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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b2836 b3553 b1478 b3399 b1241 b4069 b4384 b2744 b3115 b1849 b2296 b2779 b0030 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1982 b4139 b1033 b1623 b4015 b0261 b0411 b2799 b3945 b1602 b4381 b3915 b0529 b2492 b0904 b2954 b3029 b1380 b2660 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.440702 (mmol/gDw/h)
  Minimum Production Rate : 0.197783 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.894675
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.946237
  EX_pi_e : 0.820669
  EX_so4_e : 0.110977
  EX_k_e : 0.086022
  EX_fe3_e : 0.007078
  EX_mg2_e : 0.003823
  EX_cl_e : 0.002294
  EX_ca2_e : 0.002294
  EX_cu2_e : 0.000312
  EX_mn2_e : 0.000305
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.833489
  EX_co2_e : 37.243661
  EX_h_e : 5.104122
  EX_ac_e : 0.256570
  Auxiliary production reaction : 0.197783
  DM_5drib_c : 0.000296
  DM_4crsol_c : 0.000098

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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