Table 1.

Statistical Summary of E. coli Search Results

Name^a	Length^b	Number of examples^c	Information score “hits”^d	QPMEME “hits”^e	Significance^f
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
σ^s	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.
↵a TF name. Note σ⁷⁰ (15), etc., refers to σ⁷⁰ sites with 15 bp spacer between −10 and −35 boxes.
↵b length of the binding site in bp.
↵c number of known binding sites used to determine ϵ, μ parameters.
↵d number 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).
↵e number 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.

A Biophysical Approach to Transcription Factor Binding Site Discovery