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16  structures 1379  species 2261  sequences

Family: Lysine (RF00168)

Description: Lysine riboswitch

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 Lysine 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 Lysine family has been found.

Loading structure mapping...

Motif matches

There are 5 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 RM00004 CRC binding motif 4 0.085 39.2 Match Image
7 RM00008 GNRA tetraloop 18 0.383 168.1 Match Image
7 RM00010 Kink turn 1, 3' bulge 16 0.340 198.4 Match Image
7 RM00019 Sarcin-ricin motif 2 37 0.787 853.8 Match Image
7 RM00030 U-turn motif 8 0.170 113.2 Match Image

References

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

Literature references

  1. Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR Cell 2003;113:577-586. Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria. PUBMED:12787499

  2. Grundy FJ, Lehman SC, Henkin TM Proc Natl Acad Sci U S A 2003;100:12057-12062. The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. PUBMED:14523230

  3. Sudarsan N, Wickiser JK, Nakamura S, Ebert MS, Breaker RR Genes Dev 2003;17:2688-2697. An mRNA structure in bacteria that controls gene expression by binding lysine. PUBMED:14597663

  4. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS Nucleic Acids Res 2003;31:6748-6757. Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?. PUBMED:14627808

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 Wickiser JK, Barrick JE
Structure source Published; PMID:12787499
Type Cis-reg; riboswitch;
Author Wickiser JK, Barrick JE, Breaker RRORCID logo
Alignment details
Alignment Number of
sequences
full 2,214
seed 47

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 30.0
Trusted cutoff 30.1
Noise cutoff 29.7
Covariance model Download