Collection of regulogs in Comamonadaceae taxonomic group

General statistics
Genomes	11
TF regulogs	72
TF regulons	316
TF binding sites	886
RNA regulogs	4
RNA regulons	26
RNA sites	50

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
Acidovorax avenae subsp. citrulli AAC00-1	26	70	2	5	28	75
Acidovorax sp. JS42	20	73	3	5	23	78
Comamonas testosteroni KF-1	31	93	3	6	34	99
Delftia acidovorans SPH-1	45	118	3	6	48	124
Leptothrix cholodnii SP-6	19	57	2	4	21	61
Methylibium petroleiphilum PM1	25	65	2	4	27	69
Polaromonas naphthalenivorans CJ2	28	83	2	3	30	86
Polaromonas sp. JS666	32	100	2	4	34	104
Rhodoferax ferrireducens DSM 15236	26	72	2	6	28	78
Variovorax paradoxus S110	36	97	3	5	39	102
Verminephrobacter eiseniae EF01-2	28	58	2	2	30	60

Genomic distribution of regulons
Family	Type	Regulator												Function
FUR	TF	Zur	1 Zur Acidovorax avenae subsp. citrulli AAC00-1			1 Zur Delftia acidovorans SPH-1	2 Zur Polaromonas naphthalenivorans CJ2	1 Zur Polaromonas sp. JS666	2 Zur Rhodoferax ferrireducens DSM 15236					Zinc homeostasis
	TF	Zur2									2 Zur2 Verminephrobacter eiseniae EF01-2		1 Zur2 Leptothrix cholodnii SP-6	Zinc homeostasis
Fis	TF	NorR		3 NorR Acidovorax sp. JS42	2 NorR Comamonas testosteroni KF-1	2 NorR Delftia acidovorans SPH-1	2 NorR Polaromonas naphthalenivorans CJ2	2 NorR Polaromonas sp. JS666		2 NorR Variovorax paradoxus S110				Nitrosative stress response
	TF	NtrC	4 NtrC Acidovorax avenae subsp. citrulli AAC00-1	5 NtrC Acidovorax sp. JS42	4 NtrC Comamonas testosteroni KF-1	4 NtrC Delftia acidovorans SPH-1	3 NtrC Polaromonas naphthalenivorans CJ2	3 NtrC Polaromonas sp. JS666	3 NtrC Rhodoferax ferrireducens DSM 15236	5 NtrC Variovorax paradoxus S110	2 NtrC Verminephrobacter eiseniae EF01-2	1 NtrC Methylibium petroleiphilum PM1	3 NtrC Leptothrix cholodnii SP-6	Nitrogen assimilation
GntR/MocR	TF	Aave_3430	2 Aave_3430 Acidovorax avenae subsp. citrulli AAC00-1		2 Aave_3430 Comamonas testosteroni KF-1	2 Aave_3430 Delftia acidovorans SPH-1	2 Aave_3430 Polaromonas naphthalenivorans CJ2	2 Aave_3430 Polaromonas sp. JS666		2 Aave_3430 Variovorax paradoxus S110
	TF	Bpro_5165						1 Bpro_5165 Polaromonas sp. JS666
	TF	Daci_0288				1 Daci_0288 Delftia acidovorans SPH-1
	TF	Daci_0595	1 Daci_0595 Acidovorax avenae subsp. citrulli AAC00-1	1 Daci_0595 Acidovorax sp. JS42	2 Daci_0595 Comamonas testosteroni KF-1	2 Daci_0595 Delftia acidovorans SPH-1	1 Daci_0595 Polaromonas naphthalenivorans CJ2	1 Daci_0595 Polaromonas sp. JS666	1 Daci_0595 Rhodoferax ferrireducens DSM 15236	1 Daci_0595 Variovorax paradoxus S110		1 Daci_0595 Methylibium petroleiphilum PM1		Metabolite transport
	TF	Daci_1890			1 Daci_1890 Comamonas testosteroni KF-1	1 Daci_1890 Delftia acidovorans SPH-1
	TF	Daci_4286				1 Daci_4286 Delftia acidovorans SPH-1
	TF	EutR									3 EutR Verminephrobacter eiseniae EF01-2			Ectoine utilization
	TF	GabR				1 GabR Delftia acidovorans SPH-1	1 GabR Polaromonas naphthalenivorans CJ2		1 GabR Rhodoferax ferrireducens DSM 15236					Gamma-aminobutyrate utilization
	TF	GabR2					1 GabR2 Polaromonas naphthalenivorans CJ2	1 GabR2 Polaromonas sp. JS666	1 GabR2 Rhodoferax ferrireducens DSM 15236	1 GabR2 Variovorax paradoxus S110				Gamma-aminobutyrate utilization
	TF	PdxQ				1 PdxQ Delftia acidovorans SPH-1								Pyridoxine/pyridoxal homeostasis
	TF	PdxQ2				2 PdxQ2 Delftia acidovorans SPH-1								Metabolite transport; Pyridoxine/pyridoxal homeostasis
	TF	PdxQ3				1 PdxQ3 Delftia acidovorans SPH-1						1 PdxQ3 Methylibium petroleiphilum PM1		Metabolite transport; Pyridoxine/pyridoxal homeostasis
	TF	PdxR			1 PdxR Comamonas testosteroni KF-1	1 PdxR Delftia acidovorans SPH-1								Pyridoxine/pyridoxal homeostasis
	TF	PdxR3										2 PdxR3 Methylibium petroleiphilum PM1		Pyridoxine/pyridoxal homeostasis
	TF	PdxW				1 PdxW Delftia acidovorans SPH-1				1 PdxW Variovorax paradoxus S110				Pyridoxine/pyridoxal homeostasis
	TF	PdxW2											1 PdxW2 Leptothrix cholodnii SP-6	Pyridoxine/pyridoxal homeostasis
	TF	TauR			3 TauR Comamonas testosteroni KF-1	3 TauR Delftia acidovorans SPH-1				2 TauR Variovorax paradoxus S110	3 TauR Verminephrobacter eiseniae EF01-2			Taurine utilization
	TF	Vapar_1337								1 Vapar_1337 Variovorax paradoxus S110
	TF	Vapar_5644								1 Vapar_5644 Variovorax paradoxus S110	1 Vapar_5644 Verminephrobacter eiseniae EF01-2
	TF	Veis_0044									3 Veis_0044 Verminephrobacter eiseniae EF01-2
	TF	Veis_4721									1 Veis_4721 Verminephrobacter eiseniae EF01-2
	TF	YdcR				1 YdcR Delftia acidovorans SPH-1	1 YdcR Polaromonas naphthalenivorans CJ2	1 YdcR Polaromonas sp. JS666		1 YdcR Variovorax paradoxus S110		1 YdcR Methylibium petroleiphilum PM1	2 YdcR Leptothrix cholodnii SP-6
	TF	YrdX					1 YrdX Polaromonas naphthalenivorans CJ2			1 YrdX Variovorax paradoxus S110		1 YrdX Methylibium petroleiphilum PM1
GntR/Others	TF	Aave_3515	2 Aave_3515 Acidovorax avenae subsp. citrulli AAC00-1		2 Aave_3515 Comamonas testosteroni KF-1	2 Aave_3515 Delftia acidovorans SPH-1			2 Aave_3515 Rhodoferax ferrireducens DSM 15236		2 Aave_3515 Verminephrobacter eiseniae EF01-2
	TF	Daci_3053				2 Daci_3053 Delftia acidovorans SPH-1		3 Daci_3053 Polaromonas sp. JS666		2 Daci_3053 Variovorax paradoxus S110				Glycolate utilization; Lactate utilization
	TF	Daci_3836			1 Daci_3836 Comamonas testosteroni KF-1	1 Daci_3836 Delftia acidovorans SPH-1				1 Daci_3836 Variovorax paradoxus S110	2 Daci_3836 Verminephrobacter eiseniae EF01-2	2 Daci_3836 Methylibium petroleiphilum PM1	1 Daci_3836 Leptothrix cholodnii SP-6
	TF	GguR	3 GguR Acidovorax avenae subsp. citrulli AAC00-1	3 GguR Acidovorax sp. JS42	3 GguR Comamonas testosteroni KF-1	3 GguR Delftia acidovorans SPH-1	2 GguR Polaromonas naphthalenivorans CJ2	2 GguR Polaromonas sp. JS666		3 GguR Variovorax paradoxus S110		2 GguR Methylibium petroleiphilum PM1	4 GguR Leptothrix cholodnii SP-6	Glucarate utilization; Galactarate utilization; Galacturonate utilization; Glucuronate utilization
	TF	HutC	2 HutC Acidovorax avenae subsp. citrulli AAC00-1		4 HutC Comamonas testosteroni KF-1	3 HutC Delftia acidovorans SPH-1		6 HutC Polaromonas sp. JS666	1 HutC Rhodoferax ferrireducens DSM 15236	2 HutC Variovorax paradoxus S110	1 HutC Verminephrobacter eiseniae EF01-2			Histidine utilization
	TF	LldR			1 LldR Comamonas testosteroni KF-1	1 LldR Delftia acidovorans SPH-1			2 LldR Rhodoferax ferrireducens DSM 15236					Lactate utilization
	TF	MdcY							2 MdcY Rhodoferax ferrireducens DSM 15236			2 MdcY Methylibium petroleiphilum PM1	2 MdcY Leptothrix cholodnii SP-6	Malonate metabolism
	TF	PhnF										2 PhnF Methylibium petroleiphilum PM1		Phosphonate utilization
	TF	PhnR2						4 PhnR2 Polaromonas sp. JS666			2 PhnR2 Verminephrobacter eiseniae EF01-2			Phosphonoacetate utilization; Phosphonate utilization; 2-aminoethylphosphonate utilization
	TF	PrpR									1 PrpR Verminephrobacter eiseniae EF01-2			Methylcitrate utilization
	TF	SdaR							1 SdaR Rhodoferax ferrireducens DSM 15236					Glucarate utilization; Galactarate utilization
	TF	SdhR	3 SdhR Acidovorax avenae subsp. citrulli AAC00-1	3 SdhR Acidovorax sp. JS42	3 SdhR Comamonas testosteroni KF-1	3 SdhR Delftia acidovorans SPH-1	3 SdhR Polaromonas naphthalenivorans CJ2	3 SdhR Polaromonas sp. JS666	3 SdhR Rhodoferax ferrireducens DSM 15236	3 SdhR Variovorax paradoxus S110	3 SdhR Verminephrobacter eiseniae EF01-2	3 SdhR Methylibium petroleiphilum PM1	4 SdhR Leptothrix cholodnii SP-6	Tricarboxylic acid cycle
	TF	UreR	1 UreR Acidovorax avenae subsp. citrulli AAC00-1		2 UreR Comamonas testosteroni KF-1	3 UreR Delftia acidovorans SPH-1
	TF	UxuR2					2 UxuR2 Polaromonas naphthalenivorans CJ2	4 UxuR2 Polaromonas sp. JS666		5 UxuR2 Variovorax paradoxus S110	3 UxuR2 Verminephrobacter eiseniae EF01-2			Glucuronate utilization; Galacturonate utilization
	TF	UxuR3						2 UxuR3 Polaromonas sp. JS666		1 UxuR3 Variovorax paradoxus S110	1 UxuR3 Verminephrobacter eiseniae EF01-2			Glucuronate utilization
	TF	VanR			2 VanR Comamonas testosteroni KF-1	1 VanR Delftia acidovorans SPH-1	1 VanR Polaromonas naphthalenivorans CJ2	1 VanR Polaromonas sp. JS666		1 VanR Variovorax paradoxus S110	1 VanR Verminephrobacter eiseniae EF01-2			Vanillate utilization
HrcA	TF	HrcA	2 HrcA Acidovorax avenae subsp. citrulli AAC00-1	2 HrcA Acidovorax sp. JS42	2 HrcA Comamonas testosteroni KF-1	2 HrcA Delftia acidovorans SPH-1	2 HrcA Polaromonas naphthalenivorans CJ2	2 HrcA Polaromonas sp. JS666	2 HrcA Rhodoferax ferrireducens DSM 15236	2 HrcA Variovorax paradoxus S110	2 HrcA Verminephrobacter eiseniae EF01-2	2 HrcA Methylibium petroleiphilum PM1	2 HrcA Leptothrix cholodnii SP-6	Heat shock response
LacI	TF	Bpro_5109						1 Bpro_5109 Polaromonas sp. JS666			1 Bpro_5109 Verminephrobacter eiseniae EF01-2			Sugar utilization
	TF	FruR2	2 FruR2 Acidovorax avenae subsp. citrulli AAC00-1			2 FruR2 Delftia acidovorans SPH-1								Fructose utilization
	TF	GntR	2 GntR Acidovorax avenae subsp. citrulli AAC00-1	2 GntR Acidovorax sp. JS42	2 GntR Comamonas testosteroni KF-1	2 GntR Delftia acidovorans SPH-1	2 GntR Polaromonas naphthalenivorans CJ2		2 GntR Rhodoferax ferrireducens DSM 15236	2 GntR Variovorax paradoxus S110			2 GntR Leptothrix cholodnii SP-6	Gluconate utilization
	TF	GudR	2 GudR Acidovorax avenae subsp. citrulli AAC00-1				1 GudR Polaromonas naphthalenivorans CJ2	4 GudR Polaromonas sp. JS666				2 GudR Methylibium petroleiphilum PM1		Glucarate utilization
	TF	RbsR	1 RbsR Acidovorax avenae subsp. citrulli AAC00-1							1 RbsR Variovorax paradoxus S110				Ribose utilization
LexA	TF	LexA	8 LexA Acidovorax avenae subsp. citrulli AAC00-1	6 LexA Acidovorax sp. JS42	5 LexA Comamonas testosteroni KF-1	5 LexA Delftia acidovorans SPH-1	4 LexA Polaromonas naphthalenivorans CJ2	7 LexA Polaromonas sp. JS666	6 LexA Rhodoferax ferrireducens DSM 15236	6 LexA Variovorax paradoxus S110	3 LexA Verminephrobacter eiseniae EF01-2	8 LexA Methylibium petroleiphilum PM1	4 LexA Leptothrix cholodnii SP-6	SOS response
LysR	TF	MetR		2 MetR Acidovorax sp. JS42	2 MetR Comamonas testosteroni KF-1	1 MetR Delftia acidovorans SPH-1				2 MetR Variovorax paradoxus S110	2 MetR Verminephrobacter eiseniae EF01-2			Methionine biosynthesis
MerR	TF	CadR-PbrR	1 CadR-PbrR Acidovorax avenae subsp. citrulli AAC00-1	5 CadR-PbrR Acidovorax sp. JS42	5 CadR-PbrR Comamonas testosteroni KF-1	2 CadR-PbrR Delftia acidovorans SPH-1	1 CadR-PbrR Polaromonas naphthalenivorans CJ2	1 CadR-PbrR Polaromonas sp. JS666	1 CadR-PbrR Rhodoferax ferrireducens DSM 15236	1 CadR-PbrR Variovorax paradoxus S110	2 CadR-PbrR Verminephrobacter eiseniae EF01-2	2 CadR-PbrR Methylibium petroleiphilum PM1		Lead resistance; Cadmium resistance
	TF	CueR	2 CueR Acidovorax avenae subsp. citrulli AAC00-1	4 CueR Acidovorax sp. JS42	1 CueR Comamonas testosteroni KF-1	2 CueR Delftia acidovorans SPH-1	2 CueR Polaromonas naphthalenivorans CJ2	4 CueR Polaromonas sp. JS666	2 CueR Rhodoferax ferrireducens DSM 15236	3 CueR Variovorax paradoxus S110		5 CueR Methylibium petroleiphilum PM1		Copper resistance
	TF	LiuR	3 LiuR Acidovorax avenae subsp. citrulli AAC00-1	4 LiuR Acidovorax sp. JS42	5 LiuR Comamonas testosteroni KF-1	4 LiuR Delftia acidovorans SPH-1	5 LiuR Polaromonas naphthalenivorans CJ2	5 LiuR Polaromonas sp. JS666	4 LiuR Rhodoferax ferrireducens DSM 15236	1 LiuR Variovorax paradoxus S110			4 LiuR Leptothrix cholodnii SP-6	Branched-chain amino acid degradation
	TF	LiuR2							2 LiuR2 Rhodoferax ferrireducens DSM 15236					Acyclic terpenes degradation
	TF	MerR		2 MerR Acidovorax sp. JS42	1 MerR Comamonas testosteroni KF-1	1 MerR Delftia acidovorans SPH-1		2 MerR Polaromonas sp. JS666				1 MerR Methylibium petroleiphilum PM1		Mercury resistance
	TF	NmlR					1 NmlR Polaromonas naphthalenivorans CJ2		1 NmlR Rhodoferax ferrireducens DSM 15236					Carbonyl stress response
	TF	SoxR	3 SoxR Acidovorax avenae subsp. citrulli AAC00-1		2 SoxR Comamonas testosteroni KF-1	3 SoxR Delftia acidovorans SPH-1		2 SoxR Polaromonas sp. JS666		2 SoxR Variovorax paradoxus S110				Superoxide stress response
ModE	TF	FdsR								2 FdsR Variovorax paradoxus S110		2 FdsR Methylibium petroleiphilum PM1		Formate oxydation
	TF	ModE	1 ModE Acidovorax avenae subsp. citrulli AAC00-1	2 ModE Acidovorax sp. JS42	2 ModE Comamonas testosteroni KF-1	2 ModE Delftia acidovorans SPH-1			2 ModE Rhodoferax ferrireducens DSM 15236		1 ModE Verminephrobacter eiseniae EF01-2			Molybdenum homeostasis
	TF	ModE2			2 ModE2 Comamonas testosteroni KF-1	2 ModE2 Delftia acidovorans SPH-1		2 ModE2 Polaromonas sp. JS666		1 ModE2 Variovorax paradoxus S110	1 ModE2 Verminephrobacter eiseniae EF01-2			Molybdopterin biosynthesis
	TF	ModE3		2 ModE3 Acidovorax sp. JS42			2 ModE3 Polaromonas naphthalenivorans CJ2	2 ModE3 Polaromonas sp. JS666	2 ModE3 Rhodoferax ferrireducens DSM 15236	1 ModE3 Variovorax paradoxus S110		1 ModE3 Methylibium petroleiphilum PM1	2 ModE3 Leptothrix cholodnii SP-6	Tungsten homeostasis
NadQ	TF	NadQ			2 NadQ Comamonas testosteroni KF-1	2 NadQ Delftia acidovorans SPH-1								NAD biosynthesis
NikR	TF	NikR				1 NikR Delftia acidovorans SPH-1						2 NikR Methylibium petroleiphilum PM1		Nickel homeostasis
NrdR	TF	NrdR	1 NrdR Acidovorax avenae subsp. citrulli AAC00-1	2 NrdR Acidovorax sp. JS42	1 NrdR Comamonas testosteroni KF-1	1 NrdR Delftia acidovorans SPH-1	1 NrdR Polaromonas naphthalenivorans CJ2	1 NrdR Polaromonas sp. JS666	2 NrdR Rhodoferax ferrireducens DSM 15236	1 NrdR Variovorax paradoxus S110	1 NrdR Verminephrobacter eiseniae EF01-2	2 NrdR Methylibium petroleiphilum PM1	1 NrdR Leptothrix cholodnii SP-6	Deoxyribonucleotide biosynthesis
NrtR	TF	NrtR	1 NrtR Acidovorax avenae subsp. citrulli AAC00-1			2 NrtR Delftia acidovorans SPH-1	2 NrtR Polaromonas naphthalenivorans CJ2			2 NrtR Variovorax paradoxus S110				NAD biosynthesis
RpiR	TF	HexR	2 HexR Acidovorax avenae subsp. citrulli AAC00-1	2 HexR Acidovorax sp. JS42	2 HexR Comamonas testosteroni KF-1	4 HexR Delftia acidovorans SPH-1	3 HexR Polaromonas naphthalenivorans CJ2	4 HexR Polaromonas sp. JS666	4 HexR Rhodoferax ferrireducens DSM 15236		3 HexR Verminephrobacter eiseniae EF01-2		3 HexR Leptothrix cholodnii SP-6	Central carbohydrate metabolism
Rrf2	TF	IscR	1 IscR Acidovorax avenae subsp. citrulli AAC00-1	1 IscR Acidovorax sp. JS42	1 IscR Comamonas testosteroni KF-1	1 IscR Delftia acidovorans SPH-1	1 IscR Polaromonas naphthalenivorans CJ2	1 IscR Polaromonas sp. JS666	1 IscR Rhodoferax ferrireducens DSM 15236	1 IscR Variovorax paradoxus S110	1 IscR Verminephrobacter eiseniae EF01-2	1 IscR Methylibium petroleiphilum PM1	1 IscR Leptothrix cholodnii SP-6	Iron-sulfur cluster biogenesis
	TF	NsrR	2 NsrR Acidovorax avenae subsp. citrulli AAC00-1	3 NsrR Acidovorax sp. JS42			5 NsrR Polaromonas naphthalenivorans CJ2	1 NsrR Polaromonas sp. JS666	3 NsrR Rhodoferax ferrireducens DSM 15236					Nitrosative stress response
TetR	TF	FadP	5 FadP Acidovorax avenae subsp. citrulli AAC00-1	5 FadP Acidovorax sp. JS42	3 FadP Comamonas testosteroni KF-1	4 FadP Delftia acidovorans SPH-1	4 FadP Polaromonas naphthalenivorans CJ2	4 FadP Polaromonas sp. JS666	6 FadP Rhodoferax ferrireducens DSM 15236	4 FadP Variovorax paradoxus S110	4 FadP Verminephrobacter eiseniae EF01-2	4 FadP Methylibium petroleiphilum PM1	3 FadP Leptothrix cholodnii SP-6	Fatty acid degradation
	TF	LiuQ										2 LiuQ Methylibium petroleiphilum PM1	2 LiuQ Leptothrix cholodnii SP-6	Branched-chain amino acid degradation
	TF	PaaR				3 PaaR Delftia acidovorans SPH-1				2 PaaR Variovorax paradoxus S110	1 PaaR Verminephrobacter eiseniae EF01-2	2 PaaR Methylibium petroleiphilum PM1	3 PaaR Leptothrix cholodnii SP-6	Phenylacetic acid degradation
RF00050	RNA	FMN		1 FMN Acidovorax sp. JS42	1 FMN Comamonas testosteroni KF-1	1 FMN Delftia acidovorans SPH-1				1 FMN Variovorax paradoxus S110				Riboflavin biosynthesis
RF00059	RNA	TPP	3 TPP Acidovorax avenae subsp. citrulli AAC00-1	2 TPP Acidovorax sp. JS42	3 TPP Comamonas testosteroni KF-1	3 TPP Delftia acidovorans SPH-1	1 TPP Polaromonas naphthalenivorans CJ2	2 TPP Polaromonas sp. JS666	4 TPP Rhodoferax ferrireducens DSM 15236	2 TPP Variovorax paradoxus S110	1 TPP Verminephrobacter eiseniae EF01-2	2 TPP Methylibium petroleiphilum PM1	2 TPP Leptothrix cholodnii SP-6	Thiamine biosynthesis
RF01055	RNA	MOCO_RNA_motif
RF01057	RNA	SAH_riboswitch	2 SAH_riboswitch Acidovorax avenae subsp. citrulli AAC00-1	2 SAH_riboswitch Acidovorax sp. JS42	2 SAH_riboswitch Comamonas testosteroni KF-1	2 SAH_riboswitch Delftia acidovorans SPH-1	2 SAH_riboswitch Polaromonas naphthalenivorans CJ2	2 SAH_riboswitch Polaromonas sp. JS666	2 SAH_riboswitch Rhodoferax ferrireducens DSM 15236	2 SAH_riboswitch Variovorax paradoxus S110	1 SAH_riboswitch Verminephrobacter eiseniae EF01-2	2 SAH_riboswitch Methylibium petroleiphilum PM1	2 SAH_riboswitch Leptothrix cholodnii SP-6	Methionine metabolism

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

Collection of regulogs in Comamonadaceae taxonomic group

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