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

Collection of regulogs in Various betaproteobacteria taxonomic group

General statistics
Genomes 12
TF regulogs 47
TF regulons 158
TF binding sites 425
RNA regulogs 4
RNA regulons 24
RNA sites 31

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
Azoarcus sp. EbN1 13 28 2 3 15 31
Chromobacterium violaceum ATCC 12472 26 91 3 4 29 95
Dechloromonas aromatica RCB 16 58 2 3 18 61
Laribacter hongkongensis HLHK9 16 48 2 2 18 50
Methylobacillus flagellatus KT 12 24 2 4 14 28
Methylophilales bacterium HTCC2181 6 14 2 2 8 16
Methylotenera mobilis JLW8 13 31 2 2 15 33
Neisseria meningitidis MC58 9 29 1 2 10 31
Nitrosomonas europaea ATCC 19718 9 15 2 2 11 17
Nitrosospira multiformis ATCC 25196 7 11 2 2 9 13
Thauera sp. MZ1T 20 54 2 3 22 57
Thiobacillus denitrificans 11 22 2 2 13 24
Genomic distribution of regulons
Family Type Regulator Function
BirA TF BirA
1 BirA

Nitrosomonas europaea ATCC 19718
2 BirA

Nitrosospira multiformis ATCC 25196
2 BirA

Thiobacillus denitrificans
2 BirA

Chromobacterium violaceum ATCC 12472
2 BirA

Laribacter hongkongensis HLHK9
1 BirA

Methylobacillus flagellatus KT
2 BirA

Methylotenera mobilis JLW8
1 BirA

Methylophilales bacterium HTCC2181
Biotin biosynthesis
FUR TF Zur
1 Zur

Azoarcus sp. EbN1
2 Zur

Thauera sp. MZ1T
1 Zur

Nitrosomonas europaea ATCC 19718
1 Zur

Nitrosospira multiformis ATCC 25196
3 Zur

Methylobacillus flagellatus KT
Zinc homeostasis
TF Zur2
1 Zur2

Chromobacterium violaceum ATCC 12472
3 Zur2

Neisseria meningitidis MC58
1 Zur2

Laribacter hongkongensis HLHK9
Zinc homeostasis
Fis TF NtrC
5 NtrC

Azoarcus sp. EbN1
6 NtrC

Thauera sp. MZ1T
5 NtrC

Dechloromonas aromatica RCB
3 NtrC

Thiobacillus denitrificans
3 NtrC

Chromobacterium violaceum ATCC 12472
1 NtrC

Laribacter hongkongensis HLHK9
2 NtrC

Methylobacillus flagellatus KT
5 NtrC

Methylotenera mobilis JLW8
3 NtrC

Methylophilales bacterium HTCC2181
Nitrogen assimilation
GntR/MocR TF CV1517
1 CV1517

Chromobacterium violaceum ATCC 12472
TF CV1900
3 CV1900

Chromobacterium violaceum ATCC 12472
Metabolite transport
TF CV4096
1 CV4096

Chromobacterium violaceum ATCC 12472
TF Daro_1932
1 Daro_1932

Dechloromonas aromatica RCB
1 Daro_1932

Laribacter hongkongensis HLHK9
TF EbA483
2 EbA483

Azoarcus sp. EbN1
TF GabR
1 GabR

Thauera sp. MZ1T
Gamma-aminobutyrate utilization
TF Mfla_0336
1 Mfla_0336

Methylobacillus flagellatus KT
1 Mfla_0336

Methylotenera mobilis JLW8
TF PdxR
1 PdxR

Thauera sp. MZ1T
Pyridoxine/pyridoxal homeostasis
TF PdxW
1 PdxW

Thauera sp. MZ1T
Pyridoxine/pyridoxal homeostasis
TF PdxW2
1 PdxW2

Methylotenera mobilis JLW8
Pyridoxine/pyridoxal homeostasis
TF YdcR
2 YdcR

Thauera sp. MZ1T
3 YdcR

Dechloromonas aromatica RCB
1 YdcR

Thiobacillus denitrificans
1 YdcR

Chromobacterium violaceum ATCC 12472
1 YdcR

Laribacter hongkongensis HLHK9
2 YdcR

Methylobacillus flagellatus KT
1 YdcR

Methylotenera mobilis JLW8
GntR/Others TF GlcC
1 GlcC

Azoarcus sp. EbN1
1 GlcC

Nitrosomonas europaea ATCC 19718
Glycolate utilization
TF HutC
1 HutC

Chromobacterium violaceum ATCC 12472
Histidine utilization
TF LldR
1 LldR

Thauera sp. MZ1T
2 LldR

Dechloromonas aromatica RCB
2 LldR

Chromobacterium violaceum ATCC 12472
3 LldR

Neisseria meningitidis MC58
2 LldR

Laribacter hongkongensis HLHK9
Lactate utilization
TF MdcY
2 MdcY

Dechloromonas aromatica RCB
Malonate metabolism
TF MlnR
2 MlnR

Azoarcus sp. EbN1
4 MlnR

Thauera sp. MZ1T
6 MlnR

Dechloromonas aromatica RCB
Malonate metabolism
TF NagQ
9 NagQ

Chromobacterium violaceum ATCC 12472
N-acetylglucosamine utilization
TF PhnF
2 PhnF

Chromobacterium violaceum ATCC 12472
2 PhnF

Laribacter hongkongensis HLHK9
Phosphonate utilization
TF SdhR
4 SdhR

Azoarcus sp. EbN1
5 SdhR

Thauera sp. MZ1T
5 SdhR

Dechloromonas aromatica RCB
2 SdhR

Chromobacterium violaceum ATCC 12472
2 SdhR

Laribacter hongkongensis HLHK9
2 SdhR

Methylotenera mobilis JLW8
2 SdhR

Methylophilales bacterium HTCC2181
Tricarboxylic acid cycle
TF TreR
1 TreR

Chromobacterium violaceum ATCC 12472
Trehalose utilization
HrcA TF HrcA
2 HrcA

Azoarcus sp. EbN1
2 HrcA

Thauera sp. MZ1T
2 HrcA

Dechloromonas aromatica RCB
2 HrcA

Nitrosomonas europaea ATCC 19718
1 HrcA

Nitrosospira multiformis ATCC 25196
2 HrcA

Thiobacillus denitrificans
2 HrcA

Chromobacterium violaceum ATCC 12472
3 HrcA

Laribacter hongkongensis HLHK9
2 HrcA

Methylobacillus flagellatus KT
2 HrcA

Methylotenera mobilis JLW8
2 HrcA

Methylophilales bacterium HTCC2181
Heat shock response
LacI TF FruR2
2 FruR2

Chromobacterium violaceum ATCC 12472
Fructose utilization
TF GntR
1 GntR

Chromobacterium violaceum ATCC 12472
Gluconate utilization
LexA TF LexA
1 LexA

Azoarcus sp. EbN1
3 LexA

Thauera sp. MZ1T
5 LexA

Dechloromonas aromatica RCB
3 LexA

Thiobacillus denitrificans
SOS response
LysR TF MetR
2 MetR

Nitrosomonas europaea ATCC 19718
2 MetR

Nitrosospira multiformis ATCC 25196
2 MetR

Thiobacillus denitrificans
2 MetR

Chromobacterium violaceum ATCC 12472
2 MetR

Neisseria meningitidis MC58
2 MetR

Laribacter hongkongensis HLHK9
2 MetR

Methylobacillus flagellatus KT
2 MetR

Methylotenera mobilis JLW8
Methionine biosynthesis
MerR TF CadR-PbrR
2 CadR-PbrR

Thauera sp. MZ1T
2 CadR-PbrR

Dechloromonas aromatica RCB
1 CadR-PbrR

Chromobacterium violaceum ATCC 12472
1 CadR-PbrR

Laribacter hongkongensis HLHK9
1 CadR-PbrR

Methylobacillus flagellatus KT
Lead resistance; Cadmium resistance
TF CueR
1 CueR

Thauera sp. MZ1T
1 CueR

Thiobacillus denitrificans
3 CueR

Methylotenera mobilis JLW8
Copper resistance
TF LiuR
2 LiuR

Azoarcus sp. EbN1
6 LiuR

Thauera sp. MZ1T
1 LiuR

Dechloromonas aromatica RCB
6 LiuR

Chromobacterium violaceum ATCC 12472
4 LiuR

Laribacter hongkongensis HLHK9
Branched-chain amino acid degradation
TF MerR
1 MerR

Nitrosomonas europaea ATCC 19718
1 MerR

Thiobacillus denitrificans
Mercury resistance
TF NmlR
2 NmlR

Neisseria meningitidis MC58
Carbonyl stress response
TF SoxR
1 SoxR

Chromobacterium violaceum ATCC 12472
Superoxide stress response
ModE TF ModE
1 ModE

Dechloromonas aromatica RCB
1 ModE

Laribacter hongkongensis HLHK9
Molybdenum homeostasis
TF ModE2
2 ModE2

Methylobacillus flagellatus KT
2 ModE2

Methylotenera mobilis JLW8
Molybdopterin biosynthesis
NadQ TF NadQ
2 NadQ

Neisseria meningitidis MC58
NAD biosynthesis
NikR TF NikR
1 NikR

Dechloromonas aromatica RCB
1 NikR

Nitrosospira multiformis ATCC 25196
Nickel homeostasis
NrdR TF NrdR
1 NrdR

Azoarcus sp. EbN1
1 NrdR

Thauera sp. MZ1T
1 NrdR

Dechloromonas aromatica RCB
1 NrdR

Nitrosomonas europaea ATCC 19718
1 NrdR

Nitrosospira multiformis ATCC 25196
1 NrdR

Thiobacillus denitrificans
3 NrdR

Chromobacterium violaceum ATCC 12472
1 NrdR

Neisseria meningitidis MC58
3 NrdR

Laribacter hongkongensis HLHK9
2 NrdR

Methylobacillus flagellatus KT
2 NrdR

Methylotenera mobilis JLW8
1 NrdR

Methylophilales bacterium HTCC2181
Deoxyribonucleotide biosynthesis
NrtR TF NrtR
2 NrtR

Thauera sp. MZ1T
2 NrtR

Chromobacterium violaceum ATCC 12472
NAD biosynthesis
RpiR TF HexR
3 HexR

Chromobacterium violaceum ATCC 12472
4 HexR

Neisseria meningitidis MC58
Central carbohydrate metabolism
Rrf2 TF IscR
3 IscR

Azoarcus sp. EbN1
2 IscR

Thauera sp. MZ1T
2 IscR

Dechloromonas aromatica RCB
1 IscR

Nitrosomonas europaea ATCC 19718
2 IscR

Nitrosospira multiformis ATCC 25196
3 IscR

Thiobacillus denitrificans
1 IscR

Chromobacterium violaceum ATCC 12472
1 IscR

Neisseria meningitidis MC58
1 IscR

Laribacter hongkongensis HLHK9
2 IscR

Methylobacillus flagellatus KT
1 IscR

Methylotenera mobilis JLW8
2 IscR

Methylophilales bacterium HTCC2181
Iron-sulfur cluster biogenesis
TF NsrR
5 NsrR

Neisseria meningitidis MC58
Nitrosative stress response
TF NsrR2
2 NsrR2

Thauera sp. MZ1T
2 NsrR2

Nitrosomonas europaea ATCC 19718
1 NsrR2

Thiobacillus denitrificans
4 NsrR2

Chromobacterium violaceum ATCC 12472
1 NsrR2

Methylobacillus flagellatus KT
2 NsrR2

Methylotenera mobilis JLW8
Nitrosative stress response
TetR TF PaaR
2 PaaR

Azoarcus sp. EbN1
2 PaaR

Thauera sp. MZ1T
Phenylacetic acid degradation
TF PsrA
1 PsrA

Azoarcus sp. EbN1
1 PsrA

Thauera sp. MZ1T
3 PsrA

Dechloromonas aromatica RCB
10 PsrA

Chromobacterium violaceum ATCC 12472
12 PsrA

Laribacter hongkongensis HLHK9
Fatty acid degradation
RF00050 RNA FMN
1 FMN

Chromobacterium violaceum ATCC 12472
Riboflavin biosynthesis
RF00059 RNA TPP
1 TPP

Azoarcus sp. EbN1
1 TPP

Thauera sp. MZ1T
1 TPP

Dechloromonas aromatica RCB
1 TPP

Nitrosomonas europaea ATCC 19718
1 TPP

Nitrosospira multiformis ATCC 25196
1 TPP

Thiobacillus denitrificans
2 TPP

Chromobacterium violaceum ATCC 12472
2 TPP

Neisseria meningitidis MC58
1 TPP

Laribacter hongkongensis HLHK9
3 TPP

Methylobacillus flagellatus KT
1 TPP

Methylotenera mobilis JLW8
1 TPP

Methylophilales bacterium HTCC2181
Thiamine biosynthesis
RF01055 RNA MOCO_RNA_motif
RF01057 RNA SAH_riboswitch
2 SAH_riboswitch

Azoarcus sp. EbN1
2 SAH_riboswitch

Thauera sp. MZ1T
2 SAH_riboswitch

Dechloromonas aromatica RCB
1 SAH_riboswitch

Nitrosomonas europaea ATCC 19718
1 SAH_riboswitch

Nitrosospira multiformis ATCC 25196
1 SAH_riboswitch

Thiobacillus denitrificans
1 SAH_riboswitch

Chromobacterium violaceum ATCC 12472
1 SAH_riboswitch

Laribacter hongkongensis HLHK9
1 SAH_riboswitch

Methylobacillus flagellatus KT
1 SAH_riboswitch

Methylotenera mobilis JLW8
1 SAH_riboswitch

Methylophilales bacterium HTCC2181
Methionine metabolism