ProteoKnight: Convolution-based phage virion protein classification and uncertainty analysis

Proteins are essential macromolecules responsible for the structural and functional mechanisms of living things. Phage structural proteins are a subclass of the protein family corresponding to the bacteriophages, which are the most prevalent kind of biological creatures [1]. The PVPs are mainly associated with building structural constituents of the bacteriophage [2], such as the baseplate and head as shown in Figure 1, enabling efficient host-phage binding for genome transfer. The amino acid sequences, particularly those involved in structure synthesis, exhibit significant diversity among phages and their respective groups [3]. Consequently, characterizing these sequences becomes a challenging yet crucial task, as the shortage of annotations for phage proteins has emerged as a hindrance in numerous research studies focused on phage genomics [4]. With the advent of high-throughput sequencing technology, rapid additions of sequences are being observed in standard biological databases [6] as shown in Figure 1, giving rise to the need for proper annotation of the sequences. Enhancement of annotations for the phage family is vital for exploring effective anti-bacterial drug synthesis [7, 8], disease diagnosis [9], food production [10], bacterial genome remodeling [11], etc. Traditionally, mass spectrometry and protein array techniques [12, 13] were utilized for characterizing these proteins. However, these methods are associated with significant time, labor, and computational expenses [1]. Similarly, alignment-based methods do not always work well with PVP categorization due to the lack of collinearity [14] in viral genomes, resulting from factors such as horizontal gene transfer, high mutation rates, etc., leading to dissimilar sequences 2 Figure 1 Structural constituents of Phage