These are single-strand (DNA) annealing proteins (SSAPs) that are related to the ERF protein of phage P22 that mediates circularization of linear double-stranded DNA following infection of the host cell (Poteete, 1982). The gene product

of PHIEF11_0044 also shows similarity to a single-stranded DNA-binding protein of a prophage of S. pyogenes MGA55005, and an SSAP of Lactococcus phage ul36.13. PHIEF11_0045 shows similarity to a replication protein of L. johnsonii prophage Lj928 (Table 1) and is presumably involved BYL719 in the replication of the φEf11 DNA. Replisome organizers, such as the DnaA protein of E. coli, function as initiators of DNA replication. They act by binding to the origin of replication (ori) and promote unwinding of the DNA. The unwound region of the DNA allows access of helicases such as DnaB/DnaC, and other proteins required for DNA polymerization, to replicate the DNA (Missich et al., 1997; Majka et al., 2001). PHIEF11_0047 contains a conserved domain of phage replisome organizer proteins from several different phages (Table 1). These include similarities in sequence to the replisome organizer domains of proteins from Listeria monocytogenes phage A118, S. aureus phage 52A, a Clostridium botulinum phage, and Streptococcus mitis phage SM10. Therefore,

PHIEF11_0047 appears to be a replisome organizer protein. Additional genes in the DNA replication/modification module include a putative methyltransferase (PHIEF11_0050), an SB431542 ASCH domain protein (PHIEF11_0054), and a SbcC domain protein (PHIEF11_0061). The domains found in these gene products are all associated with DNA replication functions. In addition, the final gene of this module (PHIEF11_0065) is similar to a gene of S. pyogenes phage SM1 that is in turn similar in sequence to a gene of Streptococcus phage NZ131.3 that functions in DNA replication (e.g. DNA polymerase III β-subunit/dnaN). PHIEF11_0062 has a significant HMM match to PF02195: ParB-like nuclease domain, suggesting a possible role in DNA replication. The location of

the lysogenized φEf11 genome within the lysogenic host TUSoD11 was investigated computationally by mapping the complete genome of φEf11 to the unfinished (draft) genome of E. faecalis strain TUSoD11 Chlormezanone (GenBank accession ACOX00000000), using NUCMER (Delcher et al., 2002). Analysis of the SHOW-COORDS output of the NUCMER package indicated the integrated genome of φEf11 spread across three contigs (ACOX01000066, 44 534 bp; ACOX01000045, 647 bp; and ACOX01000055, 103 862 bp), ordered relative to the φEf11 genome beginning with the integrase gene. Examination of the ends of alignments with TUSoD11 as the reference revealed a putative 27 bp attachment site with the sequence (ACTAAGCAAGTGCCGCCATGTGTCTGA), manifested as a direct repeat.