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Table 2 Differentially expressed proteins for phenylacetic acid, benzene degradation, and various oxidoreductases on kraft lignin

From: Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB

Uniprot IDs

Locus tag

Name

Log2 fold change

Unique peptides

Sequence coverage (%)

Mol. weight (kDa)

Intensity

  

Phenylacetic acid degradation protein

     

A0A1E3LF26

A9762_23720

Phenylacetic acid degradation protein PaaD

0.529261

3

27.3

15.022

8.65E−26

A0A1E3LF48

A9762_23735

Phenylacetic acid degradation protein PaaN

0.244067

18

58.3

60.008

1.24E−140

A0A1E3LFB3

A9762_23725

2-(1,2-Epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase

0.724358

9

56.1

27.854

1.32E−76

A0A1E3LFJ2

A9762_22495

Phenylacetic acid degradation protein

0.790541

4

36.3

15.888

3.07E−15

A0A1E3LHE3

A9762_23715

Phenylacetate–coenzyme A

0.514503

14

57.5

47.386

1.43E−109

A0A1E3LQE8

A9762_10500

Phenylacetic acid degradation protein

1.426558

5

44.4

14.521

5.16E−22

  

Peroxidases

     

A0A1E3LDX8

A9762_24250

Dyp-type peroxidase

1.43239

15

72

40.756

1.29E−104

A0A1E3LHN8

A9762_20355

Peroxidase

− 1.69967

18

90.6

23.753

0

A0A1E3LPA6

A9762_00985

Chloroperoxidase

− 1.927944

16

84.7

30.075

8.73E−175

A0A1E3LF97

A9762_25345

Peroxidase-like protein

1.353771

7

59

18.981

4.85E−31

A0A1E3LNE3

A9762_13620

Laccase

− 0.13346

10

57.5

28.644

5.45E−43

  

Oxidases

     

A0A1E3LC86

A9762_26490

Glycolate oxidase subunit GlcE

1.96696

9

38.1

38.774

4.18E−40

A0A1E3LDU3

A9762_25250

Aldehyde oxidase

1.94888

25

43.2

106.43

3.40E−153

A0A1E3LG04

A9762_25240

Cytochrome C oxidase Cbb3

1.88749

12

44.8

44.919

5.64E−68

A0A1E3LL61

A9762_17965

Glycolate oxidase iron–sulfur subunit

1.88269

5

14.3

46.4

1.56E−20

A0A1E3LCC6

A9762_07195

Oxidase

1.12594

23

67.7

43.498

4.04E−279

A0A1E3LQ45

A9762_00290

FAD-linked oxidase

0.7576

46

47.6

148.68

8.22E−260

A0A1E3LDS7

A9762_25555

Ubiquinol oxidase subunit 2

− 0.72481

3

21.5

35.767

2.50E−21

A0A1E3LLY2

A9762_16250

l-Aspartate oxidase

− 1.51593

5

14.2

58.534

1.25E−24

A0A1E3LRG9

A9762_02095

Cytochrome c oxidase assembly protein

− 1.76256

6

49.8

22.192

2.52E−27

A0A1E3LCR8

A9762_26505

2-Hydroxy-acid oxidase

− 1.92172

13

43.3

51.242

1.38E−99

  

Oxidoreductases

     

A0A1E3L9T7

A9762_09290

NADH–quinone oxidoreductase subunit I

1.983

13

54.6

18.63

1.26E−66

A0A1E3LC99

A9762_26255

Oxidoreductase

1.46342

9

62.5

26.21

1.99E−100

A0A1E3LAC9

A9762_09275

NADH oxidoreductase (quinone) subunit F

0.86275

19

70.7

47.093

5.72E−135

A0A1E3LMK8

A9762_03120

NADP oxidoreductase

0.82498

10

55.5

32.458

3.02E−38

A0A1E3LHK5

A9762_23470

FAD-dependent oxidoreductase

0.33833

3

14.7

38.458

4.28E−15

A0A1E3LLW4

A9762_03220

GMC family oxidoreductase

0.24372

23

54.8

64.908

3.74E−163

A0A1E3LFG3

A9762_22500

NADP-dependent oxidoreductase

0.05857

13

63.4

35.64

5.98E−106

A0A1E3LKB2

A9762_03335

Oxidoreductase

− 0.24038

18

82.3

31.785

3.07E−157

A0A1E3LGB9

A9762_21450

YggW family oxidoreductase

− 0.68269

3

10.3

45.723

1.71E−14

A0A1E3LC87

A9762_26930

Fe–S oxidoreductase

− 1.47441

6

49.8

26.119

2.01E−34

A0A1E3LG91

A9762_21265

Vanillate O-demethylase ferredoxin subunit

− 1.5017

15

57.9

33.723

1.13E−114

A0A1E3LG83

A9762_21255

Vanillate O-demethylase oxidoreductase

0.298001

15

48.1

50.745

1.80E−76

A0A1E3LFZ4

A9762_25310

FAD-dependent oxidoreductase

− 1.67016

5

17.9

54.42

2.53E−15

A0A1E3LA58

A9762_09270

NADH-quinone oxidoreductase subunit E

− 1.69506

9

80.1

18.129

9.41E−90

A0A1E3LFR2

A9762_22175

Oxidoreductase

− 1.8627

9

61.8

30.679

4.89E−178

A0A1E3LCB2

A9762_09255

NADH-quinone oxidoreductase subunit B

− 1.96385

10

72.3

17.519

1.56E−64

A0A1E3LEJ8

A9762_05735

Oxidoreductase

− 1.97509

18

85.7

26.372

6.17E−220

A0A1E3LKX1

A9762_15740

Quinone oxidoreductase

− 1.99406

18

90.7

34.556

1.06E−219

  

Oxygenases

     

A0A1E3LHN5

A9762_23090

2-Nitropropane dioxygenase

1.84558

3

15.1

38.789

7.50E−15

A0A1E3LFU3

A9762_22350

Quercetin 2,3-dioxygenase

1.82796

7

51.5

26.31

4.21E−24

A0A1E3LFX1

A9762_21815

Homogentisate 1,2-dioxygenase

1.51818

13

56.9

48.611

5.10E−81

A0A1E3LPA9

A9762_00970

4-Hydroxyphenylpyruvate dioxygenase

1.43964

2

5.9

40.191

3.14E−09

A0A1E3LFB4

A9762_23095

2-Nitropropane dioxygenase

1.31977

9

45.1

39.332

6.27E−61

A0A1E3LDU6

A9762_24595

Phytanoyl-CoA dioxygenase

− 0.60384

6

38.3

27.846

2.72E−52

A0A1E3LF51

A9762_25450

Putative dioxygenase

− 0.666263

9

88.7

15.676

1.86E−122

A0A1E3LIM3

A9762_17955

Dioxygenase

− 0.91661

8

52

29.958

6.54E−31

A0A1E3LI70

A9762_22255

2-Nitropropane dioxygenase

− 1.45193

12

64.4

33.509

1.71E−146

A0A1E3LIR0

A9762_17450

Protocatechuate 3,4-dioxygenase subunit alpha

− 1.63442

13

83.4

21.895

2.50E−246

A0A1E3LJ07

A9762_17445

Protocatechuate 3,4-dioxygenase subunit beta

− 1.71052

16

78.4

26.513

2.43E−152

A0A1E3LG93

A9762_21285

Protocatechuate 4,5-dioxygenase subunit alpha

− 1.83931

6

80.7

13.769

6.11E−47

A0A1E3LG93

A9762_21285

Protocatechuate 4,5-dioxygenase subunit beta

− 1.83931

6

80.7

13.769

6.11E−47

A0A1E3LEL8

A9762_04935

Antibiotic biosynthesis monooxygenase

− 1.86712

6

81.8

11.026

1.02E−172

A0A1E3LBV9

A9762_07570

2OG-Fe(II) oxygenase

− 1.682965

7

50.7

30.695

9.21E−31

A0A1E3LL67

A9762_14910

2OG-Fe(II) oxygenase

− 0.037474

8

43

37.152

3.47E−45

  

Benzoate degradation

     

A0A1E3LBS0

A9762_08405

2-Aminobenzoate–CoA ligase

1.569646

5

15.2

59.58

4.06E−18

A0A1E3LF67

A9762_23480

3-Octaprenyl-4-hydroxybenzoate carboxy-lyase (Fragment)

− 1.471879

4

32.4

15.528

1.01E−27

A0A1E3LLJ4

A9762_17745

3-Octaprenyl-4-hydroxybenzoate carboxy-lyase

1.567849

11

32.8

57.345

1.54E−68

A0A1E3LM76

A9762_12465

2-Nonaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase

− 1.895105

5

47.4

23.511

1.50E−34

A0A1E3LDW9

A9762_24905

Carboxymethylenebutenolidase

− 1.707803

8

49

27.008

1.57E−119

A0A1E3LDA6

A9762_06440

Carboxymethylenebutenolidase

− 1.951469

18

77

31.135

1.41E−118

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