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 (70 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 56
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2502 b2744 b3708 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b0937 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b0261 b2799 b1602 b0507 b3709 b2913 b3161 b0112 b0452 b1539 b2492 b0904 b1781 b3001 b1533 b3825 b1380 b0325 b1473 b1600 b1771 b4141 b1798 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.336462 (mmol/gDw/h)
  Minimum Production Rate : 0.281215 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.840956
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.604152
  EX_pi_e : 1.168198
  EX_so4_e : 0.365943
  EX_k_e : 0.065675
  EX_fe2_e : 0.005404
  EX_mg2_e : 0.002919
  EX_ca2_e : 0.001751
  EX_cl_e : 0.001751
  EX_cu2_e : 0.000239
  EX_mn2_e : 0.000232
  EX_zn2_e : 0.000115
  EX_ni2_e : 0.000109

Product: (mmol/gDw/h)
  EX_h2o_e : 51.039717
  EX_co2_e : 34.839323
  EX_h_e : 5.392759
  EX_ac_e : 1.174466
  Auxiliary production reaction : 0.281215
  EX_ade_e : 0.000377
  DM_5drib_c : 0.000226
  DM_4crsol_c : 0.000075

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.

Last updated: 21-Sep-2023
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