| Type | Species* | Rfam accession number†|
---|---|---|---|
Ribozyme | Group I intron | Thermus thermophila [1] | RF00028 |
 |  | More than 20,000 sequences from all three kingdoms‡ |  |
 |  | Didymium iridis (branching enzyme, group I intron derivative) [46] |  |
 | Group II intron | Saccharomyces cerevisiae mitochondria [17,18] | RF00029 |
 |  | More than 8,000 sequences from all three kingdoms‡ |  |
 | Hammerhead | Tobacco ringspot virus satellite RNA (sTRSV) [3] | RF00008 |
 |  | Several additional satellite RNAs of plant viruses§ | RF00163 |
 |  | Viroids of the Avsunviroidae family [99,100] |  |
 |  | Carnation small viroid-like RNA (CarSV RNA) [101] |  |
 |  | Satellite DNAs of various amphibian species [102,103], Schistosoma mansoni [30] and Dolichopoda cave crickets [31] |  |
 |  | Arabidopsis thaliana genome [33] |  |
 | Hairpin | Tobacco ringspot virus satellite RNA (sTRSV) [4] | RF00173 |
 |  | Two additional satellite RNAs of plant viruses: sCYMV and sARMV [104] |  |
 | HDV | Human hepatitis delta virus RNA [6] | RF00094 |
 |  | Homo sapiens genome (intronic) [29] |  |
 | RNase P | Escherichia coli [2] | RF00010 |
 |  | More than 1,000 sequences from various Bacterial phyla¶ | RF00011 |
 |  | Archeal phyla: Crenarchaeota, Euryarchaeota [105] | RF00373 |
 | VS | Neurospora crassa Varkud satellite [8] | NL |
Catalytic riboswitch | Glms riboswitch | Bacillus subtilis [14] | RF00234 |
 |  | Bacterial phyla: Actinobacteria, Firmicutes |  |
Riboswitch | Adenine¥ | B. subtilis [106] | RF00167 |
 |  | Bacterial phyla: Proteobacteria, Firmicutes |  |
 | Coenzyme B12 | E. coli and Salmonella typhimurium btuB mRNAs [107] | RF00174 |
 |  | Bacterial phyla: Actinobacteria, Proteobacteria, Deinococcus-thermus, Bacteroidetes, Spirochaetes, Chloroflexi, Firmicutes, Fusobacteria, Cyanobacteria, Thermogales |  |
 | Flavin mononucleotide (FMN) | 20 Gram-positive and Gram-negative bacteria [23,24,108] | RF00050 |
 |  | Bacterial phyla: Actinobacteria, Deinococcus-thermus, Thermus/deinococcus group, Proteobacteria, Firmicutes, Thermotogae, Fusobacteria, Thermogales |  |
 | Guanine¥ | B. subtilis [25] | RF00167 |
 |  | Bacterial phyla: Proteobacteria, Firmicutes |  |
 | Glycine | B. subtilis [109] | RF00154 |
 |  | Bacterial phyla: Actinobacteria, Proteobacteria, Fusobacteria, Firmicutes |  |
 | Lysine | B. subtilis [25,110-112] | RF00168 |
 |  | Bacterial phyla: Proteobacteria, Thermogales, Firmicutes |  |
 | Intracellular magnesium | S. enterica [113] | NL |
 | S-adenosylmethionine (SAM) | B. subtilis [114-116] | RF00162 |
 |  | Bacterial phyla: Cyanobacteria, Actinobacteria, Proteobacteria, Firmicutes |  |
 | Thiamine pyrophosphate (TPP) | Rhizobium etli [117] | RF00059 |
 |  | Bacterial phyla: Actinobacteria, Deinococcus-thermus, Bacteroidetes, Proteobacteria, Thermus/deinococcus group, Spirochaetes, Chloroflexi, Firmicutes, Fusobacteria, Cyanobacteria, Thermogales |  |
 |  | Eukaryal phyla: Metazoa, Cercozoa, Fungi, Viridiplantae |  |
 |  | Archeal phyla: Euryarchaeota |  |