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

Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes -- version 3.2 --

Collection of regulogs in Micrococcineae taxonomic group

Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes
-- version 3.2 --