Table 1

Summary information on identified RAYTs and REPs

Host strain

RAYT symbol

RAYT accession

REP sequenceA)

Nr. of REP copies B)

rayt-BIME association


Citrobacter koseri ATCC BAA-895

Ckos

YP_001455335

GTAG

    GCCcGgT
AA
    GCG
aaG
    CGC
C
    aCCgGGC

GTAG

    GCCgGaT
AA
    gGCGc
tt
    GCGCC
gCC
    atccGGC

9/46/77

16/23/65

N


Enterobacter sakazakii ATCC BAA-894

Esak

YP_001437784

GTAG

    GGcGGGT
AA
    GCG
gAG
    CGCACCCgCC

GTAG

    GGtGGGT
AA
    GCGc
A
    GCGCACCCaCC

3/89/159

39/117/180

N


Escherichia coli str. K-12 substr. MG1655

Ecol

NP_414763

GTAG

    G
a
    cgGAT
AA
    GgCGt
tC
    ACGcC
GC
    ATCcG
G
    C
A

GTAG

    GcatGAT
AA
    GaCGc
gcCA
    gCGtC
GC
    ATCa
G
    GC
A

4/52/126

4/19/46

Y


Salmonella enterica subsp. enterica serovar Typhi str. CT18

Sent

NP_458983

TGTAG

    GCCGGAT
AA
    Ggcg
tagc
    CGCCATCCGGC

TGTAG

    GCCGGAT
AAGcaacgCGCC
    ATCCGGC

1/10/16

1/2/6

N


Klebsiella pneumoniae 342

Kpne

YP_002239241

GTAG

    GCCcggc
AA
    GCGc
A
    GCGC
C
    gccgGGC

GTAG

    GCCggat
AA
    gGCG
aAGc
    CGCCatccGGC

8/12/20

2/11/13

Y


Haemophilus parasuis SH0165

Hpar

YP_002476161

GTAG

    GGTGGGTC
TT
    GACCCACC

20/22/42

N


Haemophilus influenzae Rd KW20

Hinf

NP_438385

GTAG

    GGTGGGCT
Tc
    AGCCCACC

GTAG

    GGTGGGCT
Tt
    AGCCCACC

6/14/21

5/16/21

Y


Coxiella burnetii Dugway 5J108-111

Cbur

YP_001425023

GTAG

    GTTGGGCT
GAGCTTGCGA
    AGCCCAAC

29/38/40

N


Thioalkalivibrio sp. HL-EbGR7

T_sp

YP_002514838

GTAG

    GTCGGCCT
TC
    AGGCCGAC

38/53/118

N


Pseudomonas mendocina ymp

Pmen

YP_001186231

GTAG

    CCCGGAT
GCA
    ATCCGGG

75/136/162

N


Pseudomonas putida KT2440

Pput1

NP_747277

TGTGGGA

    GCGGGC
gT
    GCCCGC
GAA

TGTGGGA

    GCGGGC
aT
    GCCCGC
GAA

62/193/286

35/172/285

N


Pseudomonas putida GB-1

Pput2

YP_001671454

TGTGGGA

    GCGGGT
Tt
    ACCCGC
GAA

TGTGGGA

    GCGGGT
Tc
    ACCCGC
GAA

62/95/130

14/80/104

N


Pseudomonas putida KT2440

Pput3

NP_742731

TGTGGGA

    GCGGC
CTT
    Gc
GT
    CGC
GA

TGTGGGA

    GCG
G
    C
CTTGt
    G
T
    CGC
GA

21/53/69

27/62/72

N


Pseudomonas putida W619

Pput4

YP_001751446

TGTAGGA

    GCGGC
CTT
    Gc
GT
    CGC
GAA

TGTAGGA

    GCG
G
    C
CTTGt
    G
T
    CGC
GAA

24/112/189

77/174/205

Y


Pseudomonas entomophila L48

Pent1

YP_608776

TGTAGGA

    GCGGAT
TC
    ATCCGC
GAT

116/171/443

N


Pseudomonas entomophila L48

Pent2

YP_610581

GTAGGA

    GCCAGC
TT
    GCTGGC
GAA

89/101/564

N


Pseudomonas fluorescens SBW25

Pflu1

YP_002873491

GTGGGA

    GGGGGC
TT
    GCCCCC
GAT

387/557/607

N


Pseudomonas fluorescens SBW25

Pflu2

YP_002871781

GTGGCGA

    GGGAGC
TT
    GCTCCC
GCT

104/192/232

Y


Pseudomonas fluorescens SBW25

Pflu3

YP_002873800

TGTgGTGA

    GCGGGC
TT
    GCCC
C
    GC
GCT

TGTaGTGA

    GCGGGC
TT
    GCCC
C
    GC
GCT

83/217/263

119/229/257

Y


Xanthomonas axonopodis pv. citri str. 306

Xaxo

NP_641493

GTAGGA

    GCGC
A
    CC
t
    GGGCGC
GAC

GTAGGA

    GCGC
A
    CC
c
    GGGCGC
GAC

9/49/85

23/58/88

Y


Xanthomonas campestris pv. campestris str. ATCC 33913

Xcam

NP_636415

GTAGGA

    GCGCGC
TC
    GCGCGC
GA

48/177/223

Y


Stenotrophomonas maltophilia R551-3

Smal1

YP_002030358

TGTAG

    AGCCGAGC
CCAT
    GCTCGGCT

49/90/113

N


Stenotrophomonas maltophilia R551-3

Smal2

YP_002029847

GGTAG

    CGCCGGGC
CAT
    GCCCGGCG

259/329/355

N


Stenotrophomonas maltophilia K279a

Smal3

YP_001970973

GGTGG

    GTGCCGACC
GTT
    GGTCGGCAC

52/75/99

N


Stenotrophomonas maltophilia K279a

Smal4

YP_001972572

GGTAG

    TGCCGGCC
GCT
    GGCCGGCA

427/556/644

Y


Stenotrophomonas sp. SKA14

S_sp1

YP_002706198

AGTAG

    ATCCACGC
CAT
    GCGTGGAT

69/147/182

N


Stenotrophomonas sp. SKA14

S_sp2

YP_002708831

GGTGG

    GTGCCAACC
TT
    GGTTGGCAC

37/84/131

N


(A) REP sequences, as found flanking the rayt gene, in 5´→3´ direction. When upstream and downstream REPs differ, both are denoted (differing bases in lower case). Palindromic parts are underlined. Conserved head sequences are written in bold. (B) Number of REP sequences in host strain's genome, in following order: completely identical copies/copies with 1 mismatch/copies with 2 mismatches.

Nunvar et al. BMC Genomics 2010 11:44   doi:10.1186/1471-2164-11-44

Open Data