Collection of regulogs in Mycobacteriaceae taxonomic group

General statistics
Genomes	9
TF regulogs	30
TF regulons	154
TF binding sites	512
RNA regulogs	12
RNA regulons	80
RNA sites	131

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
Mycobacterium abscessus ATCC 19977	21	65	11	14	32	79
Mycobacterium avium 104	12	46	9	15	21	61
Mycobacterium flavescens PYR-GCK	17	55	10	17	27	72
Mycobacterium leprae TN	9	20	4	6	13	26
Mycobacterium marinum M	13	44	10	17	23	61
Mycobacterium smegmatis str. MC2 155	25	88	10	19	35	107
Mycobacterium sp. JLS	24	77	8	13	32	90
Mycobacterium tuberculosis H37Rv	13	47	9	15	22	62
Mycobacterium vanbaalenii PYR-1	20	70	9	15	29	85

Genomic distribution of regulons
Family	Type	Regulator										Function
ArgR	TF	ArgR	1 ArgR Mycobacterium smegmatis str. MC2 155	1 ArgR Mycobacterium tuberculosis H37Rv	1 ArgR Mycobacterium abscessus ATCC 19977	1 ArgR Mycobacterium avium 104	1 ArgR Mycobacterium marinum M	1 ArgR Mycobacterium leprae TN	1 ArgR Mycobacterium vanbaalenii PYR-1	1 ArgR Mycobacterium flavescens PYR-GCK	1 ArgR Mycobacterium sp. JLS	Arginine biosynthesis
ArsR	TF	ArsR	2 ArsR Mycobacterium smegmatis str. MC2 155	2 ArsR Mycobacterium tuberculosis H37Rv	2 ArsR Mycobacterium abscessus ATCC 19977		1 ArsR Mycobacterium marinum M		1 ArsR Mycobacterium vanbaalenii PYR-1	3 ArsR Mycobacterium flavescens PYR-GCK	2 ArsR Mycobacterium sp. JLS	Arsenic resistance
	TF	SutR	1 SutR Mycobacterium smegmatis str. MC2 155						1 SutR Mycobacterium vanbaalenii PYR-1	1 SutR Mycobacterium flavescens PYR-GCK	1 SutR Mycobacterium sp. JLS	Sulfur metabolism
	TF	Znr	1 Znr Mycobacterium smegmatis str. MC2 155	1 Znr Mycobacterium tuberculosis H37Rv		1 Znr Mycobacterium avium 104	1 Znr Mycobacterium marinum M	1 Znr Mycobacterium leprae TN	2 Znr Mycobacterium vanbaalenii PYR-1	2 Znr Mycobacterium flavescens PYR-GCK	1 Znr Mycobacterium sp. JLS	Zinc homeostasis
DeoR	TF	MSMEG_3264	2 MSMEG_3264 Mycobacterium smegmatis str. MC2 155								2 MSMEG_3264 Mycobacterium sp. JLS	Erythritol utilization; D-threitol utilization
	TF	MSMEG_3606	2 MSMEG_3606 Mycobacterium smegmatis str. MC2 155								2 MSMEG_3606 Mycobacterium sp. JLS	D-threitol utilization
DtxR	TF	MntR	2 MntR Mycobacterium smegmatis str. MC2 155	1 MntR Mycobacterium tuberculosis H37Rv	1 MntR Mycobacterium abscessus ATCC 19977	1 MntR Mycobacterium avium 104	2 MntR Mycobacterium marinum M		2 MntR Mycobacterium vanbaalenii PYR-1	2 MntR Mycobacterium flavescens PYR-GCK	2 MntR Mycobacterium sp. JLS	Manganese homeostasis
FUR	TF	Zur	6 Zur Mycobacterium smegmatis str. MC2 155	6 Zur Mycobacterium tuberculosis H37Rv	4 Zur Mycobacterium abscessus ATCC 19977	6 Zur Mycobacterium avium 104	5 Zur Mycobacterium marinum M	1 Zur Mycobacterium leprae TN	9 Zur Mycobacterium vanbaalenii PYR-1	4 Zur Mycobacterium flavescens PYR-GCK	6 Zur Mycobacterium sp. JLS	Zinc homeostasis
GntR/MocR	TF	MSMEG_4140	4 MSMEG_4140 Mycobacterium smegmatis str. MC2 155		1 MSMEG_4140 Mycobacterium abscessus ATCC 19977				1 MSMEG_4140 Mycobacterium vanbaalenii PYR-1	1 MSMEG_4140 Mycobacterium flavescens PYR-GCK	2 MSMEG_4140 Mycobacterium sp. JLS	Metabolite transport
	TF	PdxQ	2 PdxQ Mycobacterium smegmatis str. MC2 155		2 PdxQ Mycobacterium abscessus ATCC 19977							Pyridoxine/pyridoxal homeostasis; Metabolite transport
	TF	PdxQ3			1 PdxQ3 Mycobacterium abscessus ATCC 19977							Pyridoxine/pyridoxal homeostasis
	TF	PdxR2			1 PdxR2 Mycobacterium abscessus ATCC 19977							Pyridoxine/pyridoxal homeostasis
	TF	PdxR3	2 PdxR3 Mycobacterium smegmatis str. MC2 155		1 PdxR3 Mycobacterium abscessus ATCC 19977				1 PdxR3 Mycobacterium vanbaalenii PYR-1	1 PdxR3 Mycobacterium flavescens PYR-GCK	1 PdxR3 Mycobacterium sp. JLS	Pyridoxine/pyridoxal homeostasis
	TF	PdxW				2 PdxW Mycobacterium avium 104	2 PdxW Mycobacterium marinum M					Pyridoxine/pyridoxal homeostasis
GntR/Others	TF	IolR	3 IolR Mycobacterium smegmatis str. MC2 155						3 IolR Mycobacterium vanbaalenii PYR-1	3 IolR Mycobacterium flavescens PYR-GCK		Inositol utilization
	TF	LldR	2 LldR Mycobacterium smegmatis str. MC2 155								2 LldR Mycobacterium sp. JLS	Lactate utilization
	TF	Mce2R	1 Mce2R Mycobacterium smegmatis str. MC2 155	1 Mce2R Mycobacterium tuberculosis H37Rv	1 Mce2R Mycobacterium abscessus ATCC 19977				1 Mce2R Mycobacterium vanbaalenii PYR-1		1 Mce2R Mycobacterium sp. JLS	Fatty acid metabolism
	TF	PhnF	5 PhnF Mycobacterium smegmatis str. MC2 155		2 PhnF Mycobacterium abscessus ATCC 19977				4 PhnF Mycobacterium vanbaalenii PYR-1		3 PhnF Mycobacterium sp. JLS	Phosphonate utilization; 2-aminoethylphosphonate utilization
HrcA	TF	HrcA	4 HrcA Mycobacterium smegmatis str. MC2 155	3 HrcA Mycobacterium tuberculosis H37Rv	3 HrcA Mycobacterium abscessus ATCC 19977	3 HrcA Mycobacterium avium 104	3 HrcA Mycobacterium marinum M	3 HrcA Mycobacterium leprae TN	4 HrcA Mycobacterium vanbaalenii PYR-1	4 HrcA Mycobacterium flavescens PYR-GCK	4 HrcA Mycobacterium sp. JLS	Heat shock response
IclR	TF	LtbR	2 LtbR Mycobacterium smegmatis str. MC2 155	2 LtbR Mycobacterium tuberculosis H37Rv	2 LtbR Mycobacterium abscessus ATCC 19977	2 LtbR Mycobacterium avium 104	2 LtbR Mycobacterium marinum M		2 LtbR Mycobacterium vanbaalenii PYR-1	2 LtbR Mycobacterium flavescens PYR-GCK	2 LtbR Mycobacterium sp. JLS	Leucine biosynthesis
LacI	TF	RhaR	1 RhaR Mycobacterium smegmatis str. MC2 155								1 RhaR Mycobacterium sp. JLS	Rhamnose utilization
LexA	TF	LexA	8 LexA Mycobacterium smegmatis str. MC2 155	11 LexA Mycobacterium tuberculosis H37Rv	8 LexA Mycobacterium abscessus ATCC 19977	9 LexA Mycobacterium avium 104	9 LexA Mycobacterium marinum M	3 LexA Mycobacterium leprae TN	7 LexA Mycobacterium vanbaalenii PYR-1	8 LexA Mycobacterium flavescens PYR-GCK	7 LexA Mycobacterium sp. JLS	SOS response
MerR	TF	HspR	4 HspR Mycobacterium smegmatis str. MC2 155	3 HspR Mycobacterium tuberculosis H37Rv	3 HspR Mycobacterium abscessus ATCC 19977	3 HspR Mycobacterium avium 104	3 HspR Mycobacterium marinum M	2 HspR Mycobacterium leprae TN	4 HspR Mycobacterium vanbaalenii PYR-1	4 HspR Mycobacterium flavescens PYR-GCK	4 HspR Mycobacterium sp. JLS	Heat shock response
NrdR	TF	NrdR	4 NrdR Mycobacterium smegmatis str. MC2 155	2 NrdR Mycobacterium tuberculosis H37Rv	2 NrdR Mycobacterium abscessus ATCC 19977	2 NrdR Mycobacterium avium 104	2 NrdR Mycobacterium marinum M	2 NrdR Mycobacterium leprae TN	2 NrdR Mycobacterium vanbaalenii PYR-1	2 NrdR Mycobacterium flavescens PYR-GCK	2 NrdR Mycobacterium sp. JLS	Deoxyribonucleotide biosynthesis
NrtR	TF	NrtR	2 NrtR Mycobacterium smegmatis str. MC2 155	2 NrtR Mycobacterium tuberculosis H37Rv	2 NrtR Mycobacterium abscessus ATCC 19977	2 NrtR Mycobacterium avium 104	2 NrtR Mycobacterium marinum M	2 NrtR Mycobacterium leprae TN	2 NrtR Mycobacterium vanbaalenii PYR-1	2 NrtR Mycobacterium flavescens PYR-GCK	2 NrtR Mycobacterium sp. JLS	NAD biosynthesis
RpiR	TF	EutR							2 EutR Mycobacterium vanbaalenii PYR-1		2 EutR Mycobacterium sp. JLS	Ethanolamine utilization
TetR	TF	AcnR	2 AcnR Mycobacterium smegmatis str. MC2 155	1 AcnR Mycobacterium tuberculosis H37Rv	2 AcnR Mycobacterium abscessus ATCC 19977	2 AcnR Mycobacterium avium 104	1 AcnR Mycobacterium marinum M	1 AcnR Mycobacterium leprae TN	2 AcnR Mycobacterium vanbaalenii PYR-1	2 AcnR Mycobacterium flavescens PYR-GCK	2 AcnR Mycobacterium sp. JLS	Tricarboxylic acid cycle
	TF	AmtR	1 AmtR Mycobacterium smegmatis str. MC2 155		2 AmtR Mycobacterium abscessus ATCC 19977						2 AmtR Mycobacterium sp. JLS	Nitrogen metabolism
	TF	BioQ	3 BioQ Mycobacterium smegmatis str. MC2 155		3 BioQ Mycobacterium abscessus ATCC 19977				3 BioQ Mycobacterium vanbaalenii PYR-1	3 BioQ Mycobacterium flavescens PYR-GCK	3 BioQ Mycobacterium sp. JLS	Biotin biosynthesis
	TF	PaaR			4 PaaR Mycobacterium abscessus ATCC 19977							Phenylacetic acid degradation
RF00059	RNA	TPP	3 TPP Mycobacterium smegmatis str. MC2 155	2 TPP Mycobacterium tuberculosis H37Rv	2 TPP Mycobacterium abscessus ATCC 19977	2 TPP Mycobacterium avium 104	2 TPP Mycobacterium marinum M	2 TPP Mycobacterium leprae TN	2 TPP Mycobacterium vanbaalenii PYR-1	4 TPP Mycobacterium flavescens PYR-GCK	3 TPP Mycobacterium sp. JLS	Thiamine biosynthesis
RF00080	RNA	yybP-ykoY	2 yybP-ykoY Mycobacterium smegmatis str. MC2 155	1 yybP-ykoY Mycobacterium tuberculosis H37Rv	1 yybP-ykoY Mycobacterium abscessus ATCC 19977		1 yybP-ykoY Mycobacterium marinum M		4 yybP-ykoY Mycobacterium vanbaalenii PYR-1	2 yybP-ykoY Mycobacterium flavescens PYR-GCK	2 yybP-ykoY Mycobacterium sp. JLS
RF00174	RNA	Cobalamin	5 Cobalamin Mycobacterium smegmatis str. MC2 155	2 Cobalamin Mycobacterium tuberculosis H37Rv	2 Cobalamin Mycobacterium abscessus ATCC 19977	3 Cobalamin Mycobacterium avium 104	3 Cobalamin Mycobacterium marinum M	2 Cobalamin Mycobacterium leprae TN	1 Cobalamin Mycobacterium vanbaalenii PYR-1	2 Cobalamin Mycobacterium flavescens PYR-GCK	1 Cobalamin Mycobacterium sp. JLS	Cobalamin biosynthesis
RF00230	RNA	T-box(Ile)	1 T-box(Ile) Mycobacterium smegmatis str. MC2 155	1 T-box(Ile) Mycobacterium tuberculosis H37Rv	1 T-box(Ile) Mycobacterium abscessus ATCC 19977		1 T-box(Ile) Mycobacterium marinum M	1 T-box(Ile) Mycobacterium leprae TN	1 T-box(Ile) Mycobacterium vanbaalenii PYR-1	1 T-box(Ile) Mycobacterium flavescens PYR-GCK		Amino acid metabolism
RF00379	RNA	ydaO-yuaA	1 ydaO-yuaA Mycobacterium smegmatis str. MC2 155	1 ydaO-yuaA Mycobacterium tuberculosis H37Rv	1 ydaO-yuaA Mycobacterium abscessus ATCC 19977	1 ydaO-yuaA Mycobacterium avium 104	1 ydaO-yuaA Mycobacterium marinum M	1 ydaO-yuaA Mycobacterium leprae TN	1 ydaO-yuaA Mycobacterium vanbaalenii PYR-1	1 ydaO-yuaA Mycobacterium flavescens PYR-GCK	1 ydaO-yuaA Mycobacterium sp. JLS	Osmotic stress response; Cell wall metabolism
RF00380	RNA	ykoK	1 ykoK Mycobacterium smegmatis str. MC2 155	2 ykoK Mycobacterium tuberculosis H37Rv	1 ykoK Mycobacterium abscessus ATCC 19977	3 ykoK Mycobacterium avium 104	2 ykoK Mycobacterium marinum M					Magnesium homeostasis
RF00442	RNA	ykkC-yxkD				1 ykkC-yxkD Mycobacterium avium 104			1 ykkC-yxkD Mycobacterium vanbaalenii PYR-1	1 ykkC-yxkD Mycobacterium flavescens PYR-GCK		Multidrug resistance
RF00504	RNA	Glycine	1 Glycine Mycobacterium smegmatis str. MC2 155	2 Glycine Mycobacterium tuberculosis H37Rv	1 Glycine Mycobacterium abscessus ATCC 19977	1 Glycine Mycobacterium avium 104	2 Glycine Mycobacterium marinum M		1 Glycine Mycobacterium vanbaalenii PYR-1	1 Glycine Mycobacterium flavescens PYR-GCK	1 Glycine Mycobacterium sp. JLS	Glycine metabolism
RF00515	RNA	PyrR	1 PyrR Mycobacterium smegmatis str. MC2 155	1 PyrR Mycobacterium tuberculosis H37Rv	1 PyrR Mycobacterium abscessus ATCC 19977	1 PyrR Mycobacterium avium 104	1 PyrR Mycobacterium marinum M		1 PyrR Mycobacterium vanbaalenii PYR-1	1 PyrR Mycobacterium flavescens PYR-GCK	1 PyrR Mycobacterium sp. JLS	Pyrimidine metabolism
RF00557	RNA	L10_leader			1 L10_leader Mycobacterium abscessus ATCC 19977							Ribosome biogenesis
RF00634	RNA	SAM-IV	2 SAM-IV Mycobacterium smegmatis str. MC2 155	1 SAM-IV Mycobacterium tuberculosis H37Rv	2 SAM-IV Mycobacterium abscessus ATCC 19977	1 SAM-IV Mycobacterium avium 104	1 SAM-IV Mycobacterium marinum M		2 SAM-IV Mycobacterium vanbaalenii PYR-1	2 SAM-IV Mycobacterium flavescens PYR-GCK	2 SAM-IV Mycobacterium sp. JLS	Sulfur metabolism
RF01057	RNA	SAH_riboswitch	1 SAH_riboswitch Mycobacterium smegmatis str. MC2 155		1 SAH_riboswitch Mycobacterium abscessus ATCC 19977	1 SAH_riboswitch Mycobacterium avium 104	1 SAH_riboswitch Mycobacterium marinum M			1 SAH_riboswitch Mycobacterium flavescens PYR-GCK	1 SAH_riboswitch Mycobacterium sp. JLS	Methionine metabolism

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

Collection of regulogs in Mycobacteriaceae taxonomic group

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