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 : mnl1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b1478 b1241 b0351 b4069 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b2779 b3844 b1004 b3713 b1109 b0046 b3124 b3236 b3946 b0825 b1033 b2799 b3945 b1602 b4381 b3915 b2492 b0904 b1380 b2660 b0514 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.368034 (mmol/gDw/h)
  Minimum Production Rate : 0.578660 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.720045
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.974731
  EX_pi_e : 0.933667
  EX_so4_e : 0.092678
  EX_k_e : 0.071838
  EX_fe3_e : 0.005911
  EX_mg2_e : 0.003193
  EX_ca2_e : 0.001916
  EX_cl_e : 0.001916
  EX_cu2_e : 0.000261
  EX_mn2_e : 0.000254
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 41.506565
  EX_co2_e : 27.801715
  EX_h_e : 8.203141
  EX_pyr_e : 3.989057
  EX_ac_e : 0.826534
  Auxiliary production reaction : 0.578660
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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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