FIG. 3.

Map of the DMS3 genome. The arrows represent the predicted phage DMS3 ORFs and the predicted direction of gene transcription, with the ORF number appearing in bold above the arrow (see Table S2 in the supplemental material for more details regarding each ORF). Black arrows represent genes that were at least partially detected by both GeneMark.hmm and BLASTX, while gray arrows represent genes that were detected only by GeneMark.hmm. White areas represent intergenic regions. The organisms and phages included in the similarity profile were selected for having matches based on BLASTP expect values of less than 1e-19. The bacteriophage genomic sequences in the alignment and the abbreviation for each organism can be found in the lower right of the figure. The boxes labeled other (OT) represent similarity with expect values of less than 1e-19 for an organism that is not one of the 13 listed. The shaded boxes under each gene represent different degrees of similarity to detected genes based on the BLASTP expect values (the key is in the lower right of the figure). The “#” symbol represents the organism with the lowest expect value from BLASTP when the corresponding DMS3 ORF was analyzed. The “&” symbol indicates the organism most closely related to the DMS3 ORF by phylogenic analysis. The genes contained in each transcriptional unit are listed in the upper right of the figure.