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Nucleic Acids Research, 2001, Vol. 29, No. 1 169-170
© 2001 Oxford University Press

SRPDB (Signal Recognition Particle Database)

Jan Gorodkin, Bjarne Knudsen, Christian Zwieb1,* and Tore Samuelsson2

Department of Genetics and Ecology, The Institute of Biological Sciences, University of Aarhus, Building 540, Ny Munkegade, DK-8000 Aarhus C, Denmark, 1Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708-3154, USA and 2Department of Medical Biochemistry, University of Göteborg, Box 440, SE-405 30 Göteborg, Sweden

Signal recognition particle (SRP) is a stable cytoplasmic ribonucleoprotein complex that serves to translocate secretory proteins across membranes during translation. The SRP Database (SRPDB) provides compilations of SRP components, ordered alphabetically and phylogenetically. Alignments emphasize phylogenetically-supported base pairs in SRP RNA and conserved residues in the proteins. Data are provided in various formats including a column arrangement for improved access and simplified computational usability. Included are motifs for identification of new sequences, SRP RNA secondary structure diagrams, 3-D models and links to high-resolution structures. This release includes 11 new SRP RNA sequences (total of 129), two protein SRP9 sequences (total of seven), two protein SRP14 sequences (total of 10), two protein SRP19 sequences (total of 16), 10 new SRP54 (ffh) sequences (total of 66), two protein SRP68 sequences (total of seven) and two protein SRP72 sequences (total of nine). Seven sequences of the SRP receptor {alpha}-subunit and its FtsY homolog (total of 51) are new. Also considered are ß-subunit of SRP receptor, Flhf, Hbsu, CaM kinase II and cpSRP43. Access to SRPDB is at http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html and the European mirror http://www.medkem.gu.se/dbs/SRPDB/SRPDB.html

* To whom correspondence should be addressed. Tel: +1 903 877 7689; Fax: +1 903 877 5731; Email: zwieb{at}uthct.edu


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