6  structures 3281  species 4153  sequences

Family: FMN (RF00050)

Description: FMN riboswitch (RFN element)

Summary

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry FMN 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.

Submit a new alignment

We're happy receive updated seed alignments for new or existing families. Submit your new alignment and we'll take a look.

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...

Tree controls

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The tree shows the occurrence of this RNA across different species. 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 FMN family has been found.

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Motif matches

There are 3 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 30 0.208 312.3 Match Image
7 RM00024 T-loop 16 0.111 173.2 Match Image
7 RM00030 U-turn motif 14 0.097 154.6 Match Image

References

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

Literature references

  1. Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS Nucleic Acids Res 2002;30:3141-3151. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. PUBMED:12136096

  2. Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA Trends Genet 1999;15:439-442. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. PUBMED:10529804

  3. Winkler WC, Cohen-Chalamish S, Breaker RR Proc Natl Acad Sci U S A 2002;99:15908-15913. An mRNA structure that controls gene expression by binding FMN. PUBMED:12456892

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 Vitreshchak A
Structure source Published; PMID:12456892
Type Cis-reg; riboswitch;
Author Vitreshchak A, Gelfand M, Bateman AORCID logo
Alignment details
Alignment Number of
sequences
full 4,009
seed 144

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
Gathering cutoff 74.0
Trusted cutoff 74.2
Noise cutoff 73.9
Covariance model Download