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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 71
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b1278 b3708 b3008 b1479 b0871 b0030 b2407 b3236 b0583 b1779 b4117 b3962 b1982 b1525 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b1746 b4267 b0675 b1415 b2904 b1014 b4014 b0261 b2976 b0822 b2799 b0726 b0507 b3709 b1907 b2913 b2406 b4115 b3161 b0112 b4265 b2975 b0114 b3603 b0886 b1539 b2492 b0904 b2578 b1533 b2835 b1380 b2965 b0693 b0508 b1473 b0494 b0516 b4266 b3662 b1985   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.379398 (mmol/gDw/h)
  Minimum Production Rate : 0.127740 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.728382
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.322815
  EX_pi_e : 0.749190
  EX_so4_e : 0.552751
  EX_k_e : 0.074056
  EX_fe2_e : 0.006094
  EX_mg2_e : 0.003291
  EX_ca2_e : 0.001975
  EX_cl_e : 0.001975
  EX_cu2_e : 0.000269
  EX_mn2_e : 0.000262
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_h2o_e : 50.470365
  EX_co2_e : 37.107059
  EX_h_e : 3.541761
  EX_acald_e : 1.237864
  EX_met__L_e : 0.329471
  Auxiliary production reaction : 0.127740
  EX_alltn_e : 0.000425
  DM_5drib_c : 0.000255
  EX_dxylnt_e : 0.000254
  DM_4crsol_c : 0.000085

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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