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ProLysED - Prokaryotic Lysis Enzymes Database


NAR Molecular Biology Database Collection entry number 609
Firdaus Raih, M.1, Ahmad, H.A.2, Sharum, M.Y.2, Mohamed, R.1,2
1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43650 Bangi, Malaysia
2Interim Lab., National Institute for Genomics and Molecular Biology, Heliks Emas Block, UKM-MTDC Smart Technology Centre, 43650 Bangi, Malaysia

Database Description

Proteases catalyze the cleavage of peptide bonds in other proteins. These proteins represent one of the three largest groups of industrial enzymes and account for up to 60% of the total worldwide sale of enzymes. Bacterial proteases have a diverse range of function and mechanisms of action. They can be responsible for complex processes under normal physiological circumstances as well as in abnormal patho-physiological conditions. ProLysED (Prokaryotic Lysis Enzymes Database) is a metaserver integrated database for protease systems of bacterial origin and includes regulatory and inhibitor proteins in the dataset. The datasets were retrieved from the SWISS-PROT - sequences and annotation; and PDB - sequence and structural information. This data retrieval process was carried out using a combination of keyword searches and limiting the searches to only bacterial species. Further comparative analyses were carried against other known and well characterized proteases. These entries were then annotated further manually. MySQL (http://www.mysql.com) was used as the core relational database while the interfacing was done mainly using PHP (http://www.php.net). ProLysED is structured according to the following interlinked databases for basic data, sequences, structures, internal annotation and user interface. The basic data database contains information for protease class, bacterial species, GenBank Acession number, basic description and E.C. number and data source. The sequences and structures contain sequence data in FASTA format and structural data as PDB formatted files respectively. The internal annotation database contains further annotation of protease activity, inhibitor information and any other extra annotation which is not available in the original data source. The user database controls user access and usage sessions. Data without protein structure information can be submitted via metaserver to the following external services PHD, 3DPSSM, SAM-T99 and PSI-PRED through user sessions with results being returned by the respective services via email. The database is automatically updated using a Perl agent at fortnightly intervals. Updated datasets are extracted in XML format using the specified search terms. The Perl script parses the files for updates, authenticates the organism source to be prokaryotic and automatically updates the MySQL database. Any further annotation is then carried out by manually. Cross references to GenBank, PDB, the SCOP, MEROPS, PDBSum and CATH structural database as well as an external BLAST to SWISSPROT is also interfaced from ProLysED. A specific ProLysED BLAST server with the database limited to bacterial proteases and related systems is also provided. Data entries with corresponding structural data in the form of PDB formatted files is also viewable via the Chime molecular viewer plug-in (http://www.mdli.com). These structures are selectable from the bacterial protease structures data integrated within ProLysED.

Acknowledgements

The authors would like to acknowledge the National Biotechnology and Bioinformatics Network (NBBnet, http://www.nbbnet.gov.my), Malaysia and the Interim Lab., National Inst. for Genomics and Molecular Biology Malaysia (http://genome.ukm.my), which is hosting this resource. We are also grateful for miscellanous technical input and feedback from Ahmad Fuad Hilmi Muhammad, as well as assistance with the data quality control from Ayu Haslin, Norazlin and Yazeereen.


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