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 : 6pgc_m
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 62: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 24
  Gene deletion: PHATRDRAFT_26934 PHATRDRAFT_13987 PHATRDRAFT_draft877 PHATRDRAFT_34010 PHATRDRAFT_42015 PHATRDRAFT_12031 PHATRDRAFT_44906 PHATRDRAFT_30145 PHATRDRAFT_55192 PHATRDRAFT_30519 Phatr3_EG02269 PHATRDRAFT_51128 PHATRDRAFT_29456 PHATRDRAFT_23598 PHATRDRAFT_46664 PHATRDRAFT_859 PHATRDRAFT_32849 PHATRDRAFT_draft1517 PHATRDRAFT_28585 PHATRDRAFT_49505 PHATRDRAFT_8945 PHATRDRAFT_41686 PHATRDRAFT_23365 Phatr3_EG02292   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.063499 (mmol/gDw/h)
  Minimum Production Rate : 0.204233 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_photon_e : 1000.000000
  EX_co2_e : 4.407925
  EX_h2o_e : 3.422171
  EX_no3_e : 1.760000
  EX_pi_e : 0.220000
  EX_h_e : 0.126256
  EX_so4_e : 0.033722
  EX_mg2_e : 0.001135

Product: (mmol/gDw/h)
  EX_o2_e : 5.459508
  DM_no3_c : 1.449222
  Auxiliary production reaction : 0.204233
  DM_biomass_c : 0.063499
  SK_for_c : 0.054098
  DM_dmsp_c : 0.022429

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