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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b1241 b0351 b4069 b2744 b3708 b2930 b4232 b3697 b3925 b2297 b2458 b2779 b3617 b3236 b2797 b3117 b1814 b4471 b3946 b0825 b0261 b4388 b4381 b2868 b0114 b2366 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.563791 (mmol/gDw/h)
  Minimum Production Rate : 0.552945 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.353601
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.912626
  EX_pi_e : 0.543836
  EX_so4_e : 0.141974
  EX_k_e : 0.110048
  EX_fe2_e : 0.009055
  EX_mg2_e : 0.004891
  EX_ca2_e : 0.002935
  EX_cl_e : 0.002935
  EX_cu2_e : 0.000400
  EX_mn2_e : 0.000390
  EX_zn2_e : 0.000192
  EX_ni2_e : 0.000182
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.954531
  EX_co2_e : 25.851210
  EX_h_e : 10.427432
  EX_ac_e : 1.865536
  EX_glyc__R_e : 0.557828
  Auxiliary production reaction : 0.552945
  EX_xan_e : 0.014752
  DM_5drib_c : 0.000127
  DM_4crsol_c : 0.000126

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