17  structures 0  species 0  sequences

Motif: SRP_S_domain (RM00020)

Description: Signal recognition particle small S-domain

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 Signal recognition particle RNA 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:

Structures

There are 17 PDB entires which have been used to build the motif model.

The table of results below may be sorted by clicking on the column titles, or restored to the original order here.

Original order PDB ID PDB chain ID PDB Residues
2 28sp A 2 - 27
2 3ktw C 48 - 92
2 1qzw B 2 - 46
2 1cq5 A 1 - 43
2 2pxd B 3 - 47
2 2pxe B 3 - 47
2 2pxf B 3 - 47
2 2pxb B 3 - 47
2 2pxk B 3 - 47
2 2iy3 B 31 - 75
2 2pxv B 3 - 47
2 2pxq B 3 - 47
2 1dul B 3 - 47
2 2pxp B 3 - 47
2 2pxt B 3 - 47
2 1duh A 1 - 45
2 1lng B 48 - 92

Family matches

There are 8 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 RF00017 Metazoan signal recognition particle RNA 91 1.000 4302.3 Match Image
3 RF00169 Bacterial small signal recognition particle RNA 261 1.000 11121.6 Match Image
3 RF01502 Fungal signal recognition particle RNA 35 0.700 1198.8 Match Image
3 RF01570 Dictyostelium signal recognition particle 3 1.000 69.4 Match Image
3 RF01854 Bacterial large signal recognition particle RNA 90 0.978 4544.5 Match Image
3 RF01855 Plant signal recognition particle RNA 63 1.000 2604.7 Match Image
3 RF01856 Protozoan signal recognition particle RNA 9 0.500 391.9 Match Image
3 RF01857 Archaeal signal recognition particle RNA 53 1.000 2414.0 Match Image

References

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

Literature references

  1. Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T Nucleic Acids Res 2003;31:363-364. SRPDB: Signal Recognition Particle Database. PUBMED:12520023

  2. Regalia M, Rosenblad MA, Samuelsson T Nucleic Acids Res 2002;30:3368-3377. Prediction of signal recognition particle RNA genes. PUBMED:12140321

  3. Rosenblad MA, Larsen N, Samuelsson T, Zwieb C RNA Biol. 2009;6:508-516. Kinship in the SRP RNA family. PUBMED:19838050

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 Gardner PP
Structure source N/A
Type Stem Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 216 45.28 51

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
Gathering cutoff 20.0
Covariance model Download the Infernal CM for the motif here