7714  structures 0  species 0  sequences

Clan: SSU (CL00111)


SSU clan

This clan contains the SSU families.

This clan contains 5 families and the total number of sequence regions in the clan is 44,564.

Literature references

  1. Nawrocki EP, Kolbe DL, Eddy SR, Bioinformatics. 2009;25:1335-7.: Infernal 1.0: inference of RNA alignments. 19307242
  2. Eddy SR, PLoS Comput Biol. 2008;4:e1000069.: A probabilistic model of local sequence alignment that simplifies statistical significance estimation. 18516236
  3. Madera M, Bioinformatics. 2008;24:2630-2631.: Profile Comparer: a program for scoring and aligning profile hidden Markov models. 18845584
  4. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ, Nucleic Acids Res. 2008;36:D154-8.: miRBase: tools for microRNA genomics. 17991681


This clan contains the following 5 member families:

SSU_rRNA_bacteria SSU_rRNA_archaea SSU_rRNA_eukarya SSU_rRNA_microsporidia SSU_trypano_mito


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.

Loading structure mapping...

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
SSU_trypano_mito (RF02545) 12 (0.0%) View
SSU_rRNA_microsporidia (RF02542) 353 (0.8%) View
SSU_rRNA_eukarya (RF01960) 21,572 (48.4%) View
SSU_rRNA_archaea (RF01959) 546 (1.2%) View
SSU_rRNA_bacteria (RF00177) 22,081 (49.5%) View