c-di-GMP_II riboswitch clan

Clan c-di-GMP_II riboswitch included the first reported c-di_GMP_II riboswitch [2] and two variants c-di-GMP-II-GAG and c-di-GMP-II-GCG reported in [1]

This clan contains 3 families and the total number of sequence regions in the clan is 685.

Literature references

1. Weinberg Z, Nelson JW, Lunse CE, Sherlock ME, Breaker RR, Proc Natl Acad Sci U S A. 2017;114:E2077.: Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity. 28265071
2. Lee ER, Baker JL, Weinberg Z, Sudarsan N, Breaker RR, Science. 2010;329:845-848.: An allosteric self-splicing ribozyme triggered by a bacterial second messenger. 20705859

Members

This clan contains the following 3 member families:

c-di-GMP-II c-di-GMP-II-GAG c-di-GMP-II-GCG

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
c-di-GMP-II-GCG (RF03170)	6 (0.9%)	View
c-di-GMP-II-GAG (RF03169)	138 (20.1%)	View
c-di-GMP-II (RF01786)	541 (79.0%)	View