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 : air_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b1241 b0351 b3752 b0871 b2925 b2097 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b2690 b0937 b1033 b4015 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b3654 b2868 b3714 b3664 b1727 b4064 b4464 b0755 b3612 b0529 b2492 b0904 b3927 b1380 b3662 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.378588 (mmol/gDw/h)
  Minimum Production Rate : 0.022383 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.396646
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.155866
  EX_pi_e : 0.387571
  EX_so4_e : 0.095336
  EX_k_e : 0.073898
  EX_fe2_e : 0.006081
  EX_mg2_e : 0.003284
  EX_ca2_e : 0.001971
  EX_cl_e : 0.001971
  EX_cu2_e : 0.000268
  EX_mn2_e : 0.000262
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 43.956211
  EX_co2_e : 28.562285
  EX_h_e : 8.785551
  EX_pyr_e : 5.239786
  Auxiliary production reaction : 0.022383
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000084

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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