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

Gene deletion strategy (35 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3752 b3115 b1849 b2296 b1850 b3617 b2407 b1779 b1982 b0261 b0411 b0507 b4381 b0112 b0114 b0529 b2492 b0904 b0515 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.454577 (mmol/gDw/h)
  Minimum Production Rate : 0.669040 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.298467
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.734250
  EX_pi_e : 1.107528
  EX_so4_e : 0.114472
  EX_k_e : 0.088730
  EX_fe2_e : 0.007301
  EX_mg2_e : 0.003943
  EX_ca2_e : 0.002366
  EX_cl_e : 0.002366
  EX_cu2_e : 0.000322
  EX_mn2_e : 0.000314
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.523717
  EX_co2_e : 24.057221
  EX_h_e : 9.267606
  EX_thymd_e : 1.070798
  Auxiliary production reaction : 0.669040
  EX_ac_e : 0.264648
  EX_alltn_e : 0.001775
  DM_5drib_c : 0.001571
  DM_4crsol_c : 0.001367
  EX_glyclt_e : 0.001266

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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