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 : 5pg35pg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b2066 b4069 b2502 b2744 b3708 b3008 b0910 b3115 b1849 b2296 b1982 b2797 b3117 b1814 b4471 b2498 b4374 b0675 b2361 b2291 b0261 b0452 b0114 b2366 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.737435 (mmol/gDw/h)
  Minimum Production Rate : 0.156128 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.777753
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.792707
  EX_pi_e : 1.023590
  EX_so4_e : 0.185701
  EX_k_e : 0.143942
  EX_fe2_e : 0.011844
  EX_mg2_e : 0.006397
  EX_ca2_e : 0.003838
  EX_cl_e : 0.003838
  EX_cu2_e : 0.000523
  EX_mn2_e : 0.000510
  EX_zn2_e : 0.000251
  EX_ni2_e : 0.000238
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 49.259251
  EX_co2_e : 25.214453
  EX_h_e : 8.877515
  EX_ac_e : 0.429324
  Auxiliary production reaction : 0.156128
  EX_ura_e : 0.133597
  DM_5drib_c : 0.000495
  DM_4crsol_c : 0.000164

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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