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 : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4467 b1478 b1241 b4069 b3708 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2779 b1238 b1004 b3713 b1109 b0046 b3236 b2797 b3117 b1814 b4471 b3946 b0825 b4015 b2799 b3945 b1602 b4381 b2406 b3915 b3654 b3714 b3664 b4064 b4464 b2366 b2492 b0904 b1533 b1380 b2660 b1695 b1518 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.386554 (mmol/gDw/h)
  Minimum Production Rate : 0.188325 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.015823
  EX_o2_e : 281.700864
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.927979
  EX_pi_e : 0.372872
  EX_so4_e : 0.097343
  EX_k_e : 0.075453
  EX_mg2_e : 0.003353
  EX_cl_e : 0.002012
  EX_ca2_e : 0.002012
  EX_cu2_e : 0.000274
  EX_mn2_e : 0.000267
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993790
  EX_h2o_e : 544.426814
  EX_co2_e : 32.150717
  EX_ac_e : 4.672926
  Auxiliary production reaction : 0.188307
  EX_thym_e : 0.188307
  DM_mththf_c : 0.000173
  DM_5drib_c : 0.000087
  DM_4crsol_c : 0.000086

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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