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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b2836 b4382 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2407 b2388 b1982 b2797 b3117 b1814 b4471 b3565 b0261 b0114 b2366 b2492 b0904 b1533 b3927 b3437 b4268   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.739288 (mmol/gDw/h)
  Minimum Production Rate : 0.235073 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.336598
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.924534
  EX_pi_e : 1.183267
  EX_so4_e : 0.186167
  EX_k_e : 0.144304
  EX_fe2_e : 0.011874
  EX_mg2_e : 0.006413
  EX_ca2_e : 0.003848
  EX_cl_e : 0.003848
  EX_cu2_e : 0.000524
  EX_mn2_e : 0.000511
  EX_zn2_e : 0.000252
  EX_ni2_e : 0.000239
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.787522
  EX_co2_e : 26.444108
  EX_h_e : 7.928490
  EX_ac_e : 0.430403
  Auxiliary production reaction : 0.235073
  DM_5drib_c : 0.000166
  DM_4crsol_c : 0.000165

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