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 : ade_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b3617 b3665 b0675 b2361 b4381 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b0516 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.648536 (mmol/gDw/h)
  Minimum Production Rate : 1.226803 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.528050
  EX_nh4_e : 13.206027
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.625582
  EX_so4_e : 0.163314
  EX_k_e : 0.126590
  EX_fe2_e : 0.010416
  EX_mg2_e : 0.005626
  EX_ca2_e : 0.003376
  EX_cl_e : 0.003376
  EX_cu2_e : 0.000460
  EX_mn2_e : 0.000448
  EX_zn2_e : 0.000221
  EX_ni2_e : 0.000209
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 52.306982
  EX_co2_e : 22.794122
  EX_h_e : 14.352457
  EX_ac_e : 2.191556
  Auxiliary production reaction : 1.226803
  EX_alltn_e : 0.016970
  DM_mththf_c : 0.000291
  DM_5drib_c : 0.000146
  DM_4crsol_c : 0.000145

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