Table 1: Viral, bacterial, and fungal protein homology with beta-amyloid (top), NGF (middle), or tau (bottom); Predicted B cell epitope segments were compared with Borrelia burgdorferi, C. neoformans, C. pneumoniae, H. pylori, P. gingivalis and herpes viruses (HSV1, HHV6, and cytomegalovirus) proteomes by BLAST analysis. The B cell antigenicity indices are shown, and those above the server set threshold of 0.35 are in italics. The first column shows the amino acid number within the peptide or protein sequence, and the second shows the amino acid pertaining to that position. The alignments with pathogen proteins are shown. Spaces represent nonidentical amino acids and + signs amino acids with similar physicochemical properties. Only highly antigenic regions of pentapeptides or more were processed. The VGGVV sequence, antibodies to which label beta-amyloid in brain tissue, despite relatively low antigenicity, has already been reported to be identical to proteins expressed by 69 viruses including HSV-1, HSV-2, and HHV6.
(a)

Position B-AmyAmino acidB-cell indexAlignments

1D0.41C. neoformans +AE HDSG+ Borrelia burgdorferi DAE F H+SG EV H. pylori DA FRH HSV-1 +AE RH HHV-6 D FR DS P. gingivalis +AEFR C. pneumoniae DA EFRHD and +AEFR +SG
2A0.35C. neoformans AEFR D GY+V H. pylori AEF D S YE and AE+RH+ Borrelia burgdorferi AEF H+ Cytomagalovirus AEFR HD HSV-1 AE R SG HHV-6 AE+ HD P. gingivalis A+F H+S and AEFR C. pneumoniae AEF DSG
3E0.62H. pylori EFRHD HHV-6 EF DSG Borrelia Burgdorferi EFR DS C. neoformans EF R DS YE P. gingivalis E R DSGY V C. pneumoniae EF SGYEV
4F0.73C. neoformans FRHDS Borrelia burgdorferi +RH SGY++ and F H+SG H. pylori F HD EV Cytomegalovirus FR SGY P. gingivalis +RHDS C. Pneumonia F H+SGY
5R0.85C. neoformans R D GYEV H. pylori RHDS Y V and R SGYE Borrelia burgdorferi RH+ GY Cytomegalovirus RHD YE and RHDSG HSV-1 RH SG HHV-6 RHDS P. gingivalis R+DS Y+
6H0.57C. neoformans HDSGY H. pylori H. pylori +DSGY and HD G EV and HD EV Borrelia burgdorferi H+SG Y+V HSV-1 HDSG P. gingivalis HDSG C. pneumoniae ++SGY+V
7D0.69C. neoformans DSGY+V H. pylori +SG+EV HSV-1 DSGY P. gingivalis DSG+EV C. pneumoniae DSGY V
8S0.38P. gingivalis SGYEV H. pylori SGYE C. neoformans SGY++ C. pneumoniae SG+EV
9G0.63H. pylori GYEVH Borrelia burgdorferi GYE V KL+ C. neoformans GYE LV and GY++ + LV P. gingivalis GYEV C. pneumoniae GYEV and GY HH
10Y0.56H. pylori YE HH and YE+ HQ and Y++H Q and YE HHQ Cytomegalovirus YEVH Borrelia Burgdorferi YE+ KL C. neoformans YE + QK FC P. gingivalis Y++H H+K C. pneumoniae Y+V +Q LV
11E0.58H. pylori EV +QK Cytomegalovirus EV HQ L Borrelia Burgdorferi EV +KL C. neoformans EV Q LV P. gingivalis EV KLV C. pneumoniae EV QKLV
12V0.35H. pylori. +H QK Cytomegalovirus V HQ LV HHV-6 VH QK+V Borrelia Burgdorferi VH KL C. neoformans +HH LV P. gingivalis VH + LV C. pneumoniae V HQKL
13H−0.17H. pylori and C. pneumoniae HHQK Cytomegalovirus HH KL P. gingivalis HH KL
14H−0.66Borreli Burgdorferi HQKL+ C. pneumoniae and HSV-1 HQKL P. gingivalis +QKLV
15Q−1.03C. neoformans and P. gingivalis and C. pneumoniae QKLV
16K−1.47H. pylori: Cryptococcus neoformans Borrelia burgdorferi Chlamydophila pneumoniae KLVFF Human herpesvirus 1 KLVF
17L−1.34Human herpesvirus 5: Human herpesvirus 6 LVFF
18V−1.20
19F−0.93
20F−0.98
21A−0.82
22E−0.31
23D0.23
24V0.81Borrelia burgdorferi Cryptococcus neoformans Porphyromonas gingivalis VGSNK Cytomegalovirus +GSNK Helicobacter pylori Chlamydophila pneumoniae VGSN
25G1.24H. pylori Chlamydophila pneumoniae GSNK
26S1.22
27N0.90
28K0.36
29G0.30
30A−0.24
31I−0.58
32I−1.00
33G−1.14
34L−1.19
35M−1.23
36V−1.1669 viruses/phages VGGVV
37G−0.97
38G−1.02
39V−0.63
40V−0.45
41I−0.80
42A−1.06

(b)

NGF positionAmino acidB-cell indexAlignment

18A0.59C. neoformans AEPHS
19E1.16P. gingivalis EPHSES—NVP Cytomegalovirus EPHS+S
20P1.32C. neoformans P+S NVPAG and PHSES and P SESNV
21H1.78Borrelia burgdorferi HSESN C. neoformans HSES VP and HSESN P H +P+
22S1.64C. neoformans S+S VPAG T P Borrelia burgdorferi burgdorferi C. neoformans Chlamydophila pneumoniae P. gingivalis SESNV P. gingivalis S+SNVP C. pneumoniae SESNV A
23E1.68C. neoformans ESNVP and ESNV AG
24S1.51C. neoformans SNVPA
25N1.61C. neoformans Cytomegalovirus P. gingivalis NVPAG C. neoformans NV TIPQA P. gingivalis +VPAG HT
26V1.45C. neoformans P. gingivalis VPAGH C. neoformans VP AGHT C. neoformans VPAG TI and V AGHT+
27P1.36C. neoformans HSV-1 PAGHT C. neoformans PAGHT P C. neoformans PAG TIP
28A1.04C. neoformans H. pylori AGHTI C. neoformans AG H IPQA and AGHT PQ and AGHT+P and AG TIP HSV-1 HSV-2 AGH PQ and AGHT QA
29G1.00C. neoformans GHTI Q and GHT PQ and G TIPQ
30H0.93C. pneumoniae HTI QA C. neoformans HT PQA and HTIP A
31T1.05C. neoformans P. gingivalis TIPQA
32I0.95
33P0.64
34Q0.41
35A0.46
51A0.38C. neoformans AR SAPA and AR APAA and A SAPAA and ARSA AA and ARSAP A and ARS PAA and AR—SAPAA
52R0.54HSV-1 RSAPAA Borrelia burgdorferi burgdorferri RSA AA
53S0.91C. neoformans C. pneumoniae Cytomegalovirus HSV-1 HSV-2 P. gingivalis SAPAA
54A0.89
55P0.72
56A0.69
57A0.53
64A0.46C. neoformans AG TRNI and AGQT RN and AGQTR P. gingivalis AGQTR
65G0.59C. neoformans + RNITV and GQTRN
66Q0.42P. gingivalis Borrelia burgdorferi QTRNI Cytomegalovirus QTRN—IT
67T0.43C. neoformans P. gingivalis TRNIT
68R0.49C. neoformans RNIT DP and RNITV
69N0.76C. neoformans C. pneumoniae H. pylori NITVD
70I0.66
71T0.56
90S0.40C. neoformans STQPPR and STQPP AA and STQPP EA C. pneumoniae STQ PRE C. pneumoniae Cytomegalovirus STQPP HSV-1 STQ PR
91T0.63C. neoformans TQP REA and TQPPR
92Q1.06C. neoformans QPPRE
93P1.49C. neoformans PP REAA C Neoformans P. gingivalis PPREA
94P1.91C. neoformans HSV-2 H. pylori PREAA
95R2.13C. neoformans P. gingivalis REAAD and REAA TQ and RE ADT C. neoformans REAA DT and R AADT and R+AADT and READD HSV-1 REAA T Borrelia burgdorferi burgdorferi Cytomagalovirus RE ADT Cytomagalovirus REAA TQ P. gingivalis REA +TQ
96E2.13P. gingivalis EAADTQ and EA TQDLD C. neoformans EAADT+ and EAAD QD and EAAD Q and EAA TQ
97A1.92Borrelia burgdorferi burgdorferi C. neoformans AA TQD Borrelia burgdorferi burgdorferi P. gingivalis AAD QD HSV-2 AADT D HHV-6 AAD +DL C. neoformans AADT D and AA TQD and A DTQD and A TQDL and AADTQ and AADT+ D+D P. gingivalis ADTQ L H. pylori AADTQ
98A1.9Borrelia burgdorferi ADT DLD C. neoformans AD QDLD and AD QDL P. gingivalis ADT DL and AD QDL H. pylori +TQDLD
99D1.39C. neoformans DT DLD and D QDLD C. pneumoniae DTQDL
100T1.25C. neoformans H. pylori P. gingivalis TQDLD
101Q0.66Borrelia burgdorferi burgdorferi C. neoformans H. pylori P. gingivalis QDLDF H. pylori QD DFEV
102D0.73Borrelia burgdorferi burgdorferi C. neoformans H. pylori DLDFE C. neoformans DLD EVG and DLDF VG
103L0.54C. neoformans LD EVGG and LDFE GG and LDFEV and LDF VGG H. pylori LDF EVGG HSV-1 HSV-2 L+ EVGG
104D0.45Borrelia burgdorferi burgdorferi DFEVG C. neoformans DF VGGA and D EVGGA
105F0.42C. neoformans FEVGG Cytomegalovirus FE GGAA
106E0.49C. neoformans EVGGAA and EVGGA P and EVGGA and EV GAAP and E+GGAAP H. pylori EVGGA Borrelia burgdorferi burgdorferi E+GG A PF+
107V0.39P. gingivalis VGGAAP and VGGAA C. neoformans VGGAA PF and VGGAA NR and VGGAA and VG GAAP C. pneumoniae VGGA AP H. pylori VG GAAP and VGG APF and VGGAA P. gingivalis VGGAA
108G0.74C. neoformans C. pneumoniae HSV-2 GGAAP
109G0.44C. neoformans GA APFN T and GAAPF
110A0.95C. pneumoniae AAPFN Borrelia burgdorferi AAP+NR HSV-1 AAP RT
111A0.83C. neoformans APFN T RS C. neoformans H. pylori APFN TH C. pneumoniae AP N RT R RSSS
112P0.99C. neoformans PFNRT and PF RTH Borrelia burgdorferi burgdorferi PF NRT
113F0.84C. neoformans FNRT SKR
114N0.75C. neoformans NR RSKRS S and NRT R RSSS Cytomegalovirus N T RSKRS
115R0.63C. neoformans RT R SKRS and RTHRS Borrelia burgdorferi burgdorferi RTHRS
116T0.63C. neoformans THRS RS and THRSK
117H0.64C. neoformans HRS RSS and HRSKR C. Pneumonie HRSKR
118R0.94C. neoformans RSKRSS and RS RSSS and RS KRSS and RS KRSS and RSK SSS and RSKRS S P. gingivalis RSKR S and RSKRS Borrelia burgdorferi burgdorferi RSKRS
119S0.88C. neoformans SKRSSS and SKRSS C. pneumoniae H. pylori HSV-1 HSV-2 SKRSS
120K1.12C. neoformans Cytomegalovirus HHV-6 H. pylori KRSSS
121R1.13
122S1.12
123S0.83
124S0.50
144G0.52C. neoformans GDKTTA and GDKTT
145D0.54H. pylori DK TATDI Borrelia burgdorferi burgdorferi C. neoformans C. pneumoniae H. pylori DKTTA HSV-1 +KTT TD
146K0.84CF. Pneumoniae KTTAT+ C. neoformans H. pylori KTTAT
147T1.27C. neoformans HSV-1 TTATDI C. neoformans P. gingivalis TTATD
148T1.22C. neoformans TATDIK Borrelia burgdorferi burgdorferi C. neoformans C. pneumoniae H. pylori TATDI
149A1.21C. neoformans HHV-6 HHV-6B P. gingivalis ATDIK
150T1.08
151D1.01
152I0.97
153K0.61
179C0.87C. neoformans CR PNPV C. pneumoniae CRDPN P+ S RGI
180R1.40C. pneumoniae RDPNPV Borrelia burgdorferi burgdorferi RD NP VDS C. neoformans RDP PVDS and RDPNP+ and RDPNP HHV-6 HHV-6B RDPNP HSV-1 HSV-2 RDPN V
181D1.36Borrelia burgdorferi burgdorferi D NPVD and DPN VD C. neoformans DPNPV and DP PVD and DP PVDS and DPN VDS C. pneumoniae DPN VD HSV-1 DPNP S HSV-2 +P PVDS
182P1.69C. neoformans PN VDSG and PNP DSG and PNPVD P. gingivalis PNPV+S and P PVDS
183N1.72H. pylori NPVD G
184P1.85C. neoformans PV DSGCR and P PVDS RG and PVDSG Cytomagalovirus P DSG RGI P. gingivalis PV DSGC
185V1.74HSV-2 VDSG RG HSV-1 +DSG RG C. neoformans VDSG R
186D1.51C. neoformans DSGC GI and DSG RG
187S1.28Borrelia burgdorferi burgdorferi C. neoformans SGCRG and SG RGI and S CRGI
188G0.79C. neoformans GC IDSKH W and GCRG D P. gingivalis GCRGI and GCRG+
189C0.79P. gingivalis CRGID C. neoformans C GIDS
190R0.85C. neoformans R IDSK and RGIDS and RGID K H. pylori RGIDS HSV-1 HSV-2 RG+DS H. pylori RG DSK Borrelia burgdorferi burgdorferi RGID K
191G0.65C. neoformans GIDS HW and GIDSK and GIDS H Borrelia burgdorferi burgdorferi H. pylori P. gingivalis GIDSK P. gingivalis GID KH and G DSKH H. pylori GI SKH
192I0.60Borrelia burgdorferi burgdorferi IDSKH C. neoformans P. gingivalis IDSK W
193D0.3C. neoformans DSKH W Borrelia burgdorferi burgdorferi DSK WN
194S0.40C. neoformans SKHW+
195K0.44
197W0.41
212T0.33C. neoformans TMDGKQ and TMDGK
213M0.31P. gingivalis MDGKQ
214D0.39C. neoformans DGKQAA and DGKQA C. pneumoniae DGK AA
215G0.48C. neoformans GKQAA
216K0.53
217Q0.45

(c)

Tau positionAmino acidB-cell indexAlignment

53E2.516C. neoformans (GSK3)EDGSEEP S and E+G EEPG and +DGS+EP S and ED GSEE GS and EDGS++ GS and EDGSE and +D EEPG and EDG S PGS Cytomagalovirus EDG EEP and +DG EE and ED GSEE P. gingivalis EDGSEE and E+G SEEP and EDGS EE HHV-6 HHV-6B EDGS EE C. pneumoniae E GSEE Borrelia burgdorferi E GSEE HHV-6 E GSEE
54D2.568C. neoformans DGSEEP and DGS+EPG and DGSEE G P. gingivalis DGS EPGS and DGSEE and DGS EP and DGSE EP and DGSE P Cytomegalovirus DGS EP and DG EE G C. pneumoniae DGSE GS and +G EE GS Borrelia burgdorferi DGSE+ P. gingivalis +GSEE
55G2.621C. neoformans GSEEP and G EEPG and G +EPGS and GS EEPG and GSEE G Cytomegalovirus GS+EP S P. gingivalis GS EPG H. pylori GSEE G C. pneumoniae GSEE GS
56S2.732C. neoformans SEEPG and SEE GS and S EPGS and SEEP S C. pneumoniae SEEPG and SEE GS and SE PGS P. gingivalis SEE GS and S EPGS
57E2.774C. neoformans EEPGS and +EPGS and EEPG E and EE GSE C. pneumoniae EEPGS HSV-1 HSV-2 EEPG
58E2.678HHV-6 HHV-6B EPGSE C. neoformans EPGSE and EPGS+ P. gingivalis EPGS+
59P2.564
60G2.544
61S2.556
62E2.287
171S2.315Borrelia burgdorferi SG GPED C. neoformans SG GPEDT and SGT PE and SGTGP and SG GPE and SGTG E and SG GP+ P. gingivalis SGTG E C. pneumoniae SGTG PE Cytomegalovirus SGTGP+
172G2.54C. neoformans GT PED and GTG ED and GTGPE and G GPED and GTGP D and G EDTE HSV-1 GTGPE and GTGP D and GTGP+D HSV-2 GTGP D and G GPED C. pneumoniae GTGPE H. pylori GTGP D
173T2.731HHV-6 TGPEDT and TG PEDT C. neoformans TG PEDT and TG EDT and T PEDT and TGPED C. pneumoniae TGPED H. pylori TG EDT Borrelia burgdorferi TGPE T+
174G2.709C. neoformans GPEDT and GPED TE and GP DTE and GPED E HHV-6 HHV-6B TG PEDT
175P2.807C. neoformans H. pylori P. gingivalis PEDTE
176E2.7
177D2.563
178T2.397
179E2.225
228S2.396HSV-1 SP DSPP and SPQ SP C. neoformans SPQDS and S QDSP and SP DSPP and SP DSPP and SPQD PP and PQ DSPPS and SPQ PPSK and SPQ SP and SP DSP and SPQ SP Cytomegalovirus SP DSPP P. gingivalis SP DSP Borrelia burgdorferi SP++SPP and SP D PSK
229P2.744C. neoformans PQ SPPS and P DSPPS and PQDSP and P+DSPP and PQ S PPSK and PQ SPP and PQD PP and P DSPP P. gingivalis PQDS P HSV-2 P DSPP HHV-6 PQ+ PP and PQ PP K Borrelia burgdorferi PQ+ P SK
230Q2.763C. neoformans QDSPP and ++ PPSK and QDS PS and Q SPPS P. gingivalis QD PPS C. pneumoniae QDS PS
231D2.929C. neoformans DSP PSK and DSPPS and DSP SK and D PPSK and +SPPS P. gingivalis DSP SK
232S2.882C. neoformans SPPSK
233P2.75
234P2.794
235S2.68
242D2.387C. neoformans DGRPP C. pneumoniae DG PPQ HSV-1 DG PPQ HSV-2 DGRPP and DG PP+ Cytomegalovirus DG R PQ and DG PP and +GRPP Borrelia burgdorferi DG PP
243G2.49C. neoformans GRPPQ
244R2.56
245P2.42
246P2.164
247Q2.004
331P2.259C. neoformans PGEG PE and P EGPEA and PGEGP and PGEG EA and P EGPEA and PGEG E Cytomegalovirus PGEGP EA and PG GPE C. pneumoniae PGE PEA and PGEGP H. pylori PG GPE HSV-1 HHV-6 PG GP A
332G2.681C. neoformans GEGPE and GEG EA and GE PEA and G GPEA and GEGP A and GEG EA and G+GPEA C. pneumoniae GE PEA P. gingivalis GEGPE and GEG EA
333E2.715C. neoformans P. gingivalis EGPEA HSV-2 +GPEA
334G2.634
335P2.592
336E2.463
337A2.405
414H1.819HSV-1 HSV-2 HPTPG C. neoformans HPT GSS and HP PGSS and HPTP SS and HP P SS C. pneumoniae HP PGS and +PT SS
415P2.274Cytomegalovirus P PGSS and PTPG SS C. pneumoniae PT GSS and PTPG SS
416T2.503
417P2.717
418G2.469
419S2.054
420S1.76
493P2.43HSV-1 P APKTP and P APKTP and PPAP PP and PPA PP HSV-2 PPAP TPP Cytomegalovirus P APKT and PPAP PP and PP P PPS and PP KTPP and PP A TPPS and PPA TPP C. neoformans PPAP TPPS and PPAP KTP S and PP PKTP and PP PKTP and PPAPKT and PPAP KT P. gingivalis PPAPK P C. pneumoniae PPAPK and PP PKT and PP AP PP and PP TPP Borrelia burgdorferi PAP T PS and PPA KTP and PP P TPP
494P2.77HSV-1 PAP KTP and PA KTPP HSV-2 PAPK PP HHV-6 PAP PPS C. neoformans PAPKTP S and PAPK PP P. gingivalis PAPKT C. pneumoniae PAP TP and PAPK P
495A2.94C. neoformans AP PPS P. gingivalis A KTPPS HHV-6 APKTP
496P2.89C. neoformans PKTPPS and PKTP PS and PK TPPS P. gingivalis PKT PS
497K2.95C. neoformans KTPPS
498T2.98
499P2.69
500P2.51
501S2.343
502S2.123