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 : frdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4467 b1478 b1241 b0351 b0871 b2779 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b2799 b3945 b1602 b0529 b2492 b0904 b1380 b0723 b2660 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.393292 (mmol/gDw/h)
  Minimum Production Rate : 0.012614 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.250581
  EX_o2_e : 279.896445
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.247525
  EX_pi_e : 0.404601
  EX_so4_e : 0.099039
  EX_k_e : 0.076768
  EX_mg2_e : 0.003412
  EX_ca2_e : 0.002047
  EX_cl_e : 0.002047
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993683
  EX_h2o_e : 543.817024
  EX_co2_e : 28.242009
  EX_pyr_e : 5.141951
  Auxiliary production reaction : 0.012614
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000088
  EX_glyclt_e : 0.000039

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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