Table 2. Regulation targets of transcription factor (TF).

TF	Effector	Family	No. TF binding sites	No.regulation targets [A]	No.known targets [B]	Increase [A]/[B]	Ref
AscG		LacI	13	13–19	4	3.3∼4.8	(91)
BasR	Acetyl-P	OmpR	38	33–47	11	3.0∼4.3	(92)
BetI	Choline	RutR	1	2	1	2.0	Figure 2A
CitB		CitB	11	11–15	5	2.2–3.0	(93)
Cra		LacI	194	193–296	40	4.8–7.4	(16,58)
CRP	cAMP	CRP	277	192–290	190	1.0–1.5	(57)
LeuO		LysR	140	131–173	15	8.7–11.5	(60)
Lrp		AsnC	314	218–296	43	5.1–6.9	(63)
NanR		GntR	2	3	3	∼1.0	Figure 2C
NemR		RutR	2	4	2	∼2.0	(22)
NimR		AraC	1	2	2	∼1.0	(23)
OmpR	Acetyl-P	OmpR	26	21–32	12	1.8–2.1	(37)
PgrR		LacI	11	8–11	4	2.0–2.75	(24)
RbsR		LacI	5	3–4	2	1.5–2.0	(94)
RcdA		RutR	20	11–17	8	1.4–2.1	(25)
RutR		RutR	40	35–60	7	5.0–8.6	(26)
SdiA		SdiA	31	20–27	3	6.7–9.0	(41)
SdiA	HSL-A	SdiA	43	32–54	3	10.7–18.0	(41)
SdiA	HSL-F	SdiA	26	17–29	3	5.7–9.7	(41)
SdiA	HSL-K	SdiA	37	26–41	3	8.7–13.7	(41)
SdiA	HSL-OC	SdiA	34	25–44	3	8.3–14.7	(41)
SutR		DinJ	17	13–15	4	3.3–3.8	(28)
UlaR	Acetyl-P	DeoR	2	3	2	1.0–1.5	Figure 2B
The regulation targets of these TFs were predicted by Genomic SELEX screening and afterward experimentally confirmed. Number of the known targets are from EcoCyc.
Nucleoid protein
TF	Effector	Family	No. TF binding sites	No.regulation target operons	No. targets (EcoCyc)		Ref
Dan		LysR	688				(21)
Fis		Fis	1269				Figure 3A
HNS		HNS	987				(60); Figure 3C
IHF		HU	813				Figure 3B

The binding sites of these nucleoid proteins were identified by using the in vitro SELEX screening system.