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. 2012 Jan;40(Database issue):D321-4.
doi: 10.1093/nar/gkr915. Epub 2011 Nov 12.

BYKdb: The Bacterial Protein tYrosine Kinase Database

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Free PMC article

BYKdb: The Bacterial Protein tYrosine Kinase Database

Fanny Jadeau et al. Nucleic Acids Res. .
Free PMC article

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.

Figures

Figure 1.
Figure 1.
Snapshot of the BYKdb web interface. (A) The BYKdb home page, with the resources accessible as clickable buttons (B) A pre-computed dataset of BY-kinase and TAD sequences and alignments, ordered by phylum and by cluster. (C) The multiple sequence alignment of firmicutes CD viewed in the ‘EditAlignment’ applet. (D) Dynamic queries against the BYKdb. (E) The ‘Annotate’ tool detailed results page for one input sequence.

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