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 : glyc__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b3124 b2690 b2797 b3117 b1814 b4471 b0675 b0822 b0726 b4381 b2789 b3127 b1727 b0114 b2366 b0755 b3612 b2492 b0904 b1533 b1912 b0515   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.660668 (mmol/gDw/h)
  Minimum Production Rate : 1.769196 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.943542
  EX_o2_e : 276.691696
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.206084
  EX_pi_e : 0.637284
  EX_so4_e : 0.166369
  EX_k_e : 0.128958
  EX_mg2_e : 0.005731
  EX_cl_e : 0.003439
  EX_ca2_e : 0.003439
  EX_cu2_e : 0.000468
  EX_mn2_e : 0.000457
  EX_zn2_e : 0.000225
  EX_ni2_e : 0.000213
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989389
  EX_h2o_e : 544.664042
  EX_co2_e : 27.098813
  Auxiliary production reaction : 1.903998
  EX_alltn_e : 0.017732
  EX_glyclt_e : 0.000442
  DM_5drib_c : 0.000149
  DM_4crsol_c : 0.000147

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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