22  structures 6400  species 6693  sequences

Family: tmRNA (RF00023)

Description: transfer-messenger RNA

Summary

Clan

This family is a member of clan (CL00001), which contains the following 7 members:

alpha_tmRNA beta_tmRNA cyano_tmRNA mt-tmRNA tmRNA tRNA tRNA-Sec

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Transfer-messenger RNA. More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

Sequences

Alignment

There are various ways to view or download the seed alignments that we store. You can use a sequence viewer to look at them, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

You can view Rfam seed alignments in your browser in various ways. Choose the viewer that you want to use and click the "View" button to show the alignment in a pop-up window.

Viewer:

Formatting options

You can view or download Rfam seed alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".

Alignment format:
Download/view:

Download

Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.

Submit a new alignment

We're happy receive updated seed alignments for new or existing families. Submit your new alignment and we'll take a look.

Secondary structure

This section shows a variety of different secondary structure representations for this family. More...

You can view the secondary structure of the family using the VARNA applet. You can see more information about VARNA iself here.

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Click on a node to select that node and its sub-tree.

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Tree controls

Hide

The tree shows the occurrence of this RNA across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Trees

This page displays the predicted phylogenetic tree for the alignment. More...

This tree was built using the fasttree method.

Label the trees using or

Note: You can also download the data file for the seed tree.

Structures

For those sequences which have a structure in the Protein DataBank, we generate a mapping between EMBL, PDB and Rfam coordinate systems. The table below shows the structures on which the tmRNA family has been found.

Loading structure mapping...

Motif matches

There are 7 motifs which match this family.

This section shows the Rfam motifs that match sequences within the seed alignment of this family. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order Motif Accession Motif Description Number of Hits Fraction of Hits Sum of Bits Image
7 RM00004 CRC binding motif 59 0.124 630.6 Match Image
7 RM00005 CsrA/RsmA binding motif 113 0.237 983.3 Match Image
7 RM00008 GNRA tetraloop 153 0.321 1591.1 Match Image
7 RM00010 Kink turn 1, 3' bulge 42 0.088 546.1 Match Image
7 RM00024 T-loop 352 0.738 4368.9 Match Image
7 RM00029 UNCG tetraloop 57 0.119 636.7 Match Image
7 RM00030 U-turn motif 73 0.153 949.3 Match Image

References

This section shows the database cross-references that we have for this Rfam family.

Literature references

  1. Williams KP, Bartel DP RNA 1996;2:1306-1310. Phylogenetic analysis of tmRNA secondary structure. PUBMED:8972778

  2. Felden B, Himeno H, Muto A, McCutcheon JP, Atkins JF, Gesteland RF RNA 1997;3:89-103. Probing the structure of the Escherichia coli 10Sa RNA (tmRNA). PUBMED:8990402

  3. Williams KP Nucleic Acids Res 2002;30:179-182. The tmRNA Website: invasion by an intron. PUBMED:11752287

  4. Laslett D, Canback B, Andersson S Nucleic Acids Res 2002;30:3449-3453. BRUCE: a program for the detection of transfer-messenger RNA genes in nucleotide sequences. PUBMED:12140330

  5. Zwieb C, Gorodkin J, Knudsen B, Burks J, Wower J Nucleic Acids Res. 2003;31:446-447. tmRDB (tmRNA database). PUBMED:12520048

  6. Mao C, Bhardwaj K, Sharkady SM, Fish RI, Driscoll T, Wower J, Zwieb C, Sobral BW, Williams KP RNA Biol. 2010;6:355-361. Variations on the tmRNA gene. PUBMED:19617710

External database links

Curation and family details

This section shows the detailed information about the Rfam family. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.

Curation

Seed source Published; PMID:19617710
Structure source Published; PMID:19617710
Type Gene;
Author Gardner PPORCID logo
Alignment details
Alignment Number of
sequences
full 6,216
seed 477

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 16.62 -Z 549862.597050 CM SEQDB
Gathering cutoff 47.0
Trusted cutoff 47.0
Noise cutoff 46.8
Covariance model Download