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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 64
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b4117 b0207 b3012 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b2799 b1602 b3709 b2913 b2406 b4115 b3161 b0112 b2789 b3127 b3915 b2975 b3603 b1539 b2492 b0904 b1781 b3001 b1533 b3821 b1380 b2965 b0693 b0325 b1473 b1771 b4141 b1798 b3662 b0606 b0221 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.277514 (mmol/gDw/h)
  Minimum Production Rate : 0.462552 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.670223
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.236489
  EX_pi_e : 1.655324
  EX_so4_e : 0.532428
  EX_k_e : 0.054169
  EX_fe3_e : 0.004458
  EX_mg2_e : 0.002407
  EX_ca2_e : 0.001444
  EX_cl_e : 0.001444
  EX_cu2_e : 0.000197
  EX_mn2_e : 0.000192
  EX_zn2_e : 0.000095
  EX_ni2_e : 0.000090

Product: (mmol/gDw/h)
  EX_h2o_e : 50.768070
  EX_co2_e : 33.725389
  EX_h_e : 5.602633
  EX_ac_e : 1.659080
  Auxiliary production reaction : 0.462544
  EX_ade_e : 0.000311
  DM_5drib_c : 0.000186
  DM_4crsol_c : 0.000062

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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