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 : nadphx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3752 b0871 b2779 b2926 b3617 b2883 b1982 b0261 b2913 b4381 b2406 b0112 b2789 b3127 b2868 b4064 b4464 b2975 b0114 b3603 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.423473 (mmol/gDw/h)
  Minimum Production Rate : 0.688305 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.665913
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.393973
  EX_pi_e : 2.473398
  EX_so4_e : 0.106639
  EX_k_e : 0.082659
  EX_fe2_e : 0.006801
  EX_mg2_e : 0.003674
  EX_ca2_e : 0.002204
  EX_cl_e : 0.002204
  EX_cu2_e : 0.000300
  EX_mn2_e : 0.000293
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.663922
  EX_co2_e : 24.710343
  EX_h_e : 7.334930
  EX_acald_e : 1.725165
  Auxiliary production reaction : 0.688305
  EX_ade_e : 0.000474
  DM_5drib_c : 0.000284
  DM_4crsol_c : 0.000094

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