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 : 5aizc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b0512 b3115 b1849 b2296 b2779 b1850 b3617 b0160 b1982 b4374 b0675 b2361 b2291 b0261 b0507 b4388 b0112 b0114 b0529 b2492 b0904 b1380   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.403254 (mmol/gDw/h)
  Minimum Production Rate : 0.265906 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.911350
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.714127
  EX_pi_e : 0.654887
  EX_so4_e : 0.101547
  EX_k_e : 0.078712
  EX_fe2_e : 0.006477
  EX_mg2_e : 0.003498
  EX_ca2_e : 0.002099
  EX_cl_e : 0.002099
  EX_cu2_e : 0.000286
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 44.456851
  EX_co2_e : 25.278883
  EX_h_e : 10.097959
  EX_ac_e : 2.127634
  EX_alltn_e : 0.640324
  DM_5drib_c : 0.640144
  EX_glyclt_e : 0.640143
  DM_4crsol_c : 0.639963
  Auxiliary production reaction : 0.265906

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