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Nucleic Acids Research, 2003, Vol. 31, No. 1 363-364
© 2003 Oxford University Press

SRPDB: Signal Recognition Particle Database

Magnus Alm Rosenblad, Jan Gorodkin1, Bjarne Knudsen2, Christian Zwieb*,3 and Tore Samuelsson

Department of Medical Biochemistry, University of Göteborg, Box 440, SE-405 30 Göteborg, Sweden 1 Division of Genetics, The Royal Veterinary and Agricultural University, Institute of Animal Science and Animal Health, Groennegaardsvej 3, DK-1870 Frederiksberg C, Denmark 2 Bioinformatics Research Center, University of Aarhus, Høegh Guldbergsgade 10, DK-8000 Aarhus C, Denmark 3 Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708-3154, USA

*To whom correspondence should be addressed. Tel: +1 9038777689; Fax: +1 9038775731; Email: zwieb{at}uthct.edu

ABSTRACT

The Signal Recognition Particle Database (SRPDB) at http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html and http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html assists in the better understanding of the structure and function of the signal recognition particle (SRP), a ribonucleoprotein complex that recognizes signal sequences as they emerge from the ribosome. SRPDB provides alphabetically and phylogenetically ordered lists of SRP RNA and SRP protein sequences. The SRP RNA alignment emphasizes base pairs supported by comparative sequence analysis to derive accurate SRP RNA secondary structures for each species. This release includes a total of 181 SRP RNA sequences, 7 protein SRP9, 11 SRP14, 31 SRP19, 113 SRP54 (Ffh), 9 SRP68 and 12 SRP72 sequences. There are 44 new sequences of the SRP receptor alpha subunit and its FtsY homolog (a total of 99 entries). Additional data are provided for polypeptides with established or potential roles in SRP-mediated protein targeting, such as the beta subunit of SRP receptor, Flhf, Hbsu and cpSRP43. Also available are motifs for the identification of new SRP RNA sequences, 2D representations, three-dimensional models in PDB format, and links to the high-resolution structures of several SRP components. New to this version of SRPDB is the introduction of a relational database system and a SRP RNA prediction server (SRP-Scan) which allows the identification of SRP RNAs within genome sequences and also generates secondary structure diagrams.


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