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 : dhbpt_m
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 54: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: PHATRDRAFT_draft870 PHATRDRAFT_54082 PHATRDRAFT_800 PHATRDRAFT_54219 PHATRDRAFT_54477 PHATRDRAFT_12762 Phatr3_EG02232 PHATRDRAFT_26290 PHATRDRAFT_draft1023 PHATRDRAFT_draft1645 PHATRDRAFT_36256 PHATRDRAFT_49339 PHATRDRAFT_29016 PHATRDRAFT_38509 PHATRDRAFT_31906 PHATRDRAFT_14962 Phatr3_EG02361 PHATRDRAFT_41063 PHATRDRAFT_33839 PHATRDRAFT_27166 PHATRDRAFT_45592 PHATRDRAFT_54731 PHATRDRAFT_28797 PHATRDRAFT_48078 PHATRDRAFT_13005 PHATRDRAFT_50084 PHATRDRAFT_11414 Phatr3_EG02569 PHATRDRAFT_21970 PHATRDRAFT_51970 PHATRDRAFT_43697 PHATRDRAFT_45428   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.356643 (mmol/gDw/h)
  Minimum Production Rate : 0.002901 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_photon_e : 329.792762
  EX_co2_e : 28.448410
  EX_h2o_e : 24.351129
  EX_no3_e : 1.760000
  EX_so4_e : 0.184753
  EX_pi_e : 0.088557
  EX_mg2_e : 0.006374

Product: (mmol/gDw/h)
  EX_o2_e : 30.256130
  SK_for_c : 10.270561
  EX_h_e : 8.105306
  DM_biomass_c : 0.356643
  EX_etoh_e : 0.302019
  DM_dmsp_c : 0.121327
  Auxiliary production reaction : 0.002901

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