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Table 1 S. gordonii intracellular proteins and phosphoproteins, separated by 2DE and identified with LC-MS/MS

From: Intracellular Ser/Thr/Tyr phosphoproteome of the oral commensal Streptococcus gordonii DL1

Abbr

Protein

Geneb)

Acc. No.c)

pI

estimated from gel/theoreticald)

MW, Da

estimated from gel/ theoreticald)

LC-MS/MS

Ser/Thr/Tyr

phosphory-lated

+/−

MASCOT

score

No. of peptidese)

Coverage

Transmembrane transport

ABCa)

ABC transporter ATP-binding protein SP1715

SGO_1342

A8AXW3

6.7/6.25

23,000/26325

1124

18

72%

Sugar transport

HPra)

Phosphocarrier protein HPr

ptsH (SGO_1556)

A8AYH5

5.1/4.74

11,000/8935

124

2

55%

+

Glycolysis

Tpi-1a)

Triosephosphate isomerase

tpiA (SGO_0762)

A8AWA1

4.5/4.75

23,000/26524

652

9

52%

+

Tpi-2a)

   

4.3/4.75

23,000/26524

540

9

52%

-

pfk-1a)

Phosphofructokinase

pfkA (SGO_1340)

A8AXW1

6.6/5.62

35,000/35346

1043

17

49%

+

pfk-2

   

6.8/5.62

35,000/35346

1476

22

56%

+

fba-1f)

Fructose-1,6-bisphosphate aldolase, class II

Fba (SGO_1745)

A8AZ06

5.1/5.00

27,000/31394

-

-

-

-

fba-2a)

   

5.2/5.00

27,000/31394

771

12

51%

-

fba-3a)

   

5.3/5.00

27,000/31394

800

14

47%

-

fba-4f)

   

5.4/5.00

27,000/31394

-

-

-

-

fba-5a)

   

5.4/5.00

17,000/31394

164

3

11%

-

gapdh-1a)

Glyceraldehyde-3-phosphate dehydrogenase

gap (SGO_0207)

A8AUR7

5.5/5.37

39,000/35918

1153

20

51%

+

gapdh-2a)

   

5.7/5.37

39,000/35918

1299

21

79%

+

gapdh-3a)

   

5.9/5.37

39,000/35918

1304

22

58%

+

gapdh-4

   

5.5/5.37

40,000/35918

89

2

8%

-

gapdh-5

   

5.7/5.37

40,000/35918

276

4

14%

-

gapdh-6

   

6.0/5.37

39,000/35918

84

2

6%

-

gapdh-7

   

5.9/5.37

40,000/35918

325

5

16%

-

gapdh-8

   

5.2/5.37

18,000/35918

141

2

8%

-

pgk-1

Phosphoglycerate kinase

pgk (SGO_0209)

A8AUR9

4.9/4.88

45,000/42089

397

6

18%

+

pgk -2a)

   

5.0/4.88

45,000/42089

1454

23

63%

+

pgk -3a)

   

4.3/4.88

21,000/42089

340

5

17%

+

pgk -4f)

   

5.1/4.88

45,000/42089

-

-

-

-

pgk -5f)

   

5.2/4.88

45,000/42089

-

-

-

-

pgk −6

   

4.3/4.88

45,000/42089

159

3

9%

-

pgk -7a)

   

5.9/4.88

24,000/42089

431

7

18%

-

pgk -8a)

   

4.2/4.88

20,000/42089

830

11

41%

-

pgk -9a)

   

5.9/4.88

20,000/42089

561

9

28%

-

pgm-1a)

Phosphoglycerate mutase

gpma (SGO_0704)

A8AW46

5.9/5.41

22,000/26044

904

18

84%

+

pgm-2a)

   

6.1/5.41

22,000/26044

933

18

87%

+

eno-1

Enolase

eno (SGO_1426)

A8AY46

4.4/4.71

48,000/47062

1368

18

61%

+

eno −2

   

4.5/4.71

48,000/47062

1260

13

52%

+

eno −3

   

4.6/4.71

48,000/47062

1721

18

63%

+

eno -4a)

   

4.7/4.71

48,000/47062

2245

31

77%

+

eno −5

   

4.6/4.71

26,000/47062

1316

17

58%

+

eno -6a)

   

4.5/4.71

24,000/47062

460

8

26%

+

eno -7a)

   

4.1/4.71

22,000/47062

809

9

30%

+

eno -8a)

   

4.2/4.71

21,000/47062

673

9

28%

+

eno -9a)

   

4.3/4.71

21,000/47062

595

10

32%

+

eno -10a)

   

4.4/4.71

21,000/47062

989

11

34%

+

eno -11a)

   

4.4/4.71

28,000/47062

1485

15

55%

-

eno -12a)

   

4.8/4.71

25,000/47062

950

14

47%

-

eno -13a)

   

4.4/4.71

23,000/47062

460

8

26%

-

eno -14a)

   

4.2/4.71

23,000/47062

746

11

36%

-

eno -15a)

   

4.8/4.71

23,000/47062

627

9

32%

-

eno -16a)

   

4.8/4.71

22,000/47062

631

9

31%

-

eno -17a)

   

4.9/4.71

22,000/47062

636

9

31%

-

eno -18a)

   

4.4/4.71

17,000/47062

230

4

11%

-

eno −19

   

4.5/4.71

14,500/47062

931

9

41%

-

eno − 20

   

4.6/4.71

14,000/47062

533

7

23%

-

eno -21a)

   

5.0/4.71

13,000/47062

437

7

23%

-

eno -22a)

   

4.7/4.71

12,500/47062

722

9

33%

-

eno -23a)

   

4.3/4.71

11,000/47062

418

6

20%

-

eno -24a)

   

5.4/4.71

18,000/47062

684

9

27%

-

pyk-1a)

Pyruvate kinase

pyk (SGO_1339)

A8AXW0

5.15/4.94

58,000/54799

150

3

6%

+

pyk-2a)

   

5.2/4.94

58,000/54799

1474

29

62%

+

pyk-3f)

   

5.1/4.94

58,000/54799

-

-

-

-

pyk-4f)

   

5.3/4.94

58,000/54799

-

-

-

-

Cofactor biosynthesis

nadea)

NH(3)-dependent NAD(+) synthetase

nadE (SGO_0583)

A8AVT9

5.4/5.11

35,000/30248

268

3

16%

Acetoin catabolism

 

aced-1

Acetoin dehydrogenase

butA (SGO_1096)

A8AX75

5.4/5.20

26,000/26547

1008

15

77%

-

aced-2a)

   

5.7/5.20

26,000/26547

1247

17

75%

-

aced-3a)

   

5.7/5.20

24,000/26547

809

13

62%

-

Carbohydrate catabolism

deraa)

Deoxyribose-phosphate aldolase

deoC (SGO_1080)

A8AX59

4.9/4.84

20,000/23380

691

8

49%

Pyruvate conversion

ldh-1a)

L-lactate dehydrogenase

ldh (SGO_1232)

A8AXK9

5.4/5.24

36,000/35267

327

6

28%

+

ldh-2

   

5.6/5.24

36,000/35267

436

6

28%

+

ldh-3

   

5.8/5.24

36,000/35267

641

8

32%

-

adha)

Alcohol dehydrogenase

adhA (SGO_0565)

A8AVS1

5.2/4.94

39,000/35958

911

13

69%

pox

Pyruvate oxidase

spxB (SGO_0292)

A8AV01

5.3/5.06

65,000/65283

161

3

5%

Pentose phosphate pathway

 

deob

Phosphopentomutase

deoB (SGO_1264)

A8AXN8

5.3/4.96

47,000/44508

172

3

9%

+

Amino acid metabolism

alad

Alanine dehydrogenase

ald (SGO_0708)

A8AW50

6.1/5.29

45,000/38960

1378

19

63%

dapha)

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

dapH (SGO_0158)

A8AUL9

5.2/5.06

22,000/24255

291

5

25%

glya

Serine hydroxymethyltransferase

glyA, (SGO_1151)

A8AXC8

5.4/5.07

48,000/45566

583

8

28%

sed

Homoserine dehydrogenase

hom (SGO_0801)

A8AWE0

5.0/4.86

45,000/46154

245

3

11%

Nucleotide metabolism

adka)

Adenylate kinase

adk (SGO_1964)

A8AZK4

5.2/4.95

22,000/ 23,857

318

6

38%

aprta)

Adenine phosphoribosyltransferase

apt (SGO_1001)

A8AWY0

5.0/4.90

17,000/18840

875

12

74%

imdh-1

Inosine-5′-monophosphate dehydrogenase

guaB (SGO_0008)

A8AU70

5.4/5.19

58,000/52717

116

2

5%

+

imdh-2

   

5.5/5.19

56,000/52717

252

4

12%

-

pyrb

Aspartate carbamoyltransferase

pyrB (SGO_1109)

A8AX88

5.6/5.04

35,000/34741

54

1g)

4%

xprt

Xanthine phosphoribosyltransferase

xpt (SGO_1158)

A8AXD5

6.2/5.79

17,000/20849

684

12

77%

Molecular chaperone activity and/or protein folding

Dnak-1

Molecular chaperone DnaK

dnaK (SGO_0402)

A8AVA8

4.4/4.69

68,000/64724

266

4

9%

+

DnaK-2a)

   

4.5/4.69

68,000/64724

1557

26

50%

+

DnaK-3a)

   

5.2/4.69

25,000/64724

134

2

3%

+

DnaK-4f)

   

4.6/4.69

68,000/64724

-

-

-

-

DnaK-5

   

4.1/4.69

44,000/64724

254

4

10%

-

DnaK-6a)

   

5.3/4.69

36,000/64724

345

6

14%

-

GroEL-1

Molecular chaperone GroEL

groEL (SGO_1885)

A8AZE1

4.2/4.66

64,000/56754

776

13

34%

+

GroEL-2

   

4.3/4.66

64,000/56754

1500

22

47%

+

GroEL-3

   

4.4/4.66

64,000/56754

794

13

32%

-

GroES

Co-chaperone GroES

groES (SGO_1886)

A8AZE2

5.4/5.11

64,000/9681

65

1g)

2%

grpEa)

Molecular chaperone GrpE

grpE (SGO_0401)

A8AVA7

4.8/4.83

23,000/20265

186

3

18%

hyda)

Hydrolase, haloacid dehalogenase family/ peptidyl-prolyl cis-trans isomerase, cyclophilin type

SGO_0604

A8AVW0

4.2/4.74

22,000/51936

516

10

30%

tiga)

Trigger factor (chaperone)

tig (SGO_0412)

A8AVB8

4.2/4.53

55,000/47242

531

10

31%

+

Transcription

GreA

Transcription elongation factor GreA

greA (SGO_0519)

A8AVM5

4.9/4.85

15,500/17515

581

9

68%

rpoAa)

DNA-directed RNA polymerase subunit alpha

rpoA (SGO_1959)

A8AZJ9

4.5/4.70

41,000/34502

578

7

29%

rpoZ

DNA-directed RNA polymerase subunit omega

rpoZ (SGO_0595)

A8AVV1

6.7/5.82

12,000/11851

231

5

44%

y454

Probable transcriptional regulatory protein

 

A8AVG0

4.6/4.45

30,000/25722

227

4

26%

Translation

ef-G

Elongation factor G

fusA (SGO_0206)

A8AUR6

4.7/4.88

50,000/76785

53

1g)

2%

ef-Ts

Elongation factor Ts

tsf (SGO_2000)

A8AZP0

4.9/4.84

41,000/37284

326

5

20%

ef-tu-1a)

Elongation factor tu

tuf (SGO_0761)

A8AWA0

4.1/4.86

55,000/44011

519

8

31%

+

ef-tu-2

   

5–6/4.86

55,000/44011

1253

22

63%

+

ef-tu-3a)

   

4.2/4.86

34,000/44011

532

6

23%

+

ef-tu-4a)

   

4.3/4.86

25,000/44011

167

3

8%

+

ef-tu-5a)

   

4.3/4.86

29,000/44011

553

6

25%

-

ef-tu-6a)

   

4.7/4.86

23,000/44011

420

6

18%

-

ef-tu-7a)

   

5.3/4.86

20,000/44011

433

6

16%

-

rL1a)

50S ribosomal protein L1

rplA (SGO_1455)

A8AY74

5.5/9.22

23,000/24399

202

3

16%

rL4-1a)

50S ribosomal protein L4

rplD (SGO_1984)

A8AZM4

5.2/10.03

19,000/22279

285

4

26%

-

rL4-2a)

   

5.5/10.03

19,000/22279

327

4

24%

-

rL10a)

50S ribosomal protein L10

rplJ (SGO_1192)

A8AXG9

5.2/5.06

15,000/17462

1002

15

86%

rL17

50S ribosomal protein L17

rplQ (SGO_1958)

A8AZJ8

5.3/9.86

13,000/14511

141

2

17%

rrfa)

Ribosome recycling factor

frr (SGO_1451)

A8AY70

6.8/5.90

18,000/20640

421

8

46%

rS1

30S ribosomal protein S1

rpsA (SGO_1234)

A8AXL0

4.5/4.91

52,000/44149

130

2

5%

+

rS2

30S ribosomal protein S2

rpsB (SGO_2001)

A8AZP1

4.6/5.07

33,000/29125

515

8

35%

rS5-1a)

30S ribosomal protein S5

rpsE (SGO_1968)

A8AZK8

5.1/9.69

14,000/17079

335

4

33%

-

rS5–2

   

5.3/9.69

14,000/17079

283

4

33%

-

rS8a)

30S ribosomal protein S8

rpsH (SGO_1971)

A8AZL1

5.3/9.48

12,500/14753

120

2

25%

rS17

30S ribosomal protein S17

rpsQ (SGO_1976)

A8AZL6

5.0/9.92

11,000/10010

58

1g)

10%

sys-1

Serine tRNA-ligase

serS (SGO_1683)

A8AYV0

5.4/5.11

48,000/48110

342

7

21%

-

sys-2a)

   

5.7/5.11

21,000/48110

95

1g)

2%

-

Protein catabolism

clpp

ATP-dependent Clp protease proteolytic subunit

clpP (SGO_1632)

A8AYP9

4.3/4.72

18,000/21363

200

3

12%

pept

Peptidase T

pepT (SGO_1312)

A8AXT3

4.2/4.59

49,000/45200

332

4

13%

Vitamin B biosynthesis

pxka)

Pyridoxine kinase

SGO_0409

A8AVB5

5.3/5.16

23,000/27598

583

10

52%

Cell envelope biosynthesis

murda)

UDP-N-acetylmuramoylalanine D-glutamate ligase

murdD (SGO_0671)

A8AW14

5.4/5.07

46,000/48257

253

4

12%

pgama)

Phosphoglucosamine mutase

glmM (SGO_0889)

A8AWM5

4.6/4.71

52,000/48396

592

7

26%

+

rmla-1

Glucose-1-phosphate thymidylyltransferase

rfbA-1 (SGO_1009)

A8AWY8

5.1/4.92

28,000/32213

42

1g)

3%

+

rmla-2a)

   

5.3/4.92

28,000/32213

136

2

7%

+

rmlb

dTDP-glucose 4,6-dehydratase

rfbB-1 (SGO_1011)

A8AWZ0

6.3/5.55

40,000/39314

168

3

12%

Cell division

SepF

Cell division protein SepF

sepF (SGO_0677)

A8AW20

6.6/5.61

19,000/21654

367

6

41%

Antioxidant activity

soda)

Superoxide dismutase

sodA (SGO_1599)

A8AYL7

4.9/4.78

19,000/22446

474

8

46%

tox

Thiol peroxidase

Tpx (SGO_1803)

A8AZ62

4.2/4.52

16,000/18015

349

6

59%

Protein dephosphorylation

pppa)

Phosphoprotein phosphatase SGO_0599

SGO_0599

A8AVV5

4.3/4.62

23,000/26870

696

11

61%

+

  1. a) Two or more proteins were identified from this spot
  2. b) Gene name in the UniProt database as entered for S. gordonii DL1 proteins
  3. c) Accession number in the UniProt database for S. gordonii DL1
  4. d) Theoretical values for S. gordonii DL1 proteins
  5. e) The sequenced peptides identified by LC-MS/MS can be found in supplemental material (Additional file 1)
  6. f) Protein identity deduced from adjacent identified spot
  7. g) Proteins identified by only one peptide are given when only a single match was yielded from the database search