Table 1

List of novel genes found in the genome of R.pomeroyi detected by proteogenomics.

Target a

Plausible CDS start

Stop

Length (aa)

Peptides assigned

CDS Proteomic coverage

Function/Presence in other Roseobacter stains b


Non-annotated CDS

SPOA_PG001

300016

300507

164

10

73%

Unknown/observed (9e-51)

SPO_PG002

3171305

3170874

144

9

69%

Unknown/unique

SPO_PG003

1412876

1413418

181

7

73%

Unknown/observed (5e-23)

SPOA_PG004

87032

87709

226

6

27%

Unknown/unique

SPO_PG005

358784

358125

220

6

45%

Esterase-lipase/observed (5e-45)

SPO_PG006

360911

360405

169

5

54%

Unknown/unique

SPO_PG007

1483195

1482533

221

5

48%

Unknown/unique

SPO_PG008

1431167

1431595

143

5

45%

Unknown/observed (3e-56)

SPO_PG009

501740

502171

144

5

42%

Unknown/unique

SPO_PG010

2353576

2353965

130

4

42%

Unknown/observed (1e-38)

SPO_PG011

1374589

1374299

97

3

61%

Unknown/conserved (1e-43)

SPO_PG012

3703461

3702955

169

3

22%

Unknown/unique

SPO_PG013

649156

649749

198

3

23%

Unknown/unique

SPO_PG014

2482691

2482317

125

3

20%

Unknown/unique

SPO_PG015

3657397

3656924

158

3

19%

Unknown/observed (6e-50)

SPO_PG016

373055

373333

93

2

41%

Unknown/unique

SPO_PG017

1092236

1092592

119

2

34%

Unknown/unique

SPO_PG018

495167

495529

121

2

22%

Unknown/observed (4e-44)

SPO_PG019

1418666

1419187

174

2

10%

Signal transduction/conserved (1e-69)

SPO_PG020

2807747

2807223

175

2

19%

Polyketide cyclase/unique

SPO_PG021

1289473

1289829

119

2

28%

Unknown/unique

SPO_PG022

1151078

1151632

185

2

18%

Unknown/unique

SPO_PG023

1400166

1399696

157

2

24%

Unknown/unique

SPO_PG024

2628409

2629668

420

2

9%

RNA helicase/conserved (1e-175)

SPO_PG025

1322016

1322357

114

1

7%

Transcriptional regulator/unique

SPO_PG026

3883013

3882531

161

1

7%

Unknown/unique


Wrong CDS

SPO_PG027

501090

501710

207

21

77%

Unknown/unique

SPO_PG028

2429044

2427941

368

20

63%

Unknown/conserved (5e-92)

SPO_PG029

3124885

3123728

386

11

36%

Sporulation related/conserved (6e-92)

SPO_PG030

1738173

1736680

498

7

24%

Unknown/conserved (1e-175)

SPO_PG031

2905673

2906335

221

6

37%

Unknown/unique

SPO_PG032

3751605

3751147

153

6

42%

Unknown/conserved (5e-42)

SPO_PG033

2357076

2357507

144

2

18%

Excinuclease/observed (4e-35)

SPO_PG034

934724

935068

115

1

17%

Unknown/Observed (1e-27)

SPO_PG035

2751483

2750281

401

1

4%

Unknown/Conserved (1e-162)


Seq. error

SPO_PG036

562052

560282

590

3

9%

ABC transporter/conserved (0.0)

SPO_PG037

3188876

3188459

139

3

27%

Heat shock protein/observed (3e-55)

SPO_PG038

2152217

2151179

346

2

10%

Aminotransferase/conserved (1e-168)

SPO_PG039

3515528

3515111

139

1

17%

Stress protein/unique (conserved in Bacillus)


a Targets in bold represent those "one-hit-wonders" validated by RT-PCR.

b Observed indicates presence of a similar gene in less than 5 other Roseobacter strains whereas Conserved means presence in over 20 of the 36 strains searched. E-value for BLAST analysis with its nearest homologue is indicated in brackets.

Christie-Oleza et al. BMC Genomics 2012 13:73   doi:10.1186/1471-2164-13-73

Open Data