Table 2: Preliminary Alignment of HERV-K10 with IgG1Fc

HERV-K10/Autoantigen Bioinformatic Alignment Capsid/Nucleocapsid Viral Envelope


IgG1Fc  160-NGQP  92-TPEVT

Alignment Score  4/4  4/5

Replacement Score  -12

Key Rheumatoid Factor Epitopes on IgG1Fc:
256-TPEVTCVVVDVSHED-270             segment of fx2 face and b2 bend of CH2 domain
382-ESNGQPENNYKTTPP-396             b3 bend and segment fx3 face of CH3 domain

Epitopes taken from Westwood [18]. Numerals indicate amino acid position and sequence alignment (LALIGN software ( with reference to protein accession numbers: HERV-K10 Gag2 (Capsid and Nucleocapsid) (AAA88031.1), Pol/Env (AAA88033.1), IgG Fc (AF150959). Residues highlighted in bold indicate amino acid substitutions. Alignment score shown as number of identical residues/number in peptide segment. Amino acid replacement score taken from Tudos [19]. Amino acid single letter code: G=Glycine, A=Alanine, S=Serine, T=Threonine, C=Cysteine V=Valine, D=Asparate, E=Glutamate N=Asparagine, Q=Glutamine, P=Proline, K=Lysine, H=Histidine, Y=Tyrosine. Despite a low scoring amino acid replacement for A to V, the overall molecular shape could remain similar enough to enable antibody cross-reactivity.