FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology

• Published in: BMC genomics Vol. 11; no. 1; p. 81
• Main Authors: Grossetête, Sandrine, Labedan, Bernard, Lespinet, Olivier
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 01-02-2010; BioMed Central; BMC
• Subjects: Biochemistry, Molecular Biology; Bioinformatics; Computational Biology; Computational Biology - methods; Data Mining; Databases, Protein; DNA sequencing; Enzymes; Fungi; Fungi - genetics; Genetic aspects; Genome, Fungal; Genomes; Genomics; Life Sciences; Metabolic Networks and Pathways; Methods; Microbiology and Parasitology; Nucleotide sequencing; Online databases; France
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-11-81

More and more completely sequenced fungal genomes are becoming available and many more sequencing projects are in progress. This deluge of data should improve our knowledge of the various primary and secondary metabolisms of Fungi, including their synthesis of useful compounds such as antibiotics or toxic molecules such as mycotoxins. Functional annotation of many fungal genomes is imperfect, especially of genes encoding enzymes, so we need dedicated tools to analyze their metabolic pathways in depth.
FUNGIpath is a new tool built using a two-stage approach. Groups of orthologous proteins predicted using complementary methods of detection were collected in a relational database. Each group was further mapped on to steps in the metabolic pathways published in the public databases KEGG and MetaCyc. As a result, FUNGIpath allows the primary and secondary metabolisms of the different fungal species represented in the database to be compared easily, making it possible to assess the level of specificity of various pathways at different taxonomic distances. It is freely accessible at http://www.fungipath.u-psud.fr.
As more and more fungal genomes are expected to be sequenced during the coming years, FUNGIpath should help progressively to reconstruct the ancestral primary and secondary metabolisms of the main branches of the fungal tree of life and to elucidate the evolution of these ancestral fungal metabolisms to various specific derived metabolisms.