Table 1.
Motifs identified in this work
| 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 |
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).