Welcome to the Interactive Pathways Explorer

This version of iPath is now outdated. Please visit http://pathways.embl.de to access the latest version.

iPath is a web-based tool for the visualization and analysis of the metabolic pathways. The underlying global pathways map is constructed using approximately 120 KEGG pathways, and gives an overview of the complete metabolism in biological systems. Nodes in the map correspond to various chemical compounds and edges represent series of enzymatic reactions.
Various types of data can be mapped onto the default global map, changing the colors, opacity and width of any node or edge. In addition, iPath provides a set of precomputed metabolic pathway maps for various species and taxnonomic classes. All maps in iPath can be easily converted to various graphical formats..

If you find iPath useful in your work, you can cite Letunic et al. (2008) Trends Biochem Sci. 33(3):101-3 iPath: interactive exploration of biochemical pathways and networks. (PDF)

Interactive global pathways map
Interactive map
Click on the image to display the interactive version

Global map of metabolic pathways

The interactive viewer provides an easy way of navigating the global pathways map.

How to navigate the map:

  • Zoom control: mouse wheel, zoom icons or 'Page Up' and 'Page Down' keys
  • Panning the map: click the map and drag or use the arrow keys
  • Reset the view: click the '1:1' icon or press the 'Home' key

Clicking on any node or edge in the map will provide detailed information, including links to the relevant KEGG annotation pages.

In addition to the interactive version, map can be downloaded in the following graphical formats:

Analysis and data mapping
Use this form to map your data and generate a custom representation of the metabolic pathways map. You can customize the color and transparency of all edges and nodes in the map. In addition, edge width can be changed. Click the help icon below for a detailed explanation of required parameters.

Select elements to highlight

Element selection:
Upload a file with selection:

Highlight enzymes (name query):

Example:transferase
Default opacity: used for the non-selected parts of the map; between 0 and 1
Default width: used for the non-selected parts of the map; default value is 3
Species filter: only pathways present in this NCBI tax ID will be included. Check the taxonomy restricted maps page for valid IDs.
Keep original colors: if checked, non-selected parts of the map will not change to gray
Select whole pathways: when selecting using compounds or proteins, complete pathways will be highlighted
Query reaction compounds: include all reaction compounds when querying?
Set background color: White
Black
Other: 		you can change the map background here
Exported map format: DPI select the desired format and DPI for the exported map

Taxonomy restricted pathways maps
Phylogenetic tree
Click on the image to display the interactive version.

In addition to the default global map which includes data from all species in KEGG, iPath provides complete metabolic pathways maps for individual species and various taxnomic classes.

Clicking on the tree image on the left will display an interactive phylogenetic tree, generated using iTOL. You can navigate the tree using the same shortcuts which are used in the map view (mousewheel, arrows, Page Up, Page Down and Home). In addition, you can search the tree for any species or taxnomic class. The tree includes 183 species (21 Eukayota, 144 Bacteria and 18 Archaea).

Click on any species or clade in the tree to display the links to the relevant pathways map. There are two versions of each map available:

  • Non-filtered map: all enzymes present in that taxonomic class are included
  • Filtered map: enzymes which appear in different parts of the map are removed, in cases where any adjacent enzymes in the pathway are not present in that taxonomic class. The exception to this rule are cases where products of the one enzyme's reaction are utilized by the other enzyme.

This tool allows easy comparison of metabolic pathway maps for multiple species or classes.