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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 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.
Cited literature [25 references]
https://hal.inria.fr/hal-01094087
Contributor : Anthony Bretaudeau Connect in order to contact the contributor
Submitted on : Thursday, December 11, 2014 - 4:00:40 PM
Last modification on : Friday, January 7, 2022 - 3:45:01 PM
Long-term archiving on: : Thursday, March 12, 2015 - 10:57:01 AM
Contributor : Anthony Bretaudeau Connect in order to contact the contributor
Submitted on : Thursday, December 11, 2014 - 4:00:40 PM
Last modification on : Friday, January 7, 2022 - 3:45:01 PM
Long-term archiving on: : Thursday, March 12, 2015 - 10:57:01 AM
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Nucl. Acids Res.-2013-Bretaude...
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