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 : gsn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (32 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b3399 b4069 b2744 b3708 b3008 b3115 b1849 b2296 b2883 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b2291 b0261 b0411 b4381 b0114 b2366 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.744793 (mmol/gDw/h)
  Minimum Production Rate : 0.315432 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.133814
  EX_o2_e : 274.760211
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.620861
  EX_pi_e : 0.718432
  EX_so4_e : 0.187554
  EX_k_e : 0.145378
  EX_mg2_e : 0.006461
  EX_ca2_e : 0.003877
  EX_cl_e : 0.003877
  EX_cu2_e : 0.000528
  EX_mn2_e : 0.000515
  EX_zn2_e : 0.000254
  EX_ni2_e : 0.000241
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988038
  EX_h2o_e : 548.538169
  EX_co2_e : 25.406474
  EX_ac_e : 0.433608
  EX_gsn_e : 0.315432
  DM_5drib_c : 0.000500
  DM_4crsol_c : 0.000166

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