In silico analysis of the genomes

Protein-encoding open reading frames (ORFs) were predicted using Glimmer [30]. Initial functional annotation of the ORFs and percentage amino acid identities were determined using BLASTP[31] and RAST server [32]. Transfer RNAs (tRNAs) were screened in the genomes using ARAGORN [33].

The BRIG software [34] was used for genome comparison of phage genomes which gave the best hit scores using BLASTP. Consequently, ɸAPCEc01 genome was compared to E. coli phages T4, vB_EcoM_JS09, RB27, vB_EcoM-VR7, Av-05, HX01, vB_EcoM_PhAPEC2, and RB69 (GenBank numbers {"type":"entrez-nucleotide","attrs":{"text":"NC_000866","term_id":"29366675","term_text":"NC_000866"}}NC_000866, {"type":"entrez-nucleotide","attrs":{"text":"NC_024124","term_id":"897635950","term_text":"NC_024124"}}NC_024124, {"type":"entrez-nucleotide","attrs":{"text":"NC_025448","term_id":"713322590","term_text":"NC_025448"}}NC_025448, {"type":"entrez-nucleotide","attrs":{"text":"NC_014792","term_id":"314121562","term_text":"NC_014792"}}NC_014792, {"type":"entrez-nucleotide","attrs":{"text":"KM190144","term_id":"670141132","term_text":"KM190144"}}KM190144, {"type":"entrez-nucleotide","attrs":{"text":"NC_018855","term_id":"408905850","term_text":"NC_018855"}}NC_018855, {"type":"entrez-nucleotide","attrs":{"text":"NC_024794","term_id":"682124280","term_text":"NC_024794"}}NC_024794, and {"type":"entrez-nucleotide","attrs":{"text":"NC_004928","term_id":"32453484","term_text":"NC_004928"}}NC_004928, respectively), and to Shigella phage Shf125875 (GenBank {"type":"entrez-nucleotide","attrs":{"text":"KM407600","term_id":"678223442","term_text":"KM407600"}}KM407600). ɸAPCEc02 genome was compared to E. coli phages rv5, 2 JES-2013, vB_EcoM_FFH2, and vB_EcoM-FV3 (GenBank numbers {"type":"entrez-nucleotide","attrs":{"text":"NC_011041","term_id":"194172859","term_text":"NC_011041"}}NC_011041, {"type":"entrez-nucleotide","attrs":{"text":"NC_022323","term_id":"543170177","term_text":"NC_022323"}}NC_022323, {"type":"entrez-nucleotide","attrs":{"text":"NC_024134","term_id":"640883453","term_text":"NC_024134"}}NC_024134, and {"type":"entrez-nucleotide","attrs":{"text":"NC_019517","term_id":"422936321","term_text":"NC_019517"}}NC_019517, respectively). ɸAPCEc03 genome was compared to E. coli phages T5, bV_EcoS_AKFV33, DT57C, DT571/2, and vB_EcoS_FFH1 (GenBank numbers {"type":"entrez-nucleotide","attrs":{"text":"NC_005859","term_id":"46401737","term_text":"NC_005859"}}NC_005859, {"type":"entrez-nucleotide","attrs":{"text":"NC_017969","term_id":"388570360","term_text":"NC_017969"}}NC_017969, {"type":"entrez-nucleotide","attrs":{"text":"KM979354","term_id":"735997779","term_text":"KM979354"}}KM979354, {"type":"entrez-nucleotide","attrs":{"text":"KM979355","term_id":"735997913","term_text":"KM979355"}}KM979355, and {"type":"entrez-nucleotide","attrs":{"text":"KJ190157","term_id":"601129293","term_text":"KJ190157"}}KJ190157, respectively), to Salmonella phages SPC35, Shivani, and Stitch (GenBank numbers {"type":"entrez-nucleotide","attrs":{"text":"HQ406778","term_id":"321272088","term_text":"HQ406778"}}HQ406778, {"type":"entrez-nucleotide","attrs":{"text":"KP143763","term_id":"738494471","term_text":"KP143763"}}KP143763, and {"type":"entrez-nucleotide","attrs":{"text":"KM236244","term_id":"701946893","term_text":"KM236244"}}KM236244, respectively), and to Yersinia phage phiR201 (GenBank {"type":"entrez-nucleotide","attrs":{"text":"HE956708","term_id":"1005925709","term_text":"HE956708"}}HE956708).