Table 4

Conservation of Sakai virulence-related genes in EHECs and other sequenced pathogenic E. coli strains

In silico*

No. of strains conserved



Gene

Location

Conservation in K-12

Common name/description

CFT073

UTI89

536

APEC

O157 (8)

O26 (8)

O111 (6)

O103 (6)


Genes related to adhsion (not fimbrial genes)

ECs0336

S-loop20

Partly conserved

Putative invasin

+

+

+

+

[8]

[8]

[6]

[6]

ECs0350

S-loop23

Absent

HmwA-like protein

-

-

+

-

(7)

0

0

0

ECs0362

S-loop24

Absent

AidA-I adhesin-like protein

-

-

-

-

[8]

[8]

[6]

[6]

ECs0548

S-loop43

Absent

Saa-like protein

-

+

-

+

[8]

0

0

0

ECs1360

SpLE1

Absent

Iha adhesin

+

-

-

-

[8]

[8]

[6]

2

ECs1396

SpLE1

Conserved

AidA-I adhesin-like protein

-

-

-

-

(7)

[8]

0

[6]

ECs1772

Sp9

Absent

Paa

-

-

-

-

[8]

(7)

[6]

4

ECs2006

Backbone

Absent

BigA-like protein

-

-

-

-

[8]

0

0

0

ECs2007

Backbone

Absent

BigB-like protein

-

-

-

-

[8]

0

0

0

ECs2567

Backbone

Conserved

Putative adhesin

+

+

+

+

[8]

[8]

[6]

[6]

ECs3860

SpLE3

Absent

Efa1 (interrupted)

-

-

-

-

(7)

[8]

[6]

[6]

ECs3861

SpLE3

Absent

Efa1 (partial)

-

-

-

-

(7)

[8]

[6]

[6]

ECs4559

SpLE4 (LEE)

Absent

Gamma intimin

-

-

-

-

[8]

0

0

0

ECs5290

S-loop288

Absent

Putative invasin

-

-

-

-

(7)

0

0

0

Genes confer resistance to host immune response

ECs0218

S-loop14

Absent

IcmF-like protein

-

-

-

-

[8]

[8]

[6]

[6]

ECs1236

Sp5

Absent

Lom

-

-

-

-

5

1

2

0

ECs1312

SpLE1

Absent

TraT

-

-

-

-

(7)

(7)

0

3

ECs1956

Sp10

Absent

IrsA-like protein

-

-

-

+

5

1

(5)

1

ECs3850

SpLE3

Absent

PagC-like protein

-

-

-

-

[8]

0

[6]

2

RF001

Sp5, 8

Conserved

Bor

+

+

+

+

6

[8]

1

5

RF098

Sp4, 10

Absent

Copper/zinc-superoxide dismutase

-

-

-

-

4

1

(5)

[6]

RF115

Sp3, 4, 8 - 12, 14, 15

Absent

Lom

-

-

-

+

[8]

[8]

[6]

[6]

Toxins and activators

ECs0541

S-loop42

Absent

RTX-like protein

-

-

-

-

[8]

0

0

0

ECs0542

S-loop42

Absent

RTX-like protein

-

-

-

-

[8]

0

0

0

ECs0814

Sp3

Absent

SfpA (systemic factor protein A)-like protein

-

-

-

-

[8]

[8]

[6]

[6]

ECs1205

Sp5

Absent

Shiga toxin 2 subunit A

-

-

-

-

4

1

2

1

ECs1206

Sp5

Absent

Shiga toxin 2 subunit B

-

-

-

-

3

1

2

1

ECs1282

S-loop71

Absent

Hemagglutinin/hemolysin - related protein

-

-

-

-

[8]

0

0

0

ECs1283

S-loop71

Absent

Hemolysin activator - related protein

-

-

-

-

[8]

0

0

0

ECs1382

SpLE1

Absent

HecB-like protein

-

-

-

-

5

(7)

[6]

2

ECs1652

Sp8

Absent

Putative catalase

-

-

-

-

[8]

0

0

0

ECs1677

Backbone

Conserved

Hemolysin E

-

-

-

-

[8]

[8]

[6]

[6]

ECs2973

Sp15

Absent

Stx1B

-

-

-

-

6

(7)

[6]

[6]

ECs2974

Sp15

Absent

Stx1A

-

-

-

-

6

(7)

[6]

[6]

Regulators

ECs1274

s-loop71

Absent

GrvA

-

-

-

-

[8]

0

0

0

ECs1388

SpLE1

Absent

PchD

+

-

-

+

4

(7)

2

2

ECs1588

Sp7

Absent

PchE

-

-

-

-

(7)

[8]

0

4

ECs3105

Backbone

Conserved

RcsD

+

+

+

+

[8]

[8]

[6]

[6]

ECs3106

Backbone

Conserved

RcsB

+

+

+

+

[8]

[8]

[6]

[6]

ECs3107

Backbone

Conserved

RcsC

+

+

+

+

[8]

[8]

[6]

[6]

ECs3720

ETT2

Absent

EtrA

-

-

-

-

[8]

[8]

4

4

ECs3734

ETT2

Absent

EivF

-

-

-

-

[8]

0

0

0

ECs4577

SpLE4 (LEE)

Absent

GrlA

-

-

-

-

[8]

[8]

4

(5)

ECs4578

SpLE4 (LEE)

Absent

GrlR

-

-

-

-

[8]

[8]

4

4

ECs4588

SpLE4 (LEE)

Absent

Ler

-

-

-

-

[8]

[8]

(5)

[6]

RF132

Sp4, 11, 14

Absent

PchA, B, C

-

-

-

-

[8]

(7)

[6]

[6]

Secretion machineries

ECs0540

S-loop42

Absent

CyaE-like protein

-

-

-

-

[8]

0

0

0

ECs0543

S-loop43

Absent

Putative RTX toxin secretion ATP-binding protein

-

-

-

-

[8]

0

0

0

ECs0544

S-loop44

Absent

Putative RTX toxin secretion membrane fusion protein

-

-

-

-

[8]

0

0

0

ECs3716

ETT2

Absent

EprK

-

-

-

-

[8]

[8]

(5)

(5)

ECs3717

ETT2

Absent

EprJ

-

-

-

-

[8]

[8]

4

(5)

ECs3718

ETT2

Absent

EprI

-

-

-

-

[8]

[8]

(5)

4

ECs3719

ETT2

Absent

EprH

-

-

-

-

[8]

[8]

4

(5)

ECs3721

ETT2

Absent

EpaS

-

-

-

-

[8]

[8]

(5)

(5)

ECs3722

ETT2

Absent

EpaR2

-

-

-

-

[8]

[8]

4

4

ECs3723

ETT2

Absent

EpaR1

-

-

-

-

[8]

[8]

(5)

4

ECs3724

ETT2

Absent

EpaQ

-

-

-

-

[8]

[8]

(5)

(5)

ECs3725

ETT2

Absent

EpaP

-

-

-

-

[8]

[8]

4

4

ECs3726

ETT2

Absent

EpaO

-

-

-

-

[8]

1

0

2

ECs3727

ETT2

Absent

EivJ

-

-

-

-

[8]

0

0

0

ECs3729

ETT2

Absent

EivI

-

-

-

-

[8]

0

0

0

ECs3730

ETT2

Absent

EivC

-

-

-

-

[8]

0

0

0

ECs3731

ETT2

Absent

EivA

-

-

-

-

[8]

0

0

0

ECs3732

ETT2

Absent

EivE

-

-

-

-

[8]

0

0

0

ECs3733

ETT2

Absent

EivG

-

-

-

-

[8]

0

0

0

ECs4551

SpLE4 (LEE)

Absent

Orf29

-

-

-

-

[8]

3

[6]

(5)

ECs4552

SpLE4 (LEE)

Absent

EscF

-

-

-

-

[8]

[8]

[6]

[6]

ECs4553

SpLE4 (LEE)

Absent

CesD2

-

-

-

-

[8]

[8]

[6]

[6]

ECs4555

SpLE4 (LEE)

Absent

EspD

-

-

-

-

[8]

0

0

1

ECs4556

SpLE4 (LEE)

Absent

EspA

-

-

-

-

[8]

1

0

1

ECs4557

SpLE4 (LEE)

Absent

SepL

-

-

-

-

[8]

[8]

[6]

(5)

ECs4558

SpLE4 (LEE)

Absent

EscD

-

-

-

-

[8]

0

3

2

ECs4560

SpLE4 (LEE)

Absent

CesT

-

-

-

-

[8]

6

[6]

[6]

ECs4563

SpLE4 (LEE)

Absent

CesF

-

-

-

-

[8]

0

0

0

ECs4565

SpLE4 (LEE)

Absent

SepQ

-

-

-

-

[8]

0

0

1

ECs4566

SpLE4 (LEE)

Absent

Orf16

-

-

-

-

[8]

0

(5)

0

ECs4567

SpLE4 (LEE)

Absent

Orf15

-

-

-

-

[8]

6

(5)

4

ECs4568

SpLE4 (LEE)

Absent

EscN

-

-

-

-

[8]

4

(5)

3

ECs4569

SpLE4 (LEE)

Absent

EscV

-

-

-

-

[8]

6

(5)

2

ECs4570

SpLE4 (LEE)

Absent

Orf12

-

-

-

-

[8]

4

4

2

ECs4572

SpLE4 (LEE)

Absent

Rorf8

-

-

-

-

[8]

0

0

0

ECs4573

SpLE4 (LEE)

Absent

EscJ

-

-

-

-

[8]

3

4

2

ECs4574

SpLE4 (LEE)

Absent

SepD

-

-

-

-

[8]

0

4

2

ECs4575

SpLE4 (LEE)

Absent

EscC

-

-

-

-

[8]

[8]

[6]

4

ECs4576

SpLE4 (LEE)

Absent

CesD

-

-

-

-

[8]

5

4

3

ECs4579

SpLE4 (LEE)

Absent

Rorf3

-

-

-

-

[8]

1

4

2

ECs4580

SpLE4 (LEE)

Absent

EscU

-

-

-

-

[8]

(7)

(5)

4

ECs4581

SpLE4 (LEE)

Absent

EscT

-

-

-

-

[8]

(7)

4

3

ECs4582

SpLE4 (LEE)

Absent

EscS

-

-

-

-

[8]

[8]

(5)

(5)

ECs4583

SpLE4 (LEE)

Absent

EscR

-

-

-

-

[8]

[8]

4

(5)

ECs4584

SpLE4 (LEE)

Absent

Orf5

-

-

-

-

[8]

[8]

[6]

(5)

ECs4585

SpLE4 (LEE)

Absent

Orf4

-

-

-

-

[8]

[8]

4

(5)

ECs4586

SpLE4 (LEE)

Absent

Orf3

-

-

-

-

[8]

6

[6]

(5)

ECs4587

SpLE4 (LEE)

Absent

Orf2

-

-

-

-

[8]

3

1

2

T3SS effectors (LEE encoded)

ECs4550

SpLE4 (LEE)

Absent

EspF1

-

-

-

-

[8]

0

0

0

ECs4554

SpLE4 (LEE)

Absent

EspB

-

-

-

-

[8]

0

0

0

ECs4561

SpLE4 (LEE)

Absent

Tir

-

-

-

-

[8]

0

0

0

ECs4562

SpLE4 (LEE)

Absent

Map

-

-

-

-

[8]

0

0

2

ECs4564

SpLE4 (LEE)

Absent

EspH

-

-

-

-

[8]

[8]

0

[6]

ECs4571

SpLE4 (LEE)

Absent

SepZ

-

-

-

-

[8]

0

0

0

ECs4590

SpLE4 (LEE)

Absent

EspG

-

-

-

-

[8]

1

3

2

T3SS effectors (non-LEE encoded)

ECs0061

Backbone

Conserved

EspY1

-

-

-

-

[8]

0

0

0

ECs0847

Sp3

Absent

NleC

-

-

-

-

[8]

(7)

1

1

ECs0848

Sp3

Absent

NleH1-1

-

-

-

-

[8]

1

0

3

ECs0850

Sp3

Absent

NleD

-

-

-

-

[8]

0

0

4

ECs0876

S-loop57

Absent

EspX2

-

-

-

-

[8]

0

0

0

ECs1127

Sp4

Absent

EspK

-

-

-

-

[8]

[8]

[6]

[6]

ECs1560

Sp6

Absent

EspX7

-

-

-

-

[8]

(7)

[6]

[6]

ECs1561

Sp6

Absent

EspN

-

-

-

-

[8]

(7)

(5)

[6]

ECs1567

Sp6

Absent

EspO1-1

-

-

-

-

[8]

0

[6]

1

ECs1568

Sp6

Absent

EspR1

-

-

-

-

[8]

[8]

[6]

[6]

ECs1810

Sp9

Absent

NleG2-1

-

-

-

-

(7)

(7)

[6]

1

ECs1811

Sp9

Absent

NleG2-1

-

-

-

-

(7)

(7)

0

2

ECs1812

Sp9

Absent

NleA/EspI

-

-

-

-

(7)

(7)

0

1

ECs1814

Sp9

Absent

NleH1-2

-

-

-

-

4

6

[6]

[6]

ECs1815

Sp9

Absent

NleF

-

-

-

-

4

6

[6]

[6]

ECs1824

Sp9

Absent

NleG

-

-

-

-

[8]

(7)

[6]

0

ECs1825

Sp9

Absent

EspM1

-

-

-

-

[8]

(7)

[6]

0

ECs2226

Sp12

Absent

NleG7

-

-

-

-

[8]

[8]

[6]

[6]

ECs2714

Sp14

Absent

EspJ

-

-

-

-

[8]

0

0

1

ECs3485

Sp17

Absent

EspM2

-

-

-

-

[8]

(7)

[6]

2

ECs3486

Sp17

Absent

NleG8-2

-

-

-

-

[8]

(7)

[6]

3

ECs3487

Sp17

Absent

EspW

-

-

-

-

[8]

(7)

[6]

3

ECs3855

SpLE3

Absent

EspL2

-

-

-

-

[8]

[8]

[6]

[6]

ECs3857

SpLE3

Absent

NleB1

-

-

-

-

[8]

[8]

[6]

[6]

ECs3858

SpLE3

Absent

NleE

-

-

-

-

[8]

[8]

[6]

[6]

ECs4653

S-loop252

Absent

EspY4

-

-

-

-

[8]

0

0

0

RF004

Sp4, 14

Absent

Tccp, TccP2

-

-

-

-

[8]

1

2

4

RF067

Sp10, 11

Absent

NleG2-2, NleG2-3

-

-

-

-

[8]

[8]

[6]

4

RF069

Sp10, 11, 17

Absent

NleG6-1, NleG6-2, NleG6-3

-

-

-

-

[8]

(7)

[6]

3

RF070

Sp10, 11

Absent

NleG5-1, NleG5-2

-

-

-

-

[8]

(7)

(5)

1

Plasmid encoded

pO157_01

pO157

Absent

Metalloprotease StcE

-

-

-

-

[8]

0

0

0

pO157_02

pO157

Absent

Type II secretion pathway related protein

-

-

-

-

[8]

1

0

3

pO157_03

pO157

Absent

Type II secretion pathway related protein

-

-

-

-

[8]

1

0

3

pO157_04

pO157

Absent

Type II secretion pathway related protein

-

-

-

-

[8]

1

0

3

pO157_05

pO157

Absent

Type II secretion pathway related protein

-

-

-

-

[8]

0

0

2

pO157_06

pO157

Absent

Type II secretion pathway related protein

-

-

-

-

[8]

2

0

3

pO157_07

pO157

Absent

Type II secretion pathway related protein

-

-

-

-

[8]

1

0

3

pO157_08

pO157

Absent

Type II secretion pathway related protein

-

-

-

-

[8]

0

0

3

pO157_09

pO157

Absent

Type II secretion pathway related protein

-

-

-

-

[8]

1

0

3

pO157_10

pO157

Absent

Type II secretion pathway related protein

-

-

-

-

[8]

0

0

1

pO157_11

pO157

Absent

Type II secretion pathway related protein

-

-

-

-

[8]

1

0

3

pO157_12

pO157

Absent

Type II secretion pathway related protein

-

-

-

-

[8]

1

0

3

pO157_13

pO157

Absent

Type II secretion pathway related protein

-

-

-

-

[8]

0

0

1

pO157_14

pO157

Absent

Type II secretion pathway related protein

-

-

+

+

[8]

0

0

1

pO157_17

pO157

Absent

Hemolysin C

-

-

-

-

[8]

[8]

(5)

3

pO157_18

pO157

Absent

Hemolysin A

-

-

-

-

[8]

(7)

(5)

4

pO157_19

pO157

Absent

Hemolysin B

-

-

-

-

[8]

(7)

(5)

4

pO157_20

pO157

Absent

Hemolysin D

-

-

-

-

[8]

(7)

(5)

4

pO157_39

pO157

Absent

Hemagglutinin-associated protein

-

+

-

-

[8]

5

0

1

pO157_59

pO157

Absent

Putative adherence factor, Efa1 homolog

-

-

-

-

[8]

3

0

(5)

pO157_76

pO157

Absent

KatP

-

-

-

-

6

6

(5)

2

pO157_79

pO157

Absent

EspP

-

-

-

-

[8]

(7)

[6]

4

pO157_80

pO157

Absent

Putative polysaccharide deacetylase (ecf1)

-

-

-

-

[8]

(7)

(5)

4

pO157_81

pO157

Absent

Putative LPS-1,7-N-acetylglucosamine transferase (ecf2)

-

-

-

-

[8]

(7)

(5)

4

pO157_82

pO157

Absent

Putative membrane protein (ecf3)

-

-

-

-

[8]

(7)

(5)

4

pO157_83

pO157

Absent

Putative lipid A myristoyl transferase, MsbB2 (ecf4)

-

-

-

-

[8]

(7)

(5)

4


*Conservation of O157 Sakai virulence genes in four sequenced pathogenic E. coli strains was determined according to the results of homology search using the BLASTP program. The threshold for presence (+) or absence (-) determination was ≥90% sequence identity and ≥50% aligned length coverage of a query sequence. Genes conserved in all strains are indicated by brackets in bold, and those absent only in one strain by parentheses in bold.

Ogura et al. Genome Biology 2007 8:R138   doi:10.1186/gb-2007-8-7-r138

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