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

Collection of regulogs in Micrococcineae taxonomic group

General statistics
Genomes 14
TF regulogs 40
TF regulons 220
TF binding sites 667
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
Arthrobacter aurescens TC1 27 98 0 0 27 98
Arthrobacter chlorophenolicus A6 24 85 0 0 24 85
Arthrobacter sp. FB24 25 95 0 0 25 95
Beutenbergia cavernae DSM 12333 21 51 0 0 21 51
Brachybacterium faecium DSM 4810 17 47 0 0 17 47
Brevibacterium linens BL2 17 42 0 0 17 42
Clavibacter michiganensis subsp. michiganensis NCPPB 382 13 40 0 0 13 40
Janibacter sp. HTCC2649 17 41 0 0 17 41
Jonesia denitrificans DSM 20603 13 35 0 0 13 35
Kocuria rhizophila DC2201 16 45 0 0 16 45
Kytococcus sedentarius DSM 20547 7 13 0 0 7 13
Leifsonia xyli subsp. xyli str. CTCB07 8 25 0 0 8 25
Renibacterium salmoninarum ATCC 33209 14 48 0 0 14 48
Tropheryma whipplei str. Twist 1 2 0 0 1 2
Genomic distribution of regulons
Family Type Regulator Function
ArgR TF ArgR
1 ArgR

Arthrobacter aurescens TC1
1 ArgR

Arthrobacter chlorophenolicus A6
1 ArgR

Arthrobacter sp. FB24
1 ArgR

Beutenbergia cavernae DSM 12333
1 ArgR

Brachybacterium faecium DSM 4810
2 ArgR

Brevibacterium linens BL2
2 ArgR

Janibacter sp. HTCC2649
1 ArgR

Jonesia denitrificans DSM 20603
2 ArgR

Kocuria rhizophila DC2201
1 ArgR

Kytococcus sedentarius DSM 20547
1 ArgR

Renibacterium salmoninarum ATCC 33209
Arginine biosynthesis
ArsR TF SutR
1 SutR

Arthrobacter sp. FB24
1 SutR

Brachybacterium faecium DSM 4810
1 SutR

Brevibacterium linens BL2
1 SutR

Jonesia denitrificans DSM 20603
Sulfur metabolism
CsoR TF CsoR
3 CsoR

Arthrobacter aurescens TC1
2 CsoR

Arthrobacter chlorophenolicus A6
2 CsoR

Arthrobacter sp. FB24
3 CsoR

Beutenbergia cavernae DSM 12333
2 CsoR

Brachybacterium faecium DSM 4810
1 CsoR

Brevibacterium linens BL2
1 CsoR

Janibacter sp. HTCC2649
1 CsoR

Kocuria rhizophila DC2201
2 CsoR

Kytococcus sedentarius DSM 20547
Copper resistance
DtxR TF MntR
3 MntR

Arthrobacter aurescens TC1
1 MntR

Arthrobacter chlorophenolicus A6
2 MntR

Arthrobacter sp. FB24
1 MntR

Beutenbergia cavernae DSM 12333
1 MntR

Brachybacterium faecium DSM 4810
1 MntR

Brevibacterium linens BL2
1 MntR

Jonesia denitrificans DSM 20603
1 MntR

Kocuria rhizophila DC2201
1 MntR

Leifsonia xyli subsp. xyli str. CTCB07
1 MntR

Renibacterium salmoninarum ATCC 33209
Manganese homeostasis
FUR TF Zur
4 Zur

Arthrobacter aurescens TC1
3 Zur

Arthrobacter chlorophenolicus A6
3 Zur

Arthrobacter sp. FB24
2 Zur

Beutenbergia cavernae DSM 12333
2 Zur

Brachybacterium faecium DSM 4810
5 Zur

Brevibacterium linens BL2
5 Zur

Clavibacter michiganensis subsp. michiganensis NCPPB 382
1 Zur

Janibacter sp. HTCC2649
2 Zur

Jonesia denitrificans DSM 20603
1 Zur

Kocuria rhizophila DC2201
1 Zur

Kytococcus sedentarius DSM 20547
2 Zur

Leifsonia xyli subsp. xyli str. CTCB07
4 Zur

Renibacterium salmoninarum ATCC 33209
Zinc homeostasis
GntR/MocR TF Bcav_0044
1 Bcav_0044

Beutenbergia cavernae DSM 12333
TF Bcav_0410
1 Bcav_0410

Beutenbergia cavernae DSM 12333
Metabolite transport
TF PdxQ
2 PdxQ

Arthrobacter aurescens TC1
2 PdxQ

Arthrobacter chlorophenolicus A6
2 PdxQ

Arthrobacter sp. FB24
2 PdxQ

Janibacter sp. HTCC2649
Pyridoxine/pyridoxal homeostasis; Metabolite transport
TF PdxR
1 PdxR

Brevibacterium linens BL2
1 PdxR

Jonesia denitrificans DSM 20603
1 PdxR

Kocuria rhizophila DC2201
Pyridoxine biosynthesis
TF PdxR2
2 PdxR2

Brachybacterium faecium DSM 4810
2 PdxR2

Leifsonia xyli subsp. xyli str. CTCB07
Pyridoxine biosynthesis
TF PdxR2(2)
1 PdxR2(2)

Janibacter sp. HTCC2649
Pyridoxine/pyridoxal homeostasis
TF PdxR3
1 PdxR3

Arthrobacter aurescens TC1
1 PdxR3

Arthrobacter chlorophenolicus A6
1 PdxR3

Arthrobacter sp. FB24
1 PdxR3

Beutenbergia cavernae DSM 12333
1 PdxR3

Brevibacterium linens BL2
1 PdxR3

Clavibacter michiganensis subsp. michiganensis NCPPB 382
1 PdxR3

Janibacter sp. HTCC2649
Pyridoxine/pyridoxal homeostasis
GntR/Others TF AAur_0050
2 AAur_0050

Arthrobacter aurescens TC1
2 AAur_0050

Arthrobacter chlorophenolicus A6
3 AAur_0050

Arthrobacter sp. FB24
1 AAur_0050

Brevibacterium linens BL2
2 AAur_0050

Janibacter sp. HTCC2649
1 AAur_0050

Kocuria rhizophila DC2201
1 AAur_0050

Kytococcus sedentarius DSM 20547
TF AAur_2567
1 AAur_2567

Arthrobacter aurescens TC1
1 AAur_2567

Arthrobacter chlorophenolicus A6
1 AAur_2567

Beutenbergia cavernae DSM 12333
1 AAur_2567

Brachybacterium faecium DSM 4810
1 AAur_2567

Brevibacterium linens BL2
1 AAur_2567

Jonesia denitrificans DSM 20603
1 AAur_2567

Kocuria rhizophila DC2201
1 AAur_2567

Kytococcus sedentarius DSM 20547
1 AAur_2567

Renibacterium salmoninarum ATCC 33209
Multidrug resistance; Multidrug efflux
TF AnsR
2 AnsR

Arthrobacter aurescens TC1
1 AnsR

Arthrobacter chlorophenolicus A6
2 AnsR

Arthrobacter sp. FB24
Aspartate utilization; Asparagine degradation
TF Arth_3541
2 Arth_3541

Arthrobacter aurescens TC1
4 Arth_3541

Arthrobacter chlorophenolicus A6
4 Arth_3541

Arthrobacter sp. FB24
4 Arth_3541

Clavibacter michiganensis subsp. michiganensis NCPPB 382
TF Bcav_0107
1 Bcav_0107

Beutenbergia cavernae DSM 12333
1 Bcav_0107

Clavibacter michiganensis subsp. michiganensis NCPPB 382
Multidrug efflux
TF DasR
5 DasR

Arthrobacter aurescens TC1
2 DasR

Arthrobacter chlorophenolicus A6
5 DasR

Arthrobacter sp. FB24
2 DasR

Beutenbergia cavernae DSM 12333
N-acetylglucosamine utilization
TF IolR
7 IolR

Arthrobacter aurescens TC1
6 IolR

Arthrobacter chlorophenolicus A6
5 IolR

Arthrobacter sp. FB24
4 IolR

Beutenbergia cavernae DSM 12333
4 IolR

Clavibacter michiganensis subsp. michiganensis NCPPB 382
2 IolR

Janibacter sp. HTCC2649
2 IolR

Leifsonia xyli subsp. xyli str. CTCB07
4 IolR

Renibacterium salmoninarum ATCC 33209
Inositol utilization
TF LldR
2 LldR

Arthrobacter aurescens TC1
2 LldR

Arthrobacter sp. FB24
2 LldR

Brachybacterium faecium DSM 4810
4 LldR

Brevibacterium linens BL2
1 LldR

Jonesia denitrificans DSM 20603
2 LldR

Kocuria rhizophila DC2201
2 LldR

Renibacterium salmoninarum ATCC 33209
Lactate utilization
TF LndYR
1 LndYR

Beutenbergia cavernae DSM 12333
1 LndYR

Janibacter sp. HTCC2649
Antibiotic resistance
HrcA TF HrcA
3 HrcA

Arthrobacter aurescens TC1
4 HrcA

Arthrobacter chlorophenolicus A6
4 HrcA

Arthrobacter sp. FB24
4 HrcA

Beutenbergia cavernae DSM 12333
3 HrcA

Brachybacterium faecium DSM 4810
2 HrcA

Brevibacterium linens BL2
4 HrcA

Clavibacter michiganensis subsp. michiganensis NCPPB 382
3 HrcA

Janibacter sp. HTCC2649
4 HrcA

Jonesia denitrificans DSM 20603
4 HrcA

Kocuria rhizophila DC2201
3 HrcA

Kytococcus sedentarius DSM 20547
5 HrcA

Leifsonia xyli subsp. xyli str. CTCB07
3 HrcA

Renibacterium salmoninarum ATCC 33209
Heat shock response
HxlR TF QorR
2 QorR

Arthrobacter chlorophenolicus A6
1 QorR

Clavibacter michiganensis subsp. michiganensis NCPPB 382
2 QorR

Janibacter sp. HTCC2649
1 QorR

Kocuria rhizophila DC2201
Energy metabolism
IclR TF LtbR
3 LtbR

Arthrobacter aurescens TC1
3 LtbR

Arthrobacter chlorophenolicus A6
3 LtbR

Arthrobacter sp. FB24
3 LtbR

Beutenbergia cavernae DSM 12333
2 LtbR

Brachybacterium faecium DSM 4810
3 LtbR

Brevibacterium linens BL2
3 LtbR

Janibacter sp. HTCC2649
3 LtbR

Kocuria rhizophila DC2201
3 LtbR

Renibacterium salmoninarum ATCC 33209
Leucine biosynthesis
LacI TF AAur_3503
1 AAur_3503

Arthrobacter aurescens TC1
1 AAur_3503

Arthrobacter sp. FB24
Sugar utilization
TF AAur_4078
2 AAur_4078

Arthrobacter aurescens TC1
2 AAur_4078

Beutenbergia cavernae DSM 12333
3 AAur_4078

Brachybacterium faecium DSM 4810
4 AAur_4078

Jonesia denitrificans DSM 20603
Galactosides utilization
TF Arth_2426
2 Arth_2426

Arthrobacter chlorophenolicus A6
2 Arth_2426

Arthrobacter sp. FB24
1 Arth_2426

Beutenbergia cavernae DSM 12333
1 Arth_2426

Brachybacterium faecium DSM 4810
2 Arth_2426

Janibacter sp. HTCC2649
Sugar utilization
TF BgaR
2 BgaR

Clavibacter michiganensis subsp. michiganensis NCPPB 382
2 BgaR

Jonesia denitrificans DSM 20603
Galactosides utilization
TF CelR
1 CelR

Arthrobacter aurescens TC1
1 CelR

Arthrobacter chlorophenolicus A6
1 CelR

Beutenbergia cavernae DSM 12333
1 CelR

Jonesia denitrificans DSM 20603
Cellobiose utilization
TF FruR
2 FruR

Clavibacter michiganensis subsp. michiganensis NCPPB 382
3 FruR

Janibacter sp. HTCC2649
Fructose utilization
TF IolR
2 IolR

Arthrobacter aurescens TC1
4 IolR

Arthrobacter chlorophenolicus A6
Inositol utilization
TF MsmR
2 MsmR

Arthrobacter aurescens TC1
2 MsmR

Arthrobacter sp. FB24
1 MsmR

Brachybacterium faecium DSM 4810
Sugar utilization
TF RhaR
4 RhaR

Arthrobacter aurescens TC1
5 RhaR

Arthrobacter chlorophenolicus A6
7 RhaR

Arthrobacter sp. FB24
1 RhaR

Beutenbergia cavernae DSM 12333
4 RhaR

Brachybacterium faecium DSM 4810
Rhamnose utilization
LexA TF LexA
5 LexA

Arthrobacter aurescens TC1
5 LexA

Arthrobacter chlorophenolicus A6
5 LexA

Arthrobacter sp. FB24
4 LexA

Beutenbergia cavernae DSM 12333
5 LexA

Brachybacterium faecium DSM 4810
4 LexA

Brevibacterium linens BL2
4 LexA

Clavibacter michiganensis subsp. michiganensis NCPPB 382
3 LexA

Janibacter sp. HTCC2649
4 LexA

Jonesia denitrificans DSM 20603
3 LexA

Kocuria rhizophila DC2201
4 LexA

Leifsonia xyli subsp. xyli str. CTCB07
4 LexA

Renibacterium salmoninarum ATCC 33209
SOS response
NrdR TF NrdR
2 NrdR

Arthrobacter aurescens TC1
2 NrdR

Arthrobacter chlorophenolicus A6
2 NrdR

Arthrobacter sp. FB24
2 NrdR

Beutenbergia cavernae DSM 12333
2 NrdR

Brachybacterium faecium DSM 4810
1 NrdR

Brevibacterium linens BL2
1 NrdR

Clavibacter michiganensis subsp. michiganensis NCPPB 382
1 NrdR

Janibacter sp. HTCC2649
1 NrdR

Jonesia denitrificans DSM 20603
2 NrdR

Kocuria rhizophila DC2201
2 NrdR

Kytococcus sedentarius DSM 20547
1 NrdR

Leifsonia xyli subsp. xyli str. CTCB07
3 NrdR

Renibacterium salmoninarum ATCC 33209
1 NrdR

Tropheryma whipplei str. Twist
Deoxyribonucleotide biosynthesis
NrtR TF NrtR
3 NrtR

Arthrobacter aurescens TC1
1 NrtR

Arthrobacter chlorophenolicus A6
1 NrtR

Arthrobacter sp. FB24
1 NrtR

Beutenbergia cavernae DSM 12333
1 NrtR

Brachybacterium faecium DSM 4810
1 NrtR

Kocuria rhizophila DC2201
1 NrtR

Renibacterium salmoninarum ATCC 33209
NAD biosynthesis
Rex TF Rex
5 Rex

Arthrobacter aurescens TC1
5 Rex

Arthrobacter chlorophenolicus A6
5 Rex

Arthrobacter sp. FB24
3 Rex

Brevibacterium linens BL2
3 Rex

Janibacter sp. HTCC2649
4 Rex

Renibacterium salmoninarum ATCC 33209
Energy metabolism
TetR TF AmtR
2 AmtR

Arthrobacter aurescens TC1
2 AmtR

Arthrobacter sp. FB24
1 AmtR

Clavibacter michiganensis subsp. michiganensis NCPPB 382
Nitrogen metabolism
TF BioQ
3 BioQ

Brevibacterium linens BL2
2 BioQ

Clavibacter michiganensis subsp. michiganensis NCPPB 382
2 BioQ

Kocuria rhizophila DC2201
2 BioQ

Leifsonia xyli subsp. xyli str. CTCB07
2 BioQ

Renibacterium salmoninarum ATCC 33209
Biotin biosynthesis
TF PaaR
5 PaaR

Arthrobacter aurescens TC1
7 PaaR

Arthrobacter chlorophenolicus A6
7 PaaR

Arthrobacter sp. FB24
4 PaaR

Brevibacterium linens BL2
5 PaaR

Kocuria rhizophila DC2201
3 PaaR

Renibacterium salmoninarum ATCC 33209
Phenylacetic acid degradation