tmrnawebsite

is a Data Source.

The tmRNA Website is a comprehensive database of transfer-messenger RNA (tmRNA) and SmpB protein sequences involved in bacterial trans-translation. Contains 1,716 unique tmRNA sequences from bacteria and organelles, 2,258 unique SmpB sequences, with 9,387 tmRNA instances across public databases. Provides sequence alignments, structural annotations, BLAST search tools, and Krona-based phylogenetic visualization.

Compare
Domains

genomics

License

CC BY 4.0

Homepage

tmrnawebsite

Repository

Unknown

Infores ID

Unknown

FAIRsharing ID

Unknown

Product Summary

Publications

The tmRNA website Preferred

Products

From this Resource
ID Name URL Category Format Description
tmrnawebsite.portal tmRNA Website Portal tmrna-website GraphicalInterface http Main web portal for searching and bro...
tmrnawebsite.blast tmRNA Website BLAST tmrna-website Product http BLAST search interface for tmRNA and ...
tmrnawebsite.alignments tmRNA and SmpB Alignments tmrna-website Product http Multiple sequence alignments for 632 ...
tmrnawebsite.krona-viewer tmRNA Krona Phylogenetic Viewer tmrna-website Product http Krona-based interactive phylogenetic ...
tmrnawebsite.software tmRNA Identification Software m9.figshare.28430909 Product http Software tools (tFind.pl, rFind.pl) f...
From other Resources
ID Name URL Category Format Relation Description
rnacentral.portal RNAcentral Portal rnacentral.org GraphicalInterface http had primary source Web portal for searching and browsing...
rnacentral.api RNAcentral REST API api ProgrammingInterface http had primary source REST API for programmatic access to R...
rnacentral.ftp RNAcentral FTP Archive RNAcentral Product http had primary source FTP archive with current and archived...
rnacentral.public-db RNAcentral Public Postgres Database public-database DataModelProduct postgres had primary source Public PostgreSQL database for direct...

Details

The tmRNA Website

Overview

The tmRNA Website is a comprehensive resource for transfer-messenger RNA (tmRNA) and its partner protein SmpB, which together resolve problems arising when bacterial ribosomes reach the end of mRNA with no stop codon through a process called trans-translation.

Database Content

tmRNA Sequences

  • 1,716 unique tmRNA sequences: 1,454 one-piece and 262 two-piece tmRNAs
  • 9,387 instances across public databases (RefSeq, GenBank, etc.)
  • Phylogenetic breakdown: 1,594 bacterial, 0 archaeal, 122 organellar (79 oomycete/jakoid mitochondria, 42 algal plastids, 1 chromatophore)
  • 734 unique proteolysis tag sequences

SmpB Sequences

  • 2,258 unique SmpB sequences
  • 4,125 instances including 24 potentially pseudogenized/frameshifted/truncated sequences
  • SmpB proteins linked with their corresponding tmRNA partners

Trans-Translation Biology

tmRNA Function

tmRNA uses both tRNA-like and mRNA-like properties during trans-translation:

  1. When a ribosome stalls on non-stop mRNA, alanine-charged tmRNA enters as substrate for peptidyl transfer
  2. Ribosome switches from defective mRNA to the ‘resume codon’ of tmRNA
  3. Translation continues, adding a peptide tag that signals proteolysis
  4. Frees stalled ribosome and marks non-stop mRNA for degradation

SmpB Role

The protein SmpB is a partner throughout trans-translation, bound to tmRNA and occupying space normally occupied by the anticodon stem-loop.

Key Features

Sequence Discovery Pipeline

  • Detection tools: tRNAscan-SE, BRUCE, ARAGORN, plus custom rFind.pl
  • Processing: tFind.pl wrapper for comprehensive tmRNA identification
  • Software availability: Tools freely available for public download

Annotations

  • tmRNA features: Length, sequence, genomic location, proteolysis tag, CCA coordinates, introns (when present), two-piece tmRNA structural details
  • SmpB annotations: Amino acid sequence, genomic coordinates, orientation relative to ssrA gene
  • Secondary structures: Images provided where available

Search and Analysis Tools

  • BLAST searches: Available for both tmRNA and SmpB
  • Sequence alignments: 632 tmRNA and 2,258 SmpB distinct alignments
  • Krona visualization: Modified metagenome taxonomy viewer enabling navigation to individual tmRNA pages while displaying phylogenetic distribution

Data Distribution

  • Found in nearly all bacterial genomes (except six recalcitrant genomes)
  • Present in some organelles
  • SmpB genes found in all bacterial genomes studied (sometimes with severe defects) and in eukaryotic nuclear genomes with signals targeting transport to organelles encoding tmRNA

Data Sources

  • Primary genomic data: RefSeq (2,168 organisms plus 1,755 plasmids and 581 viruses)
  • Additional sequence databases: NCBI est, gss, htgs, nt, other_genomic, patnt, refseq_genome, tsa_nt, wgs
  • Contributions to: RNAcentral, International Nucleotide Sequence Database Archive (GenBank/ENA/DDBJ) as third-party annotation
  • tmRDB: Additional tmRNA database
  • Rfam: RNA families database including tmRNA
  • RNAcentral: Central repository receiving tmRNA Website contributions

Website Status

The tmRNA Website was originally hosted at Sandia National Laboratories (http://bioinformatics.sandia.gov/tmrna/), but that host is no longer available (HTTP 404 as of 2026). The resource has migrated to RNAcentral, where it is served as the dedicated “tmRNA Website” expert database (https://rnacentral.org/expert-database/tmrna-website). The associated software (tFind.pl, rFind.pl) and data files are deposited at figshare (https://doi.org/10.6084/m9.figshare.28430909). This migration is described in Nawrocki, Petrov & Williams, “Expansion of the tmRNA sequence database and new tools for search and visualization,” NAR Genomics and Bioinformatics 2025 (doi:10.1093/nargab/lqaf019).

Funding

Research fully supported by the Laboratory Directed Research and Development program at Sandia National Laboratories.

Citation

Hudson CM, Williams KP. The tmRNA website. Nucleic Acids Research. 2015;43(D1):D138-D140. doi:10.1093/nar/gku1109

Is this information incorrect or incomplete? Request an update.

Created: September 09, 2025 | Last modified: June 22, 2026