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 : pg160_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1855 b3831 b2744 b1278 b3614 b0910 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b2361 b2291 b0411 b1701 b1805 b4138 b4123 b0621 b2197 b3918 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.567764 (mmol/gDw/h)
  Minimum Production Rate : 0.299862 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 16.512793
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.937065
  EX_pi_e : 0.847531
  EX_so4_e : 0.142974
  EX_k_e : 0.110824
  EX_fe2_e : 0.009119
  EX_mg2_e : 0.004925
  EX_cl_e : 0.002955
  EX_ca2_e : 0.002955
  EX_cu2_e : 0.000403
  EX_mn2_e : 0.000392
  EX_zn2_e : 0.000194
  EX_ni2_e : 0.000183
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 39.520386
  EX_co2_e : 21.322369
  EX_h_e : 6.906362
  EX_succ_e : 0.592060
  EX_ura_e : 0.402629
  Auxiliary production reaction : 0.299862
  DM_5drib_c : 0.000128
  DM_4crsol_c : 0.000127

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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