Table 4

Distribution of VAP ORFs identified in the microarray study

Location

ORF

Function

Lineage I-LSPA 111111

PT2-LSPA 211111

Lineage II-LSPA 222222


n = 15

n = 4

n = 12

S-loop#14/OI#7

ECs0237 (Z0268)

RhsG core protein with extension

100%

100%

0%

S-loop#14/OI#7

ECs0238 (Z0269)

hypothetical protein

100%

100%

0%

S-loop#14

ECs0239

hypothetical protein

100%

100%

0%

S-loop#16

ECs0272

putative transcription antitermination protein

100%

100%

0%

S-loop#16/OI#8

ECs0273 (Z0308)

hypothetical protein

100%

100%

0%

S-loop#16/OI#8

ECs0274 (Z0309)

repressor protein CI

100%

100%

0%

S-loop#16

ECs0275

Cro repressor

100%

100%

0%

S-loop#16/OI#8

ECs0276 (Z0310)

regulatory protein cII

100%

100%

0%

S-loop#16/OI#8

ECs0277 (Z0311)

replication protein

100%

100%

0%

S-loop#16/OI#8

ECs0279 (Z0313)

replication protein

100%

100%

0%

S-loop#16/OI#8

ECs0280 (Z0317)

putative tail fiber protein

100%

100%

0%

S-loop#69/OI#45

ECs1160 (Z1424)1

putative integrase

93%

0%

0%

S-loop#69/OI#45

ECs1161 (Z1425)1

putative excisionase

93%

0%

0%

S-loop#69/OI#45

ECs1162 (Z1426)1

hypothetical protein

93%

0%

0%

S-loop#69/OI#45

ECs1163 (Z1428)1

hypothetical protein

93%

0%

0%

S-loop#69/OI#45

ECs1219 (Z1475)2

putative small subunit terminase

93%

100%

8%

S-loop#69/OI#45

ECs1220 (Z1476)2

putative terminase large subunit

93%

100%

8%

S-loop#69/OI#45

ECs1221 (Z1477)2

putative portal protein

93%

100%

8%

S-loop#69/OI#45

ECs1222 (Z1478)2

hypothetical protein

93%

100%

8%

S-loop#69/OI#45

ECs1223 (Z1479)2

hypothetical protein

93%

100%

8%

S-loop#69/OI#45

ECs1224 (Z1480)2

hypothetical protein

93%

100%

8%

S-loop#69/OI#45

ECs1225 (Z1481)2

hypothetical protein

93%

100%

8%

S-loop#69

ECs1226 2

hypothetical protein

93%

100%

8%

S-loop#69/OI#45

ECs1227 (Z1482)2

hypothetical protein

93%

100%

8%

S-loop#69/OI#45

ECs1228 (Z1483)2

putative tail fiber protein

93%

100%

8%

S-loop#69/OI#45

ECs1232 (Z1486)2

hypothetical protein

93%

100%

8%

S-loop#69/OI#45

ECs1233 (Z1487)2

putative tail tip fiber protein

93%

100%

8%

S-loop#69

ECs1234 2

putative outer membrane protein

93%

100%

8%

S-loop#69/OI#45

ECs1235 (Z1488)2

hypothetical protein

93%

100%

8%

S-loop#69/OI#45

ECs1236 (Z1489)2

putative outer membrane precursor

93%

100%

8%

S-loop#69/OI#45

ECs1237 (Z1490)2

hypothetical protein

93%

100%

8%

S-loop#69/OI#45

ECs1238 (Z1491)2

hypothetical protein

93%

100%

8%

S-loop#69/OI#45

ECs1239 (Z1492)2

hypothetical protein

93%

100%

8%

S-loop#69/OI#45

ECs1240 (Z1493)2

hypothetical protein

93%

100%

8%

S-loop#69/OI#45

ECs1241 (Z1494)2

hypothetical protein

93%

100%

8%

S-loop#69/OI#45

ECs1242 (Z1495)2

hypothetical protein

93%

100%

8%

S-loop#72/OI#43,48

ECs1377 (Z1635)

hypothetical protein

100%

100%

0%

S-loop#72/OI#43,48

ECs1378 (Z1636)

hypothetical protein

100%

100%

0%

S-loop#72/OI#43,48

ECs1379 (Z1637)

hypothetical protein

100%

100%

0%

S-loop#72/OI#43,48

ECs1382 (Z1640)

HecB-like protein

100%

100%

0%

S-loop#72/OI#43,48

ECs1383 (Z1641)

hypothetical protein

100%

100%

0%

S-loop#72/OI#43,48

ECs1384 (Z1642)

hypothetical protein

100%

100%

0%

S-loop#72/OI#43,48

ECs1385

hypothetical protein

100%

100%

0%

S-loop#72/OI#43,48

ECs1386 (Z1643)

hypothetical protein

100%

100%

0%

S-loop#72/OI#43,48

ECs1387 (Z1644)

hypothetical protein

100%

100%

0%

S-loop#72/OI#43,48

ECs1388

putative transcriptional regulator, pchD

100%

100%

0%

S-loop#72/OI#43,48

ECs1389 (Z1645)

hypothetical protein

100%

100%

0%

S-loop#72/OI#43,48

ECs1390 (Z1646)

hypothetical protein

100%

100%

0%

S-loop#78/OI#51

ECs1574 (Z1836)

putative integrase

100%

0%

0%

S-loop#78

ECs1576 (Z1839)

hypothetical protein

100%

0%

0%

S-loop#78/OI#51

ECs1578 (Z1840)

hypothetical protein

100%

0%

0%

S-loop#78

ECs1579

hypothetical protein

100%

0%

0%

S-loop#78/OI#51

ECs1580 (Z1841)

hypothetical protein

100%

0%

0%

S-loop#78

ECs1581

hypothetical protein

100%

0%

0%

S-loop#78/OI#51

ECs1582 (Z1842)

hypothetical protein

100%

0%

0%

S-loop#78

ECs1583

hypothetical protein

100%

0%

0%

S-loop#78/OI#51

ECs1584 (Z1843)

hypothetical protein

100%

0%

0%

S-loop#78

ECs1585

hypothetical protein

100%

0%

0%

S-loop#78/OI#51

ECs1590 (Z1847)

putative major head protein

100%

0%

0%

S-loop#78/OI#51

ECs1591 (Z1848)

putative prohead protease

100%

0%

0%

S-loop#78/OI#51

ECs1592 (Z1849)

putative head portal protein

100%

0%

0%

S-loop#78/OI#51

ECs1593 (Z1850)

putative head-tail adaptor

100%

0%

0%

S-loop#78/OI#51

ECs1594 (Z1851)

hypothetical protein

100%

0%

0%

S-loop#78/OI#51

ECs1595 (Z1852)

hypothetical protein

100%

0%

0%

S-loop#78

ECs1596

hypothetical protein

100%

0%

0%

S-loop#78/OI#51

ECs1597 (Z1853)

putative terminase small subunit

100%

0%

0%

S-loop#78/OI#51

ECs1598 (Z1854)

putative terminase large subunit

100%

0%

0%

S-loop#78/OI#51

ECs1599 (Z1856)

hypothetical protein

100%

0%

0%

S-loop#78/OI#51

ECs1600 (Z1857)

hypothetical protein

100%

0%

0%

S-loop#83/OI#55 upstream region

ECs1691 (Z1959)

orf, hypothetical protein; ycgR

100%

100%

0%

S-loop#83/OI#55 upstream region

ECs1692 (Z1960)

orf, hypothetical protein; ymgE

100%

100%

0%

S-loop#83/OI#55

ECs1693 (Z1961)

putative TonB dependent outer membrane receptor

100%

100%

0%

S-loop#83/OI#55

ECs1694 (Z1962)

molybdenum transport protein

100%

100%

0%

S-loop#83

ECs1695

hypothetical protein

100%

100%

0%

S-loop#83/OI#55

ECs1696 (Z1963)

hypothetical protein

100%

100%

0%

S-loop#83/OI#55

ECs1697 (Z1964)

putative ferric enterobactin transport ATP-binding protein

100%

100%

0%

S-loop#83/OI#55

ECs1698 (Z1965)

putative ABC transporter permease protein

100%

100%

0%

S-loop#83/OI#55

ECs1699 (Z1966)

putative ATP-binding protein of ABC transporter

100%

100%

0%

S-loop#83/OI#55

ECs1700 (Z1967)

hypothetical protein

100%

100%

0%

S-loop#83

ECs1701 (Z1968)

trehalase, periplasmic; treA

100%

100%

0%

S-loop#83 downstream region

ECs1702

trehalase, periplasmic; treA

100%

100%

0%

S-loop#83/OI#55 downstream region

ECs1703 (Z1969)

putative PTS system enzyme I; ycgC

100%

100%

0%

S-loop#83/OI#55 downstream region

ECs1704 (Z1970)

putative dihydroxyacetone kinase (EC 2.7.1.2); b1199

100%

100%

0%

S-loop#83/OI#55 downstream region

ECs1705 (Z1971)

putative dihydroxyacetone kinase (EC 2.7.1.2); b1200

100%

100%

0%

S-loop#85/OI#71

ECs1815 (Z6020)

NleF

100%

100%

0%

S-loop#85/OI#71

ECs1814 (Z6021)

NleH1-2 homolog of Shigella OspG

100%

100%

0%

Sp10

ECs1929 (Z2415)

putative integrase; b1345

100%

0%

0%

Sp10

ECs1930 (Z2414)3

hypothetical protein; ydaQ

100%

0%

8%

Sp10

ECs1931 (Z2413)3

hypothetical protein; ydaC

100%

0%

8%

Sp10

ECs1932 (Z2412)

restriction alleviation and modification enhancement; lar

100%

0%

0%

Sp10

ECs1937 (Z2404)

phage superinfection exclusion protein; sieB

100%

0%

0%

Sp10

ECs19384

hypothetical protein

87%

0%

0%

Sp10

ECs1939 (Z2403)

hypothetical protein, ydfA

100%

0%

0%

S-loop#91 (in Sp10)

ECs1941 (Z2400)

putative transcriptional regulator

100%

0%

0%

S-loop#91 (in Sp10)

ECs1942 (Z2399)

regulatory protein

100%

0%

0%

S-loop#92 (in Sp10)

ECs1944 (Z2397)

hypothetical protein

100%

0%

0%

S-loop#92 (in Sp10)

ECs1947 (Z2395)

hypothetical protein

100%

0%

0%

S-loop#93 (in Sp10)

ECs1950 (Z2392)

hypothetical protein

100%

0%

0%

S-loop#93 (in Sp10)

ECs1951 (Z2391)

hypothetical protein

100%

0%

0%

S-loop#93 (in Sp10)

ECs1952 (Z2390)

hypothetical protein

100%

0%

0%

S-loop#93 (in Sp10)

ECs1953 (Z2389)

putative methyltransferase

100%

0%

0%

S-loop#93 (in Sp10)

ECs1954 (Z2387)

hypothetical protein

100%

0%

0%

S-loop#93 (in Sp10)

ECs1955 (Z2386)

hypothetical protein

100%

0%

0%

S-loop#153

ECs29893

putative regulatory protein

93%

0%

0%

S-loop#153/OI#93

ECs2990 (Z3358)5

putative prophage repressor CI

93%

0%

0%

S-loop#153/OI#93

ECs2991 (Z3359)5

hypothetical protein

93%

0%

0%

S-loop#153/OI#93

ECs2992 (Z3360)5

putative membrane protein

93%

0%

0%

S-loop#153/OI#93

ECs2993 (Z3361)5

putative regulatory protein

93%

0%

0%

S-loop#153

ECs29943

hypothetical protein

93%

0%

0%

S-loop#153/OI#93

ECs2995 (Z3362)5

putative superinfection exclusion protein

93%

0%

0%

S-loop#286/OI#172

ECs5242 (Z5878)

putative integrase

80%

100%

0%

S-loop#286/OI#172

ECs5245 (Z5881)

orf; Unknown function

80%

100%

0%

S-loop#286/OI#172

ECs5246 (Z5882)

hypothetical protein

80%

100%

0%

S-loop#286

ECs5247

hypothetical protein

80%

100%

0%

S-loop#286/OI#172

ECs5248 (Z5884)

hypothetical protein

80%

100%

0%

S-loop#286/OI#172

ECs5249 (Z5885)

putative resolvase

80%

100%

0%

S-loop#286/OI#172

ECs5250 (Z5886)

hypothetical protein

80%

100%

0%

S-loop#286/OI#172

ECs5251 (Z5887)

hypothetical protein

80%

100%

0%

S-loop#286/OI#172

ECs5252 (Z5888)

putative transcription regulator

80%

100%

0%

OI#172

Z5889

orf; Unknown function

80%

100%

0%

KI#71

b1142

orf, hypothetical protein; ymfH

0%

0%

100%

KI#71

b1147

orf, hypothetical protein; ymfL

0%

0%

100%

KI#71

b1148

orf, hypothetical protein; ymfM

0%

0%

100%

KI#71

b1152

orf, hypothetical protein; b1152

0%

0%

100%

KI#121

b2360

orf, hypothetical protein; b2360

0%

100%

100%

KI#121

b2361

orf, hypothetical protein; b2360

0%

100%

100%

KI#121

b2362

orf, hypothetical protein; b2362

0%

0%

100%

KI#121

b2363

orf, hypothetical protein; b2363

0%

0%

100%

backbone

b1201

putative sensor-type regulator; b1201

0%

100%

100%

backbone

b1202

putative adhesion and penetration protein; b1202

0%

100%

100%

backbone

ECs2126 (b1519)

putative enzyme

100%

100%

0%

backbone

ECs2127 (b1520)

orf, hypothetical protein

100%

100%

0%


1Divergent in lineage II strains and the lineage I strain 97701.

2 Divergent in lineage I strain 97701 and 11/12 lineage II strains

3 ECS1930-ECS1931 were divergent in 11/12 lineage II and 4 lineage I/II strains. They were present in the lineage I strains and one lineage II strain.

4ECs1938 was divergent in lineage II strains, however, it was absent in lineage I strains 63154 and E2328.

5Divergent in Lineage II strains and the lineage I strain LRH6.

Zhang et al. BMC Genomics 2007 8:121   doi:10.1186/1471-2164-8-121

Open Data