|
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 |
||||