Table 1

Sources of riboswitch sequence alignments and molecular structures

References


Riboswitch class

Rfam accession

Seed alignment

Other alignments

Molecular structures


Thiamine pyrophosphate (TPP)

RF00059

[41]

[48]

[71-73]

Adenosylcobalamin (AdoCbl)

RF00174

[39]

[20]

Lysine

RF00168

[37]

[21]

Glycine

RF00504

[6]

S-Adenosylmethionine class 1 (SAM-I)

RF00162

[94]

[9,52]

[78]

Flavin mononucleotide (FMN)

RF00050

[56]

Guanine and adenine (purine)

RF00167

[22]

[95-97]

Glucosamine-6-phosphate (GlcN6P)

RF00234

[23]

[28,30]

7-Aminoethyl 7-deazaguanine (preQ1)

RF00522

[40]

S-Adenosylmethionine class 2 (SAM-II)

RF00521

[18]


Riboswitches are named for the metabolite that they sense with standard abbreviations in parentheses. Rfam database numbers are provided for each riboswitch along with references to the seed alignments we used to train covariance models for database searches in this study, other published multiple sequence alignments, and three-dimensional molecular structures.

Barrick and Breaker Genome Biology 2007 8:R239   doi:10.1186/gb-2007-8-11-r239

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