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 : 5aizc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4069 b4384 b2744 b3708 b3752 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2883 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b2440 b0261 b3945 b4381 b2406 b2868 b4064 b4464 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.352081 (mmol/gDw/h)
  Minimum Production Rate : 0.223711 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.856921
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.475548
  EX_pi_e : 0.563330
  EX_so4_e : 0.088661
  EX_k_e : 0.068724
  EX_fe2_e : 0.005655
  EX_mg2_e : 0.003054
  EX_ca2_e : 0.001833
  EX_cl_e : 0.001833
  EX_cu2_e : 0.000250
  EX_mn2_e : 0.000243
  EX_zn2_e : 0.000120
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 43.843584
  EX_co2_e : 27.567412
  EX_h_e : 9.521908
  EX_pyr_e : 5.185057
  Auxiliary production reaction : 0.223711
  EX_ac_e : 0.204977
  EX_ade_e : 0.000394
  DM_5drib_c : 0.000236
  DM_4crsol_c : 0.000079

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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