BioMed Research International / 2011 / Article / Tab 1

Research Article

Prediction of B-cell Linear Epitopes with a Combination of Support Vector Machine Classification and Amino Acid Propensity Identification

Table 1

Epitopes predicted in the PC dataset after analysis with LEPS.

Antigen : length (UniProt IDa)LEPS-predicted EpitopesExperimental epitopesRef.

PrP : 253
(P04156)
M1ANLGCWML9
R37YPGQG42[28]
Q52GG54[28]
Q91GGGT95[28]
N100KPSKPKTNMKHMA113[28]
G123GLGGYMLG131[28]
S143DYEDRYYRENMHRYPN159H140FGSDY 145[28]
Q160VYYRPMD167[28]
F198TETD202[28]
Y218ERESQAYYQRGS230

GAPDH : 338
(P20287)
A4KVGING10
A21AFLKNTVDV30
V31SVNDPFIDL40V31SVNDPFIDLEYM43 [29]
K48RDSTHGTFPGEVSTENGKLKVNG58EVSTENGKLKVNGKLISVHCERDP82 [29]
KL73
C78ERDPANIPWDKDGA92
A108QAHIKNNRAK118G100VFTTIDKAQAHIKN114 [29]
S123APSADAPM131
V136NENSYEKS144
V148SNASCTTN156
K163VIHDKFEIV172K163VIHDKFEIVE173 [29]
V188VDGPSSKLWRDGRGAM204
A210STGAAKAVG219
L225NGKLT230
R235VPTPDVSV243
R249LGKGASYEE258
F287VGSTSSS294S268GPLKGILEYTEDEVVSSDFVG289 [29]
I302SLNNNF308
Y315DNEFGY321
I329THMHKVDHA338

Ara h 1 : 626
(P43238)
K26SSPYQKKTENPC38K26SSPYQKK33[30]
Q47QEPDDLK54Q48EPDDLKQKA57[30]
E66YDPRCVY73[30]
P75RGHTGTTNQRSPPGERTRGRQPGE90RTRGRQPGDYDDDRR105[30]
DYDDDRRQPRREEGGRWGPAGPRER108REEGGRW115[30]
REREEDWRQPREDWRRPSHQQPRE124REEDWRQ131[30]
KIRPEGREGEQEWGTPGSHVREETSRE134DWRRPSHQQPRKIRPEG151[30]
NN173
P295GQFEDFF302[30]
Y312LQGFSRN319[30]
F325NAEFNEIRR334[30]
Q345EERGQRR352[30]
K381SVSKKGSEEEGDI394D393ITNPINLRE402[30]
N409NFGKLFEVK418[30]
G463NLELV468[30]
K472EQQQRGRREEEEDEDEEEEGSN
EV497
R498RYTARLKEG507[30]
E525LHLLGFGIN534[30]
H539RIFLAGDKD548[30]
I551DQIEKQAKDLAFPGSGE568[30]
P587QSQSQSPSSPEKESPEKEDQEEEN
QGGKGP617

SARS N : 422
(Q19QW0)
A36RPKQRRPQGLPNNTASWFT55 [31]
H60GKEEL65
T77NSGPDDQ84
L140NTPKDHIGTRNPNNN155
A156ATVLQLPQGTTLPKGFYAEGSRGG180 [31]
T266KQYNVTQAFGRRGP280 [31]
N286FGDQDLIRQGTDYK300 [31]
K356HIDAYKTFPPTEPKKDKKK375 [31]
R386QKKQPTVTLLPAADMDDFSRQLQN410 [31]

ZP3 : 399
(O77685, residue 24–422)
T31QSPAPGSSFSP42T31QSPAPGSSFSPPPVVA47[32]
Q71AAELTLGPSACAPVPAEPLSK92[32]
H101ECGSELQMTPDSLIYSTVLHY122[32]
P124NLSQ128L126SQSPLVLRSSP137[32]
G156IQPTWVPFHSTLSREQ172[32]
D251SSSIFISPRPG262[32]
V291TATDQAPSPLN302[32]
A311DEWLPVEGPRD322[32]
Q346EPGNPSEFEADLMLGPLVLSEAENGP372[32]

AIV-H4 : 511
(A3KF09, residue17–527)
Q17NYTGNPVIC26D107TCYPFDVPEYQSLR121 [33]
F137QWNTVKQNGKSGACKRANVNDFFNRLNWLVK [33]
S169DGNAYP175SDGNAYPLQNLTKINNGDYARLYIWGVHHPSTDT202
N206LYKNNPGRVTVSTK220 [33]
T224SVVPNIGSGPLVRGGQSGRVSXYWTIV250 [33]
V257FNTIGNLIAPRGHYKLNNQKKSTILNTAIPIGSC
SKCHTDKGSLSTTKPFQNISRIAVGDCPRYV
QGSLKLATGMRNIPEKASRGLFGAI349
[33]
D455SEMNKLFERVRRQL469 [33]
A473EDKGNGCFEIFHKCDNN490 [33]
N512RFQIQGVKLTQGYM526 [33]

AIV-H5 : 568
(A5HNY9)
A25NNSTEQVDTIMEKNVTVTHAQDILEKTHNGKL57 [33]
E85FLNVPEWSYIVEKINPANDLCYP108 [33]
C151PYQGRSSFFRNVVW165 [33]
D199AAEQTRLYQNPTTY213 [33]
R223SKVNGQSGRMEFFWTILKPNDAINFESNGNFIA [33]
ENAYKIV273
L472RDNAKELGNGCFEFYHR489 [33]
E284LEYGNCNTKC294

AIV-H12 : 527 (C7FPM3, residue 1–527)T35LIEQNVPVT44D31TVNTLIEQNVPVTQVEELVH51 [33]
K127YERVKMFDFTKWNVTYTGTSKACNNTSNQGS [33]
YRSMRWLTLKSGQFPVQTDEY180
F190TWAIHHPPTSDEQVKLYKNPNSLSSVTTDEINR [33]
FRPNIGPRPL234
Q238QGRMDYYWAVLKPGQTV255 [33]
T259NGNLIAPEYGHLITGKSHGRILKNDLPIGQCTTEC294 [33]
T310SKHYIGKCPKYIPS324 [33]
R334NVPQAQDRGLFGAIAGFIEG354 [33]
I430TDIWAYNAELLVLLENQKTLDEHDANVRNLHD [33]
VR465
G478CFEILHKCDDGCMDTIKNGT498 [33]
Q502DYEEESKLERQRINGVKLEENSTYK527 [33]

DEN-3 E-glycoprotein : 493 (D2JWZ8, residue 281–773)T331QLATLRKLCIEGKI345[34]
D351SRCPTQGEAVLPEEQDPNY370[34]
Q411YENLKYTVIITVHTGDQHQVGNETQGVT
AEITPQASTTE450
[34]
L476LTMKNKAWMVHRQW490[34]
S533QEGA537Q526EVVVLGSQEGAMHT540[34]
W669YKKGSSI676
L707NSLG711

O. tsutsugamushi 47-kDa antigen : 466 (Q53246)H21SKSLLNQKAVLPQQKSDMHIN42[35]
T65NIGISLNNKVSKYQQEV82[35]
V97TNENVIAGR106[35]
Y145ATFGDSNQS154[35]
V173TNGIISSKGRDMG186[35]
F193IQTNAAIHM202[35]
H201MGSFGGPMF210[35]
I233PSNTVLEAV242[35]
L245KKGEKIR252L245KKGEKIRRG254[35]
L333LRNGKSMTLKCKIIANK350[35]
Q357SNDQSLVVN366[35]
L373TPDLVKKYNITSA386[35]

HPV L1 protein : 510 (A8BQ01)D41VYVTRTNVYYHGGSSRLLTVGHPYYSIKKSNN
VAVPKV80
[36]
V122GRGQPL128V90KLPDPNKFGLPDADLYDPDTQRLLWACVGVEVG
RGQPLGV130
[36]
T205TIEDGDMVET215[36]
D219ICTNTCKYPDYLKMAAEPY238[36]
G235DSMFFSLRREQMFTRHFFNRGGKMGDTIPD285[36]
R326AQGHNNGMCW336
S350TNVSLCATEA360[36]
F370KEYLRHMEEYDLQFIFQLCKITLTPEIMAY400[36]
V416PPPPSASL424
K440PTPPKTPTDP450P450YASLTFWDVDLSESFSMDLD470[36]
G497TPPPTSKRKRV508

Bacillus anthracis, PA domain III and IV : 248 (P13423, residue 488–735)N538PSDPLETTKPDMT551R532RIAAVNPSDPLETTKPDMT551[37]
A596ELNATNIYTVL607[37]
I620RDKRFHYDRNNIAVGADES639[37]
L692NISSLRQDGKT703[37]
N720PNYK724L716YISNPNYKVNVYAVTKENT735[37]

aBecause some of the epitopes in the PC dataset were partial antigen fragments, the serial numbers for the residues in each epitope were assigned according to the sequence information retrieved from the UniProt database [38]. The overlapping amino acids between the experimentally verified and predicted epitopes are shown in bold.

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