23  structures 0  species 0  sequences

Clan: c-di-GMP_I_riboswitch (CL00126)


c-di-GMP_I riboswitch clan

Riboswitches are metabolite binding domains within certain messenger RNAs that serve as precision sensors for their corresponding targets. Allosteric rearrangement of mRNA structure is mediated by ligand binding, and this results in modulation of gene expression. A class of riboswitches that selectively recognises cyclic dinucleotides c-di-GMP and c-di-AMP was report first in [2]. c-di-GMP_I riboswitch clan included the first reported c-di_GMP_I riboswitch and the variants c-di-GMP-I-UAU and c-di-GMP-I-GGC reported in [1].

This clan contains 3 families and the total number of sequence regions in the clan is 4,880.

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. Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, Link KH, Breaker RR, Science 2008;321:411-413.: Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP 18635805


This clan contains the following 3 member families:

c-di-GMP-I c-di-GMP-I-GGC c-di-GMP-I-UAU


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.

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Secondary structures

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-I-UAU (RF03168) 17 (0.3%) View
c-di-GMP-I-GGC (RF03167) 805 (16.5%) View
c-di-GMP-I (RF01051) 4,058 (83.2%) View