Alzheimer's Disease: A Pathogenetic Autoimmune Disorder Caused by Herpes Simplex in a Gene-Dependent Manner

Table 3

Major susceptibility gene products and members of other key signalling networks in Alzheimer’s disease (Sbjct) aligning with the translated HSV-1 genome (Query). The 6 amino acids with the highest B cell antigenicity index are highlighted in grey (see Table 1). Spaces denote a nonidentical amino acid; dashes represent gaps and + = conserved amino acid (similar physicochemical properties).

Human protein	Alignment with the HSV-1 translated genome
APOE4; 1B68A GI:15826311	Query 139585		139568
	Sbjct 111		116
	PICALM NP_009097.2 phosphatidylinositol binding clathrin assembly protein		Query 35856		35873
Sbjct 601		606
Complement receptor 1 complement receptor type 1 isoform S precursor NP_000642.3		Query 39696			39679
	Sbjct 2029	2034
	Clusterin isoform 1 NP_001822	Query 48155			48138
Sbjct 30		35
APP processing and related
3DXCA chain A, crystal structure of the intracellular domain of human APP in complex with Fe65	Query 78347		78364
	Sbjct 64		69
	EAX09965.1 amyloid beta (A4) precursor protein (peptidase nexin-II, Alzheimer)		Query 102020		102064
Sbjct 359		373
NP_958816.1 amyloid beta A4 protein isoform b precursor		Query 75494			75447
	Sbjct 536	550
	NP_620428.1 beta-secretase 1 isoform B preproprotein	Query 96347			96376
Sbjct 7		16
NP_620477.1 beta-secretase 2 isoform B preproprotein BACE2		Query 148387			148334
	Sbjct 5	23
	AAM92013.1beta-site APP-cleaving enzyme BACE1	Query 59005			58955
Sbjct 59		69
Query 115596		115576
Sbjct 70		76
EAW81096.1 presenilin 1 (Alzheimer disease 3), isoform CRA_f		Query 134424			134398
		Sbjct 240			247
	EAW69799.1 presenilin 2 (Alzheimer disease 4), isoform CRA_d	Query 40896			40873
Sbjct 152		159
NP_758844.1 gamma-secretase subunit PEN-2		Query 151699			151716
	Sbjct 55	60
	Query 142209	142186
	Sbjct 60	67
	NP_004960.2 insulin-degrading enzyme isoform 1 precursor	Query 25849			25875
		Sbjct 58			66
NP_061916.3 amyloid beta A4 precursor protein-binding family B member interacting protein APBB1IP		Query 26756			26673
	Sbjct 551	571
	NP_004877.1 amyloid beta A4 precursor protein-binding family A member 3 [Homo]	Query 148163			148119
Sbjct 132		143
NP_001633.1 amyloid-like protein 2 isoform 1 APLP2		Query 73214			73116
	Sbjct 579	597
	Query 63557	63595
	Sbjct 266	277
	NP_001123886.1 amyloid beta A4 precursor protein-binding family A member 2 isoform	Query 20300			20323
		Sbjct 212			219
AAL79526.1AF394214_1 adaptor protein FE65a2		Query 63303			63335
	Sbjct 572	582
	NP_663722.1 amyloid beta A4 precursor protein-binding family B member 1 isoform	Query 51630			51604
Sbjct 130		138
Query Q12830.3BPTF_Fetal Alzheimer antigen; Alz-50 clon		Query 41203
	Sbjct 22
	Query O94985.1 CSTN1; Calsyntenin-1 = Alcadein	Query 43114			43131
Sbjct 12		17
NP_009292.1 alpha-synuclein isoform NACP112		Query 54520			54549
	Sbjct 46	55
	Others
Query; Q07954.1LRP1_HUMAN RecName: Full=Prolow-density lipoprotein receptor-related protein	Query 92727		92701
	Sbjct 1425		1433
	NP_000577.2 interleukin-2 precursor		Query 27667		27647
Sbjct 20		26
NP_002084.2 glycogen synthase kinase-3 beta isoform 1		Query 86718			86698
	Sbjct 3	9
	NP_065574.3 choline O-acetyltransferase isoform 2 [Homo sap]	Query 67995			68030
Sbjct 87		102
NP_003947.1 cholesterol 25-hydroxylase		Query 66447			66467
	Sbjct 64	70