The tmRDB and SRPDB resources

Ebbe Sloth Andersen, Magnus Alm Rosenblad, Niels Larsen, Jesper Cairo Westergaard, Jody Burks, Iwona K. Wower, Jacek Wower, Jan Gorodkin, Tore Samuelsson, Christian Zwieb

Research output: Contribution to journalArticle

82 Scopus citations

Abstract

Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/ dbs/tmRDB/tmRDB.html with mirror sites located at Auburn University, Auburn, Alabama (http://www.ag. auburn.edu/mirror/tmRDB/) and the Royal Veterinary and Agricultural University, Denmark (http:// tmrdb.kvl.dk/). The signal recognition particle database (SRPDB) at http://psyche.uthct.edu/dbs/ SRPDB/SRPDB.html is mirrored at http://srpdb.kvl. dk/ and the University of Goteborg (http://bio. lundberg.gu.se/dbs/SRPDB/SRPDB.html). The databases assist in investigations of the tmRNP (a ribonucleoprotein complex which liberates stalled bacterial ribosomes) and the SRP (a particle which recognizes signal sequences and directs secretory proteins to cell membranes). The curated tmRNA and SRP RNA alignments consider base pairs supported by comparative sequence analysis. Also shown are alignments of the tmRNA-associated proteins SmpB, ribosomal protein S1, alanyl-tRNA synthetase and Elongation Factor Tu, as well as the SRP proteins SRP9, SRP14, SRP19, SRP21, SRP54 (Ffh), SRP68, SRP72, cpSRP43, Flhf, SRP receptor (alpha) and SRP receptor (beta). All alignments can be easily examined using a new exploratory browser. The databases provide links to high-resolution structures and serve as depositories for structures obtained by molecular modeling.

Original languageEnglish (US)
Pages (from-to)D163-D168
JournalNucleic acids research
Volume34
DOIs
StatePublished - Jan 2006
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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    Andersen, E. S., Rosenblad, M. A., Larsen, N., Westergaard, J. C., Burks, J., Wower, I. K., Wower, J., Gorodkin, J., Samuelsson, T., & Zwieb, C. (2006). The tmRDB and SRPDB resources. Nucleic acids research, 34, D163-D168. https://doi.org/10.1093/nar/gkj142