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Journal Articles Nucleic Acids Research Year : 2012

CyanoLyase: a database of phycobilin lyase sequences, motifs and functions

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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 chromo-phores (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 anno-tated 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 characteri-zed 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 phylogen-etic analyses of all phycobilin lyases families, de-scribes 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 bibliog-raphy 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 fluores-cent markers.
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Dates and versions

hal-01094087 , version 1 (11-12-2014)

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Cite

Anthony Bretaudeau, François Coste, Florian Humily, Laurence Garczarek, Gildas Le Corguillé, et al.. CyanoLyase: a database of phycobilin lyase sequences, motifs and functions. Nucleic Acids Research, 2012, pp.6. ⟨10.1093/nar/gks1091⟩. ⟨hal-01094087⟩
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