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Motif: RBS_H_pylori (RM00015)

Description: Shine-Dalgarno sequences of the Helicobacter pylori sub-type

Summary

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam data in Wikipedia. This motif is described by a Wikipedia entry entitled Shine-Dalgarno sequence but we are unable to retrieve the article content at this time. More...

Alignments

You can either download the motif alignment or view it directly in your browser window. More...

Formatting options

You can view or download motif 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:

Family matches

There are 4 Rfam families which match this motif.

This section shows the families which have been annotated with this motif. 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 Family Accession Family Description Number of Hits Fraction of Hits Sum of Bits Image
3 RF01766 cspA thermoregulator 2 0.133 37.4 Match Image
3 RF01871 Metastasis associated lung adenocarcinoma transcript 1 2 0.118 34.0 Match Image
3 RF01888 Embryonic ventral forebrain RNA 1 conserved region 2 9 0.474 157.2 Match Image
3 RF02574 Rickettsia sRNA 10 3 1.000 57.0 Match Image

References

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

Literature references

  1. Shine J, Dalgarno L Nature. 1975;254:34-38. Determinant of cistron specificity in bacterial ribosomes. PUBMED:803646

External database links

Curation and motif details

This section shows the detailed information about the Rfam motif. 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 Predicted; Gardner PP
Structure source N/A
Type Specific Recognition Motif
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 202 39.00 44

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
Gathering cutoff 15.0
Covariance model Download the Infernal CM for the motif here