Metabolic Pathway Databases
Metabolic pathway databases are specialized repositories that
organize and provide access to information about biochemical pathways. These
pathways consist of a series of chemical reactions occurring within a cell that
lead to the conversion of one molecule into another, involving enzymes and
other molecules. Understanding these pathways is crucial for studying cellular
processes, metabolism, and how organisms adapt to their environments.
1. KEGG (Kyoto Encyclopedia of Genes and Genomes)
KEGG is one
of the most comprehensive databases for understanding high-level functions and
utilities of biological systems, such as the cell, organism, and ecosystem,
based on molecular-level information.
KEGG integrates genomic, chemical, and systemic
functional information, providing a rich source of data on genes, proteins, and
metabolic pathways. It includes pathways for metabolism, genetic information
processing, environmental information processing, cellular processes, and human
diseases.
Metabolic Pathways: KEGG's metabolic pathway maps
are among its most widely used features. These maps represent networks of
molecular interactions and reactions within a cell, including the major
metabolic cycles, such as glycolysis, the citric acid cycle, and oxidative
phosphorylation.
Tools and Applications: KEGG offers tools for
pathway mapping, allowing researchers to input gene or protein data and
visualize where these components fit within known pathways. This is
particularly useful for interpreting omics data and understanding the broader
biological context of specific genes or proteins.
2. EcoCyc
EcoCyc is a
database dedicated to the bacterium *Escherichia coli* K-12, one of the most
extensively studied model organisms in molecular biology.
EcoCyc provides detailed information about the
metabolic pathways, enzymes, and regulatory networks of *E. coli*. It includes
data on metabolic reactions, gene products, gene regulation, and transporters.
Pathway Tools: EcoCyc is built using the Pathway Tools
software, which allows for the visualization and analysis of metabolic
pathways. Users can explore individual pathways, see how they interconnect, and
analyze gene expression data in the context of these pathways.
Experimental Data: EcoCyc is heavily curated,
meaning it integrates experimental data with computational predictions,
offering a reliable resource for researchers studying E. coli metabolism and physiology.
3. MetaCyc
MetaCyc is a comprehensive metabolic pathway
database that covers a wide range of organisms, including bacteria, archaea,
plants, and animals.
MetaCyc contains information on metabolic pathways
and enzymes from many different species. It includes more than 2,500 pathways,
making it one of the most extensive collections of metabolic data available.
Pathway Diversity: MetaCyc covers primary metabolism (e.g.,
glycolysis, amino acid biosynthesis) as well as secondary metabolism, which
involves the production of compounds like antibiotics and plant secondary
metabolites. This diversity makes MetaCyc a valuable resource for understanding
the metabolic capabilities of different organisms.
Research Applications: MetaCyc is used in
research areas such as comparative genomics, metabolic engineering, and systems
biology. It also serves as a reference for annotating newly sequenced genomes
by providing a framework for predicting metabolic capabilities based on gene
content.
