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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3553 b1478 b1241 b4069 b4384 b3708 b3115 b1849 b2296 b2925 b2097 b2926 b0030 b2407 b1238 b1004 b3713 b1109 b0046 b3236 b2690 b2797 b3117 b1814 b4471 b1033 b3665 b0261 b2799 b3945 b1602 b4381 b2406 b3915 b0452 b3654 b3714 b3664 b2366 b2492 b0904 b1533 b1380 b2660 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.369617 (mmol/gDw/h)
  Minimum Production Rate : 0.616922 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.819311
  EX_o2_e : 280.780237
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.608716
  EX_pi_e : 0.356535
  EX_so4_e : 0.093078
  EX_k_e : 0.072147
  EX_mg2_e : 0.003206
  EX_ca2_e : 0.001924
  EX_cl_e : 0.001924
  EX_cu2_e : 0.000262
  EX_mn2_e : 0.000255
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994062
  EX_h2o_e : 543.178739
  EX_co2_e : 32.187377
  EX_ac_e : 3.544795
  Auxiliary production reaction : 0.616884
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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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