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 |
The RNA motifs are arranged according to ‘Classification code’ (column ‘CC’) and ‘Number of RNAs identified’ (column ‘No’)’. Effector’column includes experimentally identified or potential (marked with ‘?’) effectors of riboswitches; potential riboswitches with yet unknown effectors are marked with ‘?’; other classes of RNA motifs are indicated with ‘-‘. ‘Experimental’ column refers to in vivo or in vitro validation of a RNA motif function and/or riboswitch effector.