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Motif: RBS_E_coli (RM00014)

Description: Shine-Dalgarno sequences of the Escherichia coli sub-type


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. More...

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


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:

Family matches

There are 11 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 RF00503 RNAIII 3 0.300 43.3 Match Image
3 RF01471 Listeria sRNA rliB 2 0.500 33.2 Match Image
3 RF01473 Listeria sRNA rli41 6 1.000 111.4 Match Image
3 RF01492 Listeria sRNA rli28 2 0.095 32.7 Match Image
3 RF01570 Dictyostelium signal recognition particle 2 0.667 39.4 Match Image
3 RF01766 cspA thermoregulator 3 0.200 51.6 Match Image
3 RF01824 RNA of unknown function 20 2 0.333 28.6 Match Image
3 RF01888 Embryonic ventral forebrain RNA 1 conserved region 2 10 0.526 146.7 Match Image
3 RF02052 Enterobacterial sRNA STnc630 8 0.800 123.8 Match Image
3 RF02574 Rickettsia sRNA 10 2 0.667 32.7 Match Image
3 RF02644 S. pyogenes small RNA Spy490380c 4 1.000 65.6 Match Image


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.


Seed source Predicted; Gardner PP
Structure source N/A
Type Specific Recognition Motif
Author Gardner PP
Alignment details
Alignment Number of
Average length Sequence
identity (%)
seed 202 39.00 41

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
Gathering cutoff 14.0
Covariance model Download the Infernal CM for the motif here