title: BYKdb: the Bacterial protein tYrosine Kinase database.
abstract: Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. These enzymes have been shown to control several biological functions in the bacterial cells. In recent years biochemical studies, sequence analyses and structure resolutions allowed the deciphering of a common signature. However, BY-kinase sequence annotations in primary databases remain incomplete. This prompted us to develop a specialized database of computer-annotated BY-kinase sequences: the Bacterial protein tyrosine-kinase database (BYKdb). BY-kinase sequences are first identified, thanks to a workflow developed in a previous work. A second workflow annotates the UniProtKB entries in order to provide the BYKdb entries. The database can be accessed through a web interface that allows static and dynamic queries and offers integrated sequence analysis tools. BYKdb can be found at http://bykdb.ibcp.fr.
authors.affiliation: Unité Bases Moléculaires et Structurales des Systèmes Infectieux, UMR 5086 CNRS - Université Claude Bernard Lyon 1, IBCP FR 3302 - 7, Passage du Vercors, 69367 Lyon CEDEX 07, France.
authors.forename: Fanny
authors.initials: F
authors.lastname: Jadeau
authors.forename: Christophe
authors.initials: C
authors.lastname: Grangeasse
authors.forename: Lei
authors.initials: L
authors.lastname: Shi
authors.forename: Ivan
authors.initials: I
authors.lastname: Mijakovic
authors.forename: Gilbert
authors.initials: G
authors.lastname: Deléage
authors.forename: Christophe
authors.initials: C
authors.lastname: Combet
mesh_terms: D001419:Bacteria / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry*; D030562:Databases, Protein; D058977:Molecular Sequence Annotation; D011505:Protein-Tyrosine Kinases / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins; D011505:Protein-Tyrosine Kinases
references.citation: Trends Biochem Sci. 2000 Mar;25(3):147-50
references.pmid: 10694887
references.citation: Trends Biochem Sci. 2007 Feb;32(2):86-94
references.pmid: 17208443
references.citation: J Biol Chem. 1989 May 5;264(13):7085-8
references.pmid: 2540171
references.citation: Bioinformatics. 1998;14(9):755-63
references.pmid: 9918945
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D214-9
references.pmid: 21051339
references.citation: Bioinformatics. 2008 Nov 1;24(21):2427-30
references.pmid: 18772155
references.citation: Crit Rev Microbiol. 1988;15(4):297-338
references.pmid: 3060316
references.citation: EMBO J. 1982;1(8):945-51
references.pmid: 6329717
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51
references.pmid: 16381856
references.citation: Trends Cell Biol. 2000 Jan;10(1):32-8
references.pmid: 10603474