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 : bwco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b0474 b2518 b1241 b0351 b3831 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2781 b2407 b1759 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b1033 b4161 b0261 b4381 b2406 b0112 b0114 b0509 b3125 b2366 b2492 b0904 b1533 b3821 b3918 b4042 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.510410 (mmol/gDw/h)
  Minimum Production Rate : 0.239159 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.041050
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.285108
  EX_pi_e : 1.209821
  EX_so4_e : 1.085167
  EX_tungs_e : 0.239159
  EX_k_e : 0.099628
  EX_fe2_e : 0.008198
  EX_mg2_e : 0.004428
  EX_ca2_e : 0.002657
  EX_cl_e : 0.002657
  EX_cu2_e : 0.000362
  EX_mn2_e : 0.000353
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 48.262389
  EX_co2_e : 23.797816
  EX_h_e : 9.399855
  EX_ac_e : 3.806276
  Auxiliary production reaction : 0.239159
  EX_thym_e : 0.092386
  DM_oxam_c : 0.000571
  DM_5drib_c : 0.000342
  EX_glyclt_e : 0.000341
  DM_4crsol_c : 0.000114

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