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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).
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Genome Biology

ISSN: 1474-760X

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