TABLE 3.

Computer ranking of intergenic ς⁵⁴ sites^a

Typeb	Score	Gene	Ntr inductionc	Distanced		Function
				Down	Up
X	95.4	rtcBA	—	38	134p	RNA terminal phosphate cyclase
	92.8	rpoH	—	40	188t	Heat shock sigma factor
X	90.2	glnK-amtB	10–20	52	112t	Alternate Ntr regulator and ammonia transport
X	89.6	prpBCDE	—	46	176p	Propionate catabolism
(X)	88.6	yhdWXYZ	2–9	187	334t	Putative amino acid transport operon
X	88.6	zraP	2	34	196p	Zinc tolerance
(X)	88.0	gltlJKL	3–6	?	99t	Interrupted glutamate-aspartate transport genes
X	88.0	hypABCDE-fhlA	—	37	165p	Formate hydrogen lyase
	86.0	b2710-ygbD	—	47	48p	Flavodoxin, oxidoreductase
X	85.9	atoDAEB	?	45	134t	Acetoacetate metabolism
X	85.5	astCADBE	7–11	72	357p	Arginine degradation
	85.4	kch	—	264	20t	Potassium channel
X	85.2	nac	15–50	55	255p	Regulator of nitrogen assimilation genes
	83.9	yfhKGA	—	190	288t	Two-component regulatory system
(X)	83.8	yeaGH	2–4	103	316p	Possible operon, unknown function
X	83.3	glnALG	11–24	83	273p	Nitrogen assimilation and regulation of Ntr response
X	80.7	glnHPQ	5–9	54	333t	Glutamine transport
X	80.0	pspABCDE	1.5–2.5	51	84p	Phage shock
X	79.1	hycABCDEFGHI	—	36	159p	Formate hydrogen lyase
	78.8	ybhK	—	55	325p	RocR-like protein
	77.3	yaiS	—	33	656p	Hypothetical protein, 136 residues
(X)	76.8	b1012-1006	24–47	28	201p	Possible pyrimidine catabolic operon
(X)	76.6	ddpXABCDE	52–60	44	198t	d-Ala–d-Ala dipeptide transport and dipeptidase
	76.5	topA	—	201	162p	Topoisomerase I
X	76.2	zraSR (hydHG)	—	40	190p	Two-component regulatory system for zinc tolerance
X	72.6	fdhF	—	51	130t	Formate hydrogen lyase
X	72.3	argT-hisJQMP	10–18	68	181t	Arginine and histidine transport
X	70.7	ygjG	3–6	136	355p	An omega-transaminase
(X)	68.1	chaC	4–5	74	46t	Ca/H antiporter, in chaBC intercistronic region?
X	64.5	hydN-hypF	—	37	95t	Formate hydrogen lyase
(X)	63.9	potFGHI	5–6	59	275t	Putrescine transport
(X)	62.2	ycjJ	3	192	39t	Putative amino acid transporter

^aThere are over 200 sites with a computer score over 60. This table provides details of all sites with (i) verified ς⁵⁴-dependent promoters, (ii) potential sites before genes that are induced by nitrogen limitation, and (iii) sites with a score of 76 or higher (there are only seven such sites that fail to meet either criterion a or b). These criteria might exclude some authentic ς⁵⁴-dependent promoters. The following is a list of all the other intergenic sites. The following genes have sites with a score from 70.0 to 75.9 (from highest to lowest): yigL, ygeW, b2343, b2878, yjcB-vacB, ytfJ, crl, acrD, ptrA, clpPX, mutH, csgBA, b2878, pyrG, sohA, yehR, rmf, mscL, mdoB, gcvTHP, intF, and yfaO. The following sites have a ranking between 65.0 and 69.9: b1983, b2670, yhcC, yabI, malK-lamB-malM, hyfABCDEFGHIR, sgcCQ, yehZYXW, yejH, metZ, yhfA, ybcLM, proP, purC, ygiF, b1440-1444, yeaQ, yigM; b0833-0834, yefM, gdhA, rfe-wzzE, emrD, cysDNC, gcvA, yhfZY, ychH, b2380-2382, caiF, xseB-ispA-dxs, hcaA1, xdhABC (b2866-2868), ndh, pgpB, b1722, tolC, galETKM, ymcC, degQ, yheB, b0540, aer, glyQS, cadCBA, b2374, arsR, mviN, yieP, b2420, and ygdP-ptsP. The following sites have a ranking between 60.1 and 64.9: ybgE, fumB, b0805, ompF, ygdH, accBC, yciK-btuR, brnQ, acs, yceC-yceF, purM, ybcLM, b1017, kbl-tdh, b1625, yjhQP, aroG, zipA, yiiP, cybC, yjjJ, dinG, prsA, ydcD, emrD, secE, mog, ybiH, b0836, ymdD, dnaA, sapABCDF, slyA, b1826, sanA, yjdE, intB, hyaABCDEF, yhcL, yjhA, b2444-2445, tktA, bglX, yafW, dsbB, yfjZ-ypjF, yicK, panD, ycbG, rplY, yigK, yafK, yahA, araE, dfp, yfcD, feaB, gnd, yhhI, ybiA, dicF, b3000-b2999, yhaM, ydiQ, yagA, yhfA, ilvGMEDA, adiY, yjgL, trpR, osmB, sgaT, yjhQ, ydiQ, yecH, upp-uraA, rfe-wzzE (again), map, ybiT, trpEDCBA, b1592, fepB, yrbG, cydA, ssrA, yhcC, yhgN, yhjR, metA, talB, lpxC, b1432, hisS, mreB, rrfF, xylB, pfkA, hslVU, yjhR, ahpF, b1506, yihG, sbp, nhaA, proBA, hrpA, nirC-cysG, and yigK. 

^bX, the site is a verified ς⁵⁴-dependent promoter; (X), a probable ς⁵⁴-dependent promoter as suggested by computer identification of an appropriately located site and induction by nitrogen limitation. 

^cNtr induction refers to the elevation of expression induced by nitrogen limitation as determined by microarray analysis. Dashes indicate no induction. The number indicates the range of the increase for the most highly induced gene of the operon. 

^d“Down” indicates the distance from the 3′ end of the ς⁵⁴ site to the first base of the downstream structural gene. “Up” indicates the distance from the 5′ end of the ς⁵⁴ site to the most proximal base of the nearest upstream gene. The notation p or t indicates whether the promoter or the terminator, respectively, of the adjacent upstream gene is nearest the ς⁵⁴ site. The implication is that a promoter region may require a larger region. The size of the intergenic region is the sum of down plus up plus the 16 bases of the ς⁵⁴ site.