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

Collection of regulogs in Ralstonia taxonomic group

General statistics
Genomes 6
TF regulogs 69
TF regulons 277
TF binding sites 957
RNA regulogs 10
RNA regulons 46
RNA sites 66

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
Cupriavidus taiwanensis 48 169 8 11 56 180
Ralstonia eutropha H16 57 198 7 10 64 208
Ralstonia eutropha JMP134 49 156 9 13 58 169
Ralstonia metallidurans CH34 47 178 7 10 54 188
Ralstonia pickettii 12J 40 137 8 13 48 150
Ralstonia solanacearum GMI1000 36 119 7 9 43 128
Genomic distribution of regulons
Family Type Regulator Function
CRP TF Dnr
2 Dnr

Ralstonia eutropha H16
1 Dnr

Cupriavidus taiwanensis
2 Dnr

Ralstonia metallidurans CH34
1 Dnr

Ralstonia eutropha JMP134
2 Dnr

Ralstonia solanacearum GMI1000
1 Dnr

Ralstonia pickettii 12J
Denitrification
FUR TF Fur
19 Fur

Ralstonia eutropha H16
16 Fur

Cupriavidus taiwanensis
18 Fur

Ralstonia metallidurans CH34
11 Fur

Ralstonia eutropha JMP134
14 Fur

Ralstonia solanacearum GMI1000
10 Fur

Ralstonia pickettii 12J
Iron homeostasis
TF Zur
3 Zur

Ralstonia eutropha H16
2 Zur

Cupriavidus taiwanensis
3 Zur

Ralstonia metallidurans CH34
2 Zur

Ralstonia eutropha JMP134
4 Zur

Ralstonia solanacearum GMI1000
4 Zur

Ralstonia pickettii 12J
Zinc homeostasis
Fis TF NorR
4 NorR

Ralstonia eutropha H16
2 NorR

Cupriavidus taiwanensis
2 NorR

Ralstonia metallidurans CH34
2 NorR

Ralstonia eutropha JMP134
2 NorR

Ralstonia solanacearum GMI1000
2 NorR

Ralstonia pickettii 12J
Nitrosative stress response
TF NtrC
4 NtrC

Ralstonia eutropha H16
4 NtrC

Cupriavidus taiwanensis
5 NtrC

Ralstonia metallidurans CH34
5 NtrC

Ralstonia eutropha JMP134
3 NtrC

Ralstonia solanacearum GMI1000
3 NtrC

Ralstonia pickettii 12J
Nitrogen assimilation
GntR/MocR TF GabR
1 GabR

Ralstonia eutropha H16
1 GabR

Cupriavidus taiwanensis
2 GabR

Ralstonia metallidurans CH34
2 GabR

Ralstonia solanacearum GMI1000
2 GabR

Ralstonia pickettii 12J
Gamma-aminobutyrate utilization
TF H16_A0963
1 H16_A0963

Ralstonia eutropha H16
1 H16_A0963

Cupriavidus taiwanensis
1 H16_A0963

Ralstonia metallidurans CH34
1 H16_A0963

Ralstonia eutropha JMP134
1 H16_A0963

Ralstonia pickettii 12J
TF H16_A0970
3 H16_A0970

Ralstonia eutropha H16
2 H16_A0970

Cupriavidus taiwanensis
1 H16_A0970

Ralstonia metallidurans CH34
2 H16_A0970

Ralstonia eutropha JMP134
1 H16_A0970

Ralstonia solanacearum GMI1000
1 H16_A0970

Ralstonia pickettii 12J
TF H16_A2655
2 H16_A2655

Ralstonia eutropha H16
2 H16_A2655

Cupriavidus taiwanensis
2 H16_A2655

Ralstonia metallidurans CH34
2 H16_A2655

Ralstonia eutropha JMP134
1 H16_A2655

Ralstonia solanacearum GMI1000
1 H16_A2655

Ralstonia pickettii 12J
Metabolite transport
TF H16_B0275
1 H16_B0275

Ralstonia eutropha H16
2 H16_B0275

Ralstonia eutropha JMP134
TF H16_B1411
2 H16_B1411

Ralstonia eutropha H16
1 H16_B1411

Ralstonia eutropha JMP134
TF H16_B1468
3 H16_B1468

Ralstonia eutropha H16
3 H16_B1468

Cupriavidus taiwanensis
1 H16_B1468

Ralstonia metallidurans CH34
2 H16_B1468

Ralstonia eutropha JMP134
TF OapR
1 OapR

Ralstonia eutropha H16
1 OapR

Cupriavidus taiwanensis
1 OapR

Ralstonia metallidurans CH34
1 OapR

Ralstonia eutropha JMP134
1 OapR

Ralstonia solanacearum GMI1000
1 OapR

Ralstonia pickettii 12J
Gamma-aminobutyrate utilization
TF PdxQ
1 PdxQ

Ralstonia eutropha H16
1 PdxQ

Cupriavidus taiwanensis
Pyridoxine/pyridoxal homeostasis
TF PdxQ3
1 PdxQ3

Ralstonia eutropha H16
Metabolite transport; Pyridoxine/pyridoxal homeostasis
TF PdxR2
2 PdxR2

Ralstonia metallidurans CH34
Pyridoxine/pyridoxal homeostasis
TF PdxW
1 PdxW

Ralstonia solanacearum GMI1000
2 PdxW

Ralstonia pickettii 12J
Pyridoxine/pyridoxal homeostasis
TF RALTA_A0216
1 RALTA_A0216

Ralstonia eutropha H16
1 RALTA_A0216

Cupriavidus taiwanensis
1 RALTA_A0216

Ralstonia metallidurans CH34
1 RALTA_A0216

Ralstonia eutropha JMP134
1 RALTA_A0216

Ralstonia pickettii 12J
TF TauR
3 TauR

Ralstonia eutropha H16
4 TauR

Cupriavidus taiwanensis
2 TauR

Ralstonia eutropha JMP134
Taurine utilization
TF YdcR
2 YdcR

Ralstonia eutropha H16
3 YdcR

Cupriavidus taiwanensis
2 YdcR

Ralstonia eutropha JMP134
TF YrdX
1 YrdX

Ralstonia eutropha H16
TF YrdX3
1 YrdX3

Ralstonia eutropha H16
2 YrdX3

Ralstonia metallidurans CH34
2 YrdX3

Ralstonia eutropha JMP134
1 YrdX3

Ralstonia solanacearum GMI1000
TF YrdX3(2)
1 YrdX3(2)

Ralstonia metallidurans CH34
GntR/Others TF GguR
4 GguR

Ralstonia eutropha H16
4 GguR

Cupriavidus taiwanensis
6 GguR

Ralstonia metallidurans CH34
5 GguR

Ralstonia eutropha JMP134
2 GguR

Ralstonia solanacearum GMI1000
2 GguR

Ralstonia pickettii 12J
Glucarate utilization; Galactarate utilization
TF H16_B1761
2 H16_B1761

Ralstonia eutropha H16
2 H16_B1761

Ralstonia eutropha JMP134
TF H16_B2241
1 H16_B2241

Ralstonia eutropha H16
1 H16_B2241

Cupriavidus taiwanensis
1 H16_B2241

Ralstonia pickettii 12J
Alkanesulfonates utilization
TF HutC
3 HutC

Ralstonia eutropha H16
3 HutC

Cupriavidus taiwanensis
3 HutC

Ralstonia metallidurans CH34
4 HutC

Ralstonia eutropha JMP134
2 HutC

Ralstonia solanacearum GMI1000
3 HutC

Ralstonia pickettii 12J
Histidine utilization
TF HypR
2 HypR

Ralstonia metallidurans CH34
Proline and 4-hydrohyproline utilization
TF LldR
2 LldR

Ralstonia eutropha H16
2 LldR

Cupriavidus taiwanensis
2 LldR

Ralstonia metallidurans CH34
2 LldR

Ralstonia eutropha JMP134
Lactate utilization
TF MlnR
1 MlnR

Ralstonia eutropha H16
1 MlnR

Cupriavidus taiwanensis
1 MlnR

Ralstonia metallidurans CH34
1 MlnR

Ralstonia eutropha JMP134
Malonate metabolism
TF NagQ
2 NagQ

Ralstonia eutropha H16
N-acetylglucosamine utilization
TF PhnF
2 PhnF

Ralstonia eutropha H16
2 PhnF

Cupriavidus taiwanensis
2 PhnF

Ralstonia metallidurans CH34
2 PhnF

Ralstonia eutropha JMP134
Phosphonate utilization
TF PhnR2
2 PhnR2

Ralstonia eutropha H16
2 PhnR2

Cupriavidus taiwanensis
4 PhnR2

Ralstonia eutropha JMP134
2-aminoethylphosphonate utilization
TF Rmet_5631
3 Rmet_5631

Ralstonia eutropha H16
6 Rmet_5631

Cupriavidus taiwanensis
2 Rmet_5631

Ralstonia metallidurans CH34
2 Rmet_5631

Ralstonia eutropha JMP134
Glycolate utilization; Lactate utilization
TF SdaR
1 SdaR

Ralstonia eutropha H16
1 SdaR

Cupriavidus taiwanensis
1 SdaR

Ralstonia metallidurans CH34
1 SdaR

Ralstonia eutropha JMP134
Glucuronate utilization; Glucarate utilization; Galactarate utilization
TF SdhR
6 SdhR

Ralstonia eutropha H16
6 SdhR

Cupriavidus taiwanensis
7 SdhR

Ralstonia metallidurans CH34
5 SdhR

Ralstonia eutropha JMP134
4 SdhR

Ralstonia solanacearum GMI1000
8 SdhR

Ralstonia pickettii 12J
Tricarboxylic acid cycle
TF UraR
5 UraR

Ralstonia eutropha H16
4 UraR

Cupriavidus taiwanensis
3 UraR

Ralstonia metallidurans CH34
3 UraR

Ralstonia eutropha JMP134
2 UraR

Ralstonia solanacearum GMI1000
2 UraR

Ralstonia pickettii 12J
Pyrimidine utilization
TF UreR
5 UreR

Ralstonia eutropha H16
1 UreR

Ralstonia solanacearum GMI1000
1 UreR

Ralstonia pickettii 12J
TF UxuR3
2 UxuR3

Cupriavidus taiwanensis
Glucuronate utilization
HrcA TF HrcA
2 HrcA

Ralstonia eutropha H16
2 HrcA

Cupriavidus taiwanensis
2 HrcA

Ralstonia metallidurans CH34
2 HrcA

Ralstonia eutropha JMP134
2 HrcA

Ralstonia solanacearum GMI1000
2 HrcA

Ralstonia pickettii 12J
Heat shock response
LacI TF FruR2
2 FruR2

Ralstonia solanacearum GMI1000
2 FruR2

Ralstonia pickettii 12J
Fructose utilization
TF HpxR
1 HpxR

Ralstonia eutropha H16
1 HpxR

Cupriavidus taiwanensis
1 HpxR

Ralstonia eutropha JMP134
Xanthine utilization
TF PtxS
2 PtxS

Ralstonia eutropha H16
1 PtxS

Ralstonia pickettii 12J
2-ketogluconate utilization
TF RSc1790
1 RSc1790

Ralstonia eutropha H16
1 RSc1790

Cupriavidus taiwanensis
1 RSc1790

Ralstonia metallidurans CH34
1 RSc1790

Ralstonia solanacearum GMI1000
1 RSc1790

Ralstonia pickettii 12J
Sugar utilization
TF RbsR
1 RbsR

Ralstonia solanacearum GMI1000
1 RbsR

Ralstonia pickettii 12J
Ribose utilization
TF Reut_C5892
1 Reut_C5892

Ralstonia eutropha JMP134
Sugar utilization
TF Rmet_4647
2 Rmet_4647

Ralstonia metallidurans CH34
2 Rmet_4647

Ralstonia eutropha JMP134
TF ScrR
2 ScrR

Ralstonia solanacearum GMI1000
Sucrose utilization
LexA TF LexA
10 LexA

Ralstonia eutropha H16
11 LexA

Cupriavidus taiwanensis
10 LexA

Ralstonia metallidurans CH34
9 LexA

Ralstonia eutropha JMP134
5 LexA

Ralstonia solanacearum GMI1000
5 LexA

Ralstonia pickettii 12J
SOS response
LysR TF GulR
2 GulR

Ralstonia solanacearum GMI1000
2 GulR

Ralstonia pickettii 12J
Glucuronate utilization; Galacturonate utilization; Galactarate utilization; Glucarate utilization
TF MetR
2 MetR

Ralstonia eutropha H16
2 MetR

Cupriavidus taiwanensis
2 MetR

Ralstonia metallidurans CH34
2 MetR

Ralstonia eutropha JMP134
2 MetR

Ralstonia solanacearum GMI1000
2 MetR

Ralstonia pickettii 12J
Methionine biosynthesis
MerR TF CadR-PbrR
2 CadR-PbrR

Ralstonia eutropha H16
2 CadR-PbrR

Cupriavidus taiwanensis
8 CadR-PbrR

Ralstonia metallidurans CH34
2 CadR-PbrR

Ralstonia eutropha JMP134
1 CadR-PbrR

Ralstonia solanacearum GMI1000
6 CadR-PbrR

Ralstonia pickettii 12J
Lead resistance; Cadmium resistance
TF CueR
3 CueR

Ralstonia eutropha H16
2 CueR

Cupriavidus taiwanensis
4 CueR

Ralstonia metallidurans CH34
2 CueR

Ralstonia eutropha JMP134
2 CueR

Ralstonia solanacearum GMI1000
5 CueR

Ralstonia pickettii 12J
Copper resistance
TF LiuR
5 LiuR

Ralstonia eutropha H16
5 LiuR

Cupriavidus taiwanensis
5 LiuR

Ralstonia metallidurans CH34
4 LiuR

Ralstonia eutropha JMP134
6 LiuR

Ralstonia solanacearum GMI1000
6 LiuR

Ralstonia pickettii 12J
Branched-chain amino acid degradation
TF MerR
1 MerR

Ralstonia eutropha H16
7 MerR

Ralstonia metallidurans CH34
2 MerR

Ralstonia eutropha JMP134
1 MerR

Ralstonia pickettii 12J
Mercury resistance
TF NmlR
1 NmlR

Ralstonia pickettii 12J
Carbonyl stress response
TF SoxR
1 SoxR

Ralstonia eutropha H16
1 SoxR

Cupriavidus taiwanensis
1 SoxR

Ralstonia metallidurans CH34
Superoxide stress response
ModE TF FdsR
2 FdsR

Ralstonia eutropha H16
2 FdsR

Cupriavidus taiwanensis
2 FdsR

Ralstonia metallidurans CH34
2 FdsR

Ralstonia eutropha JMP134
Formate oxydation
TF ModE
1 ModE

Ralstonia eutropha H16
1 ModE

Cupriavidus taiwanensis
2 ModE

Ralstonia metallidurans CH34
1 ModE

Ralstonia eutropha JMP134
1 ModE

Ralstonia solanacearum GMI1000
2 ModE

Ralstonia pickettii 12J
Molybdenum homeostasis
TF ModE3
2 ModE3

Ralstonia eutropha H16
2 ModE3

Cupriavidus taiwanensis
2 ModE3

Ralstonia metallidurans CH34
2 ModE3

Ralstonia eutropha JMP134
2 ModE3

Ralstonia solanacearum GMI1000
2 ModE3

Ralstonia pickettii 12J
Tungsten homeostasis
NrdR TF NrdR
2 NrdR

Ralstonia eutropha H16
1 NrdR

Cupriavidus taiwanensis
2 NrdR

Ralstonia metallidurans CH34
1 NrdR

Ralstonia eutropha JMP134
2 NrdR

Ralstonia solanacearum GMI1000
3 NrdR

Ralstonia pickettii 12J
Deoxyribonucleotide biosynthesis
RpiR TF HexR
2 HexR

Ralstonia eutropha H16
2 HexR

Cupriavidus taiwanensis
2 HexR

Ralstonia metallidurans CH34
2 HexR

Ralstonia eutropha JMP134
2 HexR

Ralstonia solanacearum GMI1000
2 HexR

Ralstonia pickettii 12J
Central carbohydrate metabolism
Rrf2 TF IscR
1 IscR

Ralstonia eutropha H16
1 IscR

Cupriavidus taiwanensis
1 IscR

Ralstonia metallidurans CH34
1 IscR

Ralstonia eutropha JMP134
1 IscR

Ralstonia solanacearum GMI1000
1 IscR

Ralstonia pickettii 12J
Iron-sulfur cluster biogenesis
TF NsrR
2 NsrR

Ralstonia eutropha H16
2 NsrR

Cupriavidus taiwanensis
4 NsrR

Ralstonia metallidurans CH34
2 NsrR

Ralstonia eutropha JMP134
4 NsrR

Ralstonia solanacearum GMI1000
5 NsrR

Ralstonia pickettii 12J
Nitrosative stress response
TetR TF FadP
15 FadP

Ralstonia eutropha H16
15 FadP

Cupriavidus taiwanensis
14 FadP

Ralstonia metallidurans CH34
15 FadP

Ralstonia eutropha JMP134
11 FadP

Ralstonia solanacearum GMI1000
11 FadP

Ralstonia pickettii 12J
Fatty acid degradation
TF LiuQ
2 LiuQ

Ralstonia eutropha H16
1 LiuQ

Cupriavidus taiwanensis
2 LiuQ

Ralstonia metallidurans CH34
2 LiuQ

Ralstonia eutropha JMP134
Branched-chain amino acid degradation
TF PaaR
3 PaaR

Ralstonia eutropha H16
3 PaaR

Cupriavidus taiwanensis
3 PaaR

Ralstonia metallidurans CH34
3 PaaR

Ralstonia eutropha JMP134
3 PaaR

Ralstonia solanacearum GMI1000
3 PaaR

Ralstonia pickettii 12J
Phenylacetic acid degradation
TF PsrA
2 PsrA

Ralstonia eutropha H16
2 PsrA

Cupriavidus taiwanensis
1 PsrA

Ralstonia metallidurans CH34
2 PsrA

Ralstonia eutropha JMP134
1 PsrA

Ralstonia solanacearum GMI1000
1 PsrA

Ralstonia pickettii 12J
Fatty acid degradation
TF RutR
1 RutR

Ralstonia eutropha H16
1 RutR

Cupriavidus taiwanensis
1 RutR

Ralstonia metallidurans CH34
1 RutR

Ralstonia eutropha JMP134
Pyrimidine utilization
RF00050 RNA FMN
1 FMN

Ralstonia eutropha H16
1 FMN

Cupriavidus taiwanensis
1 FMN

Ralstonia metallidurans CH34
1 FMN

Ralstonia eutropha JMP134
1 FMN

Ralstonia solanacearum GMI1000
1 FMN

Ralstonia pickettii 12J
Riboflavin biosynthesis
RF00059 RNA TPP
1 TPP

Ralstonia eutropha H16
1 TPP

Cupriavidus taiwanensis
1 TPP

Ralstonia metallidurans CH34
1 TPP

Ralstonia eutropha JMP134
1 TPP

Ralstonia solanacearum GMI1000
1 TPP

Ralstonia pickettii 12J
Thiamine biosynthesis
RF00080 RNA yybP-ykoY
1 yybP-ykoY

Ralstonia eutropha H16
1 yybP-ykoY

Cupriavidus taiwanensis
1 yybP-ykoY

Ralstonia metallidurans CH34
1 yybP-ykoY

Ralstonia eutropha JMP134
1 yybP-ykoY

Ralstonia solanacearum GMI1000
3 yybP-ykoY

Ralstonia pickettii 12J
RF00174 RNA Cobalamin
1 Cobalamin

Ralstonia eutropha H16
1 Cobalamin

Cupriavidus taiwanensis
1 Cobalamin

Ralstonia metallidurans CH34
1 Cobalamin

Ralstonia eutropha JMP134
2 Cobalamin

Ralstonia solanacearum GMI1000
1 Cobalamin

Ralstonia pickettii 12J
Cobalamin biosynthesis
RF00442 RNA ykkC-yxkD
2 ykkC-yxkD

Ralstonia eutropha JMP134
Multidrug resistance
RF00504 RNA Glycine
2 Glycine

Ralstonia eutropha H16
2 Glycine

Cupriavidus taiwanensis
2 Glycine

Ralstonia metallidurans CH34
2 Glycine

Ralstonia eutropha JMP134
1 Glycine

Ralstonia solanacearum GMI1000
2 Glycine

Ralstonia pickettii 12J
Glycine metabolism
RF01051 RNA GEMM_RNA_motif
1 GEMM_RNA_motif

Ralstonia pickettii 12J
Second messenger response
RF01057 RNA SAH_riboswitch
1 SAH_riboswitch

Ralstonia eutropha H16
1 SAH_riboswitch

Cupriavidus taiwanensis
1 SAH_riboswitch

Ralstonia metallidurans CH34
1 SAH_riboswitch

Ralstonia eutropha JMP134
1 SAH_riboswitch

Ralstonia solanacearum GMI1000
1 SAH_riboswitch

Ralstonia pickettii 12J
Methionine metabolism
RF01068 RNA mini-ykkC
1 mini-ykkC

Cupriavidus taiwanensis
1 mini-ykkC

Ralstonia eutropha JMP134
Multidrug resistance
RF01070 RNA sucA
1 sucA

Ralstonia eutropha H16
1 sucA

Cupriavidus taiwanensis
1 sucA

Ralstonia metallidurans CH34
1 sucA

Ralstonia eutropha JMP134
1 sucA

Ralstonia solanacearum GMI1000
1 sucA

Ralstonia pickettii 12J
Tricarboxylic acid cycle