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 : adphep_LD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2836 b3399 b4382 b0586 b4384 b2744 b3708 b3008 b0871 b2779 b2925 b2097 b0160 b2407 b0120 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0675 b2361 b0261 b2406 b0112 b2868 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.398737 (mmol/gDw/h)
  Minimum Production Rate : 0.091492 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.330158
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.765576
  EX_pi_e : 0.567609
  EX_so4_e : 0.100410
  EX_k_e : 0.077831
  EX_fe2_e : 0.006404
  EX_mg2_e : 0.003459
  EX_ca2_e : 0.002075
  EX_cl_e : 0.002075
  EX_cu2_e : 0.000283
  EX_mn2_e : 0.000276
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 39.341002
  EX_co2_e : 27.526543
  EX_h_e : 8.789563
  EX_glyc__R_e : 4.849543
  Auxiliary production reaction : 0.091492
  EX_hxan_e : 0.000446
  DM_5drib_c : 0.000268
  DM_4crsol_c : 0.000089

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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