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 : adn_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b4069 b4384 b2744 b3115 b1849 b2296 b2779 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1982 b0477 b4139 b0411 b1602 b4381 b2868 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b3029 b1380 b2660 b1771 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.466986 (mmol/gDw/h)
  Minimum Production Rate : 0.215789 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.670897
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.123927
  EX_pi_e : 0.450458
  EX_so4_e : 0.117596
  EX_k_e : 0.091152
  EX_mg2_e : 0.004051
  EX_fe2_e : 0.003854
  EX_fe3_e : 0.003646
  EX_ca2_e : 0.002431
  EX_cl_e : 0.002431
  EX_cu2_e : 0.000331
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.834921
  EX_co2_e : 38.128110
  EX_h_e : 5.646890
  EX_ac_e : 0.271873
  Auxiliary production reaction : 0.215789
  EX_ade_e : 0.000314
  DM_mththf_c : 0.000209
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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