Observations in PhageD x StaphK comparison.

• Once again, using positional information approximately doubles the number of identifiable genes, and discovers unannotated genes in the previously published phage.
• In head tail region, apparent mosaicism is false.  It is due to a segment of a 3rd phage having been sequenced at about the same level of divergence.
• In ribonucleotide reductase region, apparent acquisitions from host genome is false.  The gene order and fine structure analysis indicates the involvement of gene conversion.  The true history would therefore be expected to be very different than indicated by which pair of sequences had the best blast score.
• Base plate assembly proteins are showing some rearrangements versus other myoviruses, including addition of a lysozyme domain.
• Some of the indels appear to be deletions that cut into the C terminus of the remaining gene.
• Tail genes are apparently in the order of assembly, but in reverse of transcriptional orientation.  In bacteriophage lambda, the tail genes appear in order of assembly and are transcribed in this order, leading to the suggestion that there may be synchronized waves of proteins made to coordinate with assembly.  Phage D appears to indicate that there is some other reason for gene order to coordinate with assembly order.
• Omp homologues in middle of tail module may suggest inclusion in tail structure.
• Fibers may have spectrin like structure.  eg. orf114 fits 1QUU.