BLASTp analysis

The blastp (algorithm version: BLASTP 2.11.0+ [25]) search was performed with T cell epitopes for RA, as query sequences, against the following organism groups: Bacteria (taxid: 2), Fungi (taxid: 4751) and Viruses (taxid: 10239). The remaining parameters were set at default values.

The obtained hits were further filtered according to the following criteria: percent identity ≥ 80%, query cover ≥ 80%, no gaps allowed, and e-value < 1. The protein sequences corresponding to the hits obtained by blasting the T cell epitope sequences over Bacteria/Fungi/Viruses were retrieved from the NCBI (https://www.ncbi.nlm.nih.gov/protein). Unique accession numbers for blasted and filtered bacterial, fungal and viral proteins were further used for retrieving the corresponding taxonomy information. Source Organism Lists for retrieved protein hits (BLASTp results) were obtained through the NCBI Entrez System.