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

Gene deletion strategy (56 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4069 b4384 b3708 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b0030 b2407 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b2440 b0261 b4381 b2406 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b0516 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.352090 (mmol/gDw/h)
  Minimum Production Rate : 0.223716 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.857388
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.475262
  EX_pi_e : 0.563344
  EX_so4_e : 0.088663
  EX_k_e : 0.068725
  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 : 43.842889
  EX_co2_e : 27.567748
  EX_h_e : 9.521503
  EX_pyr_e : 5.184941
  Auxiliary production reaction : 0.223716
  EX_ac_e : 0.204982
  EX_alltn_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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