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 : icit_x
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 48: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: PHATRDRAFT_2793 PHATRDRAFT_31994 PHATRDRAFT_54082 PHATRDRAFT_800 PHATRDRAFT_18337 PHATRDRAFT_16140 Phatr3_EG02232 PHATRDRAFT_draft1186 PHATRDRAFT_55126 PHATRDRAFT_52208 PHATRDRAFT_12757 PHATRDRAFT_45017 Phatr_9124 PHATRDRAFT_14762 PHATRDRAFT_22122 Phatr3_EG02251 PHATRDRAFT_36913 PHATRDRAFT_1769 PHATRDRAFT_50742 PHATRDRAFT_19708 Phatr3_EG02361 PHATRDRAFT_49056 PHATRDRAFT_18323 PHATRDRAFT_29004 PHATRDRAFT_54493 PHATRDRAFT_43194 PHATRDRAFT_48078 PHATRDRAFT_15140 PHATRDRAFT_20504 Phatr3_EG01947 PHATRDRAFT_11414 Phatr3_EG02569 PHATRDRAFT_21970 PHATRDRAFT_42245 PHATRDRAFT_39772 PHATRDRAFT_51970 PHATRDRAFT_15777 PHATRDRAFT_44482 PHATRDRAFT_43697 PHATRDRAFT_12452 Phatr3_EG02611 PHATRDRAFT_15536   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.359607 (mmol/gDw/h)
  Minimum Production Rate : 0.002986 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_photon_e : 1000.000000
  EX_co2_e : 23.239302
  EX_h2o_e : 16.990044
  EX_no3_e : 1.760000
  EX_pi_e : 0.089293
  EX_so4_e : 0.063953
  EX_mg2_e : 0.006427

Product: (mmol/gDw/h)
  EX_o2_e : 27.929111
  EX_h_e : 1.307955
  Auxiliary production reaction : 0.975180
  DM_biomass_c : 0.359607
  SK_for_c : 0.306368

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