7  structures 0  species 0  sequences

Motif: twist_up (RM00026)

Description: Twist up Motif

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 Internal loop 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 7 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 2zkr Y 27 - 46
2 3iz9 C 29 - 48
2 3bbo B 31 - 50
2 1nkw 9 33 - 53
2 1c2x C 31 - 51
2 1giy B 33 - 53
2 1S72 9 29 - 50

Family matches

There is 1 Rfam family which matches 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 RF00001 5S ribosomal RNA 571 0.802 15073.8 Match Image

References

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

Literature references

  1. Zhong C, Zhang S Nucleic Acids Res. 2012;40:1307-17. Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment. PUBMED:21976732

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 Published; PMID:21976732
Structure source N/A
Type Internal Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 9 20.56 69

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate CM
Gathering cutoff 19.0
Covariance model Download the Infernal CM for the motif here