TABLE 2.

Candidate Per boxes identified upstream of Borrelia ORFs^a

Gene	Putative identificationb	Putative Per box sequence(s)c	Position relative to ATG start site	No. of matches/total	Location in Borrelia genome	Comment (reference)
BB0083	Hypothetical protein	TTAAAATAATTATTA	−52	13/15	Chromosome
		TTTTAATTATTATAT	−94	13/15
BB0084	NifS protein (nifS)	ATATAATAATTAAAA	−49	13/15	Chromosome	Putative cysteine desulfurase (20)
		TAATAATTATTTTAA	−91	13/15
BB0166	4-α-Glucano transferase (malQ)	TGATATTTATTATAA	−66	13/15	Chromosome
BB0167	Outer membrane protein (tpn50)	TTATAATAAATATCA	−88	13/15	Chromosome
BB0565	Purine-binding chemotaxis protein (cheW-2)	TGATAATAATTATTA	−253	13/15	Chromosome	First gene in BB0565-BB0570 chemotaxis operon (15)
BB0657	Ribose 5-phosphate isomerase (rpi)	TACTAATAATTATAA	−116	13/15	Chromosome
BB0658	Phosphoglycerate mutase (gpmA)	TTATAATTATTAGTA	−47	13/15	Chromosome
BB0664	Hypothetical protein	TTATAATAATCATAT	−13	13/15	Chromosome
		TTAAAATCCTTATAA	−33	13/15
BB0665	Conserved hypothetical protein	TTATAAGGATTTTAA	−24	13/15	Chromosome
		ATATGATTATTATAA	−44	13/15
BB0689	Hypothetical proteind	ATATAATTATTATAA	−71	14/15	Chromosome
BB0690	Neutrophil-activating protein (NapA)	TTATAATAATTATAT	+6	14/15	Chromosome	Per box located −28 relative to second ATG start site
BBA69	Hypothetical protein	TTAATATAATTATAA	−71	13/15	Plasmid lp54
BBE22	Pyrazinamidase/nicotinamidase (pncA)	TATTAATAATTATAA	−255	13/15	Plasmid lp25	Gene required for mammalian infection (49)
		TTAATATTATTATAA	−374	13/15
BBG06	Conserved hypothetical protein	TTATAATTATAATAT	−145	13/15	Plasmid lp28-2	First gene in 4-gene plasmid maintenance locus (14)
		TTTTTATAATTATAA	−148	13/15
BBH40	Putative transposase-like protein	TTATAATTATAAAAA	−18	13/15	Plasmid lp28-3
BBI16	Hypothetical proteind	TTATAATAAATATAA	−55	14/15	Plasmid lp28-4	Virulent strain-associated repetitive antigen A (58)
		TTTAAATAATTATAA	−237	13/15
BBI28	Hypothetical proteind	TTATAATAAGTATAA	−47	14/15	Plasmid lp28-4	Homologue of BBI16
BBI41	Hypothetical protein	TTATAATTATAAAAA	−18	13/15	Plasmid lp28-4	Homologue of BBH40
		ATATTATAATTATAA	−21	13/15
BBI42	Putative outer membrane proteind	TTATAATTATAATAT	−317	13/15	Plasmid lp28-4
		TTTTTATAATTATAA	−320	13/15
BBJ19	Conserved hypothetical protein	TAATAATAATTATTA	−37	13/15	Plasmid lp38	First gene in 4-gene plasmid maintenance locus (14)
BBK01	Hypothetical proteind	TTATAATAATTATTC	−41	13/15	Plasmid lp36
BBK15	Putative P35 antigen	TAATATTTATTATAA	−191	13/15	Plasmid lp36
		TTATAATGATTACTA	−208	13/15
BBK47	Hypothetical proteind	TTATAATTATTATTA	−79	14/15	Plasmid lp36	B31 equivalent of N40 arp gene encoding arthritis-related protein (21)
BBK49	Hypothetical proteind	TTATAATTATTATTA	−79	14/15	Plasmid lp36	Homologue of BBK47
BBL36	Conserved hypothetical protein	TTATAAATATTATAG	−275	13/15	Plasmid cp32-8	Per box located within 180-bp inverted repeat of unknown function (14)
		TTTTATTAATTATAA	−332	13/15
BBM33	Conserved hypothetical protein	TAATTATAATTATAA	−52	13/15	Plasmid cp32-6	Last gene in 4-gene plasmid maintenance locus (14)
		TTAAAATAATTATAA	−58	14/15

^aCandidate Per boxes were identified by BlastN analysis of the B. burgdorferi genome employing an Expect value of 1,000 and a word length of 11. Sequences were excluded if they did not meet the following criteria: (i) no more than 400 nt upstream of a putative translational start site, (ii) no deeper than 50 nt into an upstream coding region, (iii) a minimum of 13 matches to the Per consensus sequence, and (iv) associated ORF at least 200 bp in size.

^bPutative identifications were from the TIGR website (http://www.tigr.org).

^cMatches to the Per consensus sequence (TTATAAT-ATTATAA) appear in boldface.

^dPutative lipoprotein.