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 : adn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b4382 b1241 b0351 b4384 b3752 b0871 b2779 b2925 b2097 b2407 b1004 b3713 b1109 b0046 b3236 b2690 b0207 b3012 b1982 b4015 b2799 b1602 b2913 b2239 b3915 b1727 b0529 b2492 b0904 b1781 b3001 b3927 b1380 b0325 b1771 b3662 b1517 b0606 b0221 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.373566 (mmol/gDw/h)
  Minimum Production Rate : 0.013916 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.485400
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.105302
  EX_pi_e : 0.360344
  EX_so4_e : 0.094072
  EX_k_e : 0.072917
  EX_fe3_e : 0.006001
  EX_mg2_e : 0.003241
  EX_cl_e : 0.001944
  EX_ca2_e : 0.001944
  EX_cu2_e : 0.000265
  EX_mn2_e : 0.000258
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 43.921471
  EX_co2_e : 28.593301
  EX_h_e : 8.820068
  EX_pyr_e : 5.310771
  EX_adn_e : 0.013913
  EX_ade_e : 0.000251
  DM_mththf_c : 0.000167
  DM_5drib_c : 0.000084
  DM_4crsol_c : 0.000083

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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