Systematic identification of stem-loop containing sequence families in bacterial genomes

BMC Genomics

Table 4 Secondary structure prediction analysis of families.

Species	Family	P	Conserved structure	Conserved SLS position	SLS folding aptitude	Type
B. anthracis	Bcr1	0.99	s	+	+	I
B. halodurans	Bhal-1	0.98	s	+	++	I
	Bhal-2	0.99	c		-	I
C. perfringens	Clop-1	0.96	s	+	+	I
C. tetani	Clot-1	0.95	s	+	++	I
E. faecalis	Efa-1	0.85	s	+	+++	I
	Efa-2	1.00	s	+	-	G
L. johnsonii	Lac-1	0.97	c	+°	-	G
S. aureus	Sta-1	0.84	s	+	+++	I
	Sta-2	1.00	s	+	++	S
	Sta-3	0.97	s	+	+	I
B. melithensis	Bru-RS	0.98	s	+	+	I
R. conorii	Rpe-4	0.73	s	+	-	I
	Rpe-5	1.00	s	+	+	I
	Rpe-6	0.45	-	+°	+
	Rpe-7	0.99	s	+	++
M. genitalium	Myg-1	0.06	-	+°	-	I
M. pneumoniae	Myp-1	0.00	-	+°	-	G
	Myp-2	0.95	s	+	++	G
	Myp-3	0.89	s	+	-	G
	Myp-4	0.09	-	+°	-	G
	Myp-5	0.74	s	+	-	G
	Myp-6	0.55	c		-	G
	Myp-7	0.67	s	+	-	G
C. diphtheriae	Cod-1	0.97	s	+	+++	I
	Cod-2	0.98	s		-	G
	Cod-3	0.99	s	+	+++
M. tuberculosis	Myt-1	0.74	s	+	+++
	Myt-8	0.90	s	+	++
M. leprae	REPLEP	1.00	c	+°	-	I
	RLEP	1.00	s	+	++	S
	Myl-1	0.61	s	+	++	S
	Myl-2	0.97	s	+	+	S
B. bronchiseptica	Bor-1	0.86	s	+	++	I
	Bor-2	1.00	s	+	-	I
B. pertussis	Bor-1	0.93	s	+	++	I
N. meningitides	ATR	1.00	s	+	-	I
	Nem-2	0.93	s	+	+
	Nem-4	0.93	s	+	+++	I
	dRS3	0.98	c		-	I
	NEMIS	1.00	s	+	+	I
	Rep2	0.98	s	+	+	I
P. multocida	Pam-1	0.96	s	+	+++	S
E. coli	BoxC	0.99	c	+°	-
	Eco-1	0.18	-	+°	-	G
	ERIC	0.94	s	+	++	S
	PU-BIME	0.94	s	+	+
H. influenzae	Hin-1	0.96	s	+	+	I
P. aeruginosa	Pae-1	0.97	s	+	++	I
	Pae-3	0.26	-	+°	-	G
	Pae-4	0.93	s	+	++
P. putida	Ppu-1	0.97	s	+	+	I
	Ppu-2	1.00	s	+	+++	S
	Ppu-4	0.95	s	+	-	I
	Ppu-9	0.54	s	+	-	I
S. typhi	PU-BIME	0.97	c		-	I
	PU*-BIME	0.98	s	+	-
S. typhimurium	PU-BIME	0.98	s	+	-
	Sal-1	0.94	c		-	I
	Sal-2	1.00	c		-	G
Y. pestis	ERIC	0.90	s	+	-	I
	YPAL	1.00	s	+	+++	I
	YPAL*	0.96	c		-	I

The ability to form a consensus secondary structure was evaluated by RNAz: the prediction scores are reported in column "P" for each family. The type of predicted structure is indicated in column "conserved structure", where "s" indicates a s tem-loop based structure, while "c" indicates a more c omplex structure, where a stem-loop compatible with the original search is not present. For each family, the aligned localization of the original SLSs is indicated by '+' in column "conserved SLS position"; when SLS alignment is not in agreement with the RNAz prediction, a '°' is added to the '+' symbol. The column marked "SLS folding aptitude" reports the behavior of family elements in the RANDFOLD test: the number of '+' symbols describes the percent of positive elements ('+++' if 90% or above; '++' if 70–90%; '+' if 50–70%; '-' if less than 50%). The localization of family members, as already described in Table 3, is also reported in the last column.

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