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Table 1 Characterization of UPMs in protein families identified by RMA

From: A reinforced merging methodology for mapping unique peptide motifs in members of protein families

protein familya

UPM

Position

loop coverage (%)b

Molecular recognitionc

Refs

RNaseA d

     

Rnase1

MDSDSSPSSSSTY#

13–25

70

 

[48]

 

GQGNCYKSNSSMHITD#

68–83

31

 

[48]

 

KERHI#

102–106

0

 

[48]

 

FDASVEDST#

120–128

50

 

[48]

Rnase2

QQCTNAMQVI

21–30

60

 

[49]

 

MTCPSNKTR#

60–68

100

 

[49]

 

HSGSQ#

73–77

50

αRNase2e

[49],f

 

TPANMFYI#

101–108

0

 

[49]

Rnase3

ISLNPPRCTIAMR#

16–28

100

 

[50]

 

RCPHNRTLNN#

61–70

90

mAb 3C1e

[50],f

 

RSRFRVP#

73–79

29

 

[50]

 

INPGAQ

86–91

83

 

[50]

 

YADRPGRRF#

98–106

0

 

[50]

 

PRDSPRY#

116–122

100

D112-P123 Abe

[12, 50]

Rnase4

VHPEETGG#

13–20

64

 

[51]

 

RKMTLYH

32–38

86

 

[51]

 

IHEDIWNIR

46–54

0

 

[51]

 

CSTTNIQ#

57–63

100

 

[51]

 

EGVVK

73–77

0

 

[51]

 

RDTGS#

82–86

50

 

[51]

 

IASTRRVVI#

97–105

0

 

[51]

Rnase5

THFLT

7–11

0

 

[25]

 

KAICEN#

54–59

100

 

[25]

 

PHRENLRISKSSF#

64–76

14

protein-cell interactiong

[13, 25]

 

WPPCQY#

89–94

60

 

[25]

EGFR

     

ErbB

CQGTSN#

31–36

50

 

[14]

 

LSNYDA

144–149

0

 

[14]

 

SINATNI

350–356

100

EGF binding

[14]

 

RTDLHAF

414–420

100

 

[14]

 

TKQHGQF#

430–436

100

 

[14]

 

TSGQKT#

483–488

33

 

[14]

ErbB2

HLDMLRHLYQ

42–51

0

αErbB2 N-terme

[33] Stratagene Cat: B50175

 

ILWKDIFHK

144–152

100

 

[33]

 

GLGMEHL

321–327

100

 

[33]

 

APLQPEQ

367–373

100

 

[33]

 

HNGAYSL

414–420

71

 

[33]

 

CFVHTVPWDQLFR

452–464

100

 

[33]

ErbB3

YIEKNDKLC#

129–137

33

 

[52]

 

FAHEAECFSCH#

524–534

0

 

[52]

MMP d

     

MMP1

RGDHRD#

66–71

-g

  
 

SHSTDIG#

128–134

-

  
 

GRSQNPVQPI#

162–171

-

  
 

WAVQGQN

250–256

-

  
 

RTVKHI

273–278

-

αMMP1e

Santa Cruz Cat: sc-21731

 

YKRSM#

304–308

-

  
 

MIAHD

315–319

-

  
 

HGTRQYKF

341–348

-

  
 

KTKRILTLQKAN#

351–362

-

  

MMP3

QWTKDTTGT#

103–111

100

 

[15]

 

TDLTRFR

145–151

100

 

[15]

 

TEPVP

178–182

-

  
 

GTPANC#

186–191

-

  
 

KSLRKLEP#

218–225

-

αMMP3d

Santa Cruz Cat: sc-21732

 

PKQIAE#

324–329

-

  

Smad

     

Smad4

MDNMSITNT

1–9

-

  
 

TTNGAH

62–67

-

DNA binding

[20]

 

KHVKYCQY

110–117

-

  
 

IQTIQH

179–184

-

  
 

HPGHYWPVH

297–305

-

  
 

HKIYPSAYIK

427–436

0

 

[18]

 

AISLSA

481–486

0

 

[18]

 

GPDYPRQSI#

510–518

100

Ski binding

[18]

 

EVLHTMPIADPQPL

538–551

64

TGFβreceptor binding

[18]

  1. a The members of each protein family were analyzed by RMA. The proteins possessing resolved 3-D structures or epitope information are listed in column 1.
  2. b The loop coverage of each identified UPM was calculated and shown as the percentage localized within a loop in accordance with the 3-D structure.
  3. c The UPMs with known protein-molecule interaction are indicated.
  4. d The protein sequences do not include the signal peptides of RNases and pre-pro regions of MMPs.
  5. eThe epitopes of the antibodies containing or within the identified UPMs are indicated.
  6. fThe epitopes of the mAbs identified in this article are indicated.
  7. gThis UPM is responsible for the protein-cell interaction for the angiogenesis of RNase5.
  8. h"-", No 3-D structural information is currently available.
  9. #UPMs overlap with the potential antigenic regions by 70% as predicted by PROTEAN.