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 : xdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b4467 b3399 b3831 b4069 b2744 b3752 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b2690 b3908 b1656 b0207 b3012 b1982 b4139 b0675 b2361 b0261 b0411 b2799 b1602 b2913 b4381 b2406 b1727 b0114 b0529 b2492 b0904 b1781 b3001 b1380 b0325 b1771 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.337571 (mmol/gDw/h)
  Minimum Production Rate : 0.146954 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.312449
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.233558
  EX_pi_e : 0.619531
  EX_so4_e : 0.085007
  EX_k_e : 0.065892
  EX_mg2_e : 0.002928
  EX_fe2_e : 0.002786
  EX_fe3_e : 0.002636
  EX_ca2_e : 0.001757
  EX_cl_e : 0.001757
  EX_cu2_e : 0.000239
  EX_mn2_e : 0.000233
  EX_zn2_e : 0.000115
  EX_ni2_e : 0.000109

Product: (mmol/gDw/h)
  EX_h2o_e : 43.885688
  EX_co2_e : 27.966968
  EX_h_e : 9.182813
  EX_pyr_e : 5.242266
  EX_ac_e : 0.196529
  EX_3hpp_e : 0.189570
  Auxiliary production reaction : 0.146954
  EX_glyclt_e : 0.009211
  DM_5drib_c : 0.000227
  DM_4crsol_c : 0.000075

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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