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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b3708 b0910 b3115 b1849 b2296 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b2797 b3117 b1814 b4471 b2799 b1602 b4381 b2406 b3915 b3654 b3714 b3664 b4064 b4464 b1539 b2492 b0904 b1781 b3001 b1533 b1380 b0325 b2660 b1771 b4141 b1798 b3662 b1517 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.455709 (mmol/gDw/h)
  Minimum Production Rate : 0.345406 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.198744
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.648647
  EX_pi_e : 0.439579
  EX_so4_e : 0.114757
  EX_k_e : 0.088951
  EX_fe3_e : 0.007319
  EX_mg2_e : 0.003953
  EX_ca2_e : 0.002372
  EX_cl_e : 0.002372
  EX_cu2_e : 0.000323
  EX_mn2_e : 0.000315
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.139367
  EX_co2_e : 37.309551
  EX_h_e : 6.186891
  Auxiliary production reaction : 0.345406
  EX_ac_e : 0.265307
  DM_mththf_c : 0.000204
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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