Table I. Putative Ptr1- and Ptr2-binding sites in the genome of M.jannaschii.

Site	Coordinates	Location	Potentially regulated gene	Function
Ptr1
ATCGCATTTGAAT	145 989–145 977	MJ0149	MJ0150	conserved hypothetical protein
TACGCATTGCGAA	147 231–147 219	IG	MJ0152	carbon monoxide dehydrogenase α-subunit (putative)
TTTTTATTGCGTA	159 707–159 719	IG	MJ0157	hypothetical protein
TTAATTTTGCGTA	677 806–677 818	MJ0752	MJ0751	transposase-related protein
ATGACATTGCGTA	685 027–685 039	MJ0762	MJ0761	conserved hypothetical protein
CGTTCATTGCGTA	773 274–773 262	MJ0846	MJ0847	N5-methyl-tetrahydromethanopterin:coenzyme Mmethyltransferase, subunit E (mtrE)
CAGTGATTGCGTA	1 030 136–1 030 124	MJ1092	MJ1092	conserved hypothetical protein
TACGCATGCATTT	1 275 882–1 275 870	IG	MJ1326	GTP-binding protein, GTP1/OBG family
Ptr2
CCACGATTTTCGGTA	308 286–308 300	MJ0331	MJ0330	hypothetical protein
TAAAAATTTTCGTCC	430 798–430 784	IG	MJ0486/MJ0487	conserved hypothetical protein, phenylalanyl-tRNAsynthetase, subunit α (pheS)
TTTGGATTTTCGTAT	555 672–555 658	MJ0627	MJ0628	hypothetical protein
AGACGATTATCGTAT	668 955–668 969	IG	MJ0740	rubredoxin
AGACGATTTTTAATA	759 162–759 148	MJ0834	MJ0833	hypothetical protein
GGACGATTTTTATGT	1 277 591–1 277 605	MJ1327	MJ1327-2	adenine-specific DNA methyltransferase
AGATGATTTTCGTCA	1 650 252–1 650 266	MJ1667	MJ1666	hypothetical protein

A search in the M.jannaschii genome (Bult et al., 1996) for sites closely matching the SELEX-derived Ptr1 and Ptr2 consensus binding sites yields a number of potential candidates, some of which are listed. For each site, the coordinates of the first and last nucleotide, the location [ORF or intergenic region (IG)] and the potentially regulated gene are indicated. The nucleotide positions matching the consensus are shown in bold, and those present in at least one SELEX clone are underlined.