0  structures 1229  species 1661  sequences

Family: Guanidine-II (RF01068)

Description: Guanidine-II riboswitch aptamer (mini-ykkC)

Summary

Note on Riboswitches

This Rfam family Guanidine-II (RF01068) represents an aptamer domain of a full riboswitch Guanidine-II riboswitch aptamer (mini-ykkC). Riboswitches are non-coding RNA structures that regulate gene expression in response to ligand. Each riboswitch has two main parts: the aptamer domain and the expression platform. The aptamer domain is highly conserved to precisely bind its ligand. However, the expression platform has multiple modes of gene regulation, which introduces sequence and structure variability that increases difficulty in its detection through covariance model searching. For more information see the original publications.

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Mini-ykkC RNA motif. More...

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

Sequences

Alignment

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Alignment format:
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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

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References

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

Literature references

  1. Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR Nucleic Acids Res. 2007;35:4809-4819. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. PUBMED:17621584

  2. Sherlock ME, Malkowski SN, Breaker RR Biochemistry. 2017;56:352-358. Biochemical Validation of a Second Guanidine Riboswitch Class in Bacteria. PUBMED:28001368

  3. Huang L, Wang J, Lilley DMJ Cell Chem Biol. 2017;24:695-702. The Structure of the Guanidine-II Riboswitch. PUBMED:28529131

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 Published; PMID:17621584; Weinberg Z
Structure source Published; PMID:17621584; Weinberg Z
Type Cis-reg; riboswitch;
Author Weinberg ZORCID logo, Gardner PPORCID logo
Alignment details
Alignment Number of
sequences
full 1,589
seed 72

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 21.00 -Z 2958934 CM SEQDB
Gathering cutoff 32.0
Trusted cutoff 32.0
Noise cutoff 31.9
Covariance model Download