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 : gdpofuc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2779 b2407 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0261 b4381 b2406 b0114 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b2413 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.396868 (mmol/gDw/h)
  Minimum Production Rate : 0.091095 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.494048
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.742060
  EX_pi_e : 0.565012
  EX_so4_e : 0.099939
  EX_k_e : 0.077466
  EX_fe2_e : 0.006374
  EX_mg2_e : 0.003443
  EX_ca2_e : 0.002066
  EX_cl_e : 0.002066
  EX_cu2_e : 0.000281
  EX_mn2_e : 0.000274
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 39.477813
  EX_co2_e : 27.630311
  EX_h_e : 8.794350
  EX_glyc__R_e : 4.873595
  Auxiliary production reaction : 0.091095
  DM_oxam_c : 0.000444
  DM_5drib_c : 0.000266
  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
Contact