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 : dadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b3617 b0160 b1623 b3665 b0675 b2361 b4381 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.652852 (mmol/gDw/h)
  Minimum Production Rate : 0.696619 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.204372
  EX_o2_e : 273.013898
  EX_nh4_e : 10.533844
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.022983
  EX_so4_e : 0.164401
  EX_k_e : 0.127432
  EX_mg2_e : 0.005663
  EX_ca2_e : 0.003398
  EX_cl_e : 0.003398
  EX_cu2_e : 0.000463
  EX_mn2_e : 0.000451
  EX_zn2_e : 0.000223
  EX_ni2_e : 0.000211
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989515
  EX_h2o_e : 549.951164
  EX_co2_e : 23.660338
  EX_acald_e : 1.287711
  Auxiliary production reaction : 0.696619
  DM_mththf_c : 0.000292
  DM_5drib_c : 0.000147
  DM_4crsol_c : 0.000146

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