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 : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (114 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b1241 b0351 b3831 b3403 b3752 b0871 b2925 b2097 b2926 b1850 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b2690 b1302 b2662 b4139 b2799 b0726 b3945 b1602 b2789 b3127 b0452 b1727 b2975 b3603 b2492 b0904 b3029 b1380 b2917 b2660 b0514 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.439053 (mmol/gDw/h)
  Minimum Production Rate : 1.061124 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.197118
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.741739
  EX_pi_e : 0.423514
  EX_so4_e : 0.110562
  EX_k_e : 0.085700
  EX_fe2_e : 0.007052
  EX_mg2_e : 0.003809
  EX_ca2_e : 0.002285
  EX_cl_e : 0.002285
  EX_cu2_e : 0.000311
  EX_mn2_e : 0.000303
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.258961
  EX_co2_e : 37.333777
  EX_h_e : 5.095617
  EX_pyr_e : 1.061419
  EX_etoh_e : 0.730421
  DM_5drib_c : 0.000099
  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.

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Last updated: 21-Sep-2023
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