Table 3: Viral, bacterial, and fungal protein homology with beta-amyloid; beta-amyloid 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 and T cell antigenicity indices are shown, and those above the server set threshold of 0.35 (B cell epitope) or 0.5 (T cell epitope) are highlighted in bold. The first column shows the amino acid sequence of beta-amyloid1-42 and 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 [230].

B cellT cellAlignments

D0.410.04+AE HDSG+ C. Neoformans DAE F H+SG EV Borrelia burgdorferi DAEF H. Pylori DA FRH H. Pylori +AE RH HSV-1 D FR DS HHV-6 +AEFR P. Gingivalis DA EFRHD and +AEFR +SG C. Pneumoniae
A0.350.78AEFR D GY+V C. Neoformans AEF D S YE H. pylori AE+RH+ H. pylori AEF H+ Borrelia burgdorferi AEFR HD Cytomegalovirus AE R SG HSV-1 AE+ HD HHV-6 A+F H+S and AEFR P. Gingivalis AEF DSG C. Pneumoniae
E0.620.02EFRHD H. Pylori EF DSG HHV-6 EFR DS Borrelia Burgdorferi EF R DS YE C. Neoformans E R DSGY V P. Gingivalis EF SGYEV C. Pneumoniae
F0.730.93FRHDS C. Neoformans +RH SGY++ Borrelia burgdorferi F HD EV H. Pylori F H+SG H. Pylori FR SGY Cytomegalovirus +RHDS P. Gingivalis F H+SGY C. Pneumonia
R0.850.05R D GYEV C. Neoformans R SGYE H. pylori RHDS Y V H. pylori RH+ GY Borrelia burgdorferi RHDSG Cytomegalovirus RHD YE cytomegalovirus RH SG HSV-1 RHDS HHV-6 R+DS Y+ P. Gingivalis
H0.570.14HDSGY C. Neoformans HD G EV H. pylori +DSGY H. pylori H+SG Y+V Borrelia burgdorferi H+SG HSV-1 HDSG P. Gingivalis ++SGY+V C. Pneumoniae
D0.690.03DSGY+V C. Neoformans +SG+EV H. pylori DSGY HSV-1 DSG+EV P. Gingivalis DSGY V C. Pneumoniae
S0.380.02SGYEV P. Gingivalis SGYE H. pylori SGY++ C. Neoformans SG+EV C. Pneumoniae
G0.630.04GYEVH H. pylori GYE V KL+ Borrelia Burgdorferi GYE LV and GY++ + LV C. Neoformans GYEV P. Gingivalis GYEV and GY HH C. Pneumoniae
Y0.560.96YE HH and YE+ HQ and Y++H Q and YE HHQ H. pylori YEVH Cytomegalovirus YE+ KL Borrelia Burgdorferi YE + QK FC. Neoformans Y++H H+K P. Gingivalis Y+V +Q LV C. Pneumoniae
E0.580.02EV +QK H. pylori EV HQ L Cytomegalovirus EV +KL Borrelia Burgdorferi EV Q LV C. Neoformans EV KLV P. Gingivalis EV QKLV C. Pneumoniae
V0.350.90.+H QK H. pylori V HQ LV Cytomegalovirus VH QK+V HHV-6 VH KL Borrelia Burgdorferi +HH LV C. Neoformans VH + LV P. Gingivalis V HQKL C. Pneumoniae
H−0.170.10HHQK H. pylori and C. Pneumoniae HH KL Cytomegalovirus HH KL P. Gingivalis
H−0.660.11HQKL+ Borreli Burgdorferi HQKL C. Pneumoniae and HSV-1 +QKLV P. Gingivalis
Q−1.030.03QKLV C. Neoformans and P. Gingivalisand C. Pneumoniae
K−1.470.93KLVFF H. pylori: Cryptococcus neoformans Borrelia Burgdorferi Chlamydophila pneumoniae KLVF Human herpesvirus 1
L−1.340.95LVFF Human herpesvirus 5: Human herpesvirus 6
V−1.200.68
F−0.930.69
F−0.980.74
A−0.820.05
E−0.310.05
D0.230.11
V0.810.88VGSNK Borrelia burgdorferi Cryptococcus neoformans Porphyromonas gingivalis +GSNK Cytomegalovirus VGSN Helicobacter pylori Chlamydophila pneumoniae
G1.240.03GSNK Helicobacter Pylori Chlamydophila pneumoniae
S1.220.03
N0.900.03
K0.360.30
G0.300.10
A−0.240.05
I−0.580.07
I−1.000.13
G−1.140.03
L−1.190.72
M−1.230.13
V−1.160.23VGGVV 69 viruses/phages
G−0.970.03
G−1.020.03
V−0.630.23
V−0.450.33
I−0.800.95
A−1.060.83