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

Anthony Bretaudeau 1 François Coste 2 Florian Humily 3 Laurence Garczarek 4 Gildas Le Corguillé 5 Christophe Six 4 Morgane Ratin 4 Olivier Collin 1 Wendy M Schluchter 6 Frédéric Partensky 4, 5
1 Plateforme bioinformatique GenOuest [Rennes]
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, UR1 - Université de Rennes 1, Plateforme Génomique Santé Biogenouest®, Inria Rennes – Bretagne Atlantique
2 Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
3 MAPP - MArine Phototrophic Prokaryotes
ADMM - Adaptation et diversité en milieu marin
4 ADMM - Adaptation et diversité en milieu marin
5 SBR - Station biologique de Roscoff [Roscoff]
6 Department of Biological Sciences [New Orleans]
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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UPMC | UNIV-RENNES1 | INRIA | IRISA | ADMM | IRISA-D7 | ADMM-MAPP | INSTITUT-TELECOM | UR1-UFR-ISTIC | CMM | UNIV-RENNES | INSA-GROUPE | SORBONNE-UNIVERSITE | SU-SCIENCES | FR2424

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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, Oxford University Press, 2012, pp.6. ⟨10.1093/nar/gks1091⟩. ⟨hal-01094087⟩

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