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 : pap_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (10 of 10: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b2502 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0675 b2361 b0261 b4381 b2406 b0452 b0114 b2366 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.635254 (mmol/gDw/h)
  Minimum Production Rate : 0.126118 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.706717
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.508614
  EX_pi_e : 0.865006
  EX_so4_e : 0.159970
  EX_k_e : 0.123997
  EX_fe2_e : 0.010203
  EX_mg2_e : 0.005511
  EX_ca2_e : 0.003306
  EX_cl_e : 0.003306
  EX_cu2_e : 0.000450
  EX_mn2_e : 0.000439
  EX_zn2_e : 0.000217
  EX_ni2_e : 0.000205
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 47.152168
  EX_co2_e : 26.739756
  EX_h_e : 8.465131
  EX_pyr_e : 1.962906
  Auxiliary production reaction : 0.126118
  DM_oxam_c : 0.017333
  DM_5drib_c : 0.000426
  DM_4crsol_c : 0.000142

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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