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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b4467 b1478 b0474 b2518 b1241 b4069 b4384 b2744 b3708 b3752 b3115 b1849 b2296 b2779 b2925 b2097 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b4374 b2361 b2291 b2799 b3945 b1602 b2913 b2406 b0114 b2366 b2492 b0904 b1533 b1380 b3662 b1517 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.370768 (mmol/gDw/h)
  Minimum Production Rate : 0.564528 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.015684
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.570039
  EX_pi_e : 0.922173
  EX_so4_e : 0.093367
  EX_k_e : 0.072371
  EX_fe2_e : 0.005955
  EX_mg2_e : 0.003216
  EX_ca2_e : 0.001930
  EX_cl_e : 0.001930
  EX_cu2_e : 0.000263
  EX_mn2_e : 0.000256
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 43.811503
  EX_co2_e : 32.324466
  EX_h_e : 8.224258
  EX_ac_e : 3.594493
  Auxiliary production reaction : 0.564528
  EX_glyclt_e : 0.092697
  EX_ade_e : 0.000250
  EX_mththf_e : 0.000166
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000083

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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