Characterization and genome sequencing of two Propionibacterium acnes phages displaying pseudolysogeny

BMC Genomics

Table 1 Putative regulatory elements

Phage	Position	gp	Sequence	Score
Promoters
PA6	5620-5655	gp7	GTGCAG GGGGTGGTGTTGATGGGTATCAT TTTGAAG	73/16
PA6	7124-7159	gp11	TTGATA TTGTTGTTTGTTTTTTGTTTGAT ATTGTTT	33/58
PA6	28708-28742	gp46	TTAAAG CTTATAGGTATAATAATATAAT ATAAGTA	68/31
PA6	3740-3704	gp50	TAGTAA GTGCCCTCTCTTTTGTCGTATAAT CCGACCT	80/10
PA6	20693-20656	gp30	TTGACA CAAGCACTAGACACAGTGCTACAAT AAAACCA	72/66
PA6	28763-28724	gp45	TTTATA ACTTATAAGCTTTAATACTTATATTAT ATTATTA	61/39
PAD20	5618-5653	gp7	GTGCAG GGGGTGGTGTTGATGGGTATCAT TTTGAAG	73/16
PAD20	7104-7140	gp11	CTGAGT AAACGTATTTGTTTTTGTTTTAAT GTAATTG	55/3
PAD20	28024-28063	gp46	TTAAAG TTAACCATCAGTCTTAAACTTTAATAT TATAACC	61/31
PAD20	3738-3704	gp50	GTGAGT GCCCTTTCTTTTGTCGTATAAT CCGACCT	80/5
PAD20	20473-20436	gp30	TTGACA CAAGCCCTCAACACAGTGCTACAAT AAAACCA	72/66
PAD20	28084-28048	gp45	TTATAA GCTTTAATACTTATAGGTTATAAT ATTAAAG	90/24
PAS50	5615-5650	gp7	GTGCAG GGGGTGGTGTTGATGGGTATCAT TTTGAAG	73/16
PAS50	7101-7137	gp11	CTGAGT AAACGTATTTGTTTTTGTTTTAAT GTAATTG	55/3
PAS50	27980-28014	gp46	TTAAAG CTTATAGGTATAATAATATAAT ATAAGTA	68/31
PAS50	3740-3704	gp50	TAGTAA GTGCCCTTTCCTTAGTCGTATAAT CCGACCT	80/10
PAS50	20641-20604	gp30	TTGACA CAAGCCCTCAACACAGTGCTACAAT AAAACCA	72/66
PAS50	28035-27996	gp45	TTTATA ACTTATAAGCTTTAATACTTATATTAT ATTATTA	61/39
Terminators				MFE
PA6	16665-16713	gp21	GTGCCCCAGCGG TGCTGCCAC GATTGTGTGG TGGTTGCCGCTGGGGCAC	-39.9
PAD20	16682-16730	gp21	GTGCCCCAGCGG TGCTGCCAC GATCGTGTGG TGGTTGCCGCTGGGGCAC	-39.9
PAS50	16604-16652	gp21	GTGCCCCAGCGG TGCTGCCAC GATCGTGTGG TGGTTGCCGCTGGGGCAC	-39.9

The gp number represents the ORF directly after the regulatory element. Bold letters indicate the putative -10 and -35 site of the promoters, and the palindromes in the terminators. The score is given as -10/-35 for the promoters based on BPROM as described in Methods, and as minimal free energy (MFE) in kcal/mol for the terminators.

ISSN: 1471-2164