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.702839
  EX_pi_e : 1.482601
  EX_so4_e : 0.116886
  EX_k_e : 0.090602
  EX_fe3_e : 0.007455
  EX_mg2_e : 0.004027
  EX_ca2_e : 0.002416
  EX_cl_e : 0.002416
  EX_cu2_e : 0.000329
  EX_mn2_e : 0.000321
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.660266
  EX_co2_e : 37.302116
  EX_h_e : 4.542606
  Auxiliary production reaction : 0.344955
  EX_ac_e : 0.270230
  DM_mththf_c : 0.000208
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000104

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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