reversible protein phosphorylation is a major mechanism in the regulation of fundamental signaling events in all living organisms . in bacteria ,
four types of phosphorylation systems were described : ( i ) the two - component system ( 1 ) , ( ii ) the phosphoenolpyruvate ( pep ) transferase system ( pts ) ( 2 ) , ( iii ) the eukaryotic - like system ( 3 ) and ( iv ) the bacterial tyrosine kinase ( by - kinase ) system ( 4 ) .
those four types differ in the nature of the phosphorylated amino acids ( s , t , y , h and d ) and the phosphate donor ( adenosine tri - phosphate ( atp ) or pep ) .
by - kinases comprise two domains : a two - pass transmembrane activator domain ( tad ) that includes a large extra cellular part , and an intracellular catalytic domain ( cd ) .
the by - kinases cd encompasses three walker - like motifs ( 5 ) , called a , a and b , and a c - terminal tyrosine - rich region named y cluster ( yc ) .
these two domains can either be linked in a single polypeptide ( in proteobacteria and actinobacteria ) , or split into two different proteins , encoded by two adjacent genes ( in firmicutes ) . in this case
, it has been shown that by - kinases activity was effective only if the cd was interacting with the region following the second transmembrane segment of tad .
a number of studies have demonstrated the importance of by - kinases in several facets of the physiology of the bacterial cell .
more precisely , their best characterized function concerns the regulation of the export and the biosynthesis of bacterial extracellular polysaccharide that are recognized important virulence factors .
since these enzymes are not homologs of their eukaryotic counterparts , by - kinases are particularly interesting in the search of new therapeutic targets to combat bacterial pathogens .
we present here the bacterial tyrosine kinase database ( bykdb ) , developed in order to collect , store and manage by - kinase sequences with standardized annotations .
the sequences are identified by using an in silico workflow described in a previous work ( 6 ) .
diverse sequences identified by the workflow have been validated experimentally since then ( dr mijakovic , personal communication ) .
the sequences are automatically annotated and stored in the database by a second automated workflow .
the database can be queried via a www interface and the query results can be further analyzed with the numerous integrated analysis tools .
the bykdb is updated on a monthly basis from the uniprot knowledgebase ( uniprotkb ) ( 7 ) , and stored in the postgresql relational database management system ( rdbms ) .
the programs for the sequence identification and annotation , as well as for the querying and the management of the database are implemented in java and sql programming languages .
the first step of the database building procedure is the identification of by - kinase sequences , thanks to the 
it relies on the hmmer software package ( version 3.0 of march 2010 ) ( 8) .
the by - kinases tad is matched by the pfam profile pf02706 ( 9 ) , in a region including the first transmembrane segment .
since this profile identifies proteins that are not by - kinases , and does not identify cd of two - parts by - kinases , it is not sufficient to unambiguously identify by - kinases .
hmmsearch result sets are analyzed to lead to three clusters of sequences . the first cluster is constituted by sequences matching both hmm profiles (  tadcd cluster ) .
the second cluster contains sequences with the tad and cd encoded by two proteins (  tad and 
the sequences of the third cluster only match the cd profile and have no identified tad (  orphancd cluster ) .
the sequences are further divided into two categories (  confirmed and  unsure ) according to a filter ( isbyk ) .
this filter checks if a sequence contains all the necessary cd motifs ( walker - like motifs and tyrosine cluster ) with the right spacing between them ( 6 ) .
the  annotatebyk process ensures the second step of the procedure , i.e. the sequence annotation .
the annotation starts with the uniprotkb entries extracted according to the ac of the relevant sequences identified in the first step .
indeed , the accession numbers , the creation date , the organism and the sequence of each entry are conserved . in the description line ( de ) , the recommended name field is set to  bacterial tyrosine kinase or to  adaptator of bacterial tyrosine kinase depending on the type of sequences . in the keywords list ( kw ) are added the 
tadcd. the domains and motifs with their start and end positions in the sequence are also added to the feature ( ft ) lines , respectively as domain and site fields . besides , for each sequences of the second group , a cross - reference to the related tad entry is added and reciprocally for the tad entry .
the user can navigate through the site , thanks to the menubar or the home page buttons .
( 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 .
( 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 .
the  annotate tool detailed results page for one input sequence . in the static part , the user can find general information about by - kinases with links to other external resources (  byk link ) .
the user can also access pre - computed datasets (  dataset link ) sorted according to the phylum and by - kinase cluster .
the datasets include by - kinase sequences in pearson / fasta format and the corresponding multiple sequence alignment .
furthermore , the alignments can be viewed and edited with the  editalignment applet developed by our team . in the dynamic part (  dynamic link )
, the user can extract his own datasets by combining multiple criteria ( e.g. species and sequence length and sequence cluster ) .
the datasets can be exported as fasta / pearson sequences , accession number lists and entry flat files for further analysis with the integrated analysis tools .
the generic analysis tools ( e.g. blast or clustal w ) are available through the nps@ server ( 10 ) , which is an integrated sequence analysis web server .
the specialized analysis tool (  annotate link ) available on the site allows the annotation of one or several sequences , which can be useful to scan protein sequences from a newly sequenced bacterial genome in order to identify by - kinases and their adaptators . in the results page
, the user can access the start / end positions and the sequences of the different domains and sites .
furthermore , the domains and sites are mapped in color on the by - kinase sequence .
the release 3.0 ( october 2011 ) comprises 2,746 sequences , including 713 cd sequences with their corresponding tad sequences , 1,169 tadcd sequences and 151 orphancd sequences .
bykdb collects by - kinase sequences , identified and annotated , thanks to a computer - automated system .
the automatic annotation process used to generate bykdb entries guarantees harmonized annotations and allows efficient keyword searches .
the bykdb website gives access to pre - computed static datasets and allows dynamic queries .
the extracted data can be further analyzed with generic or specialized bioinformatics algorithms . in the future
, the annotations will be enriched with new data ( e.g. information about protein structure ) and new analysis tools ( e.g. phylogeny ) will be added .
bykdb is funded by the agence nationale de la recherche ( anr-07-jcjc0125 - 01 bactyrkin ) and the ple rhne - alpes de bioinformatique ( prabi ) platform by the groupement d'intrt scientifique infrastructures en biologie , sant et agronomie ( gis ibisa ) .
funding for open access charge : agence nationale de la recherche ( anr-07-jcjc0125 - 01 bactyrkin ) .
 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 . 
INTRODUCTION
WEB INTERFACE
STATISTICS
CONCLUSION AND PERSPECTIVE
FUNDING