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Table 1 Summary of the datasets in RegulonDB

From: Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coliK12 DNA

Regulatory protein Number of binding sites Site size (bp) Regions with sites Regions without sites
Ada 2 28 2 2
AlpA - - - 1
AppY - - - 2
AraC 15 17 5 1
ArcA 20 61 11 9
ArgR 12 16 6 1
AsnC - - - 2
AtoC - - - 1
BetI 2 21 2 -
BirA 2 40 2 -
CRP 109 19 65 15
CadC - - - 1
Cbl 1 45 1 -
CsgD - - - 2
CspA 3 5 1 1
CynR 2 60 2 -
CysB 7 42 5 1
CytR 12 40 6 2
DeoR 7 16 2 1
DnaA 8 9 2 -
DsdC - - - 3
EbgR - - - 1
EnvY - - - 2
ExuR - - - 1
FIS 29 16 25 -
FNR 30 22 20 4
FadR 6 17 4 -
FarR 2 21 1 -
FecI 1 7 1 1
FhlA - - - 3
FruR 8 14 7 4
FucR - - - 2
Fur 9 19 4 6
GalR 4 17 1 1
GalS 2 16 1 1
GatR - - - 1
GcvA 4 29 2 -
GlpR 17 20 4 1
GntR - - - 5
GutM - - - 1
GutR - - - 1
Hns - - - 5
IHF 21 13 14 12
IclR 1 34 1 -
IlvY 4 26 2 -
KdpE 1 12 1 -
LacI 3 20 1 -
LeuO - - - 1
LexA 9 20 8 1
Lrp 22 12 11 3
LysR 1 13 1 2
MalI 4 12 2 -
MalT 9 10 4 -
MarA - - - 5
MarR - - - 1
MelR 6 18 2 1
MetJ 5 8 2 1
MetR 3 24 2 1
Mlc 2 26 1 -
MtlR - - - 1
NR_I 10 15 3 -
NadR - - - 2
NagC 8 26 4 -
NarL 20 19 9 3
NhaR - - - 1
OmpR 14 10 4 3
OxyR 4 45 4 -
PdhR 1 21 1 -
PhoB 7 17 4 1
PurR 16 16 14 3
RbsR - - - 1
RcsB 2 25 2 -
RhaR 3 20 1 -
RhaS 3 17 2 -
Rob - - - 4
SdiA - - - 1
SoxR 2 19 2 -
SoxS 4 18 3 2
TdcA 1 15 1 -
TdcR 1 12 1 -
TorR 4 10 1 -
TrpR 5 27 5 -
TyrR 15 22 8 -
UhpA 1 39 1 -
XapR 2 13 1 -
XylR 4 16 2 -
  1. RegulonDB contains information for the 86 regulons shown in this table. Of these, only 60 have at least three known binding sites for their corresponding regulatory protein. The second column indicates the total number of known sites, which are distributed in upstream regions (fourth column). The last column indicates the number of upstream regions for which there is experimental evidence suggesting regulation, but no direct proof of binding of the regulator to the upstream site is yet available. For instance, there are 12 known sites for ArgR located in only six regions (with two sites per region), plus one region for a different gene for which there is evidence of regulation by ArgR.