Database Commons
Database Commons

a catalog of worldwide biological databases

Database Profile

General information

URL: http://www.ag.auburn.edu/mirror/tmRDB/
Full name: tmRNA database
Description: The tmRDB is a tool in the study of the structures and functions of the tmRNA (earlier called "10S RNA"). As the name implies, tmRNA has properties of tRNA and mRNA combined in a single molecule. The tmRDB provides aligned, annotated and phylogenetically ordered tmRNA sequences.
Year founded: 1998
Last update: 2018-04-03
Version:
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: United States

Classification and Labelling

Data type:
RNA
Data object:
NA
Database category:
Major species:
NA
Keywords:

Contact information

University/Institution: University of Texas Health Science Center at Tyler
Address: 11937 US Highway 271, Tyler, TX 75708-3154, USA
City: Tyler
Province/State: TX
Country/Region: United States
Contact name (PI/Team): Christian Zwieb
Contact email (PI/Helpdesk): zwieb@uthct.edu

Publications

16381838
The tmRDB and SRPDB resources. [PMID: 16381838]
Andersen ES, Rosenblad MA, Larsen N, Westergaard JC, Burks J, Wower IK, Wower J, Gorodkin J, Samuelsson T, Zwieb C.

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.

Nucleic Acids Res. 2006:34(Database issue) | 72 Citations (from Europe PMC, 2022-10-01)
12520048
tmRDB (tmRNA database). [PMID: 12520048]
Zwieb C, Gorodkin J, Knudsen B, Burks J, Wower J.

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 Bioinformatics Research Center, Aarhus, Denmark (http://www.bioinf.au.dk/tmRDB/). The tmRDB collects and distributes information relevant to the study of tmRNA. In trans-translation, this molecule combines properties of tRNA and mRNA and binds several proteins to form the tmRNP. Related RNPs are likely to be functional in all bacteria. In this release of tmRDB, 186 new entries from 10 bacterial groups for a total of 274 tmRNA sequences have been added. Lists of the tmRNAs and the corresponding tmRNA-encoded tag-peptides are presented in alphabetical and phylogenetic order. The tmRNA sequences are aligned manually, assisted by computational tools, to determine base pairs supported by comparative sequence analysis. The tmRNA alignment, available in a variety of formats, provides the basis for the secondary and tertiary structure of each tmRNA molecule. Three-dimensional models of the tmRNAs and their associated proteins in PDB format give evidence for the recent progress that has been made in the understanding of tmRNP structure and function.

Nucleic Acids Res. 2003:31(1) | 48 Citations (from Europe PMC, 2022-10-01)
9847168
The tmRNA database (tmRDB). [PMID: 9847168]
Wower J, Zwieb C.

As of September, 1998, a total of 43 sequences are contained within the tmRNA database (tmRDB). The tmRNA sequences are arranged alphabetically and ordered phylogenetically. The alignment of the tmRNAs emphasizes the basepairs that are supported by comparative sequence analysis and establishes minimal secondary structures for the known tmRNAs. A corresponding alignment of the predicted tmRNA-encoded tag peptides is presented. The tmRDB also offers a small number of RNA secondary structure diagrams and PDB-formatted three-dimensional models generated with the program ERNA-3D. The data are available freely at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.++ +html

Nucleic Acids Res. 1999:27(1) | 6 Citations (from Europe PMC, 2022-10-01)
9399825
The tmRNA database (tmRDB). [PMID: 9399825]
Zwieb C, Larsen N, Wower J.

This first release of the tmRNA database (tmRDB) contains 19 tmRNA sequences, a tmRNA sequence alignment with emphasis of base pairs that are supported by comparative sequence analysis, and a tabulation of tmRNA-encoded tag peptides. The tmRNADB also offers an RNA secondary structure diagram of the Escherichia coli tmRNA, as well as PDB-formatted coordinates for three-dimensional modeling. The data are available on the World Wide Web at http://www.uthct. edu/tmRDB/tmRDB.html

Nucleic Acids Res. 1998:26(1) | 3 Citations (from Europe PMC, 2022-10-01)

Ranking

All databases:
1499/5380 (72.156%)
Gene genome and annotation:
451/1436 (68.663%)
1499
Total Rank
129
Citations
5.375
z-index

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Record metadata

Created on: 2015-07-17
Curated by:
Lin Liu [2022-09-20]
Lin Liu [2022-08-16]
huma shireen [2018-08-27]
Lina Ma [2018-06-11]
Mengwei Li [2016-02-16]
Guangyu Wang [2015-12-06]