Additional File 5 — 6S RNA grouped consensus alignment (pdf ) Folded consensus structure of the 6S RNA groups generated with

(1)

Additional File 5 — 6S RNA grouped consensus alignment (pdf )

Folded consensus structure of the 6S RNA groups generated with RNAclust (the names next to the colored square boxes indicate the family). The consensus secondary structures were calculated with RNAalifold and visualized using VARNA. The name right above the structure indicates the RNAclust group name in line with Fig. 1. Colors indicate sequence conservation within the respective LAB family.

Aerococcaceae

Aerococcus

0.0 1.0

AG A U A U C U G A G A U G U G C G U U G U A U A C A U A U U G U G U G GACCGAACACUU UAUUAUUAUAUAG G G A U U CUA A G AUC G U U G U U A C G A AU G A C A A GC CU U U UACAC

U

UG

G

A

G

U

C

AG

A

U

A

U

A

G

UG

U

G

A

AG

C

ACCUGCAAU

U

A

CUUGCGGGU

U

C

A

U

A

C

A

U

A

U

G

U

A

U

G

CAAAG

A

C

G

C

A

U

CA

U

C

G

A

U

A

C

UUU

1 10 20 30 40 50 60 70 80 90 100

110

120

130

140

150

160

170

180

190

196

5' 3'

A G A G C U C U G A A G U G U A C G U G CUAU U C U U U U AAU G U G U U G ACCGAACAAAUUUUACUAUCUAG G G A A C U G UG A A C U C C U A U G G A U G U AA C G C C U C U AUCAC

G

A

G

A

C

UA

CU

GA

A

GU

C

G

A

U

A

U

AG

C

G

UA

C

ACCUGC AAAU

U

A

UUUC GCGGGU

U

C

A

U

A

C

AGA

U

AG

AU

U

UAU

C

A

CG

GC

AC

C

AA

U

C

G

A

G

C

U

C

UA

1 10 20 30 40 50 60 70 80 90 100110

120

130

140

150

160

170

180

190196

5' 3'

Carnobacteriaceae

Carnobacteriaceae*

0.0 1.0

AG A U U U C U G A G G U G U A C G U G A U G U C CAAUAAAUGUGU U G A C C G A A C A A U U A U AUUAUUACAUUG G G A U U CA A A AG GU A UU C A A A C U G A U A A C A A GC C U U U UCACUUGG

U

A

G

U

AGAG

AUG

U

G

A

C

UG

GCG

GA

GC

C

CA

C C U G C U UAU

AUUGCG

GG

U

UC

A

AC

A

C

U

A

ACUG

G

A

C

AUAACAAAC

G

C

A

C

CAUC

G

AU

U

CUU

1 10 20 30 40 50 60 70 80 90 100

110

120

130

140 150

160

170

180

190200

5' 3'

1

(2)

Lactobacillaceae

Pediococcus

G A A G AU C U U A G G U AUU C GA A AU U A U U G G U UUCA UAUU C UUCCAACAAACAUCUAAUCGG G G A A C A C GGA UC G C A A G UG A A UU G UAGGC C U U UUA

UU

G

A

C

AU

G

CUG

U

UUG

G

U

A

U

G

UG

UA

C

ACCUUAGUUUACUUGGGU

U

A

G

A

U

A

C

U

G

C

G

A

U

A

UG

C

AAC

G

U

A

C

UAA

A

GU

U

C

U

UC

1 10 20 30 40 50 60 70 80 90

100

110

120

130

140

150

160

170

1801855'3'

0.0 1.0

Lactobacllus 1

Lactobacllus 2

Lactobacllus 3

Lactobacllus 4

Lactobacllus 5

Lactobacllus 6

Lactobacllus 7

AGUG A U C U G A G U U G A UCGA CA GAAAA G C U U A AAUGUAUAAAGUUGACC GAUCAAACUAUAAG A C G U G G G A G U U U G U AAAUA ACUACC G A A U C G G AA UAC U G C C UUGUUGCAG

GA

U

C

CA

UA

U

C

GC

U

G

C

G

AU

A

U

A

G

C

U

CAAAUUUGUGAAUUCACU

GCGGGUUCAACAAG

C

G

U

C

A

U

AU

G

C

UA

U

GU

U

AG

U

C

A

C

U

C

G

A

U

UUCUUU

1 10 20 30 40 50 60 70 80 90 100 110120

130

140

150

160170

180190

200

2075'3' UUAAAU C U G A G A U G UAC G C G U U A U C U CAUAAAUG UAAG G U U G ACCGAACACCUAUAUAUUUUGGU U U U U GGAA UA U U U A GU G G A UA A CAUGC C U AUU U A UUAUU

A

UC

G

UU

A

GG

A

G

U

UAA

G

AAGU

U

A

G

U

C

UA

U

C

G

A

U

AC

A

U

UC

ACCUGCUU

UGAGA GCGGG

UU

C

A

C

U

A

C

A

G

A

G

A

UG

A

UU

AAC

G

C

A

U

CA

UAC

G

AUUUUCA

1 10 20 30 40 50 60 70 80 90 100

110

120

130

140

150

160

170

180

190

2002045'3' A A A GUUC U A A G G U G UUC G C G C U U C C CUAUCUA U CAG U U G ACCGAACAAGUAUCGAGACCUU G G G AC C GCG AAGUG C C U A U G C C C G U G CAU GAC U AU UUCA

C

U

A

G

C

G

CU

AAG

G

A

C

G

A

G

C

G

UAC

U

G

GA

C

A

CCUGCU UAAUAUUAGCGGG

U

C

A

C

G

A

U

A

C

G

GA

A

GAUA

AAC

G

C

A

C

CAAU

U

A

G

C

U

UCA

1 10 20 30 40 50 60 70 80 90 100

110

120

130

140150

160170

180

190196 GUGGUU C U A A G G U G UAC G C G U U G U C UCA CUAC A A G U U GCCGAACAAGUAAUUCUUAAACG G G A U UG CCUAACG A U A G C GAA G AU G A CA GGC CU U UUCA

CU

UG

G

A

G

U

C

AG

A

C

GC

U

A

U

C

AG

G

C

U

UC

C

CCUGCAUUU

G

U

CAUCGCGGG

U

C

A

C

A

U

G

AC

U

G

AC

A

UU

AAC

G

C

A

C

CA

CU

U

A

G

AUCGACCA

1 10 20 30 40 50 60 70 80 90 100110120130

140

150

160170

180

1901935'3'GA A A U U C U A U G G U G UAC G C G U U G U CCAUAAUGCAGGUUUGCCUUACAGCUCUUAUUACAUU G G G A CUAGUGUUUACGU U CUGU U GGAU A A CA UG C CU U U UACA

CU

UG

G

U

A

G

U

GG

A

C

UU

G

AC

A

GC

C

G

UG

U

C

A

C C U G U C UUA

AA

CA

C

A

G

U

C

A

AC

C

U

G

A

CGG

A

C

AAAU

U

AAC

G

C

A

C

UA

A

U

G

A

G

U

UU

UUC

1 10 20 30 40 50 60 70 80 90 100

110

120

130

140

150

160

170

180

190

196 G A UU UU C U G A G G U G UGCG C GUAU U U C CAACCUUGUG U U G ACCGAUCAAGUAAUUCAUUAAU G G G AU G GACUUUUGAU U U A U U A A UC A A AG CAUGC C U UU UCACGAGG

A

G

CU

A

GUA

U

A

U

A

U

A

G

CC

G

AA

C

A

CCUGCAUCUUU

UAGCGGG

U

C

A

UA

CU

C

AG

G

A

GCA

UC

AA

CGG

C

A

C

U

A

CC

A

G

A

U

A

U

CC

1 10 20 30 40 50 60 70 80 90 100

110

120

130

140

150

160170

180

190

1955'3' AA AU UA C U A A G G U G UGC G C A U U G C U C UAAACAAA G U G U U GCCGAACAAUUAAUACUACUUUG G G A C G U A CGUUAG C U A A U UACC AU A A CAU G C CU U AUCC

UU

UG

G

U

A

G

U

A

G

C

G

A

U

A

G

U

C

A

G

C

U

C

G

U

C

ACCUGCCU

U

A

AAGCGGGU

C

A

U

A

C

U

G

A

G

C

G

UU

AAC

G

C

A

C

CA

CU

A

G

U

UCC

1 10 20 30 40 50 60 70 80 90 100

110

120

130

140

150

160

170

180

1895'3'

2

(3)

Enterococcaceae

Vagococcus

Enterococcaceae

0.0 1.0

G G A U A U C U G U G A U G U A C G C C G U A U U C UC A U U AG U G U U G ACCGAACAAAUCGUCUUACCUUG G G A A U UA A C G AG U U A U U A AU A G AA A A C A G G C C U U U UCA

CU

U

G

U

A

G

U

GA

G

U

A

G

U

A

C

AA

C

G

A

U

C

ACCUGC AUU

G

U

ACA GCGGGU

U

C

A

C

A

C

A

C

A

G

A

U

A

CA

UU

AAC

G

C

A

U

CG

A

CG

GA

UA

U

UU

1 10 20 30 40 50 60 70 80 90 100

110

120

130

140

150

160

170

180

190192

5' 3'

GGGAAAU C U G U G A U G UA C G A G U U G U C C UUU U U GUG U G U U G ACCGAACAUUUU UAUUGAUAUCUUG G G A U C C G UCU UG U G U C A A A G UU G G U A A C A U G C C U U U UCA

UU

U

G

U

A

G

U

UC

GA

A

UG

C

UU

A

G

A

C

G

U

G

GA

AC

C

A

CCUGC UUA

GA

A

UUU GCGGG

A

U

C

A

U

A

C

U

A

C

A

G

A

C

GAAU

AA

ACGG

C

A

U

CG

A

C

G

AUAUUAC

1 10 20 30 40 50 60 70 80 90 100

110

120

130

140

150

160

170

180

190

199

5' 3'

Leuconostocaceae

0.0 1.0

G A A U U C C U C A G A U A U A C G C A U U G C U A C A U C A U C A G C

U

U U U

U

C

C U U A C

A

C

C U

U U

A U U U U U C G G U U G G G A A U U C U U G A C U U A G A A G A U C U G C C C U U U C A U U C G G U A A U C U G A C A A U C U U G A U G A A C C A U C C A C C U C G A U A A

U U U

C

G

A

G

G A

A A

A U

C U G C G

U

A

G

C

G

A

U U

A A C

G

U

A

U

C A A U U G

A

G

U

G

U

C C G

1 10 20 30

40 50

60 70 80 90 100

110 120 130 140

150 160 170

180

189

3

(4)

Streptococcaceae

Lactococcus

Streptococcus

0.0 1.0

A A A G C A C U G G A A U G U G C G A A C U U A C U CA C A U U UU U G ACC

GA

CUA U A AU C GUA UUGCAUAG G G A G U U UAU G A G ACAU U C U A U A G C G U U C A A A C C A U U UAAGAAAGUAGCUGCAGUUGAUUAAAAG

CG

AG

GA

CA

C

ACCUGGC UAAC

AUUUAU AGCGGGU

U

C

A

AU

AC

UCG

AG

U

A

AG

CAUAC

G

GC

A

U

CAAUC

AG

UG

U

UU

1 10 20 30 40 50 60 70 80 90 100110120130

140

150160

170

180190

200

5' 3' 5' 3'

AAAUUG C U G U G G C A U A C G A A U U C A CA U C U A AG U G U U G ACCGACUAUUU UUU UGUAUUUUCG G G A A A CAA A A G UCU U U U U G C C A G U A U G CA A G C C G U U U UCACGCGG

A

G

C

A

C

UUCAAG

G

A

GA

C

G

AG

U

UA

C

A

CCUGC UUUUU

AAUUGU GCGGG

U

C

A

U

A

CAA

A

ACCG

U

G

A

UCACC

G

U

G

C

CAAUA

C

A

G

CUUUUUUCU

1 10 20 30 40 50 60 70 80 90 100

110120

130

140

150

160

170

180190

200204