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 : gmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (97 of 102: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b4069 b4384 b2744 b3752 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1779 b2690 b1982 b4139 b1033 b0261 b0411 b2799 b3945 b1602 b2913 b4381 b2868 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b3029 b1380 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.341058 (mmol/gDw/h)
  Minimum Production Rate : 0.157396 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.234654
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.472279
  EX_pi_e : 0.486382
  EX_so4_e : 0.085885
  EX_k_e : 0.066572
  EX_mg2_e : 0.002959
  EX_fe2_e : 0.002815
  EX_fe3_e : 0.002663
  EX_ca2_e : 0.001775
  EX_cl_e : 0.001775
  EX_cu2_e : 0.000242
  EX_mn2_e : 0.000236
  EX_zn2_e : 0.000116
  EX_ni2_e : 0.000110

Product: (mmol/gDw/h)
  EX_h2o_e : 43.977571
  EX_co2_e : 27.900206
  EX_h_e : 9.499616
  EX_pyr_e : 5.179745
  EX_ac_e : 0.198559
  EX_3hpp_e : 0.195990
  Auxiliary production reaction : 0.157396
  EX_ade_e : 0.000382
  DM_5drib_c : 0.000229
  DM_4crsol_c : 0.000076

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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