Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes
-- version 4.0 --

Collection of regulogs in Enterobacteriales taxonomic group

General statistics
Genomes 12
TF regulogs 127
TF regulons 812
TF binding sites 7659
RNA regulogs 18
RNA regulons 147
RNA sites 188

This collection involves all regulons that were tentatively predicted by applying integrative comparative genomic approach to a single taxonomic group of closely-related genomes. To infer the regulons operated by transcription factors (TFs), we combined the identification of TF binding sites and cross-genome comparison of regulons with the analysis of the genomic and functional context of candidate target genes. To infer the regulons operated by regulatory RNAs such as riboswitches, we identified candidate RNA regulatory elements using HMM profiles and further analyzed their genomic and functional context.

Studied genomes and reconstructed regulon statistics
TF RNA Total
Genomes Regulons Sites Regulons Sites Regulons Sites
Citrobacter koseri ATCC BAA-895 82 858 14 19 96 877
Edwardsiella tarda EIB202 50 386 11 15 61 401
Enterobacter sp. 638 81 765 12 15 93 780
Erwinia amylovora ATCC 49946 48 355 10 13 58 368
Erwinia carotovora subsp. atroseptica SCRI1043 67 599 14 18 81 617
Escherichia coli str. K-12 substr. MG1655 84 943 13 16 97 959
Klebsiella pneumoniae subsp. pneumoniae MGH 78578 86 804 14 19 100 823
Photorhabdus luminescens subsp. laumondii TTO1 47 407 12 14 59 421
Proteus mirabilis HI4320 52 541 12 14 64 555
Salmonella typhimurium LT2 75 819 12 16 87 835
Serratia proteamaculans 568 81 648 13 17 94 665
Yersinia pestis KIM 59 534 10 12 69 546
Genomic distribution of regulons
Family Type Regulator Function
AraC TF AraC
4 AraC

Escherichia coli str. K-12 substr. MG1655
4 AraC

Salmonella typhimurium LT2
4 AraC

Citrobacter koseri ATCC BAA-895
6 AraC

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
5 AraC

Enterobacter sp. 638
2 AraC

Erwinia amylovora ATCC 49946
2 AraC

Yersinia pestis KIM
2 AraC

Serratia proteamaculans 568
2 AraC

Erwinia carotovora subsp. atroseptica SCRI1043
Arabinose utilization
TF RhaR
1 RhaR

Escherichia coli str. K-12 substr. MG1655
1 RhaR

Salmonella typhimurium LT2
1 RhaR

Citrobacter koseri ATCC BAA-895
1 RhaR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 RhaR

Enterobacter sp. 638
1 RhaR

Yersinia pestis KIM
1 RhaR

Erwinia carotovora subsp. atroseptica SCRI1043
Rhamnose utilization
TF RhaS
3 RhaS

Escherichia coli str. K-12 substr. MG1655
5 RhaS

Salmonella typhimurium LT2
4 RhaS

Citrobacter koseri ATCC BAA-895
4 RhaS

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
4 RhaS

Enterobacter sp. 638
3 RhaS

Yersinia pestis KIM
7 RhaS

Erwinia carotovora subsp. atroseptica SCRI1043
Rhamnose utilization
ArgR TF ArgR
15 ArgR

Escherichia coli str. K-12 substr. MG1655
13 ArgR

Salmonella typhimurium LT2
14 ArgR

Citrobacter koseri ATCC BAA-895
15 ArgR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
13 ArgR

Enterobacter sp. 638
9 ArgR

Erwinia amylovora ATCC 49946
12 ArgR

Yersinia pestis KIM
11 ArgR

Serratia proteamaculans 568
13 ArgR

Erwinia carotovora subsp. atroseptica SCRI1043
10 ArgR

Edwardsiella tarda EIB202
9 ArgR

Proteus mirabilis HI4320
9 ArgR

Photorhabdus luminescens subsp. laumondii TTO1
Arginine biosynthesis; Arginine degradation
BirA TF BirA
3 BirA

Escherichia coli str. K-12 substr. MG1655
2 BirA

Salmonella typhimurium LT2
2 BirA

Citrobacter koseri ATCC BAA-895
3 BirA

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 BirA

Enterobacter sp. 638
2 BirA

Erwinia amylovora ATCC 49946
3 BirA

Yersinia pestis KIM
2 BirA

Serratia proteamaculans 568
2 BirA

Erwinia carotovora subsp. atroseptica SCRI1043
2 BirA

Edwardsiella tarda EIB202
2 BirA

Proteus mirabilis HI4320
2 BirA

Photorhabdus luminescens subsp. laumondii TTO1
Biotin biosynthesis
CRP TF Crp
245 Crp

Escherichia coli str. K-12 substr. MG1655
207 Crp

Salmonella typhimurium LT2
204 Crp

Citrobacter koseri ATCC BAA-895
196 Crp

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
186 Crp

Enterobacter sp. 638
73 Crp

Erwinia amylovora ATCC 49946
121 Crp

Yersinia pestis KIM
148 Crp

Serratia proteamaculans 568
105 Crp

Erwinia carotovora subsp. atroseptica SCRI1043
93 Crp

Edwardsiella tarda EIB202
122 Crp

Proteus mirabilis HI4320
98 Crp

Photorhabdus luminescens subsp. laumondii TTO1
Carbon catabolism
TF Fnr
82 Fnr

Escherichia coli str. K-12 substr. MG1655
68 Fnr

Salmonella typhimurium LT2
66 Fnr

Citrobacter koseri ATCC BAA-895
56 Fnr

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
54 Fnr

Enterobacter sp. 638
20 Fnr

Erwinia amylovora ATCC 49946
46 Fnr

Yersinia pestis KIM
46 Fnr

Serratia proteamaculans 568
51 Fnr

Erwinia carotovora subsp. atroseptica SCRI1043
39 Fnr

Edwardsiella tarda EIB202
50 Fnr

Proteus mirabilis HI4320
37 Fnr

Photorhabdus luminescens subsp. laumondii TTO1
Energy metabolism; Anaerobic metabolism
CsoR TF RcnR
2 RcnR

Escherichia coli str. K-12 substr. MG1655
2 RcnR

Salmonella typhimurium LT2
2 RcnR

Citrobacter koseri ATCC BAA-895
2 RcnR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Cobalt resistance; Nickel resistance
DeoR TF AgaR
3 AgaR

Escherichia coli str. K-12 substr. MG1655
3 AgaR

Citrobacter koseri ATCC BAA-895
3 AgaR

Enterobacter sp. 638
N-acetylgalactosamine utilization
TF DeoR
4 DeoR

Escherichia coli str. K-12 substr. MG1655
3 DeoR

Salmonella typhimurium LT2
2 DeoR

Citrobacter koseri ATCC BAA-895
2 DeoR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 DeoR

Enterobacter sp. 638
2 DeoR

Erwinia amylovora ATCC 49946
1 DeoR

Yersinia pestis KIM
1 DeoR

Serratia proteamaculans 568
3 DeoR

Erwinia carotovora subsp. atroseptica SCRI1043
2 DeoR

Edwardsiella tarda EIB202
3 DeoR

Proteus mirabilis HI4320
Deoxyribonucleoside utilization
TF FucR
2 FucR

Escherichia coli str. K-12 substr. MG1655
1 FucR

Salmonella typhimurium LT2
3 FucR

Citrobacter koseri ATCC BAA-895
3 FucR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 FucR

Edwardsiella tarda EIB202
Fucose utilization
TF GlpR
6 GlpR

Escherichia coli str. K-12 substr. MG1655
6 GlpR

Salmonella typhimurium LT2
6 GlpR

Citrobacter koseri ATCC BAA-895
6 GlpR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
5 GlpR

Enterobacter sp. 638
4 GlpR

Erwinia amylovora ATCC 49946
3 GlpR

Yersinia pestis KIM
4 GlpR

Serratia proteamaculans 568
4 GlpR

Erwinia carotovora subsp. atroseptica SCRI1043
4 GlpR

Edwardsiella tarda EIB202
5 GlpR

Proteus mirabilis HI4320
3 GlpR

Photorhabdus luminescens subsp. laumondii TTO1
Glycerol utilization
TF SrlR
1 SrlR

Escherichia coli str. K-12 substr. MG1655
1 SrlR

Salmonella typhimurium LT2
1 SrlR

Citrobacter koseri ATCC BAA-895
1 SrlR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 SrlR

Serratia proteamaculans 568
Sorbitol utilization
TF UlaR
2 UlaR

Escherichia coli str. K-12 substr. MG1655
2 UlaR

Salmonella typhimurium LT2
2 UlaR

Citrobacter koseri ATCC BAA-895
2 UlaR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 UlaR

Edwardsiella tarda EIB202
Ascorbate utilization
DtxR TF MntR
4 MntR

Escherichia coli str. K-12 substr. MG1655
4 MntR

Salmonella typhimurium LT2
5 MntR

Citrobacter koseri ATCC BAA-895
4 MntR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
4 MntR

Enterobacter sp. 638
4 MntR

Erwinia amylovora ATCC 49946
2 MntR

Serratia proteamaculans 568
Manganese homeostasis
FUR TF Fur
30 Fur

Escherichia coli str. K-12 substr. MG1655
29 Fur

Salmonella typhimurium LT2
49 Fur

Citrobacter koseri ATCC BAA-895
34 Fur

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
36 Fur

Enterobacter sp. 638
14 Fur

Erwinia amylovora ATCC 49946
29 Fur

Yersinia pestis KIM
36 Fur

Serratia proteamaculans 568
36 Fur

Erwinia carotovora subsp. atroseptica SCRI1043
16 Fur

Edwardsiella tarda EIB202
35 Fur

Proteus mirabilis HI4320
28 Fur

Photorhabdus luminescens subsp. laumondii TTO1
Iron homeostasis
TF Zur
5 Zur

Escherichia coli str. K-12 substr. MG1655
5 Zur

Salmonella typhimurium LT2
11 Zur

Citrobacter koseri ATCC BAA-895
5 Zur

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
5 Zur

Enterobacter sp. 638
3 Zur

Erwinia amylovora ATCC 49946
4 Zur

Yersinia pestis KIM
9 Zur

Serratia proteamaculans 568
6 Zur

Erwinia carotovora subsp. atroseptica SCRI1043
3 Zur

Edwardsiella tarda EIB202
5 Zur

Proteus mirabilis HI4320
3 Zur

Photorhabdus luminescens subsp. laumondii TTO1
Zinc homeostasis
Fis TF NorR
2 NorR

Escherichia coli str. K-12 substr. MG1655
2 NorR

Salmonella typhimurium LT2
2 NorR

Citrobacter koseri ATCC BAA-895
2 NorR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 NorR

Enterobacter sp. 638
2 NorR

Serratia proteamaculans 568
2 NorR

Erwinia carotovora subsp. atroseptica SCRI1043
Nitrosative stress response
TF NtrC
12 NtrC

Escherichia coli str. K-12 substr. MG1655
7 NtrC

Salmonella typhimurium LT2
10 NtrC

Citrobacter koseri ATCC BAA-895
11 NtrC

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
11 NtrC

Enterobacter sp. 638
8 NtrC

Erwinia amylovora ATCC 49946
7 NtrC

Yersinia pestis KIM
9 NtrC

Serratia proteamaculans 568
6 NtrC

Erwinia carotovora subsp. atroseptica SCRI1043
4 NtrC

Edwardsiella tarda EIB202
3 NtrC

Proteus mirabilis HI4320
4 NtrC

Photorhabdus luminescens subsp. laumondii TTO1
Nitrogen assimilation
GntR/MocR TF EAM_2333
1 EAM_2333

Erwinia amylovora ATCC 49946
TF Ent638_1108
1 Ent638_1108

Enterobacter sp. 638
TF GabR
1 GabR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 GabR

Erwinia amylovora ATCC 49946
1 GabR

Yersinia pestis KIM
1 GabR

Serratia proteamaculans 568
1 GabR

Erwinia carotovora subsp. atroseptica SCRI1043
Gamma-aminobutyrate utilization
TF PdxR
2 PdxR

Erwinia carotovora subsp. atroseptica SCRI1043
Pyridoxine/pyridoxal homeostasis
TF PdxR2
2 PdxR2

Salmonella typhimurium LT2
2 PdxR2

Citrobacter koseri ATCC BAA-895
2 PdxR2

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 PdxR2

Enterobacter sp. 638
2 PdxR2

Serratia proteamaculans 568
Pyridoxine/pyridoxal homeostasis
TF PdxR3
1 PdxR3

Citrobacter koseri ATCC BAA-895
1 PdxR3

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 PdxR3

Enterobacter sp. 638
Pyridoxine biosynthesis
TF PdxW
1 PdxW

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 PdxW

Enterobacter sp. 638
Pyridoxine/pyridoxal homeostasis
TF Spro_0112
1 Spro_0112

Serratia proteamaculans 568
TF Spro_2017
1 Spro_2017

Serratia proteamaculans 568
TF Spro_3347
1 Spro_3347

Serratia proteamaculans 568
Metabolite transport
TF Spro_3719
1 Spro_3719

Salmonella typhimurium LT2
1 Spro_3719

Citrobacter koseri ATCC BAA-895
1 Spro_3719

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 Spro_3719

Enterobacter sp. 638
1 Spro_3719

Serratia proteamaculans 568
2 Spro_3719

Erwinia carotovora subsp. atroseptica SCRI1043
TF TauR
1 TauR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Taurine utilization
TF YE4144
1 YE4144

Serratia proteamaculans 568
1 YE4144

Erwinia carotovora subsp. atroseptica SCRI1043
Metabolite transport
TF YdcR
1 YdcR

Escherichia coli str. K-12 substr. MG1655
1 YdcR

Salmonella typhimurium LT2
1 YdcR

Citrobacter koseri ATCC BAA-895
2 YdcR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 YdcR

Enterobacter sp. 638
1 YdcR

Erwinia amylovora ATCC 49946
2 YdcR

Serratia proteamaculans 568
1 YdcR

Erwinia carotovora subsp. atroseptica SCRI1043
1 YdcR

Proteus mirabilis HI4320
1 YdcR

Photorhabdus luminescens subsp. laumondii TTO1
TF YjiR
1 YjiR

Escherichia coli str. K-12 substr. MG1655
1 YjiR

Citrobacter koseri ATCC BAA-895
1 YjiR

Enterobacter sp. 638
1 YjiR

Serratia proteamaculans 568
1 YjiR

Erwinia carotovora subsp. atroseptica SCRI1043
GntR/Others TF CelR
1 CelR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 CelR

Enterobacter sp. 638
1 CelR

Erwinia carotovora subsp. atroseptica SCRI1043
Cellobiose utilization
TF DgoR
1 DgoR

Escherichia coli str. K-12 substr. MG1655
1 DgoR

Salmonella typhimurium LT2
1 DgoR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 DgoR

Enterobacter sp. 638
2 DgoR

Serratia proteamaculans 568
1 DgoR

Erwinia carotovora subsp. atroseptica SCRI1043
Galactonate utilization
TF ExuR
4 ExuR

Escherichia coli str. K-12 substr. MG1655
8 ExuR

Citrobacter koseri ATCC BAA-895
7 ExuR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
7 ExuR

Enterobacter sp. 638
5 ExuR

Yersinia pestis KIM
7 ExuR

Serratia proteamaculans 568
4 ExuR

Erwinia carotovora subsp. atroseptica SCRI1043
6 ExuR

Edwardsiella tarda EIB202
Galacturonate utilization
TF FadR
12 FadR

Escherichia coli str. K-12 substr. MG1655
12 FadR

Salmonella typhimurium LT2
11 FadR

Citrobacter koseri ATCC BAA-895
12 FadR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
12 FadR

Enterobacter sp. 638
7 FadR

Erwinia amylovora ATCC 49946
11 FadR

Yersinia pestis KIM
11 FadR

Serratia proteamaculans 568
9 FadR

Erwinia carotovora subsp. atroseptica SCRI1043
4 FadR

Edwardsiella tarda EIB202
9 FadR

Proteus mirabilis HI4320
11 FadR

Photorhabdus luminescens subsp. laumondii TTO1
Fatty acid degradation
TF GlcC
2 GlcC

Escherichia coli str. K-12 substr. MG1655
Glycolate utilization
TF HpxS
1 HpxS

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 HpxS

Erwinia amylovora ATCC 49946
1 HpxS

Serratia proteamaculans 568
Allantoin utilization
TF HutC
1 HutC

Salmonella typhimurium LT2
3 HutC

Citrobacter koseri ATCC BAA-895
4 HutC

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 HutC

Enterobacter sp. 638
4 HutC

Erwinia amylovora ATCC 49946
4 HutC

Yersinia pestis KIM
4 HutC

Serratia proteamaculans 568
2 HutC

Photorhabdus luminescens subsp. laumondii TTO1
Histidine utilization
TF HypR
1 HypR

Erwinia amylovora ATCC 49946
Proline and 4-hydrohyproline utilization
TF LldR
1 LldR

Escherichia coli str. K-12 substr. MG1655
1 LldR

Salmonella typhimurium LT2
1 LldR

Citrobacter koseri ATCC BAA-895
1 LldR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 LldR

Enterobacter sp. 638
Lactate utilization
TF NanR
3 NanR

Escherichia coli str. K-12 substr. MG1655
1 NanR

Salmonella typhimurium LT2
1 NanR

Citrobacter koseri ATCC BAA-895
1 NanR

Enterobacter sp. 638
1 NanR

Edwardsiella tarda EIB202
Sialic acid utilization
TF PMI3555
2 PMI3555

Proteus mirabilis HI4320
2 PMI3555

Photorhabdus luminescens subsp. laumondii TTO1
TF PdhR
6 PdhR

Escherichia coli str. K-12 substr. MG1655
5 PdhR

Salmonella typhimurium LT2
5 PdhR

Citrobacter koseri ATCC BAA-895
4 PdhR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
5 PdhR

Enterobacter sp. 638
1 PdhR

Erwinia amylovora ATCC 49946
4 PdhR

Yersinia pestis KIM
3 PdhR

Serratia proteamaculans 568
2 PdhR

Erwinia carotovora subsp. atroseptica SCRI1043
3 PdhR

Edwardsiella tarda EIB202
3 PdhR

Proteus mirabilis HI4320
2 PdhR

Photorhabdus luminescens subsp. laumondii TTO1
Pyruvate metabolism
TF PhnF
1 PhnF

Escherichia coli str. K-12 substr. MG1655
1 PhnF

Citrobacter koseri ATCC BAA-895
1 PhnF

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 PhnF

Enterobacter sp. 638
1 PhnF

Yersinia pestis KIM
1 PhnF

Serratia proteamaculans 568
Phosphonate utilization
TF PhnR
3 PhnR

Salmonella typhimurium LT2
3 PhnR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Phosphonate utilization; 2-aminoethylphosphonate utilization
TF PhnR1
2 PhnR1

Serratia proteamaculans 568
2-aminoethylphosphonate utilization
TF RspR
1 RspR

Escherichia coli str. K-12 substr. MG1655
1 RspR

Salmonella typhimurium LT2
2 RspR

Citrobacter koseri ATCC BAA-895
2 RspR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 RspR

Enterobacter sp. 638
1 RspR

Serratia proteamaculans 568
1 RspR

Erwinia carotovora subsp. atroseptica SCRI1043
L-gulonate utilization
TF Spro_0637
2 Spro_0637

Serratia proteamaculans 568
TF Spro_1420
1 Spro_1420

Serratia proteamaculans 568
2 Spro_1420

Erwinia carotovora subsp. atroseptica SCRI1043
Nitrogen metabolism
TF UxuR
9 UxuR

Escherichia coli str. K-12 substr. MG1655
4 UxuR

Salmonella typhimurium LT2
6 UxuR

Yersinia pestis KIM
4 UxuR

Erwinia carotovora subsp. atroseptica SCRI1043
6 UxuR

Edwardsiella tarda EIB202
3 UxuR

Photorhabdus luminescens subsp. laumondii TTO1
Glucuronate utilization
TF YihL
1 YihL

Escherichia coli str. K-12 substr. MG1655
1 YihL

Serratia proteamaculans 568
1 YihL

Edwardsiella tarda EIB202
HxlR TF QorR
2 QorR

Escherichia coli str. K-12 substr. MG1655
2 QorR

Salmonella typhimurium LT2
2 QorR

Citrobacter koseri ATCC BAA-895
2 QorR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 QorR

Enterobacter sp. 638
1 QorR

Yersinia pestis KIM
2 QorR

Erwinia carotovora subsp. atroseptica SCRI1043
2 QorR

Proteus mirabilis HI4320
Energy metabolism
IclR TF AllR
3 AllR

Escherichia coli str. K-12 substr. MG1655
3 AllR

Salmonella typhimurium LT2
Allantoin utilization
TF IclR
1 IclR

Escherichia coli str. K-12 substr. MG1655
1 IclR

Salmonella typhimurium LT2
1 IclR

Citrobacter koseri ATCC BAA-895
1 IclR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 IclR

Enterobacter sp. 638
1 IclR

Yersinia pestis KIM
1 IclR

Serratia proteamaculans 568
1 IclR

Erwinia carotovora subsp. atroseptica SCRI1043
1 IclR

Proteus mirabilis HI4320
1 IclR

Photorhabdus luminescens subsp. laumondii TTO1
Glyoxylate bypass
TF KdgR
10 KdgR

Escherichia coli str. K-12 substr. MG1655
12 KdgR

Salmonella typhimurium LT2
17 KdgR

Citrobacter koseri ATCC BAA-895
18 KdgR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
21 KdgR

Enterobacter sp. 638
14 KdgR

Yersinia pestis KIM
5 KdgR

Serratia proteamaculans 568
31 KdgR

Erwinia carotovora subsp. atroseptica SCRI1043
5 KdgR

Edwardsiella tarda EIB202
Pectin and polygalacturonate utlization
TF YiaJ
2 YiaJ

Escherichia coli str. K-12 substr. MG1655
2 YiaJ

Salmonella typhimurium LT2
2 YiaJ

Citrobacter koseri ATCC BAA-895
2 YiaJ

Serratia proteamaculans 568
L-lyxose utilization
LacI TF AscG
2 AscG

Escherichia coli str. K-12 substr. MG1655
3 AscG

Citrobacter koseri ATCC BAA-895
4 AscG

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
5 AscG

Enterobacter sp. 638
2 AscG

Erwinia amylovora ATCC 49946
3 AscG

Serratia proteamaculans 568
5 AscG

Erwinia carotovora subsp. atroseptica SCRI1043
Beta-glucosides utilization; Cellobiose utilization
TF BglR
2 BglR

Yersinia pestis KIM
Beta-glucosides utilization
TF CelR2
1 CelR2

Yersinia pestis KIM
1 CelR2

Serratia proteamaculans 568
Cellobiose utilization
TF CscR
2 CscR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 CscR

Serratia proteamaculans 568
2 CscR

Proteus mirabilis HI4320
Sucrose utilization
TF ECA4246
1 ECA4246

Erwinia carotovora subsp. atroseptica SCRI1043
Sugar utilization
TF EbgR
2 EbgR

Escherichia coli str. K-12 substr. MG1655
3 EbgR

Serratia proteamaculans 568
Galactosides utilization
TF FruR
24 FruR

Escherichia coli str. K-12 substr. MG1655
24 FruR

Salmonella typhimurium LT2
22 FruR

Citrobacter koseri ATCC BAA-895
22 FruR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
22 FruR

Enterobacter sp. 638
13 FruR

Erwinia amylovora ATCC 49946
17 FruR

Yersinia pestis KIM
18 FruR

Serratia proteamaculans 568
14 FruR

Erwinia carotovora subsp. atroseptica SCRI1043
13 FruR

Edwardsiella tarda EIB202
12 FruR

Proteus mirabilis HI4320
12 FruR

Photorhabdus luminescens subsp. laumondii TTO1
Central carbohydrate metabolism
TF GalR/GalS
6 GalR/GalS

Escherichia coli str. K-12 substr. MG1655
4 GalR/GalS

Salmonella typhimurium LT2
7 GalR/GalS

Citrobacter koseri ATCC BAA-895
7 GalR/GalS

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
7 GalR/GalS

Enterobacter sp. 638
4 GalR/GalS

Erwinia amylovora ATCC 49946
3 GalR/GalS

Yersinia pestis KIM
5 GalR/GalS

Serratia proteamaculans 568
5 GalR/GalS

Erwinia carotovora subsp. atroseptica SCRI1043
3 GalR/GalS

Edwardsiella tarda EIB202
3 GalR/GalS

Proteus mirabilis HI4320
Galactose utilization
TF GntR
5 GntR

Escherichia coli str. K-12 substr. MG1655
5 GntR

Salmonella typhimurium LT2
4 GntR

Citrobacter koseri ATCC BAA-895
3 GntR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
3 GntR

Enterobacter sp. 638
2 GntR

Erwinia amylovora ATCC 49946
3 GntR

Yersinia pestis KIM
5 GntR

Serratia proteamaculans 568
5 GntR

Erwinia carotovora subsp. atroseptica SCRI1043
1 GntR

Edwardsiella tarda EIB202
2 GntR

Proteus mirabilis HI4320
1 GntR

Photorhabdus luminescens subsp. laumondii TTO1
Gluconate utilization
TF IdnR
2 IdnR

Escherichia coli str. K-12 substr. MG1655
2 IdnR

Salmonella typhimurium LT2
1 IdnR

Citrobacter koseri ATCC BAA-895
2 IdnR

Serratia proteamaculans 568
Idonate utilization
TF LacI
1 LacI

Escherichia coli str. K-12 substr. MG1655
1 LacI

Citrobacter koseri ATCC BAA-895
1 LacI

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 LacI

Enterobacter sp. 638
1 LacI

Erwinia carotovora subsp. atroseptica SCRI1043
Lactose utilization
TF LfaR
2 LfaR

Citrobacter koseri ATCC BAA-895
2 LfaR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 LfaR

Enterobacter sp. 638
2 LfaR

Yersinia pestis KIM
2 LfaR

Serratia proteamaculans 568
2 LfaR

Erwinia carotovora subsp. atroseptica SCRI1043
Sugar utilization
TF MalI
2 MalI

Escherichia coli str. K-12 substr. MG1655
2 MalI

Citrobacter koseri ATCC BAA-895
2 MalI

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 MalI

Enterobacter sp. 638
2 MalI

Serratia proteamaculans 568
Maltose utilization
TF PMI2934
1 PMI2934

Proteus mirabilis HI4320
Sugar utilization
TF PtsR
1 PtsR

Enterobacter sp. 638
Sugar utilization
TF PtxS
1 PtxS

Citrobacter koseri ATCC BAA-895
1 PtxS

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 PtxS

Enterobacter sp. 638
1 PtxS

Erwinia amylovora ATCC 49946
1 PtxS

Serratia proteamaculans 568
2-ketogluconate utilization
TF PurR
28 PurR

Escherichia coli str. K-12 substr. MG1655
26 PurR

Salmonella typhimurium LT2
27 PurR

Citrobacter koseri ATCC BAA-895
27 PurR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
27 PurR

Enterobacter sp. 638
24 PurR

Erwinia amylovora ATCC 49946
20 PurR

Yersinia pestis KIM
23 PurR

Serratia proteamaculans 568
22 PurR

Erwinia carotovora subsp. atroseptica SCRI1043
20 PurR

Edwardsiella tarda EIB202
24 PurR

Proteus mirabilis HI4320
15 PurR

Photorhabdus luminescens subsp. laumondii TTO1
Purine metabolism
TF RafR
1 RafR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 RafR

Enterobacter sp. 638
1 RafR

Yersinia pestis KIM
1 RafR

Erwinia carotovora subsp. atroseptica SCRI1043
Raffinose utilization
TF RbsR
1 RbsR

Escherichia coli str. K-12 substr. MG1655
1 RbsR

Salmonella typhimurium LT2
1 RbsR

Citrobacter koseri ATCC BAA-895
1 RbsR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 RbsR

Enterobacter sp. 638
1 RbsR

Erwinia amylovora ATCC 49946
1 RbsR

Serratia proteamaculans 568
1 RbsR

Erwinia carotovora subsp. atroseptica SCRI1043
1 RbsR

Edwardsiella tarda EIB202
1 RbsR

Proteus mirabilis HI4320
1 RbsR

Photorhabdus luminescens subsp. laumondii TTO1
Ribose utilization
TF RhiR
2 RhiR

Erwinia carotovora subsp. atroseptica SCRI1043
Rhamnogalacturonides utilization
TF STM1555
1 STM1555

Salmonella typhimurium LT2
1 STM1555

Serratia proteamaculans 568
2 STM1555

Photorhabdus luminescens subsp. laumondii TTO1
Sugar utilization
TF ScrR
2 ScrR

Citrobacter koseri ATCC BAA-895
2 ScrR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 ScrR

Enterobacter sp. 638
2 ScrR

Erwinia amylovora ATCC 49946
2 ScrR

Serratia proteamaculans 568
2 ScrR

Erwinia carotovora subsp. atroseptica SCRI1043
Sucrose utilization
TF SgaR
2 SgaR

Salmonella typhimurium LT2
2 SgaR

Citrobacter koseri ATCC BAA-895
2 SgaR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 SgaR

Enterobacter sp. 638
2 SgaR

Yersinia pestis KIM
2 SgaR

Erwinia carotovora subsp. atroseptica SCRI1043
2 SgaR

Edwardsiella tarda EIB202
2 SgaR

Proteus mirabilis HI4320
2 SgaR

Photorhabdus luminescens subsp. laumondii TTO1
Ascorbate utilization
TF TalR
2 TalR

Salmonella typhimurium LT2
2 TalR

Erwinia carotovora subsp. atroseptica SCRI1043
L-talarate utilization
TF TreR
1 TreR

Escherichia coli str. K-12 substr. MG1655
1 TreR

Citrobacter koseri ATCC BAA-895
1 TreR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 TreR

Enterobacter sp. 638
1 TreR

Yersinia pestis KIM
1 TreR

Serratia proteamaculans 568
1 TreR

Proteus mirabilis HI4320
1 TreR

Photorhabdus luminescens subsp. laumondii TTO1
Trehalose utilization
TF XltR
1 XltR

Yersinia pestis KIM
Xylitol utilization
TF YcjW
2 YcjW

Escherichia coli str. K-12 substr. MG1655
2 YcjW

Enterobacter sp. 638
Sugar utilization
TF y3436
2 y3436

Yersinia pestis KIM
Sugar utilization
LexA TF LexA
26 LexA

Escherichia coli str. K-12 substr. MG1655
27 LexA

Salmonella typhimurium LT2
21 LexA

Citrobacter koseri ATCC BAA-895
22 LexA

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
23 LexA

Enterobacter sp. 638
19 LexA

Erwinia amylovora ATCC 49946
15 LexA

Yersinia pestis KIM
16 LexA

Serratia proteamaculans 568
15 LexA

Erwinia carotovora subsp. atroseptica SCRI1043
15 LexA

Edwardsiella tarda EIB202
16 LexA

Proteus mirabilis HI4320
15 LexA

Photorhabdus luminescens subsp. laumondii TTO1
SOS response
LuxR TF NarP
26 NarP

Escherichia coli str. K-12 substr. MG1655
23 NarP

Salmonella typhimurium LT2
25 NarP

Citrobacter koseri ATCC BAA-895
6 NarP

Yersinia pestis KIM
12 NarP

Serratia proteamaculans 568
13 NarP

Erwinia carotovora subsp. atroseptica SCRI1043
6 NarP

Edwardsiella tarda EIB202
4 NarP

Proteus mirabilis HI4320
1 NarP

Photorhabdus luminescens subsp. laumondii TTO1
Nitrate and nitrite respiration
TF TtrR
2 TtrR

Salmonella typhimurium LT2
2 TtrR

Serratia proteamaculans 568
2 TtrR

Edwardsiella tarda EIB202
2 TtrR

Proteus mirabilis HI4320
Tetrathionate reduction
LysR TF AbgR
2 AbgR

Escherichia coli str. K-12 substr. MG1655
2 AbgR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 AbgR

Serratia proteamaculans 568
2 AbgR

Photorhabdus luminescens subsp. laumondii TTO1
p-aminobenzoyl-glutamate utilization
TF GcvA
2 GcvA

Escherichia coli str. K-12 substr. MG1655
2 GcvA

Salmonella typhimurium LT2
2 GcvA

Citrobacter koseri ATCC BAA-895
2 GcvA

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 GcvA

Enterobacter sp. 638
2 GcvA

Erwinia amylovora ATCC 49946
2 GcvA

Yersinia pestis KIM
2 GcvA

Serratia proteamaculans 568
2 GcvA

Erwinia carotovora subsp. atroseptica SCRI1043
2 GcvA

Edwardsiella tarda EIB202
2 GcvA

Proteus mirabilis HI4320
2 GcvA

Photorhabdus luminescens subsp. laumondii TTO1
Glycine metabolism
TF IlvY
2 IlvY

Escherichia coli str. K-12 substr. MG1655
2 IlvY

Salmonella typhimurium LT2
2 IlvY

Citrobacter koseri ATCC BAA-895
2 IlvY

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 IlvY

Enterobacter sp. 638
2 IlvY

Erwinia amylovora ATCC 49946
2 IlvY

Yersinia pestis KIM
2 IlvY

Serratia proteamaculans 568
2 IlvY

Erwinia carotovora subsp. atroseptica SCRI1043
2 IlvY

Edwardsiella tarda EIB202
2 IlvY

Proteus mirabilis HI4320
2 IlvY

Photorhabdus luminescens subsp. laumondii TTO1
Branched-chain amino acid biosynthesis
TF LeuO
3 LeuO

Escherichia coli str. K-12 substr. MG1655
2 LeuO

Salmonella typhimurium LT2
1 LeuO

Citrobacter koseri ATCC BAA-895
1 LeuO

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 LeuO

Enterobacter sp. 638
1 LeuO

Yersinia pestis KIM
1 LeuO

Serratia proteamaculans 568
1 LeuO

Edwardsiella tarda EIB202
1 LeuO

Proteus mirabilis HI4320
2 LeuO

Photorhabdus luminescens subsp. laumondii TTO1
TF LysR
2 LysR

Escherichia coli str. K-12 substr. MG1655
2 LysR

Salmonella typhimurium LT2
2 LysR

Citrobacter koseri ATCC BAA-895
2 LysR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 LysR

Enterobacter sp. 638
2 LysR

Erwinia amylovora ATCC 49946
2 LysR

Yersinia pestis KIM
2 LysR

Serratia proteamaculans 568
2 LysR

Erwinia carotovora subsp. atroseptica SCRI1043
2 LysR

Edwardsiella tarda EIB202
2 LysR

Proteus mirabilis HI4320
2 LysR

Photorhabdus luminescens subsp. laumondii TTO1
Lysine biosynthesis
TF MetR
8 MetR

Escherichia coli str. K-12 substr. MG1655
8 MetR

Salmonella typhimurium LT2
10 MetR

Citrobacter koseri ATCC BAA-895
11 MetR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
10 MetR

Enterobacter sp. 638
7 MetR

Erwinia amylovora ATCC 49946
7 MetR

Yersinia pestis KIM
10 MetR

Serratia proteamaculans 568
8 MetR

Erwinia carotovora subsp. atroseptica SCRI1043
5 MetR

Edwardsiella tarda EIB202
9 MetR

Proteus mirabilis HI4320
6 MetR

Photorhabdus luminescens subsp. laumondii TTO1
Methionine biosynthesis
TF NhaR
1 NhaR

Escherichia coli str. K-12 substr. MG1655
1 NhaR

Salmonella typhimurium LT2
1 NhaR

Citrobacter koseri ATCC BAA-895
1 NhaR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 NhaR

Enterobacter sp. 638
1 NhaR

Yersinia pestis KIM
1 NhaR

Serratia proteamaculans 568
1 NhaR

Erwinia carotovora subsp. atroseptica SCRI1043
1 NhaR

Edwardsiella tarda EIB202
1 NhaR

Proteus mirabilis HI4320
1 NhaR

Photorhabdus luminescens subsp. laumondii TTO1
Osmotic stress response
TF XapR
1 XapR

Escherichia coli str. K-12 substr. MG1655
1 XapR

Citrobacter koseri ATCC BAA-895
1 XapR

Enterobacter sp. 638
1 XapR

Edwardsiella tarda EIB202
Xanthosine utilization
MarR TF MarR
1 MarR

Escherichia coli str. K-12 substr. MG1655
1 MarR

Salmonella typhimurium LT2
1 MarR

Citrobacter koseri ATCC BAA-895
1 MarR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 MarR

Enterobacter sp. 638
Antibiotic resistance
TF MprA
2 MprA

Escherichia coli str. K-12 substr. MG1655
2 MprA

Salmonella typhimurium LT2
2 MprA

Citrobacter koseri ATCC BAA-895
2 MprA

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 MprA

Enterobacter sp. 638
2 MprA

Erwinia amylovora ATCC 49946
2 MprA

Yersinia pestis KIM
2 MprA

Serratia proteamaculans 568
2 MprA

Erwinia carotovora subsp. atroseptica SCRI1043
2 MprA

Edwardsiella tarda EIB202
1 MprA

Proteus mirabilis HI4320
2 MprA

Photorhabdus luminescens subsp. laumondii TTO1
Multidrug resistance
MerR TF CueR
2 CueR

Escherichia coli str. K-12 substr. MG1655
3 CueR

Salmonella typhimurium LT2
2 CueR

Citrobacter koseri ATCC BAA-895
3 CueR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 CueR

Enterobacter sp. 638
3 CueR

Erwinia amylovora ATCC 49946
3 CueR

Yersinia pestis KIM
3 CueR

Serratia proteamaculans 568
2 CueR

Erwinia carotovora subsp. atroseptica SCRI1043
2 CueR

Edwardsiella tarda EIB202
3 CueR

Proteus mirabilis HI4320
2 CueR

Photorhabdus luminescens subsp. laumondii TTO1
Copper resistance
TF SoxR
2 SoxR

Escherichia coli str. K-12 substr. MG1655
2 SoxR

Salmonella typhimurium LT2
2 SoxR

Citrobacter koseri ATCC BAA-895
3 SoxR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
3 SoxR

Enterobacter sp. 638
2 SoxR

Erwinia amylovora ATCC 49946
Superoxide stress response
TF ZntR
1 ZntR

Escherichia coli str. K-12 substr. MG1655
1 ZntR

Salmonella typhimurium LT2
1 ZntR

Citrobacter koseri ATCC BAA-895
1 ZntR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 ZntR

Enterobacter sp. 638
1 ZntR

Erwinia amylovora ATCC 49946
1 ZntR

Yersinia pestis KIM
1 ZntR

Serratia proteamaculans 568
1 ZntR

Edwardsiella tarda EIB202
1 ZntR

Proteus mirabilis HI4320
1 ZntR

Photorhabdus luminescens subsp. laumondii TTO1
Zinc resistance
MetJ TF MetJ
15 MetJ

Escherichia coli str. K-12 substr. MG1655
12 MetJ

Salmonella typhimurium LT2
18 MetJ

Citrobacter koseri ATCC BAA-895
20 MetJ

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
19 MetJ

Enterobacter sp. 638
12 MetJ

Erwinia amylovora ATCC 49946
9 MetJ

Yersinia pestis KIM
18 MetJ

Serratia proteamaculans 568
17 MetJ

Erwinia carotovora subsp. atroseptica SCRI1043
7 MetJ

Edwardsiella tarda EIB202
10 MetJ

Proteus mirabilis HI4320
10 MetJ

Photorhabdus luminescens subsp. laumondii TTO1
Methionine metabolism; Methionine biosynthesis
ModE TF ModE
5 ModE

Escherichia coli str. K-12 substr. MG1655
6 ModE

Salmonella typhimurium LT2
6 ModE

Citrobacter koseri ATCC BAA-895
6 ModE

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
5 ModE

Enterobacter sp. 638
2 ModE

Erwinia amylovora ATCC 49946
3 ModE

Yersinia pestis KIM
5 ModE

Serratia proteamaculans 568
5 ModE

Erwinia carotovora subsp. atroseptica SCRI1043
5 ModE

Edwardsiella tarda EIB202
3 ModE

Proteus mirabilis HI4320
1 ModE

Photorhabdus luminescens subsp. laumondii TTO1
Molybdopterin biosynthesis; Molybdenum homeostasis
NadR TF NadR
3 NadR

Escherichia coli str. K-12 substr. MG1655
3 NadR

Salmonella typhimurium LT2
3 NadR

Citrobacter koseri ATCC BAA-895
3 NadR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
3 NadR

Enterobacter sp. 638
1 NadR

Erwinia amylovora ATCC 49946
1 NadR

Yersinia pestis KIM
3 NadR

Serratia proteamaculans 568
2 NadR

Erwinia carotovora subsp. atroseptica SCRI1043
2 NadR

Proteus mirabilis HI4320
1 NadR

Photorhabdus luminescens subsp. laumondii TTO1
NAD biosynthesis
NikR TF NikR
1 NikR

Escherichia coli str. K-12 substr. MG1655
2 NikR

Salmonella typhimurium LT2
1 NikR

Citrobacter koseri ATCC BAA-895
1 NikR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 NikR

Enterobacter sp. 638
3 NikR

Edwardsiella tarda EIB202
Nickel homeostasis
NrdR TF NrdR
3 NrdR

Escherichia coli str. K-12 substr. MG1655
3 NrdR

Salmonella typhimurium LT2
3 NrdR

Citrobacter koseri ATCC BAA-895
3 NrdR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
3 NrdR

Enterobacter sp. 638
3 NrdR

Erwinia amylovora ATCC 49946
3 NrdR

Yersinia pestis KIM
3 NrdR

Serratia proteamaculans 568
3 NrdR

Erwinia carotovora subsp. atroseptica SCRI1043
2 NrdR

Edwardsiella tarda EIB202
3 NrdR

Proteus mirabilis HI4320
3 NrdR

Photorhabdus luminescens subsp. laumondii TTO1
Ribonucleotide reductases
NrtR TF NrtR
2 NrtR

Proteus mirabilis HI4320
NAD biosynthesis
ROK TF NagC
8 NagC

Escherichia coli str. K-12 substr. MG1655
6 NagC

Salmonella typhimurium LT2
5 NagC

Citrobacter koseri ATCC BAA-895
4 NagC

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
5 NagC

Enterobacter sp. 638
2 NagC

Erwinia amylovora ATCC 49946
5 NagC

Yersinia pestis KIM
4 NagC

Serratia proteamaculans 568
3 NagC

Erwinia carotovora subsp. atroseptica SCRI1043
3 NagC

Edwardsiella tarda EIB202
4 NagC

Proteus mirabilis HI4320
3 NagC

Photorhabdus luminescens subsp. laumondii TTO1
N-acetylglucosamine utilization
RpiR TF AlsR
2 AlsR

Escherichia coli str. K-12 substr. MG1655
2 AlsR

Citrobacter koseri ATCC BAA-895
Allose utilization
TF HexR
3 HexR

Escherichia coli str. K-12 substr. MG1655
4 HexR

Salmonella typhimurium LT2
4 HexR

Citrobacter koseri ATCC BAA-895
4 HexR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
4 HexR

Enterobacter sp. 638
3 HexR

Yersinia pestis KIM
4 HexR

Serratia proteamaculans 568
4 HexR

Erwinia carotovora subsp. atroseptica SCRI1043
3 HexR

Edwardsiella tarda EIB202
4 HexR

Proteus mirabilis HI4320
3 HexR

Photorhabdus luminescens subsp. laumondii TTO1
Central carbohydrate metabolism
TF MurR
2 MurR

Escherichia coli str. K-12 substr. MG1655
2 MurR

Citrobacter koseri ATCC BAA-895
1 MurR

Proteus mirabilis HI4320
N-acetylmuramate utilization
TF NanR (SiaQ)
2 NanR (SiaQ)

Enterobacter sp. 638
Sialic acid utilization
TF SiaR
2 SiaR

Salmonella typhimurium LT2
3 SiaR

Yersinia pestis KIM
3 SiaR

Edwardsiella tarda EIB202
2 SiaR

Proteus mirabilis HI4320
Sialic acid utilization
Rrf2 TF IscR
3 IscR

Escherichia coli str. K-12 substr. MG1655
3 IscR

Salmonella typhimurium LT2
3 IscR

Citrobacter koseri ATCC BAA-895
3 IscR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
3 IscR

Enterobacter sp. 638
2 IscR

Erwinia amylovora ATCC 49946
3 IscR

Yersinia pestis KIM
3 IscR

Serratia proteamaculans 568
2 IscR

Erwinia carotovora subsp. atroseptica SCRI1043
3 IscR

Edwardsiella tarda EIB202
2 IscR

Proteus mirabilis HI4320
3 IscR

Photorhabdus luminescens subsp. laumondii TTO1
Iron-sulfur cluster biogenesis
TF NsrR
10 NsrR

Escherichia coli str. K-12 substr. MG1655
11 NsrR

Salmonella typhimurium LT2
8 NsrR

Citrobacter koseri ATCC BAA-895
6 NsrR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
8 NsrR

Enterobacter sp. 638
4 NsrR

Yersinia pestis KIM
2 NsrR

Serratia proteamaculans 568
5 NsrR

Erwinia carotovora subsp. atroseptica SCRI1043
4 NsrR

Edwardsiella tarda EIB202
6 NsrR

Proteus mirabilis HI4320
3 NsrR

Photorhabdus luminescens subsp. laumondii TTO1
Nitrosative stress response
SdaR TF SdaR
4 SdaR

Escherichia coli str. K-12 substr. MG1655
4 SdaR

Salmonella typhimurium LT2
4 SdaR

Citrobacter koseri ATCC BAA-895
4 SdaR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
4 SdaR

Enterobacter sp. 638
4 SdaR

Erwinia carotovora subsp. atroseptica SCRI1043
Glucarate utilization; Galactarate utilization
SorC TF LsrR
2 LsrR

Escherichia coli str. K-12 substr. MG1655
2 LsrR

Salmonella typhimurium LT2
2 LsrR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 LsrR

Enterobacter sp. 638
1 LsrR

Yersinia pestis KIM
2 LsrR

Photorhabdus luminescens subsp. laumondii TTO1
Quorum sensing; Biofilm formation
TF SorC
1 SorC

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Sorbose utilization
TetR TF AcrR
2 AcrR

Escherichia coli str. K-12 substr. MG1655
2 AcrR

Salmonella typhimurium LT2
2 AcrR

Citrobacter koseri ATCC BAA-895
2 AcrR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 AcrR

Enterobacter sp. 638
2 AcrR

Erwinia amylovora ATCC 49946
2 AcrR

Yersinia pestis KIM
2 AcrR

Serratia proteamaculans 568
2 AcrR

Erwinia carotovora subsp. atroseptica SCRI1043
2 AcrR

Edwardsiella tarda EIB202
2 AcrR

Proteus mirabilis HI4320
2 AcrR

Photorhabdus luminescens subsp. laumondii TTO1
Multidrug resistance
TF BetI
2 BetI

Escherichia coli str. K-12 substr. MG1655
2 BetI

Citrobacter koseri ATCC BAA-895
2 BetI

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 BetI

Erwinia amylovora ATCC 49946
2 BetI

Serratia proteamaculans 568
2 BetI

Erwinia carotovora subsp. atroseptica SCRI1043
2 BetI

Proteus mirabilis HI4320
Glycine betaine synthesis
TF FabR
3 FabR

Escherichia coli str. K-12 substr. MG1655
3 FabR

Salmonella typhimurium LT2
3 FabR

Citrobacter koseri ATCC BAA-895
3 FabR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
3 FabR

Enterobacter sp. 638
3 FabR

Erwinia amylovora ATCC 49946
4 FabR

Yersinia pestis KIM
4 FabR

Serratia proteamaculans 568
4 FabR

Erwinia carotovora subsp. atroseptica SCRI1043
4 FabR

Edwardsiella tarda EIB202
3 FabR

Proteus mirabilis HI4320
3 FabR

Photorhabdus luminescens subsp. laumondii TTO1
Fatty acid biosynthesis
TF RutR
3 RutR

Escherichia coli str. K-12 substr. MG1655
1 RutR

Salmonella typhimurium LT2
1 RutR

Citrobacter koseri ATCC BAA-895
3 RutR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 RutR

Enterobacter sp. 638
1 RutR

Erwinia amylovora ATCC 49946
2 RutR

Serratia proteamaculans 568
Pyrimidine utilization
TrpR TF TrpR
5 TrpR

Escherichia coli str. K-12 substr. MG1655
5 TrpR

Salmonella typhimurium LT2
5 TrpR

Citrobacter koseri ATCC BAA-895
4 TrpR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
5 TrpR

Enterobacter sp. 638
3 TrpR

Erwinia amylovora ATCC 49946
3 TrpR

Yersinia pestis KIM
3 TrpR

Serratia proteamaculans 568
2 TrpR

Erwinia carotovora subsp. atroseptica SCRI1043
4 TrpR

Edwardsiella tarda EIB202
2 TrpR

Proteus mirabilis HI4320
2 TrpR

Photorhabdus luminescens subsp. laumondii TTO1
Tryptophan biosynthesis
TyrR TF TyrR
8 TyrR

Escherichia coli str. K-12 substr. MG1655
8 TyrR

Salmonella typhimurium LT2
10 TyrR

Citrobacter koseri ATCC BAA-895
8 TyrR

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
8 TyrR

Enterobacter sp. 638
4 TyrR

Erwinia amylovora ATCC 49946
5 TyrR

Yersinia pestis KIM
6 TyrR

Serratia proteamaculans 568
4 TyrR

Erwinia carotovora subsp. atroseptica SCRI1043
4 TyrR

Edwardsiella tarda EIB202
5 TyrR

Proteus mirabilis HI4320
4 TyrR

Photorhabdus luminescens subsp. laumondii TTO1
Aromatic amino acid metabolism
[Other] TF PaaX
2 PaaX

Escherichia coli str. K-12 substr. MG1655
2 PaaX

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 PaaX

Serratia proteamaculans 568
Phenylacetic acid degradation
RF00050 RNA FMN
1 FMN

Escherichia coli str. K-12 substr. MG1655
1 FMN

Salmonella typhimurium LT2
1 FMN

Citrobacter koseri ATCC BAA-895
1 FMN

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 FMN

Enterobacter sp. 638
1 FMN

Erwinia amylovora ATCC 49946
1 FMN

Yersinia pestis KIM
1 FMN

Serratia proteamaculans 568
1 FMN

Erwinia carotovora subsp. atroseptica SCRI1043
1 FMN

Edwardsiella tarda EIB202
1 FMN

Proteus mirabilis HI4320
1 FMN

Photorhabdus luminescens subsp. laumondii TTO1
Riboflavin biosynthesis
RF00059 RNA TPP
3 TPP

Escherichia coli str. K-12 substr. MG1655
3 TPP

Salmonella typhimurium LT2
3 TPP

Citrobacter koseri ATCC BAA-895
4 TPP

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
3 TPP

Enterobacter sp. 638
4 TPP

Erwinia amylovora ATCC 49946
3 TPP

Yersinia pestis KIM
4 TPP

Serratia proteamaculans 568
3 TPP

Erwinia carotovora subsp. atroseptica SCRI1043
3 TPP

Edwardsiella tarda EIB202
3 TPP

Proteus mirabilis HI4320
2 TPP

Photorhabdus luminescens subsp. laumondii TTO1
Thiamine biosynthesis
RF00080 RNA yybP-ykoY
2 yybP-ykoY

Escherichia coli str. K-12 substr. MG1655
2 yybP-ykoY

Salmonella typhimurium LT2
2 yybP-ykoY

Citrobacter koseri ATCC BAA-895
2 yybP-ykoY

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
2 yybP-ykoY

Enterobacter sp. 638
1 yybP-ykoY

Erwinia amylovora ATCC 49946
1 yybP-ykoY

Yersinia pestis KIM
2 yybP-ykoY

Serratia proteamaculans 568
2 yybP-ykoY

Erwinia carotovora subsp. atroseptica SCRI1043
2 yybP-ykoY

Edwardsiella tarda EIB202
1 yybP-ykoY

Proteus mirabilis HI4320
2 yybP-ykoY

Photorhabdus luminescens subsp. laumondii TTO1
RF00114 RNA S15
1 S15

Escherichia coli str. K-12 substr. MG1655
1 S15

Salmonella typhimurium LT2
1 S15

Citrobacter koseri ATCC BAA-895
1 S15

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 S15

Enterobacter sp. 638
1 S15

Erwinia amylovora ATCC 49946
1 S15

Yersinia pestis KIM
1 S15

Serratia proteamaculans 568
1 S15

Erwinia carotovora subsp. atroseptica SCRI1043
1 S15

Edwardsiella tarda EIB202
1 S15

Proteus mirabilis HI4320
1 S15

Photorhabdus luminescens subsp. laumondii TTO1
Ribosome biogenesis
RF00168 RNA Lysine
1 Lysine

Escherichia coli str. K-12 substr. MG1655
1 Lysine

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 Lysine

Erwinia amylovora ATCC 49946
1 Lysine

Serratia proteamaculans 568
1 Lysine

Erwinia carotovora subsp. atroseptica SCRI1043
Lysine biosynthesis
RF00174 RNA Cobalamin
1 Cobalamin

Escherichia coli str. K-12 substr. MG1655
2 Cobalamin

Salmonella typhimurium LT2
3 Cobalamin

Citrobacter koseri ATCC BAA-895
2 Cobalamin

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 Cobalamin

Enterobacter sp. 638
1 Cobalamin

Yersinia pestis KIM
1 Cobalamin

Serratia proteamaculans 568
1 Cobalamin

Erwinia carotovora subsp. atroseptica SCRI1043
2 Cobalamin

Edwardsiella tarda EIB202
1 Cobalamin

Proteus mirabilis HI4320
1 Cobalamin

Photorhabdus luminescens subsp. laumondii TTO1
Cobalamin biosynthesis
RF00380 RNA ykoK
1 ykoK

Citrobacter koseri ATCC BAA-895
1 ykoK

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 ykoK

Serratia proteamaculans 568
1 ykoK

Proteus mirabilis HI4320
1 ykoK

Photorhabdus luminescens subsp. laumondii TTO1
Magnesium homeostasis
RF00442 RNA ykkC-yxkD
1 ykkC-yxkD

Erwinia carotovora subsp. atroseptica SCRI1043
Multidrug resistance
RF00504 RNA Glycine
1 Glycine

Erwinia carotovora subsp. atroseptica SCRI1043
Glycine metabolism
RF00506 RNA Thr_leader
1 Thr_leader

Escherichia coli str. K-12 substr. MG1655
1 Thr_leader

Salmonella typhimurium LT2
1 Thr_leader

Citrobacter koseri ATCC BAA-895
1 Thr_leader

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 Thr_leader

Enterobacter sp. 638
1 Thr_leader

Erwinia amylovora ATCC 49946
1 Thr_leader

Yersinia pestis KIM
1 Thr_leader

Serratia proteamaculans 568
1 Thr_leader

Erwinia carotovora subsp. atroseptica SCRI1043
1 Thr_leader

Edwardsiella tarda EIB202
1 Thr_leader

Proteus mirabilis HI4320
1 Thr_leader

Photorhabdus luminescens subsp. laumondii TTO1
Threonine biosynthesis
RF00512 RNA Leu_leader
1 Leu_leader

Escherichia coli str. K-12 substr. MG1655
1 Leu_leader

Salmonella typhimurium LT2
1 Leu_leader

Citrobacter koseri ATCC BAA-895
1 Leu_leader

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 Leu_leader

Enterobacter sp. 638
1 Leu_leader

Erwinia amylovora ATCC 49946
1 Leu_leader

Yersinia pestis KIM
1 Leu_leader

Serratia proteamaculans 568
1 Leu_leader

Erwinia carotovora subsp. atroseptica SCRI1043
1 Leu_leader

Edwardsiella tarda EIB202
1 Leu_leader

Proteus mirabilis HI4320
1 Leu_leader

Photorhabdus luminescens subsp. laumondii TTO1
Branched-chain amino acid biosynthesis
RF00513 RNA Trp_leader
1 Trp_leader

Escherichia coli str. K-12 substr. MG1655
1 Trp_leader

Salmonella typhimurium LT2
1 Trp_leader

Citrobacter koseri ATCC BAA-895
1 Trp_leader

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 Trp_leader

Enterobacter sp. 638
1 Trp_leader

Erwinia amylovora ATCC 49946
1 Trp_leader

Yersinia pestis KIM
1 Trp_leader

Serratia proteamaculans 568
1 Trp_leader

Erwinia carotovora subsp. atroseptica SCRI1043
1 Trp_leader

Edwardsiella tarda EIB202
1 Trp_leader

Proteus mirabilis HI4320
1 Trp_leader

Photorhabdus luminescens subsp. laumondii TTO1
Tryptophan biosynthesis
RF00514 RNA His_leader
1 His_leader

Escherichia coli str. K-12 substr. MG1655
1 His_leader

Salmonella typhimurium LT2
1 His_leader

Citrobacter koseri ATCC BAA-895
1 His_leader

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 His_leader

Enterobacter sp. 638
1 His_leader

Erwinia amylovora ATCC 49946
1 His_leader

Yersinia pestis KIM
1 His_leader

Serratia proteamaculans 568
1 His_leader

Erwinia carotovora subsp. atroseptica SCRI1043
1 His_leader

Edwardsiella tarda EIB202
1 His_leader

Proteus mirabilis HI4320
1 His_leader

Photorhabdus luminescens subsp. laumondii TTO1
Histidine biosynthesis
RF00558 RNA L20_leader Ribosome biogenesis
RF01051 RNA GEMM_RNA_motif
1 GEMM_RNA_motif

Citrobacter koseri ATCC BAA-895
Second messenger response
RF01055 RNA MOCO_RNA_motif
1 MOCO_RNA_motif

Escherichia coli str. K-12 substr. MG1655
1 MOCO_RNA_motif

Salmonella typhimurium LT2
1 MOCO_RNA_motif

Citrobacter koseri ATCC BAA-895
1 MOCO_RNA_motif

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 MOCO_RNA_motif

Enterobacter sp. 638
1 MOCO_RNA_motif

Erwinia amylovora ATCC 49946
1 MOCO_RNA_motif

Yersinia pestis KIM
1 MOCO_RNA_motif

Serratia proteamaculans 568
1 MOCO_RNA_motif

Erwinia carotovora subsp. atroseptica SCRI1043
1 MOCO_RNA_motif

Edwardsiella tarda EIB202
1 MOCO_RNA_motif

Proteus mirabilis HI4320
1 MOCO_RNA_motif

Photorhabdus luminescens subsp. laumondii TTO1
Molybdopterin biosynthesis
RF01056 RNA Mg_sensor
1 Mg_sensor

Escherichia coli str. K-12 substr. MG1655
1 Mg_sensor

Salmonella typhimurium LT2
1 Mg_sensor

Citrobacter koseri ATCC BAA-895
1 Mg_sensor

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 Mg_sensor

Enterobacter sp. 638
Magnesium homeostasis
RF01068 RNA mini-ykkC
1 mini-ykkC

Escherichia coli str. K-12 substr. MG1655
1 mini-ykkC

Salmonella typhimurium LT2
1 mini-ykkC

Citrobacter koseri ATCC BAA-895
1 mini-ykkC

Klebsiella pneumoniae subsp. pneumoniae MGH 78578
1 mini-ykkC

Enterobacter sp. 638
1 mini-ykkC

Serratia proteamaculans 568
1 mini-ykkC

Erwinia carotovora subsp. atroseptica SCRI1043
1 mini-ykkC

Edwardsiella tarda EIB202
1 mini-ykkC

Proteus mirabilis HI4320
1 mini-ykkC

Photorhabdus luminescens subsp. laumondii TTO1
Multidrug resistance