29  structures 2540  species 6161  sequences

Family: SAM (RF00162)

Description: SAM riboswitch (S box leader)



This family is a member of clan (CL00012), which contains the following 3 members:


Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry SAM riboswitch (S box leader). More...

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



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.


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:


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


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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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The tree shows the occurrence of this RNA across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


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.


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 SAM family has been found.

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Motif matches

There are 2 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 85 0.186 992.4 Match Image
7 RM00010 Kink turn 1, 3' bulge 271 0.594 3372.6 Match Image


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

Literature references

  1. Grundy FJ, Henkin TM Mol Microbiol 1998;30:737-749. The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. PUBMED:10094622

  2. Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR Nat Struct Biol 2003;10:701-707. An mRNA structure that controls gene expression by binding S-adenosylmethionine. PUBMED:12910260

  3. Epshtein V, Mironov AS, Nudler E Proc Natl Acad Sci U S A 2003;100:5052-5056. The riboswitch-mediated control of sulfur metabolism in bacteria. PUBMED:12702767

  4. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS Nucleic Acids Res 2004;32:3340-3353. Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. PUBMED:15215334

  5. Montange RK, Batey RT Nature. 2006;441:1172-1175. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. PUBMED:16810258

  6. Montange RK, Mondragon E, van Tyne D, Garst AD, Ceres P, Batey RT J Mol Biol. 2010;396:761-772. Discrimination between closely related cellular metabolites by the SAM-I riboswitch. PUBMED:20006621

  7. Stoddard CD, Montange RK, Hennelly SP, Rambo RP, Sanbonmatsu KY, Batey RT Structure. 2010;18:787-797. Free state conformational sampling of the SAM-I riboswitch aptamer domain. PUBMED:20637415

  8. Lu C, Ding F, Chowdhury A, Pradhan V, Tomsic J, Holmes WM, Henkin TM, Ke A J Mol Biol. 2010;404:803-818. SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch. PUBMED:20951706

  9. Baird NJ, Zhang J, Hamma T, Ferre-D'Amare AR RNA. 2012;18:759-770. YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. PUBMED:22355167

  10. Schroeder KT, Daldrop P, McPhee SA, Lilley DM RNA. 2012;18:1257-1266. Structure and folding of a rare, natural kink turn in RNA with an A*A pair at the 2b*2n position. PUBMED:22539525

  11. Daldrop P, Lilley DM RNA. 2013;19:357-364. The plasticity of a structural motif in RNA: structural polymorphism of a kink turn as a function of its environment. PUBMED:23325110

  12. Huang L, Wang J, Lilley DM Nucleic Acids Res. 2016;44:5390-5398. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function. PUBMED:27016741

  13. Huang L, Liao X, Li M, Wang J, Peng X, Wilson TJ, Lilley DMJ Nucleic Acids Res 2021;49:5916-5924. Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules. PUBMED:33978763

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.


Seed source Grundy F, Henkin T, PMID:10094622
Structure source Published; PMID:10094622
Type Cis-reg; riboswitch;
Author Griffiths-Jones SRORCID logo, Gardner PPORCID logo, Ontiveros-Palacios NORCID logo
Alignment details
Alignment Number of
full 5,704
seed 457

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 742849.287494 CM SEQDB
Gathering cutoff 44.4
Trusted cutoff 44.4
Noise cutoff 44.3
Covariance model Download