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 : glyclt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b2836 b4382 b4069 b4384 b2744 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b0583 b2883 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0261 b4381 b2406 b0112 b2868 b4064 b4464 b2975 b0114 b3603 b0509 b3125 b2366 b2492 b0904 b2578 b1533 b3927 b0508 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.588473 (mmol/gDw/h)
  Minimum Production Rate : 0.249228 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.092457
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.604890
  EX_pi_e : 0.567644
  EX_so4_e : 0.148189
  EX_k_e : 0.114866
  EX_fe2_e : 0.009451
  EX_mg2_e : 0.005105
  EX_ca2_e : 0.003063
  EX_cl_e : 0.003063
  EX_cu2_e : 0.000417
  EX_mn2_e : 0.000407
  EX_zn2_e : 0.000201
  EX_ni2_e : 0.000190
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.548664
  EX_co2_e : 26.432882
  EX_h_e : 8.577675
  EX_pyr_e : 1.329290
  EX_ac_e : 0.342601
  EX_ade_e : 0.249887
  DM_5drib_c : 0.249623
  DM_4crsol_c : 0.249359
  Auxiliary production reaction : 0.249228

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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