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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b2836 b3553 b4069 b4384 b2744 b3708 b3008 b0871 b3115 b1849 b2296 b2925 b2097 b0030 b1238 b2883 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b3945 b0507 b4381 b2406 b0112 b2868 b4064 b4464 b0114 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b0594 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.573635 (mmol/gDw/h)
  Minimum Production Rate : 0.728832 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.074115
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.656078
  EX_pi_e : 2.739826
  EX_so4_e : 0.144453
  EX_k_e : 0.111969
  EX_fe2_e : 0.009213
  EX_mg2_e : 0.004976
  EX_ca2_e : 0.002986
  EX_cl_e : 0.002986
  EX_cu2_e : 0.000407
  EX_mn2_e : 0.000396
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.812979
  EX_co2_e : 26.036939
  EX_h_e : 6.669988
  EX_pyr_e : 1.062032
  Auxiliary production reaction : 0.728832
  EX_ac_e : 0.333962
  EX_ade_e : 0.000642
  DM_5drib_c : 0.000385
  DM_4crsol_c : 0.000128

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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