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Table 2 Predicted HLA II epitopes HCV Proteins of Pakistani origin and their conservancy in Genotype 1, 2 and 3 worldwide

From: Promiscuous prediction and conservancy analysis of CTL binding epitopes of HCV 3a viral proteome from Punjab Pakistan: an In Silico Approach

Epitope start Position

Predicted T-cell epitopes

HLA alleles

HCV genotype 1

HCV Genotype 2

HCV Genotype 3

Capsid

     

43

L GVRATRKA

23

LGVRATRKTD

LGVRATRKT

LGVRATRKTD

36

L PRRGPRL G

15

LPRRGPRLG

LPRRGPRLG

LPRRGPRLG

106

W GPNDPRRR

16

WGPT DPRRR

WGPT DPRH RD

WGPNDPRRR

34

Y VLPRRGPR

24

YL LPRRGPR

YL LPRRGPR

YVLPRRGPR

21

V KFPGGGQI

8

VKFPGGGQI *

VKFPGGGQI

VKFPGGGQI

35

V LPRRGPRL

9

  

VLPRRGPRL

45

V RATRKASE

25

VRATRKT SED

VRATRKT SED

VRATRKT SED

30

V GGVY VLPR

39

VGGVYL LPR *

VGGVYL LPR

VGGVYVLPR

15

I RRPQDVKF

6

  

IRRPQDVKF

95

W LLSPRGSR

28

WLLSPRGSR

WLLSPRGSR

WLLSPRGSR

29

I VGGVYVLP

3

IVGGVYL LP *

IVGGVYL LP

IVGGVYVLP

82

W PLYGNEGC

10

WPLYGNEGC

WPLYGNEGC

WPLYGNEGC

85

Y GNEGCGWA

11

YGNEGCGWA

YGNEGCGWA *

YGNEGCGWA

33

V YVL PRRGP

1

VYL LPRRGP

VYL LPRRGP

VYVLPRRGP

Core

     

61

F LL ALLSCL

50

FLLALLSCL

FLLALLSCI

FLLALLSCL

64

L ALLSCLIH

45

LALLSCLTVDD

 

LALLSCLIH *

15

F ADLMGYIP

41

FADLMGYIP

FADLMGYIP

FADLMGYIP

24

L VGAPVGGV

44

LVGAPL GGA

 

LVGAPVGGV *

63

LL ALLSCLI

36

LLALLSCLTD

LLALLSCITD

LLALLSCLI *

62

FLL ALLSCL

24

FLLALLSCL

FLLALLSCI

FLLALLSCL *

32

V ARALAHGV

10

 

VARALAHGV

VARALAHGV

21

Y IPLVGAPV

28

YIPLVGAPL

YIPV VGAPL

YIPLVGAPV

19

M GYIPLVGA

26

MGYIPLVGA

MGYIPV VGA

MGYIPLVGA

E1

     

58

Y VGATTASI

41

  

YVGATTASI *

140

M VVAHILRL

39

  

MVVAHILRL*

2

W RNTSGLY V

27

  

WRNTSGLYV

138

V GM VVAHIL

28

   

56

V KY VGATTA

21

  

VR YVGATTAD *

9

Y VLTNARSN

31

  

YVLTNDC SNDD

161

W GVLAGLAY

15

WGVLAGM AY

WGVVF GLAY

WGI LAGLAY

93

F LVGQAFTF

11

FLVGQL FTF

 

FLVGQAFTF

181

I IMVMFSGV

91

  

IIMVMFSGV

130

M MMNWSPAV

35

MMMNWSPTAD

 

MMMNWSPAM

134

W SPAV GM VV

6

  

WSPAM GMVV *

132

M NW SPAV GM

14

  

MNWSPAM GM *

169

Y YTM QGNWA

18

  

YYS MQGNWA

47

W TPMTPTVA

21

  

WTPV TPTVA *

172

M QGNWAKVA

25

MV GNWAKVLD

MQGA WAKVID

WTPV TPTVAD *

145

I LRLPQTLF

19

  

ILRLPQTLF

E2

     

122

M LPHHRPVV

3

   

151

V FLLNPCGL

48

   

337

W EF VILVFL

4

  

WEFIV LVFL

339

F VIL VFLLL

46

  

FIV LVFLLL

35

W HINSTVLH

41

   

342

L VFLLLADA

 

LL FLLLADA

LL FLLLADA

LVFLLLADA

100

V LLAYAPRP

50

   

198

F RPLLPHRL

47

   

218

V RLGALVDT

12

   

62

F NLLDVPKA

45

   

26

L ELINTHGS

46

   

57

F YYHKF NLL

12

FYYHKFNSSD

 

FYYHKFNSTDD

83

V GPLDRCQH

26

   

58

Y YHKF NLLD

24

   

286

L LHSTTELA

17

LLHSTTEW A

 

LLHSTTELA

129

V VVGTTDPK

14

VVVGTTDKLDD

VVVGTTDRLDD *

VVVGTTDA K

320

V QYLYGVGS

46

VQYLYGVGS

 

VQYLYGVGS

159

L LVVGGLGG

14

   

293

L AILPCSFT

7

  

LAILPCSFT

335

L KWEF VIL V

4

  

LKWEFIV LV

322

Y LYGVGSGM

5

YLYGVGSSID

 

YLYGVGSGM

300

F TPMPALST

17

  

FTPMPALST

245

F YTVQGEDV

4

   

18

I VRGPEQRL

26

   

100

V LLAYAPRP

4

   

257

V WHRFTAAC

19

VE HRL TAACD *

  

206

L LQETSRGH

8

   

1

Y ITGGTAAR

8

   

267

W TRGERCDI

10

  

WTRGERCE I

310

I HLHQNIVD

11

IHLHQNIVD *

 

IHLHQNIVD

NS2

     

101

V RAHVLVRL

51

  

VRAHVLVRL

62

V ILLTSLLY

50

  

VILLTSLLY *

73

L VFDIAKLL

24

LVFDIT KLLD *

LVFDIT KLLD *

LI FDIT KLLD

153

L KDLAVATE

7

  

LKDLAVATE *

113

F VRSVTGGK

37

   

130

V GRWFNTYL

11

  

VGRWFNTYL *

123

F QMAILSVG

31

  

FQMI ILH VGD

137

Y LYDHLAPM

21

  

YLYDHLAPM

74

V FDIAKLLIA

23

VFDIT KLLL A D *

VFDIT KLLL AD

 

107

LV RLCMFVR

36

  

LVRLCML VR

108

V RLCMFVRS

51

  

VRLCML VRS *

89

YF VRAHV LV

33

  

YFVRAHVLV

11

IL VLFGFFT

15

   

37

Y AICRCESA

18

 

IIN GLPVSAD

YT ICRCESAD *

33

W WNQY AICR

8

  

WWNQYT ICRD

185

I LCGLPVSA

10

IIN GLPVSA *

IIN GLPVSA

ILCGLPVSA

145

M QHWAAAGL

18

  

MQHWAAAGL

50

V PPLLARGS

21

  

VPS LLARGSD *

88

LY LIQAAIT

35

  

LYLIQT AITD *

158

V ATEPVIFS

14

VAV EPVV FSD

VAV EPVV FS

VATEPVIFS

37

Y AICRCESA

19

  

YTICRCESAD *

175

W GADTAACG

11

WGADTAACG *

WGADTAACG *

WGADTAACG

NS3

     

4

V QVLSTATQ

46

VQIV STATQ

VQVLSSV TQD

 

43

L QMYTNVDQ

42

   

129

V CTRGVAKA

21

VCTRGVAKA

VCA RGVAKSDD *

 

24

W TVYHGAGS

13

WTVYHGAGT

WTVYHGAGN

 

84

VI PARRRGD

18

VIPV RRRGD *

  

138

L QF IPVETL

45

   

140

F IPVETLST

43

FIPVEN LG TD

  

6

V LSTATQTF

19

IV STATQTF

  

53

L VGWPAPPG

29

LVGWPAPQ G

LVGWPS PPGD

 

27

Y HGAGSRTL

22

YHGAGT RTI

  

14

F LGTTLGGV

10

   

77

L VTREADVI

25

LVTRH ADVI D *

LVTRN ADVID *

 

98

L SPRPLACL

12

 

LSPRPLST LD

 

124

IF RAAVCTR

44

   

NS4a

     

23

V VIVGHIEL

43

VVIVGR II LDD

VVIVGR IV LDD

VVIVGHIEL

3

W VLLGGVL AA

43

WVLV GGVLAA

WVLV GGVLAA

WVLLGGVLAA

4

V LL GGVL AAL

40

VLV GGVLAAL

VLV GGVLAAL

VLLGGVLAAL

38

V PDKEVLY Q

11

  

VPDKEVLYQ *

24

V IVGHI ELG

8

  

VIVGHIELG

10

L AALAAY CLS

8

LAALAAYCLT *

LAALAAYCLS

LAALAAYCLS

16

Y CLSVGCV V

6

 

YCLST GCVVD

YCLSVGCVV

26

V GHIELGGK

9

  

VGHIELGGK

25

I VGHIELGG

29

  

IVGHIELGG

20

V GCVVIVGH

15

  

VGCVVIVGH

9

VL AALAAY C

9

VLAALAAYC*

VLAALAAYC

VLAALAAYC

29

I ELGGKPAL

14

  

IELGGKPAL

NS4b

     

81

FF NILGGWV

41

  

FFNILGGWV

153

V NLLPAILS

51

VNLLPAILS

VNLLPAILS

VNLLPAILS

152

VV NLLPAIL

51

   

39

W NF VSGI QY

16

WNFI SGIQY

WNFI SGIQY

WNFVSGIQY

165

L VVGVICAA

35

LVVGVV CAA

LVVGVV CAA

LVVGVICAA

82

F NILGGWVA

32

FNILGGWVA

FNILGGWVA

FNILGGWVA

81

FF NILGGWV

5

  

FFNILGGWV

63

LM AFAASVT

9

LMAFT ASI TD

LMAFT AA VTDD

LMAFT ASVTD

27

W QKLEAFWH

35

 

WQKLEV FWAD

WQKLEAFWH *

167

V GVICAALL

11

VGVV CAAI L

VGVV CAAI L

VGVICAAI L

45

I QYLAGLST

35

IQYLAGLST

IQYLAGLST

IQYLAGLST

64

M AFAASVTS

23

MAFT ASI TS

MAFT AA VTSDD

MAFT ASVTSD

84

I LGGWVATH

24

ILGGWVAAQDD

ILGGWVAAQDD

ILGGWVATH

103

VV SGLAGAA

10

 

VGA GLAGAAD

VVSGLAGAA

166

VV GVICAAL

31

VVGVV CAAI

VVGVV CAAI

VGVICAAI L

85

L GGWVATHL

3

LGGWVAAQ LDD

LGGWVAAQ LDD

LGGWVATHL

60

V ASLMAFAA

15

  

VASLMAFT AD

41

F VSGI QYLA

8

FI SGIQYLA

FI SGIQYLA

FVSGIQYLA

139

F KIMGGELP

21

 

FKIMS GEV PD

FKIMGGEF P *

9

L QRATQQQA

14

  

LQRATQQQA *

122

L DILAGYGA

6

  

LDILAGYGA *

104

V SGLAGAAI

3

  

VSGLAGAAI

NS5a_1a

     

39

M RLAGPRTC

51

MRIV GPRTC *

FISCQKGYRD *

MRLAGPRTC*

3

F ISCQKGYK

22

FF SCQR GYKDD *

 

FISCQKGYK *

19

V VSTRCPCG

25

  

VM STRCPCG *

NS5a_1b

     

73

L LRDEITF V

20

LLRDEV TFQD*

LLRDEV TFQ D **

LLRDEITFV *

16

W RVAANSYV

33

WRVAAEE YVDD *

WRVAASE YVD

WRVAANSYV

55

F TEVDGVRL

4

FTEL DGVRL*

FTEVDGVRL **

FTEVDGVRL

80

FV VGLNSYA

25

  

FVVGLNSYA *

32

F HYITGATE

16

  

FHYITGATE

61

V RLHRYAPP

27

VRLHRYAPA*

 

VRLHRYAPP *

87

Y AIGSQLPC

20

YVV GSQLPC *

VRLHRYAPAD **

YAIGSQLPC *

23

YV EVRRVGD

14

YVEVT RVGDD *

YVEVT RVGDD **

YVEVRRVGD

  1. Bold amino acid residues in T-cell Epitope column indicates the anchor residues
  2. Bold individual amino acid residues in HCV Genotype 1, 2 and 3 columns indicated the variation in peptide in comparison to the predicted epitope
  3. *Indicates that one of the protein sequence selected for epitope conservancy either does not respond or have conservancy lower then 70%
  4. ** Indicates that only one of the protein sequence from selected sequences respond to epitope conservancy
  5. D Indicates that amino acid residue in case of single/double variation diverted their group compared to primary epitope using pI value
  6. DD Indicates that both amino acid residues in case of double variation diverted their group compared to primary epitope using pI value