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Table 2 Swiss-Prot sequence features matching peptide patterns

From: Characterization of oligopeptide patterns in large protein sets

Dataset

wf

wof

Feature (Number of peptide patterns)

POP-A-Swissprot

46

54

NP_BIND 25, ACT_SITE 7, REPEAT 6, MOTIF 4, BINDING 4, ZN_FING 3, METAL 2

POP-A-genome

52

48

METAL 22, ZN_FING 15, NP_BIND 7, ACT_SITE 3, DISULFID 3, CARBOHYD 2, VAR_SEQ 2, LIPID 1, SIGNAL 1, MUTAGEN 1, REPEAT 1

POP-B-Swissprot

13

87

METAL 6, ACT_SITE 5, MOTIF 2, NP_BIND 1

POP-B-genome

67

33

METAL 33, ZN_FING 18, DISULFID 7, BINDING 6, ACT_SITE 4, TRANSMEM 2, VAR_SEQ 2, STRAND 2, REPEAT 1, SE_CYS 1, SITE 1, TURN 1, HELIX 1

POP-E-Swissprot

24

76

METAL 10, TRANSMEM 5, DNA_BIND 5, DISULFID 3, ZN_FING 2, BINDING 1, ACT_SITE 1

POP-E-genome

39

61

TRANSMEM 10, ZN_FING 6, DISULFID 6, REPEAT 5, VAR_SEQ 4, COMPBIAS 2, METAL 2, CARBOHYD 2, VARIANT 1, BINDING 1, PROPEP 1, CONFLICT 1

NEP-A-Swissprot

16

84

TRANSMEM 16

NEP-A-genome

6

94

TRANSMEM 5, PEPTIDE 1

NEP-B-Swissprot

10

90

TRANSMEM 7, VAR_SEQ 1, COMPBIAS 1, COILED 1

NEP-B-genome

38

62

DISULFID 12, VAR_SEQ 8, REPEAT 6, TRANSMEM 5, COMPBIAS 3, METAL 2, ZN_FING 2, VARIANT 1, COILED 1, STRAND 1

NEP-E-Swissprot

7

93

TRANSMEM 3, VAR_SEQ 2, COMPBIAS 1, NP_BIND 1

NEP-E-genome

14

86

TRANSMEM 4, DISULFID 4, STRAND 3, ZN_FING 1, MOTIF 1, PROPEP 1

ORP-A-Swissprot

10

44

METAL 3, BINDING 2, ACT_SITE 1, DISULFID 1, MOTIF 1, TRANSMEM 1, HELIX 1

ORP-A-genome

0

6

 

ORP-B-Swissprot

7

93

METAL 4, BINDING 3, NP_BIND 1

ORP-B-genome

29

71

TRANSMEM 17, STRAND 4, HELIX 3, METAL 2, DNA_BIND 1, ACT_SITE 1, TURN 1, ZN_FING 1, DISULFID 1, CROSSLNK 1

ORP-E-Swissprot

24

76

METAL 10, ZN_FING 9, DNA_BIND 3, NP_BIND 1, TRANSMEM 1

ORP-E-genome

40

60

ZN_FING 22, DISULFID 5, COMPBIAS 2, REPEAT 2, CARBOHYD 2, TRANSMEM 2, LIPID 1, DNA_BIND 1, HELIX 1, COILED 1, VAR_SEQ 1, PROPEP 1

URP-A-Swissprot

13

87

COMPBIAS 7, METAL 4, VAR_SEQ 3, ZN_FING 2, REPEAT 1, COILED 1

URP-A-genome

79

21

ZN_FING 49, COMPBIAS 10, TRANSMEM 6, DISULFID 6, REPEAT 3, DNA_BIND 2, SIGNAL 2, ACT_SITE 2, NP_BIND 1, METAL 1, CARBOHYD 1, VAR_SEQ 1

URP-B-Swissprot

23

77

ZN_FING 10, METAL 8, DNA_BIND 3, NP_BIND 1, TRANSMEM 1

URP-B-genome

47

53

ZN_FING 24, DISULFID 9, COMPBIAS 2, TRANSMEM 2, HELIX 2, CARBOHYD 2, REPEAT 1, SIGNAL 1, METAL 1 TURN 1, NP_BIND 1, COILED 1, PROPEP 1, LIPID 1

URP-E-Swissprot

6

94

NP_BIND 2, METAL 2, BINDING 1, ACT_SITE 1

URP-E-genome

31

69

TRANSMEM 19, HELIX 4, STRAND 4, METAL 2, TURN 2, DNA_BIND 1, ACT_SITE 1, ZN_FING 1, CROSSLNK 1

  1. Known Swiss-Prot sequence features of peptide patterns were retrieved by matching peptide patterns against Swiss-Prot entries. Features that matched fewer than 20% of the sequence hits of a peptide pattern or were ambiguous (see Methods section) were excluded. The table shows the fraction of feature-associated patterns for each peptide set and the respective number of patterns associated with each feature. Individual data on each pattern are given in Additional files 3 and 4. wf, with feature, number of peptide patterns that matches a sequence feature type in at least 20% of all the sequence hits in Swiss-Prot (release 51.5); wof, without feature, number of peptide patterns that does not meet the criteria of wf.
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BMC Genomics

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