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 : prbatp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (29 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b1241 b0351 b4069 b4384 b3752 b2297 b2458 b3617 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b0261 b1602 b4381 b2406 b1727 b0114 b0529 b2492 b0904 b1380 b2660 b3662 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.355398 (mmol/gDw/h)
  Minimum Production Rate : 0.433525 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.104596
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.491408
  EX_pi_e : 2.076919
  EX_so4_e : 0.089496
  EX_k_e : 0.069371
  EX_fe2_e : 0.005708
  EX_mg2_e : 0.003083
  EX_ca2_e : 0.001850
  EX_cl_e : 0.001850
  EX_cu2_e : 0.000252
  EX_mn2_e : 0.000246
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 52.576626
  EX_co2_e : 34.030756
  EX_h_e : 6.258537
  EX_etoh_e : 0.746638
  EX_his__L_e : 0.495172
  Auxiliary production reaction : 0.433525
  EX_ac_e : 0.206908
  DM_5drib_c : 0.000238
  DM_4crsol_c : 0.000079

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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