Table 3 Abundant proteins in the proteomes of seed-borne strains compared with nodule strains

Spot no.

Gene ID

Protein

Function

COG

Mascot score

Sequence coverage

Matched peptides

Ratio

CIAT652

CCGM1

 24

RLPCCGM1_c3018

SucB

Dihydrolipoamide succinyltransferase

C

115

27

13/28

-

679.8

-

 41

RLPCCGM1_c0918

PdhA

Pyruvate dehydrogenase (acetyl-transferring) protein subunit alpha

C

71

25

9/36

503.7

1013.7

2.0

 8

RLPCCGM1_p0657

RepA

Plasmid partitioning protein RepAb

D

73

28

10/32

21.8

77.3

3.5

 5

RLPCCGM1_c0705

AldA

Alanine dehydrogenase

E

150

34

13/29

143.1

442.6

3.1

 7

RLPCCGM1_c1335

SufS

Cysteine desulfurase

E

72

19

7/19

14.5

46.9

3.2

 14

RLPCCGM1_p1587

FdhA

Glutathione-independent formaldehyde dehydrogenase

E

118

42

16/32

3.3

62.8

19.0

 25

RLPCCGM1_c1870

IlvI

Acetolactate synthase 3 catalytic subunit

E

73

17

8/30

-

59.4

-

 29

RLPCCGM1_c3812

ArgD

Acetylornithine transaminase

E

143

49

14/35

-

97.4

-

 6

RLPCCGM1_c0701

CpdB

Bifunctional 2′,3′-cyclic nucleotide 2′-phosphodiesterase/3′-nucleotidase periplasmic protein

F

96

18

11/27

-

46.5

-

 11

RLPCCGM1_c3249

PurH

Bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase

F

105

31

11/31

6.7

41.5

6.2

 2

RLPCCGM1_c2616

Pgk

Phosphoglycerate kinase

G

118

36

11/25

17.5

41.3

2.4

 9

RLPCCGM1_c2662

PykA

Pyruvate kinase

G

86

29

9/43

9.6

37.6

3.9

 34

RLPCCGM1_c1984

-

Family 1 extracellular solute-binding protein

G

130

45

13/35

-

127.5

-

 38

RLPCCGM1_c3763

FrcB

Fructose ABC transporter substrate-binding protein

G

75

25

5/8

-

156

-

 40

RLPCCGM1_c2613

Gap

Glyceraldehyde 3-phosphate dehydrogenase

G

67

35

8/29

-

191.9

-

 3

RLPCCGM1_c4187

Dxs

1-deoxy-D-xylulose-5-phosphate synthase

H

108

26

12/24

9.7

25.8

2.7

 23

RLPCCGM1_c3273

CoaE

Dephospho-CoA kinase

H

57

23

5/23

-

53

-

 26

RLPCCGM1_c4205

RibA

Riboflavin biosynthesis protein

H

69

24

7/21

-

75

-

 36

RLPCCGM1_c3299

AhcY

S-adenosyl-L-homocysteine hydrolase

H

142

34

13/28

-

146.6

-

 39

RLPCCGM1_c2569

SerC

Phosphoserine aminotransferase

H

113

43

12/39

-

190.4

-

 17

RLPCCGM1_c3650

FadB

Enoyl-CoA hydratase

I

70

35

8/30

-

20.8

-

 18

RLPCCGM1_c3059

-

Oxidoreductase

I

87

44

12/55

-

21

-

 35

RLPCCGM1_c3416

FabB

3-oxoacyl-ACP synthase

I

89

33

12/49

-

127.6

-

 1

RLPCCGM1_c1345

TyrS

Tyrosyl-tRNA synthetase

J

101

27

12/37

20.7

44

2.1

 15

RLPCCGM1_c2760

-

Acetyltransferase

J

40

37

10/44

-

19.1

-

 13

RLPCCGM1_c1935

MurD

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase

M

139

31

13/26

-

15.2

-

 33

RLPCCGM1_c2681

ExoN

UTP--glucose-1-phosphate uridylyltransferase

M

162

51

14/40

-

122.2

-

 10

RLPCCGM1_c3962

FlaC

Flagellin C protein

N

80

32

8/29

29.6

178.8

6.0

 21

RLPCCGM1_p1412

HtpG

Heat shock protein 90

O

103

45

13/35

-

31.3

-

 22

RLPCCGM1_c1051

PpiA

Peptidyl-prolyl cis-trans isomerase A

O

55

30

4/29

-

38.1

-

 31

RLPCCGM1_p1186

-

Glutathione S-transferase YghU

O

60

30

6/23

-

113.8

-

 4

RLPCCGM1_p1923

KatG

Catalase

P

89

23

12/35

26.8

81.6

3.0

 16

RLPCCGM1_c0709

SseA

Thiosulfate sulfurtransferase

P

138

55

12/34

-

20.7

-

 27

RLPCCGM1_c2174

-

Methanol dehydrogenase regulator MoxR-like protein

R

108

52

14/48

-

76.8

-

 28

RLPCCGM1_c3573

-

Oxidoreductase

R

80

37

12/48

-

76.8

-

 30

RLPCCGM1_c2292

IdhA

Myo-inositol 2-dehydrogenase

R

87

44

12/55

-

102.8

-

 19

RLPCCGM1_c4033

-

Isoprenylcysteine carboxyl methyltransferase

S

62

35

6/54

-

21.8

-

 37

RLPCCGM1_c2285

-

Hypothetical protein

S

76

42

9/39

-

153.1

-

 12

RLPCCGM1_p0713

-

Sensory box/GGDEF family protein

T

54

10

9/29

32.6

314.2

9.6

 20

RLPCCGM1_p2036

CpaC

Pilus assembly protein

U

135

32

12/47

-

25.2

-

 32

RLPCCGM1_p1459

-

Hypothetical protein

-

67

22

6/16

23

119.3

5.2

Spot no.

Gene ID

Protein

Function

COG

Mascot score

Sequence coverage

Matched peptides

Ratio

CIAT652

CCGM1

 47

RHECIAT_PC0000173

-

Putative oxidoreductase

C

132

21

15/27

6.5

-

-

 62

RHECIAT_CH0002031

PdhA2

Pyruvate dehydrogenase subunit beta

C

114

37

18/39

51.5

-

-

 67

RHECIAT_CH0004343

-

Aldehyde dehydrogenase

C

52

17

6/31

86.1

-

-

 69

RHECIAT_CH0001680

NuoE1

NADH dehydrogenase subunit E

C

147

51

17/45

119.3

-

-

 75

RHECIAT_CH0000039

PckA

Phosphoenolpyruvate carboxykinase

C

99

33

13/38

400.7

-

-

 76

RHECIAT_CH0002032

PdhC

Dihydrolipoamide S-acetyltransferase

C

101

33

12/25

909.1

-

-

 49

RHECIAT_PC0000423

-

Putative oligopeptide ABC transporter substrate-binding protein

E

56

8

7/23

7.6

2.9

2.6

 50

RHECIAT_CH0003659

PotD

Spermidine/putrescine ABC transporter substrate-binding protein

E

60

25

7/24

243.5

23.9

10.2

 60

RHECIAT_CH0002150

-

Peptide ABC transporter substrate-binding protein

E

218

44

22/38

39.9

-

-

 72

RHECIAT_CH0001992

MetC

Cystathionine beta-lyase

E

81

38

9/22

190.4

-

-

 73

RHECIAT_CH0000879

GuaB

Inosine 5′-monophosphate dehydrogenase

F

192

44

21/47

210.1

-

-

 51

RHECIAT_CH0003979

LacZ2

Beta-D-galactosidase

G

129

18

11/14

16.8

-

-

 55

RHECIAT_CH0000213

GpmA

Phosphoglyceromutase

G

214

84

18/52

23.7

-

-

 61

RHECIAT_CH0003393

XylF

Xylose ABC transporter substrate-binding protein

G

113

32

10/41

46.7

-

-

 64

RHECIAT_CH0003248

-

Omega amino acid--pyruvate transaminase

H

147

47

14/26

67.8

-

-

 42

RHECIAT_CH0001955

AccC

Acetyl-CoA carboxylase biotin carboxylase subunit

I

77

33

9/26

795.2

364.4

2.2

 53

RHECIAT_CH0003282

BdhA

D-beta-hydroxybutyrate dehydrogenase

I

81

28

6/8

19.3

-

-

 48

RHECIAT_PA0000110

FusAa

Elongation factor G

J

55

16

8/27

6.8

-

-

 54

RHECIAT_CH0004024

PrfA

Peptide chain release factor 1

J

119

41

14/40

19.9

-

-

 58

RHECIAT_CH0001897

ValS

Valyl-tRNA synthetase

J

85

12

8/12

26.5

-

-

 59

RHECIAT_CH0002285

ThrS

Threonyl-tRNA synthetase

J

124

23

16/34

31.3

-

-

 65

RHECIAT_CH0000980

GlyS

Glycyl-tRNA synthetase subunit beta

J

192

38

23/37

71.6

-

-

 66

RHECIAT_CH0002242

MetS

Methionyl-tRNA synthetase

J

105

26

10/22

72.1

-

-

 57

RHECIAT_CH0001733

-

Nucleoside-diphosphate-sugar epimerase

M

57

19

5/22

26.4

-

-

 74

RHECIAT_CH0003488

NoeJ

Mannose-1-phosphate guanylyltransferase (GDP) protein

M

145

48

18/52

243.4

-

-

 46

RHECIAT_CH0001879

-

Peroxidase

O

67

35

8/29

119.2

23.7

5.0

 52

RHECIAT_CH0001895

Pcm1

Protein-L-isoaspartate(D-aspartate) O-methyltransferase

O

93

38

6/16

19

-

-

 63

RHECIAT_CH0002260

PpiD1

Peptidyl-prolyl cis-trans isomerase D signal peptide protein

O

57

16

6/14

67.7

-

-

 70

RHECIAT_CH0004147

-

Nitrate/sulfonate/bicarbonate ABC transporter substrate-binding protein

P

106

42

11/29

127.6

-

-

 71

RHECIAT_CH0002820

-

Ferrichrome ABC transporter substrate-binding protein

P

135

52

12/23

146.6

-

-

 56

RHECIAT_PC0000681

VbsO

L-lysine 6-monooxygenase (NADPH) protein

Q

105

32

11/23

25.5

-

-

 43

RHECIAT_CH0004212

-

ABC transporter substrate-binding protein

R

99

36

9/29

360.8

-

-

 44

RHECIAT_CH0004405

-

Hypothetical protein

S

89

33

8/38

253.5

111.4

2.3

 68

RHECIAT_CH0002473

-

Hypothetical protein

S

109

31

14/38

94.5

-

-

 45

RHECIAT_CH0004199

TypA

GTP-binding protein TypA/BipA

T

151

34

21/42

215.3

-

-

Spot no.

Gene ID

Protein

Function

COG

Mascot score

Sequence coverage

Matched peptides

Ratio

CFNEI73

CCGM7

 2

SAMCCGM7_Ch3507

AcnA

Aconitate hydratase

C

69

17

11/31

-

185.6

-

 3

SAMCCGM7_Ch3374

SucB

Dihydrolipoamide succinyltransferase

C

99

25

11/21

-

127

-

 4

SAMCCGM7_Ch1973

FumC

Fumarate hydratase class II

C

100

21

10/20

-

105.8

-

 8

SAMCCGM7_pC0039

TctC

Tricarboxylate transport protein

C

64

30

6/11

-

45.4

-

 11

SAMCCGM7_Ch0047

PckA

Phosphoenolpyruvate carboxykinase

C

88

20

11/30

6.5

143.9

22.1

 12

SAMCCGM7_Ch2624

Ald

Aldehyde dehydrogenase

C

65

17

7/18

-

17.3

-

 20

SAMCCGM7_Ch3356

AtpD

ATP synthase subunit beta

C

111

38

13/34

41.4

407.9

9.9

 28

SAMCCGM7_Ch1381

NuoG

NADH-quinone oxidoreductase subunit G

C

111

23

13/27

9.3

52.4

5.6

 29

SAMCCGM7_Ch2523

AcoD

Acetaldehyde dehydrogenase 2

C

133

27

14/33

65.9

259.8

3.9

 31

SAMCCGM7_Ch3358

AtpA

ATP synthase subunit alpha

C

97

29

14/41

78.5

290.4

3.7

 16

SAMCCGM7_Ch1849

CarB

Carbamoyl-phosphate synthase large subunit

E

74

10

11/20

7.5

103.4

13.8

 17

SAMCCGM7_Ch2552

LeuA

2-isopropylmalate synthase

E

118

27

13/23

-

11.4

-

 18

SAMCCGM7_pA0276

-

Homoserine dehydrogenase

E

72

22

9/28

-

11.2

-

 26

SAMCCGM7_Ch1267

GlyA

Pyridoxal-phosphate-dependent serine hydroxymethyltransferase

E

85

21

9/22

11.9

75.8

6.4

 19

SAMCCGM7_Ch3100

-

5′-nucleotidase

F

122

22

12/19

11.1

120.3

10.8

 35

SAMCCGM7_Ch3605

PurH

Bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase

F

80

23

10/31

140.6

278.9

2.0

 24

SAMCCGM7_Ch3149

Pgm

Phosphoglucomutase Pgm

G

61

12

5/7

6.4

-

-

 30

SAMCCGM7_Ch2630

ChvE

Multiple sugar-binding periplasmic receptor

G

55

24

6/25

34.2

127.5

3.7

 32

SAMCCGM7_Ch3057

FbaB

Fructose-bisphosphate aldolase

G

70

32

9/34

27.2

95.8

3.5

 33

SAMCCGM7_Ch3054

Gap

Glyceraldehyde-3-phosphate dehydrogenase

G

80

29

7/15

33.7

109.3

3.2

 21

SAMCCGM7_Ch0041

AhcY

S-adenosyl-L-homocysteine hydrolase

H

81

26

10/29

21.2

169

8.0

 14

SAMCCGM7_Ch1196

FabF

3-oxoacyl-ACP synthase

I

66

16

7/17

-

16.8

-

 1

SAMCCGM7_Ch2527

RplY

50S ribosomal protein L25

J

199

72

17/32

-

498.9

-

 7

SAMCCGM7_Ch1428

GatB

Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B

J

72

18

7/19

-

59.6

-

 23

SAMCCGM7_Ch0231

Pnp

Polyribonucleotide nucleotidyltransferase

J

122

29

17/38

35.5

270.8

7.6

 9

SAMCCGM7_Ch0831

GroEL

Chaperonin

O

95

28

14/36

12.8

380.2

29.7

 25

SAMCCGM7_pC0433

ClpV

Protease

O

63

15

10/32

-

7

-

 5

SAMCCGM7_Ch0999

CysN

Sulfate adenylyltransferase subunit 1

P

121

45

15/44

-

65.2

-

 13

SAMCCGM7_pC1570

-

Iron ABC transport system, solute-binding protein

P

89

19

17/11

-

17.1

-

 22

SAMCCGM7_pC1145

-

Ferrichrome-iron receptor

P

149

19

13/16

-

7.8

-

 27

SAMCCGM7_pC1571

-

Iron ABC transport system, solute-binding protein

P

105

26

11/23

20.6

123.5

6.0

 34

SAMCCGM7_pC1766

Fct

Ferrichrysobactin receptor

P

174

35

18/31

2.6

7.4

2.8

 6

SAMCCGM7_Ch2381

-

ABC transporter ATP-binding protein

R

126

31

17/30

-

60.4

-

 10

SAMCCGM7_pA0100

VirB10

Type IV secretion system protein

U

150

32

12/19

-

23.8

-

 15

SAMCCGM7_pC0430

ImpC

Type VI secretion system protein

U

96

23

10/21

14

206

14.7

Spot no.

Gene ID

Protein

Function

COG

Mascot score

Sequence coverage

Mached peptides

Ratio

CFNEI73

CCGM7

 37

SAMCFNEI73_Ch3492

LpdA

Dihydrolipoamide dehydrogenase

C

134

37

13/23

48.2

-

-

 44

SAMCFNEI73_Ch3194

-

Hypothetical protein

C

93

44

9/22

21.6

-

-

 47

SAMCFNEI73_Ch0872

AtpF

ATP synthase subunit B’

C

94

35

7/18

51

3.4

15.0

 53

SAMCFNEI73_Ch1106

-

Electron transfer flavoprotein-ubiquinone oxidoreductase

C

105

24

11/22

10.4

-

-

 54

SAMCFNEI73_Ch0062

GlcB

Malate synthase G

C

156

27

14/19

15.1

1.7

8.9

 57

SAMCFNEI73_Ch0755

MmsA

Methylmalonate-semialdehyde dehydrogenase

C

132

33

17/29

66.6

12.8

5.2

 70

SAMCFNEI73_Ch1382

NuoD

NADH-quinone oxidoreductase subunit D

C

135

42

20/54

45.7

21

2.2

 72

SAMCFNEI73_Ch3505

SdhA

Succinate dehydrogenase flavoprotein subunit

C

96

20

10/15

42.5

19.9

2.1

 36

SAMCFNEI73_pC0436

FliY

Cystine-binding periplasmic protein

E

63

26

6/17

63.4

-

-

 43

SAMCFNEI73_Ch1350

ArgC

N-acetyl-gamma-glutamyl-phosphate reductase

E

66

29

7/27

23.5

-

-

 49

SAMCFNEI73_pC0934

HutU

Urocanate hydratase

E

93

21

13/34

13.2

-

-

 51

SAMCFNEI73_Ch2492

IlvB

Acetolactate synthase large subunit

E

82

14

7/10

12.1

-

-

 52

SAMCFNEI73_Ch0061

-

Hydantoinase/oxoprolinase family protein

E

71

17

7/16

10.5

-

-

 59

SAMCFNEI73_Ch3399

MetH

Methionine synthase

E

208

25

24/29

4.6

-

-

 63

SAMCFNEI73_Ch0442

DapD

2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase

E

55

20

7/42

38.3

10.6

3.6

 65

SAMCFNEI73_Ch2207

MetH2

Methionine synthase

E

79

28

8/37

25.4

7.9

3.2

 69

SAMCFNEI73_Ch0208

-

Extracellular solute-binding protein, family 5

E

74

21

12/47

30

11

2.7

 71

SAMCFNEI73_Ch1748

-

Peptide ABC transporter substrate-binding protein

E

93

24

13/34

32.5

15.1

2.2

 62

SAMCFNEI73_Ch3182

Pgk

Phosphoglycerate kinase

G

113

41

12/26

146.7

39.3

3.7

 66

SAMCFNEI73_Ch3273

GlgX

Glycogen debranching protein

G

131

23

12/18

6.7

2.1

3.2

 58

SAMCFNEI73_pC1978

ThiC

Phosphomethylpyrimidine synthase

H

113

33

17/37

23.9

5

4.8

 64

SAMCFNEI73_Ch1162

NadB

L-aspartate oxidase

H

156

31

15/23

33.7

9.7

3.5

 48

SAMCFNEI73_pC0946

MmgC

Acyl-CoA dehydrogenase

I

83

32

13/40

13.9

-

-

 46

SAMCFNEI73_Ch1475

FusA

Elongation factor G

J

93

22

12/24

15.8

-

-

 42

SAMCFNEI73_Ch1028

-

ATPase component BioM of energizing module of biotin ECF transporter

L

136

40

15/36

23.8

-

-

 39

SAMCFNEI73_pC1683

RkpQ

N-acylneuraminate-9-phosphate synthase

M

202

55

16/39

25.6

-

-

 50

SAMCFNEI73_Ch1571

KdsA

2-dehydro-3-deoxyphosphooctonate aldolase

M

106

43

16/54

12.4

-

-

 67

SAMCFNEI73_Ch2467

MurE

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase

M

166

34

13/19

26.3

8.7

3.0

 40

SAMCFNEI73_Ch1644

Pcm

Protein-L-isoaspartate O-methyltransferase

O

140

57

11/20

24.9

-

-

 61

SAMCFNEI73_Ch1368

LonA

Endopeptidase La

O

62

12

9/20

55

14.3

3.8

 68

SAMCFNEI73_pC1783

-

Phosphate ABC transporter substrate-binding protein

P

78

27

7/24

104.4

36.3

2.9

 45

SAMCFNEI73_Ch3296

-

Cobalamin synthesis protein/P47K family protein

R

69

25

9/37

17.9

-

-

 55

SAMCFNEI73_Ch3670

-

Hypothetical protein

R

72

16

8/19

8.2

-

-

 38

SAMCFNEI73_pB0529

TraI

Autoinducer synthesis protein

T

157

75

15/39

30.5

-

-

 60

SAMCFNEI73_Ch1589

NtrC

Nitrogen assimilation regulatory protein

T

63

19

7/20

26.2

6

4.4

 56

SAMCFNEI73_pB0525

TrbE

Conjugal transfer protein

U

177

27

20/32

7.9

-

-

 41

SAMCFNEI73_pC1268

-

Peroxiredoxin

V

95

37

8/22

24.8

-

-