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 : ametam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (5 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4069 b2744 b3708 b3008 b2297 b2458 b0160 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0114 b1539 b2492 b0904 b1533 b3927 b3821   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.739176 (mmol/gDw/h)
  Minimum Production Rate : 0.187868 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.026577
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.110241
  EX_pi_e : 0.713013
  EX_so4_e : 0.374007
  EX_k_e : 0.144282
  EX_fe2_e : 0.011872
  EX_mg2_e : 0.006412
  EX_ca2_e : 0.003847
  EX_cl_e : 0.003847
  EX_cu2_e : 0.000524
  EX_mn2_e : 0.000511
  EX_zn2_e : 0.000252
  EX_ni2_e : 0.000239
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.753893
  EX_co2_e : 25.792025
  EX_h_e : 7.785782
  EX_ac_e : 0.618205
  Auxiliary production reaction : 0.187868
  DM_5drib_c : 0.000496
  DM_4crsol_c : 0.000165

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.

Last updated: 21-Sep-2023
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