Score as provided by TransTermHP, only terminators with a score above 90 are shown. Features of the JG004 genome A schematic EVP4593 clinical trial representation of the genome, with its predicted CDSs, the tRNA locations, some functional assignments and overall genetic organization is shown in Dorsomorphin Figure 3 and Additional file 1, Table S1. The genome of phage JG004 shows 11.3% intergenic space. This is comparable with the genome of the host P. aeruginosa PAO1 which has 10.6% non-coding regions [25]. Putative functions could be assigned to

only 30 (18.5%) genes based on sequence similarities (Figure 3). Although phage JG004 and PAK-P1 share strong similarities, we found 19 genes with no similarities to PAK-P1 including 13 genes with no significant similarities to any protein in the 3-MA ic50 database.

The proteins with no similarity to other proteins are small proteins with a size between 47 aa and 112 aa. It is still difficult to accurately predict short genes with computational methods [26], therefore, these predictions are uncertain. Figure 3 Genome of JG004. Schematic representation of the JG004 genome with its assumed tRNAs, genes and some functional assignments. The arrowheads point in the direction of transcription. Gene 46-57 represent the tRNAs of phage JG004. Predicted terminator structures are indicated as hairloop structures. No significant match to proteins annotated as integrase, repressor or transposase was found, suggesting that this phage is a virulent phage which is in concordance with the results of the highly related phage PAK-P1 [27]. Gene 66 has similarities to RNA polymerases (e-value: 6e-41) suggesting that the phage JG004 is probably not dependent on the host transcriptional machinery. Moreover, genes encoding for enzymes of the DNA replication machinery were found, suggesting that the DNA replication is also independent from the host. We found genes with similarities to a DNA polymerase (gene 111; e-value: 0.0), a DNA

helicase/primase (gene 110; e-value: 0.0), a thymidylate synthetase (gene 130; e-value: 6e-70), a ribonucleoside-diphosphate reductase (gene 132, 133; e-values: 0.0) and to a putative exodeoxyribunuclease (gene 117; e-value: 1e-28). A terminase like gene (gene Coproporphyrinogen III oxidase 59; e-value: 0.0) could also be detected. Phage terminases are DNA packaging enzymes and are among the most conserved proteins found in phages. Some terminases also contain endonuclease activity to cut DNA into the genome length of the respective phage [28]. Two putative endonucleases were also detected (gene 36, 70; e-values: 2e-8, 3e-14). Endonucleases could be involved in the DNA packaging process or in host nucleic acid damaging. Interestingly, the putative endonuclease gene 70 has no homologue in phage PAK-P1. Moreover, one putative methyltransferase was found (gene 61; e-value: 4e-8).