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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3553 b3399 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b0160 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0675 b2361 b0261 b0822 b1602 b4381 b2406 b0452 b1727 b0114 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b1380 b3447 b2660 b0516 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.387582 (mmol/gDw/h)
  Minimum Production Rate : 0.236501 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.606421
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.947564
  EX_pi_e : 0.373864
  EX_so4_e : 0.097602
  EX_k_e : 0.075653
  EX_fe2_e : 0.006227
  EX_mg2_e : 0.003362
  EX_ca2_e : 0.002017
  EX_cl_e : 0.002017
  EX_cu2_e : 0.000275
  EX_mn2_e : 0.000268
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 37.850744
  EX_co2_e : 27.814363
  EX_h_e : 5.693312
  EX_12ppd__R_e : 3.328633
  EX_pyr_e : 1.370344
  Auxiliary production reaction : 0.236278
  EX_ade_e : 0.010575
  DM_5drib_c : 0.000260
  DM_4crsol_c : 0.000086

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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