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 : sbzcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4384 b3708 b3008 b3752 b0871 b2779 b2407 b1238 b1779 b0121 b1982 b2797 b3117 b1814 b4471 b0595 b0261 b3709 b4381 b2406 b3161 b0112 b2789 b3127 b2975 b0114 b3603 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b2835 b1473 b0494 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.669781 (mmol/gDw/h)
  Minimum Production Rate : 0.092243 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.033186
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.880033
  EX_pi_e : 0.922804
  EX_so4_e : 0.260907
  EX_k_e : 0.130737
  EX_fe2_e : 0.010757
  EX_mg2_e : 0.005810
  EX_ca2_e : 0.003486
  EX_cl_e : 0.003486
  EX_cu2_e : 0.000475
  EX_mn2_e : 0.000463
  EX_zn2_e : 0.000228
  EX_ni2_e : 0.000216
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.640674
  EX_co2_e : 29.553781
  EX_h_e : 6.524690
  Auxiliary production reaction : 0.092243
  DM_oxam_c : 0.000749
  DM_5drib_c : 0.000449
  DM_4crsol_c : 0.000149

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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