KEGG Pathway

NTHU Bioinformatics Core KEGG Pathway• Introduction to KEGG pathway• KEGG pathway search tool (KPST)2

NTHU Bioinformatics Core KEGG: Kyoto Encyclopedia of Genesand GenomesFrom Pathway to Genesand Molecules3

NTHU Bioinformatics Core The KEGG system is part of the JapaneseGenomeNet service.Select "KEGG: KyotoEncyclopedia of Genes andGenomes“to enter KEGG.(http://www.genome.jp/)4

NTHU Bioinformatics Core KEGG home page1. The documentaion on KEGGcan be found in "Introduction".2. The main entry point to KEGGis "KEGG2" that leads to thetable of contents page.(http://www.genome.jp/kegg/)5

NTHU Bioinformatics Core KEGG - Table of ContentsLet's go to the “KEGG PATHWAY"section of KEGG shown at the top. You can bookmark this page fora quick access to KEGG.6

NTHU Bioinformatics Core Metabolism - Reference pathwayLet's expand the portion of"Carbohydrate Metabolism". This is the overall (lowest-resolution)map of known metabolic pathways.8

NTHU Bioinformatics Core Carbohydrate MetabolismLet's choose glycolysis to see howit is represented in KEGG. This is the expanded map ofcarbohydrate metabolism showingglycolysis and TCA cycle in themiddle.9

NTHU Bioinformatics Core GlycolysisLet's click on EC 5.3.1.1. A box is an enzyme with ECnumber inside and a circle is ametabolic compound. Both are clickable to retrievemore detailed molecularinformation.10

NTHU Bioinformatics Core EC 5.3.1.1Let's examine the substrateinformation that is stored in theCOMPOUND section of LIGAND. By clicking on the box, we retrievedthe entry of EC 5.3.1.1 or triosephosphateisomerase from theENZYME section of the LIGANDdatabse. This is done by the DBGET/LinkDBsystem that is the basic retrivalsystem in the GenomeNet service.11

NTHU Bioinformatics Core Information of D-glyceraldehyde 3-phosphateLet's go back to EC 5.3.1.1. Here the information on D-glyceraldehyde 3-phosphate isdisplayed including the chemicalstructure in GIF image and the CASregistry number. By installing a proper browser, suchas ISIS/Draw, the chemical structurecan be handled in graphics.12

NTHU Bioinformatics Core EC 5.3.1.1Let's examine the E. coli genecoding for triose-phosphateisomerase. LIGAND is also linked to theGENES database that is the genecatalog database in KEGG.13

NTHU Bioinformatics Core Escherichia coli K-12 MG1655: b3919Let's go back again toEC 5.3.1.1. This is a typical entry of the GENESdatabase.14

NTHU Bioinformatics Core EC 5.3.1.1The link to the Protein DataBank (PDB) can be used toexamine the 3D structure ofthis enzyme. LIGAND is a gateway to a numberof existing molecular biologydatabases.15

NTHU Bioinformatics Core Database: PDB/ Entry: 3TIM By scrolling down the PDB entrydisplayed, it is possible to launchRasMol or Chime (if it is correctlyinstalled) to view and manipulate thestructure graphically.16

NTHU Bioinformatics Core EC 5.3.1.1In addition to the links that areexplicitly written in the entry,the DBGET/LinkDB systemprovides additional,compuationally derived links. To retrieve all links in LinkDB ata time, click on the entry namethat usually appears at the bottomof the entry.18

NTHU Bioinformatics Core Glycolysis Last time we clicked on abox (enzyme), but nowlet's click on a circle(compound),glyceraldehyde-3P.20

NTHU Bioinformatics Core E. coli specific pathway for glycolysis A green box is linked to theGENES database ratherthan the LIGAND databaseClick the green box5.3.1.1.23

NTHU Bioinformatics Core Escherichia coli K-12 MG1655: b3919 This is the same GENESentry we saw before for theE. coli gene of EC 5.3.1.1. The GENES database islinked to the graphicalGENOME map in KEGG.Click the Genome mapbutton.24

NTHU Bioinformatics Core The genome mapcontains an overallview window. Themap shows eachgene that is linked tothe GENES database25

NTHU Bioinformatics Core KEGG Pathway• Introduction to KEGG pathway• KEGG pathway search tool (KPST)26

NTHU Bioinformatics Core KPST: KEGG Pathway Search Tool(http://ibm4.life.nthu.edu.tw/KPST/)27

NTHU Bioinformatics Core KPST Tutorialhttp://ibm4.life.nthu.edu.tw/KPST/tutorial.php28