SAM clan

The SAM clan contains the RNA families SAM, SAM-IV and SAM-I/IV. Homology between these families has been established in the published literature [1].

This clan contains 3 families and the total number of sequence regions in the clan is 12,731.

Literature references

1. Weinberg Z, Regulski EE, Hammond MC, Barrick JE, Yao Z, Ruzzo WL, Breaker RR, RNA. 2008 Mar; [Epub ahead of print]: The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. 18369181

Members

This clan contains the following 3 member families:

SAM SAM-IV SAM-I-IV

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 mapping between the Rfam families in this clan, the corresponding EMBL entries, and the region of the three-dimensional structures that are available for that sequence.

This tool allows you to view the secondary structure images of two clan members side-by-side. Choose the family structures using the two drop-down menus below.

The table below shows the number of occurrences of each family throughout the sequence database. In brackets beside each number is the percentage of the total number of sequence hits for the clan that are represented by this family. The rightmost column provides a link to the alignments tab for each family.

Rfam family	Num. regions	Alignment
SAM-I-IV (RF01725)	567 (4.5%)	View
SAM-IV (RF00634)	2,360 (18.5%)	View
SAM (RF00162)	9,804 (77.0%)	View