SRPDB: Signal recognition particle database

Magnus Alm Rosenblad, Jan Gorodkin, Bjarne Knudsen, Christian Zweib, Tore Samuelsson

Research output: Contribution to journalReview article

98 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)363-364
Number of pages2
JournalNucleic acids research
Volume31
Issue number1
DOIs
StatePublished - Jan 1 2003
Externally publishedYes

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ASJC Scopus subject areas

  • Genetics

Cite this

Rosenblad, M. A., Gorodkin, J., Knudsen, B., Zweib, C., & Samuelsson, T. (2003). SRPDB: Signal recognition particle database. Nucleic acids research, 31(1), 363-364. https://doi.org/10.1093/nar/gkg107