Table 1 Functional overview of regulatory RNA families included in this study
CC | RNA motif name | Effector (for riboswitches) | No | Experimental | Rfam ID |
|---|---|---|---|---|---|
A | TPP (THI element) | thiamin pyrophosphate | 564 | known | RF00059 |
A | Cobalamin (B12 element) | adenosylcobalamin | 536 | known | RF00174 |
A | Glycine | glycine | 324 | known | RF00504 |
A | yybP-ykoY | ? | 232 | predicted | RF00080 |
A | FMN (RFN element) | flavin mononucleotide | 233 | known | RF00050 |
B | SAM (S-box) | S-adenosylmethionine | 257 | known | RF00162 |
B | pyrR | - | 211 | known | RF00515 |
B | Lysine (L-box) | lysine | 186 | known | RF00168 |
B | Purine (G-box) | guanine, adenine | 141 | known | RF00167 |
B | GEMM | cyclic di-GMP | 89 | known | RF01051 |
B | PreQ1 | pre-queuosine1 | 72 | known | RF00522 |
B | MOCO | molybdenum or tungsten cofactor? | 62 | known | RF01055 |
B | ydaO-yuaA | ATP | 59 | known | RF00379 |
B | ykkC-yxkD | ? | 58 | predicted | RF00442 |
B | mini-ykkC | ? | 67 | predicted | RF01068 |
B | ykoK (M-box) | magnesium | 48 | known | RF00380 |
B | glmS | glucosamine-6-phosphate | 44 | known | RF00234 |
B | SAH | S-adenosylhomocysteine | 27 | known | RF01057 |
C | SAM-Alpha | S-adenosylmethionine? | 39 | known | RF00521 |
C | serC | ? | 32 | predicted | RF00517 |
C | THF | tetrahydrofolate | 23 | known | RF01831 |
C | PreQ1-II | pre-queuosine1 | 17 | known | RF01054 |
C | sucA | ? | 14 | predicted | RF01070 |
C | glnA | glutamine | 13 | known | RF01739 |
C | SAM-IV | S-adenosylmethionine | 13 | known | RF00634 |
C | SAM-SAH | S-adenosylmethionine, S-adenosylhomocysteine | 13 | known | RF01727 |
C | Smk-box | S-adenosylmethionine | 13 | known | RF01767 |
C | speF | ? | 12 | predicted | RF00518 |
C | SAM-Chlorobi | S-adenosylmethionine | 11 | predicted | RF01724 |
C | ylbH | ? | 10 | predicted | RF00516 |
C | ybhL | ? | 8 | predicted | RF00520 |
C | Mg sensor | magnesium | 5 | known | RF01056 |
D | L10 leader | - | 108 | predicted | RF00557 |
D | S15 leader | - | 98 | known | RF00114 |
D | L20 leader | - | 75 | predicted | RF00558 |
D | L21 leader | - | 67 | predicted | RF00559 |
D | L19 leader | - | 61 | predicted | RF00556 |
D | L13 leader | - | 43 | predicted | RF00555 |
E | His leader | - | 49 | known | RF00514 |
E | Trp leader | - | 48 | known | RF00513 |
E | Thr leader | - | 45 | known | RF00506 |
E | Leu leader | - | 43 | known | RF00512 |
F | T-box | - | 1134 | known | RF00230 |