MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iLB1027_lipid [2].
Target metabolite : pheme_h
List of minimal gene deletion strategies (Download)

Gene deletion strategy (19 of 23: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 16
  Gene deletion: PHATRDRAFT_54082 PHATRDRAFT_12031 PHATRDRAFT_44906 Phatr3_EG02232 PHATRDRAFT_draft1186 PHATRDRAFT_52208 PHATRDRAFT_12757 PHATRDRAFT_48983 PHATRDRAFT_22404 PHATRDRAFT_50742 PHATRDRAFT_39711 PHATRDRAFT_50971 PHATRDRAFT_10306 PHATRDRAFT_16375 PHATRDRAFT_draft18 PHATRDRAFT_44384   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.048145 (mmol/gDw/h)
  Minimum Production Rate : 0.119660 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_photon_e : 1000.000000
  EX_co2_e : 15.995444
  EX_h2o_e : 7.709674
  EX_no3_e : 1.760000
  EX_h_e : 0.237124
  EX_pi_e : 0.220000
  EX_fe2_e : 0.119660
  EX_so4_e : 0.008562
  EX_mg2_e : 0.000860

Product: (mmol/gDw/h)
  EX_o2_e : 20.819852
  SK_for_c : 1.066185
  DM_indole_c : 1.045727
  Auxiliary production reaction : 0.119660
  DM_biomass_c : 0.048145
  DM_minohp_c : 0.034674

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

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: 27-Sep-2023
Contact