17  structures 1772  species 5247  sequences

Family: c-di-GMP-I (RF01051)

Description: c-di-GMP-I riboswitch aptamer

Summary

Clan

This family is a member of clan (CL00126), which contains the following 3 members:

c-di-GMP-I c-di-GMP-I-GGC c-di-GMP-I-UAU

Note on Riboswitches

This Rfam family c-di-GMP-I (RF01051) represents an aptamer domain of a full riboswitch c-di-GMP-I riboswitch aptamer. 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 Cyclic di-GMP-I riboswitch. More...

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

Sequences

Alignment

There are various ways to view or download the seed alignments that we store. You can use a sequence viewer to look at them, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

You can view Rfam seed alignments in your browser in various ways. Choose the viewer that you want to use and click the "View" button to show the alignment in a pop-up window.

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Formatting options

You can view or download Rfam seed 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:
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Download

Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.

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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

This page displays the predicted phylogenetic tree for the alignment. More...

This tree was built using the fasttree method.

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Note: You can also download the data file for the seed tree.

Structures

For those sequences which have a structure in the Protein DataBank, we generate a mapping between EMBL, PDB and Rfam coordinate systems. The table below shows the structures on which the c-di-GMP-I family has been found.

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Motif matches

There are 1 motifs which match this family.

This section shows the Rfam motifs that match sequences within the seed alignment of this family. 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 Motif Accession Motif Description Number of Hits Fraction of Hits Sum of Bits Image
7 RM00008 GNRA tetraloop 86 0.555 955.8 Match Image

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. Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, Link KH, Breaker RR Science 2008;321:411-413. Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP PUBMED:18635805

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 Weinberg Z
Structure source Published; PMID:17621584
Type Cis-reg; riboswitch;
Author Weinberg ZORCID logo
Alignment details
Alignment Number of
sequences
full 5,092
seed 155

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
Gathering cutoff 35.0
Trusted cutoff 35.0
Noise cutoff 34.9
Covariance model Download