Metabolic Pathway Databases

 

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.