Metabolic pathway databases
KEGG Database
• KEGG is the database for metabolic pathways.
• Developed by M. Kanehisa.
• The KEGG project is undertaken in the Bioinformatics
Center, Institute for Chemical Research, Kyoto Univ.
• It collects individual genomes, gene products and their
functions with biochemical and genetic information.
• Kyoto Encyclopedia of Genes and Genomes (KEGG) is a
knowledge base for systematic analysis of gene functions in
terms of the networks of genes and molecules.
• The major component of KEGG is the PATHWAY
database that consists of graphical diagrams of
biochemical pathways including most of the known
metabolic pathways and some of the known
regulatory pathways.
• The pathway information is also represented by the
ortholog group tables summarizing orthologous and
paralogous gene groups among different organisms.
• KEGG maintains the GENES database for the
gene catalogs of all organisms with complete
genomes and selected organisms with partial
genomes, which are continuously re-
annotated, as well as the LIGAND database
for chemical compounds and enzymes.
• Each gene catalog is associated with the
graphical genome map for chromosomal
locations that is represented by Java applet.
• In addition to the data collection efforts, KEGG
develops and provides various computational
tools, such as for reconstructing biochemical
pathways from the complete genome sequence
and for predicting gene regulatory networks
from the gene expression profiles.
• The KEGG databases are daily updated and
made freely available
• (http://www.genome.ad.jp/kegg/).
• KEGG is an integrated database resource consisting of the
15 main databases.
• It covers various data objects, called KEGG objects, for
computer representation of molecular systems.
• Broadly categorized into
• systems information (PATHWAY, BRITE, MODULE,
DISEASE, DRUG and ENVIRON),
• genomic information (ORTHOLOGY, GENOME and
GENES) and
• chemical information (COMPOUND, GLYCAN,
REACTION, RPAIR, RCLASS and ENZYME).
• KEGG GENES is a collection of gene catalogs for all
organisms whose genomes are completely sequenced
and made available by RefSeq.
• http://www.ncbi.nlm.nih.gov/RefSeq
• The KEGG pathway maps are graphical diagrams
representing knowledge on molecular interaction and
reaction networks for metabolism, genetic
information processing, environmental information
processing, cellular processes, organismal systems,
human diseases and drug development.
http://nar.oxfordjournals.org/content/early/2011/11/10/nar.gkr988.full
The current statistics of KEGG databases is as follows:
Number of pathways 23,574(PATHWAY database)
Number of reference pathways 265(PATHWAY database)
Number of ortholog tables 87(PATHWAY database)
Number of organisms 272(GENOME database)
Number of genes 911,584(GENES database)
Number of ortholog clusters 35,456(SSDB database)
Number of KO assignments 6,221(KO database)
Number of chemical compounds 12,737(COMPOUND database)
Number of glycans 11,017(GLYCAN database)
Number of chemical reactions 6,399(REACTION database)
Number of reactant pairs 5,953(RPAIR database)
KEGG Map of Glycolysis
• Reference pathway: a summary
of all relevant reactions and
enzymes from all organisms
• Reaction intermediates are
named
• Enzymes given by E.C. number
(linked: discussed on next slide)
• Arrows for the pathways: note
that some go both ways!
• Boxes showing neighboring
pathways (linked to pathway
maps)
• At the top:
– “Pathway entry” link gives a
description of the pathway
– Dropdown pathway list for
many organisms.
• Other reference
pathways just vary what
the links go to.
Metabolic pathway map
EMP
• Enzymes and Metabolic Pathways database, EMP,
is a unique and most comprehensive electronic
source of biochemical data.
• It covers all aspects of enzymology and
metabolism and represents the whole factual
content of original journal publications.
•The database can be queried by means of a whole
text search, taxonomy search, by accession number
(i.e., a unique key that identifies a record), or by
enzyme commission (EC) number.
MetaCyc
•MetaCyc (https://MetaCyc.org) is a comprehensive
reference database of metabolic pathways and enzymes
from all domains of life.
•It contains more than 2570 pathways derived from
>54,000 publications, making it the largest curated
collection of metabolic pathways.
•The data in MetaCyc is strictly evidence-based and richly
curated, resulting in an encyclopedic reference tool for
metabolism.
•MetaCyc is also used as a knowledge base for generating
thousands of organism-specific Pathway/Genome
Databases (PGDBs), which are available in the BioCyc
(https://BioCyc.org) and other PGDB collections.
BRENDA
BRENDA (Braunschweig Enzyme Database) represents a
comprehensive collection of enzyme and metabolic
information, based on primary literature.
The database contains data from at least 83,000 different
enzymes from 9800 different organisms, classified in
approximately 4200 EC numbers.
The development of an enzyme data information system
was started in 1987 at the German National Research
Centre for Biotechnology in Braunschweig (GBF) and is
now continued at the University of Cologne, Institute of
Biochemistry.
http://www.brenda-enzymes.info/
