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 : 2ombzl_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b4382 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2925 b2097 b2926 b2407 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0261 b2406 b0114 b1539 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.626357 (mmol/gDw/h)
  Minimum Production Rate : 0.061217 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.722197
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.826516
  EX_pi_e : 0.604187
  EX_so4_e : 0.157729
  EX_k_e : 0.122260
  EX_fe2_e : 0.010060
  EX_mg2_e : 0.005434
  EX_cl_e : 0.003260
  EX_ca2_e : 0.003260
  EX_cu2_e : 0.000444
  EX_mn2_e : 0.000433
  EX_zn2_e : 0.000214
  EX_ni2_e : 0.000202
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 46.313760
  EX_co2_e : 28.976194
  EX_h_e : 7.035212
  EX_ac_e : 1.156162
  DM_oxam_c : 0.061918
  Auxiliary production reaction : 0.061217
  DM_5drib_c : 0.000420
  DM_4crsol_c : 0.000140

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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