Table 1.

Statistical Summary of E. coli Search Results

Namea	Lengthb	Number of examplesc	Information score “hits”d	QPMEME “hits”e	Significancef
ArcA	15	14	391	52	6.3
ArgR	18	17	320	79	8.9
CRP	22	49	3093	796	27.2
CytR	18	5	745	42	4.3
DnaA	15	8	98,748	461	0.5
FadR	17	7	28	10	9.0
FarR	10	4	1893	241	3.7
FIS	35	19	7687	255	4.1
Fnr	22	14	174	36	13.9
FruR	16	12	31	23	14.8
GalR	16	7	10	9	8 × 103
GevA	20	4	15	5	5 × 103
GlpR	20	13	9132	192	1.6
H-NS	11	15	14,619	2340	2.7
IHF	48	26	82,494	359	13.6
LexA	20	19	39	39	104
LRP	25	12	90,676	4087	32.9
MalR	10	10	96	61	8.7
MetJ	16	15	404	42	1.6
MetR	15	8	344	26	3.2
NagC	23	6	72	8	7.0
NarL	16	11	2090	19	7.5
OmpR	20	9	4890	93	2.6
PhoB	22	15	258	23	14.8
PurR	26	22	47	28	27.0
σ70 (15)	27	27	11,517	635	2.2
σ70 (16)	28	48	15,867	912	2.6
σ70 (17)	29	116	41,488	3923	0.6
σ70 (18)	30	34	10,133	381	0.6
σ70 (19)	31	25	15,086	301	0.4
σ54	16	6	16	7	6.0
σs	29	15	10,669	245	2.0
SoxS	35	14	3963	49	2.2
TyrR	22	17	3843	73	6.2

See Web site http://www.biomaps.rutgers.edu/bioinformatics/QPMEME.htm. for details.

^aTF name. Note σ⁷⁰ (15), etc., refers to σ⁷⁰ sites with 15 bp spacer between −10 and −35 boxes.

^blength of the binding site in bp.

^cnumber of known binding sites used to determine ε, μ parameters.

^dnumber of candidate sites found using information theoretic weight matrix with threshold set to include most of the example sites (the 2σ cut-off; Robison et al. 1998).

^enumber of candidate sites found using QPMEME approach.

^f“Significance” defined here as a difference between actual and expected number of sites normalized to the square root of the expected number.