Cobalamin clan

The Cobalamin clan contains the RNA families for Cobalamin riboswitches and the AdoCbl riboswitch from Enterobacteria. The following bioinformatic methods were used to confirm the relationship between these families: CMSEARCH [1]. The relationship and distinction between these RNA families has been noted in the published literature [2,3].

This clan contains 3 families and the total number of sequence regions in the clan is 21,357.

Literature references

1. Nawrocki EP, Kolbe DL, Eddy SR, Bioinformatics. 2009;25:1335-7.: Infernal 1.0: inference of RNA alignments. 19307242
2. Fox KA, Ramesh A, Stearns JE, Bourgogne A, Reyes-Jara A, Winkler WC, Garsin DA, Proc Natl Acad Sci U S A. 2009;106:4435-4440.: Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis. 19246383
3. Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR;, Genome Biol. 2010;11:R31.: Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes. 20230605

Members

This clan contains the following 3 member families:

Cobalamin AdoCbl AdoCbl-II

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
AdoCbl-II (RF01689)	174 (0.8%)	View
AdoCbl (RF01482)	319 (1.5%)	View
Cobalamin (RF00174)	20,864 (97.7%)	View