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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.