Individual pathway maps from KEGG provide information on protein localization within the cell, compartmentalization into different cellular components, or of reactions within a larger metabolic process. Visualiza­tion of proteins from gene lists onto pathway maps is useful for their in­terpretation. The Algal Functional Annotation Tool utilizes the publicly available KEGG application programming interface (API) for pathway highlighting. The information linking C. reinhardtii proteins to identifiers within the KEGG database is used to determine the subset of KEGG IDs within the supplied gene list associated with a particular pathway. The Algal Functional Annotation Tool also deduces which proteins within the pathway are located within the genome of C. reinhardtii but not found in the gene list and sends the corresponding identifiers to the KEGG API to be highlighted in a different background color. This API interface is imple­mented using the SOAP architecture for web applications.