0  structures 253  species 767  sequences

Family: ar14 (RF02344)

Description: Alphaproteobacterial ar14

Summary

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry %CE%91r14 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:
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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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The tree shows the occurrence of this RNA across different species. More...

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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 4 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 RM00008 GNRA tetraloop 72 0.610 573.3 Match Image
7 RM00022 Rho independent terminator 1 83 0.703 1267.2 Match Image
7 RM00023 Rho independent terminator 2 107 0.907 1510.6 Match Image
7 RM00029 UNCG tetraloop 16 0.136 151.8 Match Image

References

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

Literature references

  1. del Val C, Romero-Zaliz R, Torres-Quesada O, Peregrina A, Toro N, Jimenez-Zurdo JI RNA Biol. 2012;9:119-129. A survey of sRNA families in alpha-proteobacteria. PUBMED:22418845

  2. Robledo M, Peregrina A, Millan V, Garcia-Tomsig NI, Torres-Quesada O, Mateos PF, Becker A, Jimenez-Zurdo JI Environ Microbiol. 2017;19:2661-2680. A conserved alpha-proteobacterial small RNA contributes to osmoadaptation and symbiotic efficiency of rhizobia on legume roots. PUBMED:28401641

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:22418845
Structure source Predicted; PMID:22418845
Type Gene; sRNA;
Author Eberhardt RORCID logo
Alignment details
Alignment Number of
sequences
full 649
seed 118

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 25.54 -Z 549862.597050 CM SEQDB
Gathering cutoff 52.0
Trusted cutoff 52.0
Noise cutoff 51.7
Covariance model Download