The tmRDB and SRPDB resources.
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.
Andersen
Ebbe Sloth
ES
Department of Molecular Biology, University of Aarhus, C.F. Moellers Allé, Building 139, 8000 Aarhus, Denmark.
Rosenblad
Magnus Alm
MA
Larsen
Niels
N
Westergaard
Jesper Cairo
JC
Burks
Jody
J
Wower
Iwona K
IK
Wower
Jacek
J
Gorodkin
Jan
J
Samuelsson
Tore
T
Zwieb
Christian
C
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
D010455:Peptides; D012329:RNA, Bacterial; D012261:Ribonucleoproteins; D018271:Signal Recognition Particle; C096222:tmRNA