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 : prbamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b2836 b3399 b2502 b2744 b3708 b3008 b0871 b2297 b2458 b2779 b2925 b2097 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b3945 b2913 b2868 b0114 b2366 b0529 b2492 b0904 b2947 b2578 b1533 b3927 b2413 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.358685 (mmol/gDw/h)
  Minimum Production Rate : 0.082304 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.064287
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.287282
  EX_pi_e : 0.510593
  EX_so4_e : 0.090325
  EX_k_e : 0.070013
  EX_fe2_e : 0.005762
  EX_mg2_e : 0.003112
  EX_ca2_e : 0.001867
  EX_cl_e : 0.001867
  EX_cu2_e : 0.000254
  EX_mn2_e : 0.000248
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 43.934616
  EX_co2_e : 27.939603
  EX_h_e : 9.076154
  EX_pyr_e : 5.366898
  Auxiliary production reaction : 0.082301
  EX_ade_e : 0.000401
  DM_5drib_c : 0.000241
  DM_4crsol_c : 0.000080

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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