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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4382 b1241 b0351 b4384 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b3617 b2407 b1779 b2797 b3117 b1814 b4471 b3946 b0825 b2868 b0114 b2366 b2492 b0904 b1533 b3821 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.375407 (mmol/gDw/h)
  Minimum Production Rate : 0.064815 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.960866
  EX_o2_e : 280.155955
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.379699
  EX_pi_e : 0.362120
  EX_so4_e : 0.094535
  EX_k_e : 0.073277
  EX_mg2_e : 0.003257
  EX_ca2_e : 0.001954
  EX_cl_e : 0.001954
  EX_cu2_e : 0.000266
  EX_mn2_e : 0.000259
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993971
  EX_h2o_e : 544.051039
  EX_co2_e : 28.166729
  EX_pyr_e : 5.258379
  Auxiliary production reaction : 0.064815
  EX_ade_e : 0.000253
  DM_5drib_c : 0.000084
  DM_4crsol_c : 0.000084

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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