The distributions, mechanisms, and structures of metabolite-binding riboswitches

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.

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