. 2003 Dec 1;31(23):6891–6903. doi: 10.1093/nar/gkg879

Table 1. Combined set sequences for generating the Spo0A-phosphate positional weight matrix, including regulatory sequences upstream from the translation start site of known spo0A directly controlled genes in B.subtilis and orthologous genes in other Bacillus species.

Gene	Species	Binding site	Position	Score
abrB^I	B.subtilis	ttgtcgaa	–59	9.93
dltA^I	B.subtilis	ttgtcgaa	–198	9.93
kinA^I	B.subtilis	atgtcgaa	–37	8.82
kinC^I	B.subtilis	ttgtcgaa	–51	9.93
narQ^II	B.subtilis	ttgtcgaa	–55	9.93
sinI^I	B.subtilis	atgtcgaa	–163	8.82
spo0A-p1^I	B.subtilis	ttgtcgaa	–182	9.93
spo0A-p2^I	B.subtilis	ttgtcgaa	–61	9.93
spo0F^I	B.subtilis	ttgacgaa	–29	7.43
spoIIE^I	B.subtilis	ttgtcaaa	–63	7.87
spoIIGA^I	B.subtilis	ttgtcgag	–130	7.35
ykaA^II	B.subtilis	ttgtcgaa	–56	9.93
yneE^II	B.subtilis	ttgtcgga	–99	6.75
yqzD^II	B.subtilis	atgtcgaa	–247	8.82
yuxH^II	B.subtilis	ttgacgaa	–54	7.43
yvyE^II	B.subtilis	atgtcgaa	–154	8.82
ywcI^II	B.subtilis	ttgttgaa	–200	6.00
abrB^I	B.halodurans	atgtcgaa	–59	8.82
BH2351 (yneE ortholog)^II	B.halodurans	ttgtcgaa	–91	9.93
BH3630 (yvyE ortholog)^II	B.halodurans	atgtcgaa	–242	8.82
kinC^I	B.halodurans	atgtcaaa	–118	6.76
spo0A^I	B.halodurans	ttgtcgaa	–112	9.93
spo0F^I	B.halodurans	ttctcgaa	–150	6.37
spoIIE^I	B.halodurans	ttgtcaaa	–60	7.87
spoIIGA^I	B.halodurans	ttgtcaaa	–30	7.87
abrB^I	B.stearothermophilus	ttgtcgaa	–58	9.93
kinC^I	B.stearothermophilus	ttttcgaa	–131	6.04
spo0A^I	B.stearothermophilus	ttgtcgaa	–158	9.93
spo0A^I	B.stearothermophilus	ttgtcgaa	–66	9.93
spo0F^I	B.stearothermophilus	ttgtcgca	–11	6.75
spoIIE^I	B.stearothermophilus	acgtcgaa	–98	5.64
spoIIGA^I	B.stearothermophilus	ttgtcaaa	–112	7.87
ykaA^II	B.stearothermophilus	ttgtcgaa	–110	9.93
yvyE^II	B.stearothermophilus	ttgtcgaa	–137	9.93
abrB^I	B.anthracis	ttgtcaaa	–67	7.87
spo0A^I	B.anthracis	ttgtcgaa	–74	9.93
spo0F^I	B.anthracis	ttgacgaa	–338	7.43
ykaA^II	B.anthracis	ttatcgaa	–312	6.04
yvyE^II	B.anthracis	ttgtcgag	–126	7.35
spo0A^I	B.megaterium	ttgtcgaa	–81	9.93
spoIIGA^I	B.megaterium	atgtcgaa	–179	8.82
spo0A^I	B.thuringiensis	ttgtcgaa	–71	9.93

Genes that are initially from training set I and training set II are labeled with ^I and ^II, respectively.