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 : ppbng_h
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 45: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 24
  Gene deletion: PHATRDRAFT_42398 PHATRDRAFT_54834 PHATRDRAFT_800 PHATRDRAFT_49229 PHATRDRAFT_55192 PHATRDRAFT_36257 Phatr3_EG02232 Phatr3_EG02269 PHATRDRAFT_draft1023 PHATRDRAFT_draft1645 PHATRDRAFT_34120 PHATRDRAFT_29016 PHATRDRAFT_draft1572 Phatr3_EG02361 PHATRDRAFT_42458 PHATRDRAFT_39711 PHATRDRAFT_20143 PHATRDRAFT_20310 PHATRDRAFT_22117 PHATRDRAFT_39772 PHATRDRAFT_45428 PHATRDRAFT_8945 PHATRDRAFT_41686 PHATRDRAFT_44384   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.356465 (mmol/gDw/h)
  Minimum Production Rate : 0.007689 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_photon_e : 1000.000000
  EX_co2_e : 18.053957
  EX_h2o_e : 14.124559
  EX_no3_e : 1.760000
  EX_h_e : 1.595763
  EX_pi_e : 0.088513
  EX_so4_e : 0.063394
  EX_mg2_e : 0.006370

Product: (mmol/gDw/h)
  EX_o2_e : 24.538542
  EX_etoh_e : 0.362696
  DM_biomass_c : 0.356465
  SK_for_c : 0.319068
  Auxiliary production reaction : 0.007689

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