Bacterial genome sequencing and progress in genomic research over the last decade has revealed the high incidence of prophage elements in bacterial genomes. Prophages contribute 10 - 20 % of bacterial genome and account for substantial inter-strain genetic variability in several bacterial species. These elements are defective and cannot form infective particles but have also been implicated in providing fitness factors. Prophage database (either in India or Israel) is a comprehensive database for prophage elements and phage remnants. The first version contains a total of 226 prophage entries covering a total of 6,628 proteins. Genome level data briefs on details of prophage location, genome size, GC content, taxonomy, and functionality of the prophages. Protein level data details possible functional and domain annotation, whether the protein is likely to be disordered and other details, which are useful as selection criteria for structural genomics initiatives. This work emphasizes the need to extend the efforts to detect and annotate prophage elements in genomes sequences. This provides a step towards the development of effective and systematic support for prophage data management and enables this to serve as a platform for prophage detection and target selection for structural genomics.