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 : fgam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4069 b4384 b2744 b3708 b3752 b2297 b2458 b2925 b2097 b2883 b1779 b1982 b2797 b3117 b1814 b4471 b3449 b3946 b0825 b0411 b4381 b2239 b2868 b4064 b4464 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.390350 (mmol/gDw/h)
  Minimum Production Rate : 0.248375 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.020539
  EX_o2_e : 281.626311
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.713812
  EX_pi_e : 0.624910
  EX_so4_e : 0.098298
  EX_k_e : 0.076194
  EX_mg2_e : 0.003386
  EX_ca2_e : 0.002032
  EX_cl_e : 0.002032
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993731
  EX_h2o_e : 543.761297
  EX_co2_e : 32.211861
  EX_ac_e : 4.888435
  Auxiliary production reaction : 0.248375
  EX_ade_e : 0.000263
  DM_mththf_c : 0.000175
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000087

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