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Introduction: Flagellin (FliC) is an essential and universal subunit of flagella in motile bacteria. Analysis of the sequence diversity of the FliC protein in the Enterobacteriaceae family may provide insight into the pathogenic strategy of these bacteria in the context of interaction with pathogen-associated molecular patterns (PAMPs). In addition, the efficacy of FliC as an adjuvant or a component of the multi-epitope vaccine has been demonstrated.  Methods: We analyzed 392 full-length and non-redundant FliC proteins from the Enterobacteriaceae family. In the first step, isoelectric pH, molecular weight (kDa), and amino acid composition of FliC protein sequences were calculated using the ProtParam program. Next, the tertiary structure of the FliC proteins and its interaction with zebrafish TLR-5 was performed. Sequence alignments were performed using ClustalW software and the curricular phylogenetic tree was depicted using MEGA-7 software and iTOL web server. Finally, we evaluated the interaction of FliC proteins of Enterobacteriaceae family with TLR-5 to find the strongest docking. Results: Physicochemical properties and multiple sequence alignments revealed that FliC has a unique characterization in each genus. However, D1 as the binding domain site associated with TLR-5 exhibited high sequence conservation and the FliC protein of S. enterica subsp. enterica had the strongest interaction with TLR-5. Conclusions: FliC protein of S. enterica subsp. enterica can be consider as a promising epitope-delivery platform. In addition, phylogenetic analysis revealed that FliC may be acceptable marker for distinguishing genera in the family Enterobacteriaceae.

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