title: The tmRDB and SRPDB resources.
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.
authors.affiliation: Department of Molecular Biology, University of Aarhus, C.F. Moellers Allé, Building 139, 8000 Aarhus, Denmark.
authors.forename: Ebbe Sloth
authors.initials: ES
authors.lastname: Andersen
authors.forename: Magnus Alm
authors.initials: MA
authors.lastname: Rosenblad
authors.forename: Niels
authors.initials: N
authors.lastname: Larsen
authors.forename: Jesper Cairo
authors.initials: JC
authors.lastname: Westergaard
authors.forename: Jody
authors.initials: J
authors.lastname: Burks
authors.forename: Iwona K
authors.initials: IK
authors.lastname: Wower
authors.forename: Jacek
authors.initials: J
authors.lastname: Wower
authors.forename: Jan
authors.initials: J
authors.lastname: Gorodkin
authors.forename: Tore
authors.initials: T
authors.lastname: Samuelsson
authors.forename: Christian
authors.initials: C
authors.lastname: Zwieb
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D030541:Databases, Genetic; D020407:Internet; D010455:Peptides / Q000378:metabolism; D010802:Phylogeny; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012261:Ribonucleoproteins / Q000737:chemistry* / Q000235:genetics / Q000502:physiology; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D018271:Signal Recognition Particle / Q000737:chemistry* / Q000235:genetics / Q000502:physiology; D014584:User-Computer Interface
chemical_list: D010455:Peptides; D012329:RNA, Bacterial; D012261:Ribonucleoproteins; D018271:Signal Recognition Particle; C096222:tmRNA