Bioinformatics analysis of bacterial protective antigens in manually curated Protegen database

Protective antigens are targeted by host acquired immunity and able to induce protection against infectious diseases. To identify enriched features that do not typically exist in non-protective protein antigens, this study analyzed 201 protective protein antigens from Gram-negative bacteria and 69 protective protein antigens from Gram-positive bacteria available in the manually curated Protegen protective antigen database. Our study found that 64% of Gram+ protective antigens are extracellular or cell wall proteins and 48% of protective antigens in Gram^-bacteria belong to extracellular or outer membrane proteins. Approximately 54% and 40% protective antigens in Gram+ and Gram-, respectively, are adhesins or adhesin-like proteins. Many conserved domains (motifs), such as Autotransporter and TonB domains, are enriched in protective antigens. A protection method based on SVM (Support Vector Machine) classification demonstrates 92% of true positive rate of sequence-based protection. This study represents a pioneer effort in the identification and prediction of specific patterns in protective antigens.