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

Collection of regulogs in Alcaligenaceae taxonomic group

General statistics
Genomes 3
TF regulogs 25
TF regulons 60
TF binding sites 157
RNA regulogs 0
RNA regulons 0
RNA sites 0

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
Bordetella avium 197N 17 45 0 0 17 45
Bordetella bronchiseptica RB50 21 53 0 0 21 53
Bordetella petrii DSM 12804 22 59 0 0 22 59
Genomic distribution of regulons
Family Type Regulator Function
GntR/MocR TF BAV2320
3 BAV2320

Bordetella avium 197N
2 BAV2320

Bordetella petrii DSM 12804
1 BAV2320

Bordetella bronchiseptica RB50
TF BAV2922
1 BAV2922

Bordetella avium 197N
1 BAV2922

Bordetella petrii DSM 12804
1 BAV2922

Bordetella bronchiseptica RB50
Metabolite transport
TF Bpet3002
1 Bpet3002

Bordetella petrii DSM 12804
TF Bpet3338
2 Bpet3338

Bordetella petrii DSM 12804
TF GabR
3 GabR

Bordetella avium 197N
2 GabR

Bordetella petrii DSM 12804
2 GabR

Bordetella bronchiseptica RB50
Gamma-aminobutyrate utilization
TF OapR
1 OapR

Bordetella avium 197N
1 OapR

Bordetella petrii DSM 12804
1 OapR

Bordetella bronchiseptica RB50
Gamma-aminobutyrate utilization
TF PdxQ
1 PdxQ

Bordetella petrii DSM 12804
Pyridoxine/pyridoxal homeostasis
TF PdxR
1 PdxR

Bordetella avium 197N
1 PdxR

Bordetella bronchiseptica RB50
Pyridoxine/pyridoxal homeostasis
TF PdxR2
1 PdxR2

Bordetella avium 197N
2 PdxR2

Bordetella bronchiseptica RB50
Pyridoxine/pyridoxal homeostasis
TF PdxW
1 PdxW

Bordetella avium 197N
1 PdxW

Bordetella petrii DSM 12804
1 PdxW

Bordetella bronchiseptica RB50
Pyridoxine/pyridoxal homeostasis
TF YdcR
2 YdcR

Bordetella bronchiseptica RB50
GntR/Others TF BAV2585
2 BAV2585

Bordetella avium 197N
3 BAV2585

Bordetella petrii DSM 12804
Nitrogen metabolism
TF Bpet4349
2 Bpet4349

Bordetella petrii DSM 12804
3 Bpet4349

Bordetella bronchiseptica RB50
Glycolate utilization; Lactate utilization
TF GlcC
3 GlcC

Bordetella petrii DSM 12804
2 GlcC

Bordetella bronchiseptica RB50
Glycolate utilization
TF MlnR
1 MlnR

Bordetella petrii DSM 12804
1 MlnR

Bordetella bronchiseptica RB50
Malonate metabolism
TF PrpR
3 PrpR

Bordetella avium 197N
2 PrpR

Bordetella petrii DSM 12804
3 PrpR

Bordetella bronchiseptica RB50
Methylcitrate utilization
TF SdhR
4 SdhR

Bordetella avium 197N
5 SdhR

Bordetella petrii DSM 12804
5 SdhR

Bordetella bronchiseptica RB50
Tricarboxylic acid cycle
TF UxuR2
1 UxuR2

Bordetella avium 197N
4 UxuR2

Bordetella petrii DSM 12804
1 UxuR2

Bordetella bronchiseptica RB50
Glucuronate utilization; Galacturonate utilization
HrcA TF HrcA
2 HrcA

Bordetella avium 197N
2 HrcA

Bordetella petrii DSM 12804
2 HrcA

Bordetella bronchiseptica RB50
Heat shock response
LexA TF LexA
7 LexA

Bordetella avium 197N
6 LexA

Bordetella petrii DSM 12804
6 LexA

Bordetella bronchiseptica RB50
SOS response
LysR TF MetR
2 MetR

Bordetella avium 197N
3 MetR

Bordetella petrii DSM 12804
2 MetR

Bordetella bronchiseptica RB50
Methionine biosynthesis
ModE TF FdsR
2 FdsR

Bordetella avium 197N
2 FdsR

Bordetella petrii DSM 12804
2 FdsR

Bordetella bronchiseptica RB50
Formate oxydation
TF ModE
1 ModE

Bordetella avium 197N
1 ModE

Bordetella petrii DSM 12804
1 ModE

Bordetella bronchiseptica RB50
Molybdopterin biosynthesis
TF ModE3
3 ModE3

Bordetella petrii DSM 12804
2 ModE3

Bordetella bronchiseptica RB50
Tungsten homeostasis
NrdR TF NrdR
1 NrdR

Bordetella avium 197N
1 NrdR

Bordetella petrii DSM 12804
1 NrdR

Bordetella bronchiseptica RB50
Deoxyribonucleotide biosynthesis