title: CyanoLyase: a database of phycobilin lyase sequences, motifs and functions.
abstract: CyanoLyase (http://cyanolyase.genouest.org/) is a manually curated sequence and motif database of phycobilin lyases and related proteins. These enzymes catalyze the covalent ligation of chromophores (phycobilins) to specific binding sites of phycobiliproteins (PBPs). The latter constitute the building bricks of phycobilisomes, the major light-harvesting systems of cyanobacteria and red algae. Phycobilin lyases sequences are poorly annotated in public databases. Sequences included in CyanoLyase were retrieved from all available genomes of these organisms and a few others by similarity searches using biochemically characterized enzyme sequences and then classified into 3 clans and 32 families. Amino acid motifs were computed for each family using Protomata learner. CyanoLyase also includes BLAST and a novel pattern matching tool (Protomatch) that allow users to rapidly retrieve and annotate lyases from any new genome. In addition, it provides phylogenetic analyses of all phycobilin lyases families, describes their function, their presence/absence in all genomes of the database (phyletic profiles) and predicts the chromophorylation of PBPs in each strain. The site also includes a thorough bibliography about phycobilin lyases and genomes included in the database. This resource should be useful to scientists and companies interested in natural or artificial PBPs, which have a number of biotechnological applications, notably as fluorescent markers.
authors.affiliation: GenOuest Platform, France.
authors.forename: Anthony
authors.initials: A
authors.lastname: Bretaudeau
authors.forename: François
authors.initials: F
authors.lastname: Coste
authors.forename: Florian
authors.initials: F
authors.lastname: Humily
authors.forename: Laurence
authors.initials: L
authors.lastname: Garczarek
authors.forename: Gildas
authors.initials: G
authors.lastname: Le Corguillé
authors.forename: Christophe
authors.initials: C
authors.lastname: Six
authors.forename: Morgane
authors.initials: M
authors.lastname: Ratin
authors.forename: Olivier
authors.initials: O
authors.lastname: Collin
authors.forename: Wendy M
authors.initials: WM
authors.lastname: Schluchter
authors.forename: Frédéric
authors.initials: F
authors.lastname: Partensky
mesh_terms: D020816:Amino Acid Motifs; D000458:Cyanobacteria / Q000201:enzymology; D030562:Databases, Protein; D020407:Internet; D008190:Lyases / Q000737:chemistry* / Q000145:classification / Q000235:genetics / Q000502:physiology; D058977:Molecular Sequence Annotation; D052980:Phycobilins / Q000378:metabolism*; D052979:Phycobiliproteins / Q000378:metabolism*; D000461:Rhodophyta / Q000201:enzymology; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D052980:Phycobilins; D052979:Phycobiliproteins; D008190:Lyases