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0  structures 42  species 48  sequences

Family: cyano_tmRNA (RF01851)

Description: Cyanobacteria 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.

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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

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Colour assignments

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

Selections

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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

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Trees

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

This tree was built using the fasttree method.

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

Motif matches

There are 3 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 RM00005 CsrA/RsmA binding motif 17 0.630 169.7 Match Image
7 RM00024 T-loop 3 0.111 31.0 Match Image
7 RM00029 UNCG tetraloop 9 0.333 140.2 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 21
seed 27

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
Gathering cutoff 70.0
Trusted cutoff 70.0
Noise cutoff 67.5
Covariance model Download