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  • Model SEED Tutorial Part 2:Model SEED Biochemistry Database

    Christopher Henry, Scott Devoid, Matt DeJongh, Aaron Best, Ross Overbeek, and Rick Stevens

    Presented by: Christopher Henry

    August 31-September 2

  • Model SEED Biochemistry Database

    Model SEED Homepage

    Viewing reactions/compound on KEGG maps

    Reactions and Compound pages

    Reaction data table

    Compound data table

    Media data table

  • You should log in here using your RAST account

    http://www.theseed.org/models/

    Use this menu to create an account

    Important server messages show up hereClick here for links to site tutorials

    With no models selected, the site shows all reactions and compounds found in the Model SEED biochemistry database

  • http://www.theseed.org/models/

    With no models selected, the site shows all reactions and compounds found in the Model SEED biochemistry database

    Click on this tab to view reaction and compound data overlaid on KEGG maps

    Search maps by name here

    Click on link to select a single map

  • Exploring the Biochemistry Database KEGG Maps

    Multiple maps can be openedHover and click on compounds to see additional data Hover and click on

    reactions to see additional reaction data

    Click on other map names to open those maps

    Click on compound link to visit compound page

  • Compound Page of Model SEED Database

    Name of compound in KEGG and publicly published models

    Table of reactions compound participates in.

    Structural Cues used to calculate G

  • 'f group G

    O

    O

    OHO

    OO

    Group Count Uncertainty

    [-OH]sec -42.2 1

    [-COO-] -82.2 2

    [-CH=]ring 4.6 3

    [>CH-]ring 5.5 2

    [-O-] -24.9 1

    [-CH2-] 0.9 1

    [>C=]ring 9.7 1

    [=CH2] 4.8 1

    Chorismate: -176.8 2.3 kcal/mol

    [>C=] 14.5 1

    Jankowski et al, Biophysical Journal, 2008

    0.4

    0.3

    0.5

    0.6

    0.9

    0.1

    1.0

    1.1

    0.7

    ( )' 'Number of groups 2

    Uncertaintyr g i

    iG Gi

    n =

    Group contribution method for estimating fGIn the group contribution method, the estimated fG of a molecular is equal to the sum of

    the estimated energies for the molecular substructures that make up the molecule

  • Exploring the Biochemistry Database KEGG Maps

    Multiple maps can be opened

    Click on other map names to open those maps

    Click on compound link to visit compound page

    Click on reaction link to visit reaction page

  • Reaction Page of Model SEED Database

    Equation contains links to compound pages

    Name of reaction in KEGG and published models.

  • Model SEED Reaction TableClick on this tab to view a table of all reactions in the Model SEED database

    ~13,000 reactions in database

  • A biochemistry database was constructed combining content from the KEGG and 13 published genome-scale models into a non-redundant set of compounds and reactions

    Reactions were then mapped to the functional roles in the SEED based on EC number, substrate names, and enzyme names:

    Acetinobacter: iAbaylyiv4 (874 rxn) M. barkeri: iAF692 (620 rxn)

    Combined SEED Database

    (12,103 rxn)

    M. genitalium: iPS189 (263 rxn)

    M. tuberculosis: iNJ661 (975 rxn)

    P. putida: iJN746 (949 rxn)

    S. aureus: iSB619 (649 rxn)

    S. cerevisiae: iND750 (1149 rxn)

    B. subtilis: iAG612 (598 rxn)

    E. coli: iAF1260 (2078 rxn)

    E. coli: iJR904 (932 rxn)

    H. pylori: iIT341 (476 rxn)

    L. lactis: iAO358 (619 rxn)

    B. subtilis: iYO844 (1020 rxn)

    (8000 rxn)

    NAD+ + NADPH NADH + NADP+

    NAD(P) transhydrogenase alpha subunit (EC 1.6.1.2)

    NAD(P) transhydrogenase subunit beta (EC 1.6.1.2)

    REACTION FUNCTIONAL ROLE GENE

    peg.100

    peg.101

    COMPLEX

    Gene complex

    Biochemistry Database in the SEED

    www.theseed.org/models/

  • Model SEED Reaction TableClick on this tab to view a table of all reactions in the Model SEED database

    Links to KEGG Map in Map tab

    SEED Functional roles of reaction

    Table is paginated

    Search by compound name

  • Model SEED Compound TableClick on this tab to view a table of all compounds in the Model SEED database

    Sort by Column headers e.g. largest and smallest mass

    Links to KEGG Maps that containcompound

  • Model SEED Media TableClick on this tab to view a table of all media formulations in the Model SEED database

    Sort and search by media name or by compound name

    Compound name and ID link to compound page

  • AcknowledgementsANL/U. Chicago Team- Robert Olson- Terry Disz- Daniela Bartels- Tobias Paczian- Daniel Paarmann- Scott Devoid- Andreas Wilke- Bill Mihalo- Elizabeth Glass- Folker Meyer- Jared Wilkening- Rick Stevens- Alex Rodriguez- Mark DSouza- Rob Edwards- Christopher Henry

    FIG Team- Ross Overbeek- Gordon Pusch- Bruce Parello- Veronika Vonstein- Andrei Ostermann- Olga Vassieva- Olga Zagnitzko - Svetlana GerdesHope College Team- Aaron Best- Matt DeJongh- Nathan Tintle - Hope college students

    Slide Number 1Slide Number 2Slide Number 3Slide Number 4Slide Number 5Slide Number 6Group contribution method for estimating fGSlide Number 8Slide Number 9Slide Number 10Slide Number 11Slide Number 12Slide Number 13Slide Number 14Acknowledgements

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