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 : adp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b2779 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b3665 b3945 b4381 b2406 b0114 b1539 b2492 b0904 b1533 b3927 b3821 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.649969 (mmol/gDw/h)
  Minimum Production Rate : 0.149578 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.428426
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.769685
  EX_pi_e : 0.926119
  EX_so4_e : 0.163675
  EX_k_e : 0.126869
  EX_fe2_e : 0.010439
  EX_mg2_e : 0.005638
  EX_ca2_e : 0.003383
  EX_cl_e : 0.003383
  EX_cu2_e : 0.000461
  EX_mn2_e : 0.000449
  EX_zn2_e : 0.000222
  EX_ni2_e : 0.000210
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 45.676821
  EX_co2_e : 26.564054
  EX_h_e : 8.325434
  EX_glyc__R_e : 1.752762
  Auxiliary production reaction : 0.149578
  EX_ade_e : 0.000437
  DM_mththf_c : 0.000291
  DM_5drib_c : 0.000146
  DM_4crsol_c : 0.000145

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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