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 (75 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 60
  Gene deletion: b1241 b0351 b3831 b4069 b4384 b3708 b1479 b3614 b0910 b3752 b3115 b1849 b2296 b2926 b2781 b2407 b3236 b1759 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1415 b1014 b0261 b2799 b3945 b0507 b3709 b2913 b4381 b2406 b3161 b0112 b2868 b2975 b0114 b3603 b1539 b2492 b0904 b3035 b1533 b3927 b2835 b1380 b3918 b1912 b0508 b1473 b0494 b4266 b3662 b2842   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.307527 (mmol/gDw/h)
  Minimum Production Rate : 0.199402 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.441917
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.495296
  EX_pi_e : 0.894847
  EX_so4_e : 0.543213
  EX_k_e : 0.060027
  EX_fe2_e : 0.004939
  EX_mg2_e : 0.002668
  EX_ca2_e : 0.001601
  EX_cl_e : 0.001601
  EX_cu2_e : 0.000218
  EX_mn2_e : 0.000213
  EX_zn2_e : 0.000105
  EX_ni2_e : 0.000099

Product: (mmol/gDw/h)
  EX_h2o_e : 49.824434
  EX_co2_e : 34.707552
  EX_h_e : 5.708184
  EX_ac_e : 1.839211
  EX_met__L_e : 0.266370
  EX_thym_e : 0.255065
  Auxiliary production reaction : 0.199402
  EX_ade_e : 0.000344
  DM_5drib_c : 0.000206
  EX_dxylnt_e : 0.000206
  DM_4crsol_c : 0.000069

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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