Table 2

Presence, cellular localization and level of conservation of a selection of genes that are either surface exposed, or known to be involved in interaction with the host and virulence

TIGR ID

R6 Id

INV104B

Length

Annotation

Predicted cell localization

Presence in Spn strains

Conservation (average % ID)

Present in S. mitisa

Present in S. oralis

Present in S. infantis


Frameshiftedb

spr1536

1,035

Neuraminidase A (NanA)

LPXTG cell-wall anchored

44

92.59

Yes

Yes

Yes

SP_0057

spr0057

1,312

Beta-N-acetylhexosaminidase (StrH)

LPXTG cell-wall anchored

44

97.59

No

Yes

Yes

SP_0069

Absent

211

Choline binding protein I (CbpI)

Choline binding, surface

6

85.73

Yes

No

No

SP_0071

Absent

1,856

Zinc metalloprotease ZmpC

LPXTG cell-wall anchored

6

89.79

Yes

No

No

SP_0082

spr0075

857

Cell wall surface anchor family protein

LPXTG cell-wall anchored

44

91.92

Yes

Yes

Yes

SP_0117

spr0097

744

Pneumococcal surface protein A (PspA)

Choline binding, surface

44

81.35

No

No

No

SP_0268

spr0247

1,280

Alkaline amylopullulanase, putative

LPXTG cell-wall anchored

44

97.53

Yes

Yes

No

SP_0314

spr0286

1,066

Hyaluronidase (HysA)

LPXTG cell-wall anchored

44

99.38

No

No

No

SP_0368

spr0328

1,767

Cell wall surface anchor family protein

LPXTG cell-wall anchored

44

96.96

No

Yes

Yes

SP_0377

spr0337

340

Choline binding protein C (CbpC)

Choline binding, surface

31

93.86

Yes

Yes

No

SP_0378

Absent

332

Choline binding protein J (CbpJ)

Choline binding, surface

36

88.97

Yes

Yes

Yes

SP_0390

spr0349

285

Choline binding protein G (CbpG)

Choline binding, surface

44

95.21

No

No

No

SP_0391

spr0350

340

Choline binding protein F (CbpF)

Choline binding, surface

16

90.33

Yes

Yes

Yes

SP_0462

Absent

893

RrgA pilus subunit, adhesin

LPXTG cell-wall anchored

8

91.66

No

No

No

SP_0463

Absent

665

RrgB pilus subunit, backbone

LPXTG cell-wall anchored

8

66.5

No

No

No

SP_0464

Absent

393

RrgC pilus subunit

LPXTG cell-wall anchored

8

99.09

No

No

No

SP_0498

spr0440

1,659

Endo-beta-N-acetylglucosaminidase, putative

LPXTG cell-wall anchored

44

97.02

Yes

Yes

Yes

SP_0641

spr0561

2,140

Serine protease, subtilase family

LPXTG cell-wall anchored

44

96.54

Yes

Yes

No

SP_0648

spr0565

2,233

Beta-galactosidase (BgaA)

LPXTG cell-wall anchored

44

96.54

Yes

Yes

No

SP_0664

spr0581

1,881

Zinc metalloprotease, putative (ZmpB)

LPXTG cell-wall anchored

43

71.13

Yes

No

Yes

SP_0667

spr0583

332

Pneumococcal surface protein, putative

Choline binding, surface

44

90

Yes

No

Yes

SP_0930

spr0831

627

Choline binding protein E (CbpE)

Choline binding, surface

44

96.64

Yes

No

No

SP_0965

spr0867

658

Endo-beta-N-acetylglucosaminidase (LytB)

Choline binding, surface

44

98.42

Yes

No

No

SP_0981

spr0884

313

Putative protease maturation protein (PpmA)

Lipoprotein

44

96.77

Yes

Yes

Yes

SP_1003

spr0907

839

Histidine triad protein

Lipoprotein

39

91.34

Yes

Yes

Yes

SP_1004

spr0908

1,039

Histidine triad protein

Lipoprotein

44

99.67

Yes

Yes

Yes

SP_1154

spr1042

2,004

Immunoglobulin A1 protease

LPXTG cell-wall anchored

44

79.85

Yes

Yes

No

SP_1174

Absent

819

Histidine triad protein

Lipoprotein

16

95.39

Yes

Yes

Yes

SP_1175

spr1061

802

Histidine triad protein

Lipoprotein

33

92.95

Yes

Yes

Yes

SP_1326

Absent

740

Putative neuraminidase (NanC)

Outer membrane/secreted

16

94.21

No

No

No

SP_1492

spr1345

202

Cell wall surface anchor family protein

LPXTG cell-wall anchored

44

91

Yes

Yes

Yes

SP_1572

spr1430

178

Non-heme iron-containing ferritin (PppA)

Surface

44

94.5

Yes

Yes

Yes

SP_1573

spr1431

490

Lysozyme (LytC)

Choline binding, surface

44

96.46

Yes

No

No

SP_1650

spr1494

309

Manganese ABC transporter, manganese-binding adhesion liprotein (PsaA)

Lipoprotein

44

97.92

Yes

Yes

Yes

SP_1687

spr1531

697

Neuraminidase B (NanB)

Surface

43

93.85

Yes

No

No

SP_1732

spr1577

Serine threonine kinase protein (StkP)

Membrane

44

95.33

Yes

Yes

Yes

SP_1772

Absent

4,776

Cell wall surface anchor family protein (PsrP)

LPXTG cell-wall anchored

14

99.7

No

No

No

SP_1833

spr1652

708

Cell wall surface anchor family protein

LPXTG cell-wall anchored

44

97.63

Yes

No

Yes

SP_1923

spr1739

471

Pneumolysin (Ply)

Secreted

44

99.5

Yes

No

No

SP_1937

spr1754

318

Autolysin (LytA)

Choline binding, surface

44

98.74

Yes

No

No

SP_1992

spr1806

221

Cell wall surface anchor family protein

LPXTG cell-wall anchored

44

99.01

No

No

No

SP_2136

spr1945

621

Choline binding protein PcpA (PcpA)

Choline binding, surface

32

99.05

Yes

No

No

SP_2190c

spr1995

693

Choline binding protein A (CbpA) (PspC)

Choline binding, surface

44

Yes

No

No

SP_2201

Absent

448

Choline binding protein D (CbpD)

Choline binding, surface

43

98.94

Yes

No

No

SP_2216

spr2021

392

Secreted 45 kDa protein (PcsB)

Secreted

44

96.75

Yes

Yes

Yes

Absent

Absent

SPNINV104_08710

410

PitB pilus 2 subunit, backbone

LPXTG cell-wall anchored

8

100

No

Yes

No

Absent

Absent

SPNINV104_08690

589

PitA pilus 2 subunit, ancillary

LPXTG cell-wall anchored

8

100

No

Yes

No


Due to the presence of unfinished genomes, we considered genes present in 43 S. pneumoniae genomes to be core. a'Yes' indicates genes that are present in at least one of the strains of S. mitis, while 'no' indicates genes that are absent in the four analyzed strains. bNanA is annotated as frameshifted in the TIGR4 strain, but it is known to be expressed by all pneumococcal strains. cPspC has been classified in 11 major variants that cannot be aligned due to different gene organization.

Donati et al. Genome Biology 2010 11:R107   doi:10.1186/gb-2010-11-10-r107

Open Data