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 : uri_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b4382 b0474 b2518 b1241 b0351 b3831 b4384 b3752 b4152 b0871 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b3946 b0825 b4161 b0411 b1602 b4138 b4123 b0621 b0452 b1727 b2492 b0904 b3029 b1380 b2660 b1771 b1206 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.356407 (mmol/gDw/h)
  Minimum Production Rate : 0.188235 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.663655
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.354659
  EX_pi_e : 0.343793
  EX_so4_e : 0.089750
  EX_k_e : 0.069568
  EX_mg2_e : 0.003092
  EX_fe2_e : 0.002941
  EX_fe3_e : 0.002783
  EX_ca2_e : 0.001855
  EX_cl_e : 0.001855
  EX_cu2_e : 0.000253
  EX_mn2_e : 0.000246
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 36.093943
  EX_co2_e : 29.172705
  EX_h_e : 4.526403
  EX_12ppd__R_e : 4.134181
  EX_succ_e : 0.371659
  Auxiliary production reaction : 0.188235
  EX_etoh_e : 0.178541
  EX_ura_e : 0.064511
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000079

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