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 (83 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 69
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b1278 b3708 b3008 b1479 b0871 b2779 b2926 b0160 b3236 b3962 b1982 b1525 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b1746 b4267 b1033 b0595 b4374 b0675 b2361 b2291 b1014 b4014 b0261 b2976 b0822 b2799 b0726 b0507 b3709 b1907 b3161 b0112 b0452 b2975 b0114 b3603 b0886 b2366 b0306 b3605 b2492 b0904 b2578 b1533 b3927 b1380 b2965 b0693 b1473 b4266 b2842 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.388171 (mmol/gDw/h)
  Minimum Production Rate : 0.086840 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.891491
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.138049
  EX_pi_e : 0.634951
  EX_so4_e : 0.522113
  EX_k_e : 0.075768
  EX_fe2_e : 0.006234
  EX_mg2_e : 0.003367
  EX_ca2_e : 0.002020
  EX_cl_e : 0.002020
  EX_cu2_e : 0.000275
  EX_mn2_e : 0.000268
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 50.423686
  EX_co2_e : 37.239417
  EX_h_e : 3.577632
  EX_acald_e : 1.179214
  EX_met__L_e : 0.337524
  Auxiliary production reaction : 0.086840
  DM_oxam_c : 0.000434
  DM_5drib_c : 0.000260
  EX_dxylnt_e : 0.000260
  DM_4crsol_c : 0.000087

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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