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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b0160 b1982 b3616 b3589 b1033 b4374 b0675 b2361 b2291 b0261 b0112 b0114 b0509 b3125 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.463809 (mmol/gDw/h)
  Minimum Production Rate : 0.888878 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.606808
  EX_o2_e : 270.835016
  EX_nh4_e : 11.231767
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.225150
  EX_so4_e : 0.116796
  EX_k_e : 0.090532
  EX_mg2_e : 0.004024
  EX_ca2_e : 0.002414
  EX_cl_e : 0.002414
  EX_cu2_e : 0.000329
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992551
  EX_h2o_e : 550.070867
  EX_co2_e : 19.159192
  EX_ac_e : 1.567217
  Auxiliary production reaction : 0.888878
  DM_oxam_c : 0.000519
  DM_5drib_c : 0.000311
  EX_glyclt_e : 0.000310
  DM_4crsol_c : 0.000103

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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