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 : malcoame_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (6 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b4384 b3708 b3008 b0871 b2925 b2097 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b2440 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 : 0.783186 (mmol/gDw/h)
  Minimum Production Rate : 0.049385 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.497056
  EX_o2_e : 274.688387
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.899759
  EX_pi_e : 0.903620
  EX_so4_e : 0.246607
  EX_k_e : 0.152872
  EX_mg2_e : 0.006794
  EX_cl_e : 0.004076
  EX_ca2_e : 0.004076
  EX_cu2_e : 0.000555
  EX_mn2_e : 0.000541
  EX_zn2_e : 0.000267
  EX_ni2_e : 0.000253
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987421
  EX_h2o_e : 548.193627
  EX_co2_e : 26.289612
  DM_oxam_c : 0.050261
  Auxiliary production reaction : 0.049385
  EX_acser_e : 0.045461
  DM_5drib_c : 0.000526
  DM_4crsol_c : 0.000175

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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