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 : air_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b0030 b2883 b1982 b3616 b3589 b0261 b0507 b4381 b2406 b0112 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.481394 (mmol/gDw/h)
  Minimum Production Rate : 1.845159 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 987.481319
  EX_o2_e : 271.194188
  EX_nh4_e : 10.737186
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.309514
  EX_so4_e : 0.121225
  EX_k_e : 0.093965
  EX_mg2_e : 0.004176
  EX_ca2_e : 0.002506
  EX_cl_e : 0.002506
  EX_cu2_e : 0.000341
  EX_mn2_e : 0.000333
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992268
  EX_h2o_e : 546.006789
  EX_co2_e : 20.376867
  EX_ac_e : 2.549216
  Auxiliary production reaction : 1.845159
  EX_ade_e : 0.000539
  DM_5drib_c : 0.000323
  EX_glyclt_e : 0.000322
  DM_4crsol_c : 0.000107

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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