0  structures 1420  species 12315  sequences

Family: T-box (RF00230)

Description: T-box leader

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 T-box leader. 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.

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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...

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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 RM00004 CRC binding motif 6 0.125 60.3 Match Image
7 RM00008 GNRA tetraloop 10 0.208 98.3 Match Image
7 RM00021 Tandem GA/AG loop 44 0.917 1653.9 Match Image

References

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

Literature references

  1. Grundy FJ, Rollins SM, Henkin TM J Bacteriol 1994;176:4518-4526. Interaction between the acceptor end of tRNA and the T box stimulates antitermination in the Bacillus subtilis tyrS gene: a new role for the discriminator base. PUBMED:8045882

  2. Grundy FJ, Collins JA, Rollins SM, Henkin TM RNA 2000;6:1131-1141. tRNA determinants for transcription antitermination of the Bacillus subtilis tyrS gene. PUBMED:10943892

  3. Winkler WC, Grundy FJ, Murphy BA, Henkin TM RNA 2001;7:1165-1172. The GA motif: an RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs. PUBMED:11497434

  4. Gerdeman MS, Henkin TM, Hines JV J Mol Biol 2003;326:189-201. Solution structure of the Bacillus subtilis T-box antiterminator RNA: seven nucleotide bulge characterized by stacking and flexibility. PUBMED:12547201

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 Barrick JE, predicted; Vitreschak A, PMID:12770710
Structure source Published; PMID:12770710
Type Cis-reg; leader;
Author Barrick JE, Bateman AORCID logo, Vitreschak AG, Gelfand MS, Gardner PPORCID logo
Alignment details
Alignment Number of
sequences
full 12,267
seed 48

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 18.50 -Z 549862.597050 CM SEQDB
Gathering cutoff 93.0
Trusted cutoff 93.0
Noise cutoff 92.9
Covariance model Download