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 : gdpfuc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3916 b2836 b3399 b4069 b2744 b3708 b3008 b3115 b1849 b2296 b0160 b1851 b1982 b1200 b2797 b3117 b1814 b4471 b0675 b2361 b2291 b0261 b4381 b2239 b3453 b0114 b2366 b1723 b2492 b0904 b2947 b1533 b3927 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.719561 (mmol/gDw/h)
  Minimum Production Rate : 0.297229 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.043667
  EX_o2_e : 273.972571
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.280015
  EX_pi_e : 1.288608
  EX_so4_e : 0.181200
  EX_k_e : 0.140453
  EX_mg2_e : 0.006242
  EX_ca2_e : 0.003745
  EX_cl_e : 0.003745
  EX_cu2_e : 0.000510
  EX_mn2_e : 0.000497
  EX_zn2_e : 0.000245
  EX_ni2_e : 0.000232
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988443
  EX_h2o_e : 547.959192
  EX_co2_e : 24.756861
  EX_ac_e : 0.418919
  Auxiliary production reaction : 0.297229
  EX_acser_e : 0.022611
  DM_5drib_c : 0.000483
  DM_4crsol_c : 0.000160
  EX_g3pe_e : 0.000058

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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