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

Collection of regulogs in Caulobacterales taxonomic group

General statistics
Genomes 4
TF regulogs 33
TF regulons 100
TF binding sites 430
RNA regulogs 8
RNA regulons 26
RNA sites 36

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
Caulobacter crescentus CB15 24 119 6 10 30 129
Caulobacter segnis ATCC 21756 25 119 6 9 31 128
Caulobacter sp. K31 29 119 7 9 36 128
Phenylobacterium zucineum HLK1 22 73 7 8 29 81
Genomic distribution of regulons
Family Type Regulator Function
ArsR TF SahR
4 SahR

Caulobacter crescentus CB15
4 SahR

Caulobacter segnis ATCC 21756
3 SahR

Caulobacter sp. K31
3 SahR

Phenylobacterium zucineum HLK1
Methionine metabolism
CRP TF FixK
6 FixK

Caulobacter crescentus CB15
7 FixK

Caulobacter segnis ATCC 21756
5 FixK

Caulobacter sp. K31
3 FixK

Phenylobacterium zucineum HLK1
Oxidative stress response; Nitrogen fixation
TF NnrR
4 NnrR

Caulobacter segnis ATCC 21756
5 NnrR

Phenylobacterium zucineum HLK1
Denitrification
FUR TF Fur
9 Fur

Caulobacter crescentus CB15
9 Fur

Caulobacter segnis ATCC 21756
7 Fur

Caulobacter sp. K31
7 Fur

Phenylobacterium zucineum HLK1
Iron homeostasis
TF Zur
6 Zur

Caulobacter crescentus CB15
5 Zur

Caulobacter segnis ATCC 21756
3 Zur

Caulobacter sp. K31
2 Zur

Phenylobacterium zucineum HLK1
Zinc homeostasis
Fis TF NtrC
4 NtrC

Caulobacter crescentus CB15
2 NtrC

Caulobacter segnis ATCC 21756
4 NtrC

Caulobacter sp. K31
3 NtrC

Phenylobacterium zucineum HLK1
Nitrogen assimilation
GntR/MocR TF PdxQ2
3 PdxQ2

Caulobacter segnis ATCC 21756
3 PdxQ2

Caulobacter sp. K31
Metabolite transport; Pyridoxine/pyridoxal homeostasis
TF PdxR3
1 PdxR3

Phenylobacterium zucineum HLK1
Pyridoxine/pyridoxal homeostasis
TF PdxW
2 PdxW

Phenylobacterium zucineum HLK1
Pyridoxine/pyridoxal homeostasis
TF YrdX3
1 YrdX3

Caulobacter crescentus CB15
1 YrdX3

Caulobacter segnis ATCC 21756
1 YrdX3

Caulobacter sp. K31
GntR/Others TF HutC
2 HutC

Caulobacter crescentus CB15
2 HutC

Caulobacter segnis ATCC 21756
3 HutC

Caulobacter sp. K31
3 HutC

Phenylobacterium zucineum HLK1
Histidine utilization
TF NagQ
5 NagQ

Caulobacter crescentus CB15
4 NagQ

Caulobacter segnis ATCC 21756
2 NagQ

Caulobacter sp. K31
N-acetylglucosamine utilization
TF PhnR
3 PhnR

Caulobacter segnis ATCC 21756
4 PhnR

Caulobacter sp. K31
Phosphonate utilization; 2-aminoethylphosphonate utilization
TF VanR
2 VanR

Caulobacter crescentus CB15
2 VanR

Caulobacter segnis ATCC 21756
1 VanR

Caulobacter sp. K31
Vanillate utilization
HrcA TF HrcA
1 HrcA

Caulobacter crescentus CB15
1 HrcA

Caulobacter segnis ATCC 21756
1 HrcA

Caulobacter sp. K31
1 HrcA

Phenylobacterium zucineum HLK1
Heat shock response
LacI TF BglR1
1 BglR1

Caulobacter crescentus CB15
1 BglR1

Caulobacter sp. K31
Beta-glucosides utilization
TF BglR2
3 BglR2

Caulobacter crescentus CB15
3 BglR2

Caulobacter segnis ATCC 21756
3 BglR2

Caulobacter sp. K31
Beta-glucosides utilization
TF BglR3
2 BglR3

Caulobacter crescentus CB15
2 BglR3

Caulobacter segnis ATCC 21756
2 BglR3

Caulobacter sp. K31
2 BglR3

Phenylobacterium zucineum HLK1
Beta-glucosides utilization
TF CC1627
4 CC1627

Caulobacter crescentus CB15
3 CC1627

Caulobacter segnis ATCC 21756
5 CC1627

Caulobacter sp. K31
2 CC1627

Phenylobacterium zucineum HLK1
Sugar utilization
TF GluR
6 GluR

Caulobacter crescentus CB15
6 GluR

Caulobacter segnis ATCC 21756
5 GluR

Caulobacter sp. K31
Carbohydrate metabolism
LexA TF LexA
12 LexA

Caulobacter crescentus CB15
11 LexA

Caulobacter segnis ATCC 21756
10 LexA

Caulobacter sp. K31
10 LexA

Phenylobacterium zucineum HLK1
SOS response
LuxR TF FixJ
1 FixJ

Caulobacter crescentus CB15
1 FixJ

Caulobacter segnis ATCC 21756
1 FixJ

Caulobacter sp. K31
1 FixJ

Phenylobacterium zucineum HLK1
Oxidative stress response
MerR TF CadR-PbrR
1 CadR-PbrR

Caulobacter sp. K31
2 CadR-PbrR

Phenylobacterium zucineum HLK1
Lead resistance; Cadmium resistance
TF CueR
3 CueR

Caulobacter sp. K31
4 CueR

Phenylobacterium zucineum HLK1
Copper resistance
TF LiuR
2 LiuR

Caulobacter crescentus CB15
2 LiuR

Caulobacter segnis ATCC 21756
3 LiuR

Caulobacter sp. K31
2 LiuR

Phenylobacterium zucineum HLK1
Branched-chain amino acid degradation
TF ZntR
1 ZntR

Caulobacter sp. K31
Zinc resistance
ModE TF ModE
2 ModE

Caulobacter crescentus CB15
3 ModE

Caulobacter sp. K31
Molybdenum homeostasis
NadQ TF NadQ
3 NadQ

Caulobacter crescentus CB15
3 NadQ

Caulobacter segnis ATCC 21756
3 NadQ

Caulobacter sp. K31
3 NadQ

Phenylobacterium zucineum HLK1
NAD biosynthesis
NrdR TF NrdR
3 NrdR

Caulobacter crescentus CB15
3 NrdR

Caulobacter segnis ATCC 21756
3 NrdR

Caulobacter sp. K31
3 NrdR

Phenylobacterium zucineum HLK1
Deoxyribonucleotide biosynthesis
Rrf2 TF IscR
1 IscR

Caulobacter crescentus CB15
1 IscR

Caulobacter segnis ATCC 21756
1 IscR

Caulobacter sp. K31
1 IscR

Phenylobacterium zucineum HLK1
Iron-sulfur cluster biogenesis
TF NsrR
2 NsrR

Caulobacter sp. K31
1 NsrR

Phenylobacterium zucineum HLK1
Nitrosative stress response
TetR TF PsrA
22 PsrA

Caulobacter crescentus CB15
19 PsrA

Caulobacter segnis ATCC 21756
21 PsrA

Caulobacter sp. K31
6 PsrA

Phenylobacterium zucineum HLK1
Fatty acid degradation
TF RutR
2 RutR

Caulobacter crescentus CB15
2 RutR

Caulobacter segnis ATCC 21756
Pyrimidine utilization
RF00050 RNA FMN
1 FMN

Phenylobacterium zucineum HLK1
Riboflavin biosynthesis
RF00059 RNA TPP
1 TPP

Caulobacter crescentus CB15
1 TPP

Caulobacter segnis ATCC 21756
1 TPP

Caulobacter sp. K31
1 TPP

Phenylobacterium zucineum HLK1
Thiamine biosynthesis
RF00080 RNA yybP-ykoY
1 yybP-ykoY

Caulobacter crescentus CB15
1 yybP-ykoY

Caulobacter segnis ATCC 21756
1 yybP-ykoY

Caulobacter sp. K31
1 yybP-ykoY

Phenylobacterium zucineum HLK1
RF00174 RNA Cobalamin
2 Cobalamin

Caulobacter crescentus CB15
3 Cobalamin

Caulobacter segnis ATCC 21756
1 Cobalamin

Caulobacter sp. K31
1 Cobalamin

Phenylobacterium zucineum HLK1
Cobalamin biosynthesis
RF00504 RNA Glycine
2 Glycine

Caulobacter crescentus CB15
1 Glycine

Caulobacter segnis ATCC 21756
2 Glycine

Caulobacter sp. K31
1 Glycine

Phenylobacterium zucineum HLK1
Glycine metabolism
RF00517 RNA serC
1 serC

Caulobacter crescentus CB15
1 serC

Caulobacter segnis ATCC 21756
1 serC

Caulobacter sp. K31
1 serC

Phenylobacterium zucineum HLK1
Serine biosynthesis
RF01055 RNA MOCO_RNA_motif
1 MOCO_RNA_motif

Caulobacter sp. K31
Molybdopterin biosynthesis; Molybdenum homeostasis
RF01068 RNA mini-ykkC
1 mini-ykkC

Caulobacter crescentus CB15
1 mini-ykkC

Caulobacter segnis ATCC 21756
1 mini-ykkC

Caulobacter sp. K31
1 mini-ykkC

Phenylobacterium zucineum HLK1
Multidrug resistance