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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (101 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b3399 b3831 b4069 b2744 b3708 b3008 b3614 b0910 b3752 b2297 b2458 b2779 b2925 b2097 b2781 b0160 b1779 b1759 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b2440 b0596 b0675 b2361 b0261 b3709 b4381 b2406 b3161 b0112 b2789 b3127 b0452 b2975 b0114 b3603 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3918 b1473   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.598238 (mmol/gDw/h)
  Minimum Production Rate : 0.310251 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.552248
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.283142
  EX_pi_e : 0.577064
  EX_so4_e : 0.150648
  EX_k_e : 0.116772
  EX_fe2_e : 0.009608
  EX_mg2_e : 0.005190
  EX_ca2_e : 0.003114
  EX_cl_e : 0.003114
  EX_cu2_e : 0.000424
  EX_mn2_e : 0.000413
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.642859
  EX_co2_e : 27.867021
  EX_h_e : 8.169275
  EX_ac_e : 1.833927
  Auxiliary production reaction : 0.310251
  EX_thym_e : 0.092678
  DM_oxam_c : 0.016323
  DM_5drib_c : 0.000401
  DM_4crsol_c : 0.000133
  EX_etha_e : 0.000048

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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