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Table 3 ESTs from adult cDNAs with predicted amino-terminal signal peptides and with homologs in C. elegans

From: Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensisand the evolution of secreted proteins in parasites

Cluster

Score

P

Conventional cDNAs

Oligo-capped cDNAs

Wormpep ID

SignalP criteria

SignalP scores

Signal in C. elegans?

Description of C. elegans gene

       

C-p

Amino acids

SP-p

SP?

  

(a) Signal peptides predicted in both N. brasiliensis and C. elegans

NBC00012

86

6e-18

4

0

CE20223

YYYYS

0.533

16

1.000

Y

Y

Unknown (similar to NBC00237)

NBC00031

80

3e-16

2

2

CE17924

YYYYS

0.932

18

0.999

Y

Y

Unknown

NBC00237

84

5e-17

1

2

CE20223

YYYYS

0.671

19

1.000

Y

Y

Unknown (similar to NBC00012)

NBC00258

145

1e-35

1

0

CE00133

YYYYS

0.524

19

0.999

Y

Y

FAR-1 fatty acid/retinol-binding protein

NBC00266

129

6e-31

1

0

CE19630

YYYYS

0.662

20

1.000

Y

Y

Unknown

NBC00314

147

3e-36

1

1

CE03639

YYYYS

0.708

19

0.987

Y

Y

Transthyretin-like family

NBC00327

94

2e-20

1

0

CE00906

YYYYS

0.542

25

0.998

Y

Y

Unknown

NBC00336

138

2e-33

1

0

CE23545

YYYYS

0.903

17

1.000

Y

Y

Unknown

NBC00354

91

4e-21

4

0

CE16530

YYYYS

0.511

17

0.943

Y

Y

Unknown

NBC00472

215

8e-57

1

0

CE04886

YYYYS

0.319

15

0.999

Y

Y

Signal sequence receptor

NBC00487

55

7e-09

1

0

CE05972

YYYYS

0.979

21

0.988

Y

Y

Unknown

NBC00495

51

3e-07

1

1

CE13171

YYYYS

0.566

19

0.999

Y

Y

Transthyretin-like family

NBC00502

176

3e-45

1

0

CE32298

YYYYS

0.634

20

1.000

Y

Y

Ectonucleotide pyrophosphatase/phosphodiesterase

NBC00592

80

1e-15

0

3

CE17924

YYYYS

0.920

16

1.000

Y

Y

Unknown

NBC00606

81

4e-16

0

2

CE02454

YYYYS

0.399

20

1.000

Y

Y

Similar to O. volvulus hypodermal antigen Ov-17

NBC00615

207

3e-54

0

1

CE04533

YYYYS

0.995

18

1.000

Y

Y

LBP-1 fatty acid-binding protein

NBC00616

61

3e-10

0

1

CE20257

YYYYS

0.754

19

0.993

Y

Y

Unknown

NBC00633

153

4e-38

0

1

CE03639

YYYYS

0.450

17

1.000

Y

Y

Transthyretin-like family

NBC00641

145

1e -35

0

1

CE33289

YYYYS

0.219

19

0.930

Y

Y

Unknown

NBC00643

102

2e-22

0

2

CE27850

YYYYS

0.961

17

0.999

Y

Y

Unknown

NBC00706

50

9e-07

0

1

CE06014

YYYYS

0.466

20

1.000

Y

Y

Unknown

NBC00720

12

3e-30

0

1

CE16958

YYYYS

0.967

19

0.998

Y

Y

NLP-13 neuropeptide

NBC00742

60

3e-10

0

1

CE16731

YYYYS

0.880

21

0.993

Y

Y

Unknown

NBC00748

50

4e-07

0

1

CE02932

YYYYS

0.804

17

0.998

Y

Y

Transthyretin-like family

NBC00767

79

7e-16

0

1

CE31662

YYYYS

0.559

17

1.000

Y

Y

Unknown

(b) Signal peptides predicted in N. brasiliensis but not C. elegans

NBC00028

104

1e-23

1

1

CE00431

YYYYS

0.731

18

0.999

Y

N

Globin

NBC00124

128

8e-31

1

1

CE00431

YYYYS

0.731

18

0.999

Y

N

Globin

NBC00144

195

7e-51

1

0

CE29663

YYNYS

0.866

19

0.963

Y

N

Transport-secretion protein

NBC00197

143

8e-35

3

6

CE00431

YYYYS

0.557

16

1.000

Y

N

Globin

NBC00272

144

2e-35

1

0

CE32475

YYNYS

0.262

22

0.513

Y

N

Unknown

NBC00328

147

4e-36

3

4

CE00431

YYYYS

0.523

17

0.999

Y

N

Globin

NBC00581

122

7e-29

0

1

CE00431

YYYYS

0.404

21

0.998

Y

N

Globin

NBC00601

93

5e-20

0

1

CE30218

YYYYS

0.535

34

0.944

Y

N

Unknown

NBC00607

159

4e-40

0

1

CE29597

YYNYS

0.529

18

0.786

Y

N

Unknown

  1. Entries in table do not match numbers in Figure 2, which includes predicted signal anchors. SignalP criteria are C-score (raw cleavage site score); S-score (signal peptide score); Y-score (combined cleavage site score); mean S score; and assignation as signal peptide (S as in all entries above; otherwise A for signal anchor or N for neither). SignalP scores are as follows: C-p: probability of predicted cleavage site being correct; amino acids: length of predicted signal peptide in amino acids; SP-p: probability of existence of signal peptide; SP?: overall prediction for signal peptide. Note that NBC00028 is almost identical to the cuticular globin of N. brasiliensis (P51536), and NBC00197 and NBC00328 are closely related, whereas NBC0124 and NBC00581 are more similar to, but not identical to, the body-wall form of globin (P51535).
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Genome Biology

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