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Table 1 Motifs identified in this work

From: Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

Motif RNA? cis-reg? Switch? Taxa Rfam
6S-flavo Y N N Bacteroidetes RF01685
aceE ? y ? γ-Proteobacteria  
Acido-1 y n n Acidobacteria RF01686
Acido-Lenti-1 y n n Acidobacteria, Lentisphaerae RF01687
Actino-pnp Y Y N Actinomycetales RF01688
AdoCbl-variant Y Y Y Marine RF01689
asd Y ? ? Lactobacillales RF01732
atoC y y ? δ-Proteobacteria RF01733
Bacillaceae-1 Y n n Bacillaceae RF01690
Bacillus-plasmid y ? n Bacillus RF01691
Bacteroid-trp y y n Bacteroidetes RF01692
Bacteroidales-1 Y ? ? Bacteroidales RF01693
Bacteroides-1 y ? n Bacteroides RF01694
Bacteroides-2 ? n n Bacteroides  
Burkholderiales-1 ? ? n Burkholderiales  
c4 antisense RNA Y N N Proteobacteria, phages RF01695
c4-a1b1 Y N N γ-Proteobacteria, phages  
Chlorobi-1 Y n n Chlorobi RF01696
Chlorobi-RRM y y n Chlorobi RF01697
Chloroflexi-1 y ? n Chloroflexus aggregans RF01698
Clostridiales-1 y n n Clostridiales, human gut RF01699
COG2252 ? y n Pseudomonadales  
Collinsella-1 y n n Actinobacteria, human gut RF01700
crcB Y Y Y Widespread, bacteria and archaea RF01734
Cyano-1 y n n Cyanobacteria, marine RF01701
Cyano-2 Y n n Cyanobacteria, marine RF01702
Desulfotalea-1 ? n n Proteobacteria  
Dictyoglomi-1 y ? ? Dictyoglomi RF01703
Downstream-peptide Y y y Cyanobacteria, marine RF01704
epsC Y y y Bacillales RF01735
fixA ? y n Pseudomonas  
Flavo-1 y n n Bacteroidetes RF01705
flg-Rhizobiales y y n Rhizobiales RF01736
flpD y ? n Euryarchaeota RF01737
gabT Y y ? Pseudomonas RF01738
Gamma-cis-1 ? y n γ-Proteobacteria  
glnA Y Y y Cyanobacteria, marine RF01739
GUCCY-hairpin ? ? n Bacteroidetes, Proteobacteria  
Gut-1 Y n n Human gut only RF01706
gyrA y y n Pseudomonas RF01740
hopC y Y ? Helicobacter RF01741
icd ? y n Pseudomonas  
JUMPstart y Y ? γ-Proteobacteria RF01707
L17 downstream element y y n Lactobacillales, Listeria RF01708
lactis-plasmid y ? n Lactobacillales RF01742
Lacto-int ? ? n Lactobacillales, phages  
Lacto-rpoB Y y n Lactobacillales RF01709
Lacto-usp Y ? ? Lactobacillales RF01710
Leu/phe leader Y Y N Lactococcus lactis RF01743
livK y y ? Pseudomonadales RF01744
Lnt y y ? Chlorobi RF01711
manA Y Y y Marine, γ-Proteobacteria, cyanophage RF01745
Methylobacterium-1 Y n n Methylobacterium, marine RF01712
Moco-II y Y ? Proteobacteria RF01713
mraW y y ? Actinomycetales RF01746
msiK Y Y ? Actinobacteria RF01747
Nitrosococcus-1 ? n n Nitrosococcus, Clostridia  
nuoG y y ? Enterobacteriales (incl. E. coli K12) RF01748
Ocean-V y n n Marine only RF01714
Ocean-VI ? ? ? Marine only  
pan Y Y ? Chloroflexi, Firmicutes, δ-Proteobacteria RF01749
Pedo-repair y ? n Pedobacter RF01715
pfl Y Y Y Several phyla RF01750
pheA ? y n Actinobacteria  
PhotoRC-I y y n Cyanobacteria, marine RF01716
PhotoRC-II Y y n Marine, cyanophage RF01717
Polynucleobacter-1 y y ? Burkholderiales, fresh water/estuary RF01718
potC y y ? Marine only RF01751
psaA Y y ? Cyanobacteria RF01752
psbNH y y n Cyanobacteria, marine RF01753
Pseudomon-1 y n n Pseudomonadales RF01719
Pseudomon-2 ? n n Pseudomonas  
Pseudomon-GGDEF ? y ? Pseudomonas  
Pseudomon-groES y y ? Pseudomonas RF01721
Pseudomon-Rho y Y n Pseudomonas RF01720
Pyrobac-1 y n n Pyrobaculum RF01722
Pyrobac-HINT ? y n Pyrobaculum  
radC Y y ? Proteobacteria RF01754
Rhizobiales-1 ? n N Rhizobiales  
Rhizobiales-2 y ? n Rhizobiales RF01723
Rhodopirellula-1 ? y ? Proteobacteria, Planctomycetes  
rmf Y y ? Pseudomonadales RF01755
rne-II Y y N Pseudomonadales RF01756
SAM-Chlorobi y Y ? Chlorobi RF01724
SAM-I-IV-variant Y Y Y Several phyla, marine RF01725
SAM-II long loops Y Y Y Bacteroidetes, marine RF01726
SAM/SAH riboswitch Y Y Y Rhodobacterales RF01727
sanguinis-hairpin ? n n Streptococcus  
sbcD y ? n Burkholderiales RF01757
ScRE ? y n Streptococcus  
Soil-1 ? n n Soil only  
Solibacter-1 ? n n Solibacter usitatus  
STAXI y ? n Enterobacteriales RF01728
sucA-II y y ? Pseudomonadales RF01758
sucC Y Y ? γ-Proteobacteria RF01759
Termite-flg Y y n Termite hind gut only RF01729
Termite-leu y ? ? Termite hind gut only RF01730
traJ-II Y Y n Proteobacteria, Enterococcus faecium RF01760
Transposase-resistance ? y n Several phyla  
TwoAYGGAY y n n Human gut, γ-Proteobacteria, Clostridiales  
wcaG Y y y Marine, cyanophage RF01761
Whalefall-1 Y n n Whalefall only RF01762
yjdF Y Y Y Firmicutes RF01764
ykkC-III y Y y Actinobacteria, δ-Proteobacteria RF01763
  1. Columns are as follows. "RNA?" : is this motif likely to represent a biological RNA? "Y" = certainly, "y" = probably, "?" = ambiguous, "n" = probably not, "N" = no. "cis-reg" : is the motif cis-regulatory? "switch?" : is the motif a riboswitch? Additional annotation and justification is in Additional File 2. "Taxa" : common taxon/taxa carrying this motif. Many motifs are discussed only in Additional file 1. "Rfam" : accession numbers of motifs that were submitted to the Rfam database for version 10.1. Note: consensus diagrams of some motifs were presented as supplementary data of a previous report [21] under simplified names: Acido-1 (previously ac-1), Dictyoglomi-1 (dct-1), Gut-1 (gt-1), manA (manA), Termite-flg (tf-1) and Whalefall-1 (wf-1).