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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3553 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b2779 b2925 b2097 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b2440 b4374 b2361 b2291 b0261 b0411 b1602 b2913 b2789 b3127 b1727 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1380 b0494 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.370634 (mmol/gDw/h)
  Minimum Production Rate : 0.424496 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.392402
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.416230
  EX_pi_e : 1.206507
  EX_so4_e : 0.093333
  EX_k_e : 0.072345
  EX_fe2_e : 0.005953
  EX_mg2_e : 0.003215
  EX_ca2_e : 0.001929
  EX_cl_e : 0.001929
  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 : 45.599540
  EX_co2_e : 31.711804
  EX_h_e : 8.881979
  EX_ac_e : 4.487113
  Auxiliary production reaction : 0.424496
  EX_his__L_e : 0.046503
  DM_oxam_c : 0.000415
  DM_5drib_c : 0.000249
  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.

Last updated: 21-Sep-2023
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