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 (59 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3553 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1779 b3946 b0825 b1033 b1602 b2913 b4381 b1727 b0114 b2492 b0904 b1380 b1695 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.376583 (mmol/gDw/h)
  Minimum Production Rate : 0.021732 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.158521
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.067063
  EX_pi_e : 0.406717
  EX_so4_e : 0.094831
  EX_k_e : 0.073506
  EX_fe2_e : 0.006048
  EX_mg2_e : 0.003267
  EX_cl_e : 0.001960
  EX_ca2_e : 0.001960
  EX_cu2_e : 0.000267
  EX_mn2_e : 0.000260
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 43.748883
  EX_co2_e : 28.467651
  EX_h_e : 8.688254
  EX_pyr_e : 5.249792
  Auxiliary production reaction : 0.021732
  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.

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Last updated: 21-Sep-2023
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