Collection of regulogs in Rhodobacterales taxonomic group

General statistics
Genomes	15
TF regulogs	76
TF regulons	386
TF binding sites	1487
RNA regulogs	13
RNA regulons	115
RNA sites	182

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
Hyphomonas neptunium ATCC 15444	14	42	8	10	22	52
Jannaschia sp. CCS1	27	130	8	10	35	140
Loktanella vestfoldensis SKA53	22	99	7	8	29	107
Oceanicaulis alexandrii HTCC2633	12	41	6	7	18	48
Oceanicola batsensis HTCC2597	24	90	7	12	31	102
Oceanicola granulosus HTCC2516	22	61	6	8	28	69
Paracoccus denitrificans PD1222	38	117	7	21	45	138
Rhodobacter sphaeroides 2.4.1	33	136	8	15	41	151
Rhodobacterales bacterium HTCC2654	24	106	8	10	32	116
Roseobacter sp. MED193	27	116	8	14	35	130
Roseovarius nubinhibens ISM	28	93	9	14	37	107
Roseovarius sp. 217	29	130	9	13	38	143
Silicibacter pomeroyi DSS-3	35	126	6	8	41	134
Silicibacter TM1040	29	116	9	18	38	134
Sulfitobacter sp. EE-36	22	84	9	14	31	98

Genomic distribution of regulons
Family	Type	Regulator																Function
ArsR	TF	SahR														1 SahR Hyphomonas neptunium ATCC 15444	3 SahR Oceanicaulis alexandrii HTCC2633	Methionine metabolism
CRP	TF	FnrN	9 FnrN Rhodobacter sphaeroides 2.4.1	8 FnrN Paracoccus denitrificans PD1222	5 FnrN Jannaschia sp. CCS1	8 FnrN Rhodobacterales bacterium HTCC2654	1 FnrN Oceanicola granulosus HTCC2516	4 FnrN Loktanella vestfoldensis SKA53	5 FnrN Oceanicola batsensis HTCC2597		9 FnrN Roseovarius sp. 217	2 FnrN Sulfitobacter sp. EE-36	9 FnrN Silicibacter TM1040	10 FnrN Silicibacter pomeroyi DSS-3	7 FnrN Roseobacter sp. MED193			Oxidative stress response; Nitrogen fixation
	TF	NnrR	4 NnrR Rhodobacter sphaeroides 2.4.1			6 NnrR Rhodobacterales bacterium HTCC2654					4 NnrR Roseovarius sp. 217							Denitrification
DeoR	TF	RhaR				2 RhaR Rhodobacterales bacterium HTCC2654	2 RhaR Oceanicola granulosus HTCC2516											Rhamnose utilization
DtxR	TF	MntR				2 MntR Rhodobacterales bacterium HTCC2654				2 MntR Roseovarius nubinhibens ISM	1 MntR Roseovarius sp. 217							Manganese homeostasis
FUR	TF	Fur														8 Fur Hyphomonas neptunium ATCC 15444	14 Fur Oceanicaulis alexandrii HTCC2633	Iron homeostasis
	TF	Irr	2 Irr Rhodobacter sphaeroides 2.4.1		3 Irr Jannaschia sp. CCS1	3 Irr Rhodobacterales bacterium HTCC2654	1 Irr Oceanicola granulosus HTCC2516	4 Irr Loktanella vestfoldensis SKA53	3 Irr Oceanicola batsensis HTCC2597	4 Irr Roseovarius nubinhibens ISM	4 Irr Roseovarius sp. 217	4 Irr Sulfitobacter sp. EE-36	3 Irr Silicibacter TM1040	4 Irr Silicibacter pomeroyi DSS-3	2 Irr Roseobacter sp. MED193			Iron homeostasis
	TF	Mur	1 Mur Rhodobacter sphaeroides 2.4.1	2 Mur Paracoccus denitrificans PD1222	1 Mur Jannaschia sp. CCS1	2 Mur Rhodobacterales bacterium HTCC2654	1 Mur Oceanicola granulosus HTCC2516	1 Mur Loktanella vestfoldensis SKA53	1 Mur Oceanicola batsensis HTCC2597	1 Mur Roseovarius nubinhibens ISM	1 Mur Roseovarius sp. 217	2 Mur Sulfitobacter sp. EE-36	2 Mur Silicibacter TM1040	2 Mur Silicibacter pomeroyi DSS-3	2 Mur Roseobacter sp. MED193			Manganese homeostasis
	TF	Zur	3 Zur Rhodobacter sphaeroides 2.4.1	3 Zur Paracoccus denitrificans PD1222	2 Zur Jannaschia sp. CCS1	2 Zur Rhodobacterales bacterium HTCC2654	2 Zur Oceanicola granulosus HTCC2516	2 Zur Loktanella vestfoldensis SKA53	3 Zur Oceanicola batsensis HTCC2597	4 Zur Roseovarius nubinhibens ISM	2 Zur Roseovarius sp. 217	3 Zur Sulfitobacter sp. EE-36	4 Zur Silicibacter TM1040	2 Zur Silicibacter pomeroyi DSS-3	2 Zur Roseobacter sp. MED193	1 Zur Hyphomonas neptunium ATCC 15444	1 Zur Oceanicaulis alexandrii HTCC2633	Zinc homeostasis
Fis	TF	NifA	7 NifA Rhodobacter sphaeroides 2.4.1															Nitrogen fixation
	TF	NtrC	4 NtrC Rhodobacter sphaeroides 2.4.1	4 NtrC Paracoccus denitrificans PD1222	9 NtrC Jannaschia sp. CCS1	6 NtrC Rhodobacterales bacterium HTCC2654	4 NtrC Oceanicola granulosus HTCC2516	5 NtrC Loktanella vestfoldensis SKA53	4 NtrC Oceanicola batsensis HTCC2597	3 NtrC Roseovarius nubinhibens ISM	5 NtrC Roseovarius sp. 217	7 NtrC Sulfitobacter sp. EE-36	5 NtrC Silicibacter TM1040	3 NtrC Silicibacter pomeroyi DSS-3	8 NtrC Roseobacter sp. MED193	2 NtrC Hyphomonas neptunium ATCC 15444		Nitrogen assimilation
GntR/MocR	TF	EutR	2 EutR Rhodobacter sphaeroides 2.4.1	1 EutR Paracoccus denitrificans PD1222				2 EutR Loktanella vestfoldensis SKA53	1 EutR Oceanicola batsensis HTCC2597	2 EutR Roseovarius nubinhibens ISM		2 EutR Sulfitobacter sp. EE-36	1 EutR Silicibacter TM1040	3 EutR Silicibacter pomeroyi DSS-3	1 EutR Roseobacter sp. MED193			Ectoine utilization
	TF	Pden_4836		1 Pden_4836 Paracoccus denitrificans PD1222
	TF	PdxQ		1 PdxQ Paracoccus denitrificans PD1222														Pyridoxine/pyridoxal homeostasis
	TF	PdxQ3								1 PdxQ3 Roseovarius nubinhibens ISM				1 PdxQ3 Silicibacter pomeroyi DSS-3				Metabolite transport; Pyridoxine/pyridoxal homeostasis
	TF	PdxR2	1 PdxR2 Rhodobacter sphaeroides 2.4.1	1 PdxR2 Paracoccus denitrificans PD1222														Pyridoxine biosynthesis
	TF	PdxR3															1 PdxR3 Oceanicaulis alexandrii HTCC2633	Metabolite transport; Pyridoxine/pyridoxal homeostasis
	TF	PdxW								1 PdxW Roseovarius nubinhibens ISM								Pyridoxine/pyridoxal homeostasis
	TF	SPOA0164							2 SPOA0164 Oceanicola batsensis HTCC2597					2 SPOA0164 Silicibacter pomeroyi DSS-3
	TF	SPOA0379									2 SPOA0379 Roseovarius sp. 217			2 SPOA0379 Silicibacter pomeroyi DSS-3
	TF	TauR	1 TauR Rhodobacter sphaeroides 2.4.1	2 TauR Paracoccus denitrificans PD1222	3 TauR Jannaschia sp. CCS1			1 TauR Loktanella vestfoldensis SKA53		2 TauR Roseovarius nubinhibens ISM	2 TauR Roseovarius sp. 217		2 TauR Silicibacter TM1040	2 TauR Silicibacter pomeroyi DSS-3	2 TauR Roseobacter sp. MED193			Taurine utilization
	TF	TauR2									2 TauR2 Roseovarius sp. 217			2 TauR2 Silicibacter pomeroyi DSS-3
GntR/Others	TF	AnsR		1 AnsR Paracoccus denitrificans PD1222														Asparagine degradation; Aspartate utilization
	TF	BioR	2 BioR Rhodobacter sphaeroides 2.4.1	4 BioR Paracoccus denitrificans PD1222								2 BioR Sulfitobacter sp. EE-36	1 BioR Silicibacter TM1040	2 BioR Silicibacter pomeroyi DSS-3	1 BioR Roseobacter sp. MED193			Biotin biosynthesis
	TF	GlcC		1 GlcC Paracoccus denitrificans PD1222														Glycolate utilization
	TF	HutC	2 HutC Rhodobacter sphaeroides 2.4.1	2 HutC Paracoccus denitrificans PD1222			2 HutC Oceanicola granulosus HTCC2516			3 HutC Roseovarius nubinhibens ISM	4 HutC Roseovarius sp. 217		3 HutC Silicibacter TM1040	2 HutC Silicibacter pomeroyi DSS-3	2 HutC Roseobacter sp. MED193	2 HutC Hyphomonas neptunium ATCC 15444	2 HutC Oceanicaulis alexandrii HTCC2633	Histidine utilization
	TF	HypR		4 HypR Paracoccus denitrificans PD1222			4 HypR Oceanicola granulosus HTCC2516			1 HypR Roseovarius nubinhibens ISM								Proline and 4-hydrohyproline utilization
	TF	HypR2		2 HypR2 Paracoccus denitrificans PD1222						3 HypR2 Roseovarius nubinhibens ISM			4 HypR2 Silicibacter TM1040	2 HypR2 Silicibacter pomeroyi DSS-3	3 HypR2 Roseobacter sp. MED193			Proline and 4-hydrohyproline utilization
	TF	LldR		2 LldR Paracoccus denitrificans PD1222		2 LldR Rhodobacterales bacterium HTCC2654												Lactate utilization
	TF	MdcY		2 MdcY Paracoccus denitrificans PD1222														Malonate metabolism
	TF	NagQ		2 NagQ Paracoccus denitrificans PD1222	2 NagQ Jannaschia sp. CCS1								2 NagQ Silicibacter TM1040	2 NagQ Silicibacter pomeroyi DSS-3				N-acetylglucosamine utilization
	TF	Pden_0318		2 Pden_0318 Paracoccus denitrificans PD1222
	TF	Pden_3389		2 Pden_3389 Paracoccus denitrificans PD1222	2 Pden_3389 Jannaschia sp. CCS1					2 Pden_3389 Roseovarius nubinhibens ISM	2 Pden_3389 Roseovarius sp. 217							Glycolate utilization; Lactate utilization
	TF	PhnF		2 PhnF Paracoccus denitrificans PD1222	2 PhnF Jannaschia sp. CCS1	2 PhnF Rhodobacterales bacterium HTCC2654		2 PhnF Loktanella vestfoldensis SKA53	2 PhnF Oceanicola batsensis HTCC2597	2 PhnF Roseovarius nubinhibens ISM	2 PhnF Roseovarius sp. 217	2 PhnF Sulfitobacter sp. EE-36	1 PhnF Silicibacter TM1040	2 PhnF Silicibacter pomeroyi DSS-3	2 PhnF Roseobacter sp. MED193			Phosphonate utilization
	TF	RspR		1 RspR Paracoccus denitrificans PD1222										2 RspR Silicibacter pomeroyi DSS-3				L-gulonate utilization
	TF	SPOA0375									2 SPOA0375 Roseovarius sp. 217			2 SPOA0375 Silicibacter pomeroyi DSS-3
	TF	UxuR											2 UxuR Silicibacter TM1040					Glucuronate utilization
	TF	UxuR1	2 UxuR1 Rhodobacter sphaeroides 2.4.1															Glucuronate utilization; Galacturonate utilization
HrcA	TF	HrcA	1 HrcA Rhodobacter sphaeroides 2.4.1	1 HrcA Paracoccus denitrificans PD1222	1 HrcA Jannaschia sp. CCS1	1 HrcA Rhodobacterales bacterium HTCC2654	1 HrcA Oceanicola granulosus HTCC2516	1 HrcA Loktanella vestfoldensis SKA53	1 HrcA Oceanicola batsensis HTCC2597	1 HrcA Roseovarius nubinhibens ISM	1 HrcA Roseovarius sp. 217	1 HrcA Sulfitobacter sp. EE-36	1 HrcA Silicibacter TM1040	1 HrcA Silicibacter pomeroyi DSS-3	1 HrcA Roseobacter sp. MED193	1 HrcA Hyphomonas neptunium ATCC 15444	1 HrcA Oceanicaulis alexandrii HTCC2633	Heat shock response
LacI	TF	AfrR			2 AfrR Jannaschia sp. CCS1													1,5-Anhydro-d-Fructose utilization
	TF	AglR			2 AglR Jannaschia sp. CCS1	2 AglR Rhodobacterales bacterium HTCC2654	2 AglR Oceanicola granulosus HTCC2516	2 AglR Loktanella vestfoldensis SKA53					2 AglR Silicibacter TM1040					Alpha-glucosides utilization
	TF	CceR (GapR)	8 CceR (GapR) Rhodobacter sphaeroides 2.4.1	10 CceR (GapR) Paracoccus denitrificans PD1222	12 CceR (GapR) Jannaschia sp. CCS1	12 CceR (GapR) Rhodobacterales bacterium HTCC2654	5 CceR (GapR) Oceanicola granulosus HTCC2516	9 CceR (GapR) Loktanella vestfoldensis SKA53	10 CceR (GapR) Oceanicola batsensis HTCC2597	8 CceR (GapR) Roseovarius nubinhibens ISM	8 CceR (GapR) Roseovarius sp. 217	8 CceR (GapR) Sulfitobacter sp. EE-36	11 CceR (GapR) Silicibacter TM1040	13 CceR (GapR) Silicibacter pomeroyi DSS-3	11 CceR (GapR) Roseobacter sp. MED193			Central carbohydrate metabolism
	TF	FruR2	2 FruR2 Rhodobacter sphaeroides 2.4.1															Fructose utilization
	TF	IolR			4 IolR Jannaschia sp. CCS1			4 IolR Loktanella vestfoldensis SKA53					4 IolR Silicibacter TM1040					Inositol utilization
	TF	Jann_1107			4 Jann_1107 Jannaschia sp. CCS1		1 Jann_1107 Oceanicola granulosus HTCC2516											Sugar utilization
	TF	Jann_1459	2 Jann_1459 Rhodobacter sphaeroides 2.4.1	2 Jann_1459 Paracoccus denitrificans PD1222	2 Jann_1459 Jannaschia sp. CCS1				2 Jann_1459 Oceanicola batsensis HTCC2597									Sugar utilization
	TF	Jann_3936			2 Jann_3936 Jannaschia sp. CCS1													Sugar utilization
	TF	KglR		1 KglR Paracoccus denitrificans PD1222														Sugar utilization
	TF	OB2597_06045							2 OB2597_06045 Oceanicola batsensis HTCC2597									Sugar utilization
	TF	OG2516_10476					2 OG2516_10476 Oceanicola granulosus HTCC2516											Sugar utilization
	TF	RbsR2	2 RbsR2 Rhodobacter sphaeroides 2.4.1															Ribose utilization
	TF	RbtR	2 RbtR Rhodobacter sphaeroides 2.4.1															Ribitol utilization
	TF	SPO0590			4 SPO0590 Jannaschia sp. CCS1					2 SPO0590 Roseovarius nubinhibens ISM	2 SPO0590 Roseovarius sp. 217			2 SPO0590 Silicibacter pomeroyi DSS-3	2 SPO0590 Roseobacter sp. MED193			Sugar utilization
	TF	SPOA0336										2 SPOA0336 Sulfitobacter sp. EE-36		2 SPOA0336 Silicibacter pomeroyi DSS-3				Sugar utilization
	TF	SmoR		3 SmoR Paracoccus denitrificans PD1222	2 SmoR Jannaschia sp. CCS1		2 SmoR Oceanicola granulosus HTCC2516	2 SmoR Loktanella vestfoldensis SKA53	2 SmoR Oceanicola batsensis HTCC2597			2 SmoR Sulfitobacter sp. EE-36	2 SmoR Silicibacter TM1040					Sorbitol utilization; Mannitol utilization
	TF	SocR	1 SocR Rhodobacter sphaeroides 2.4.1															Santhopine utilization
LexA	TF	LexA	7 LexA Rhodobacter sphaeroides 2.4.1	7 LexA Paracoccus denitrificans PD1222	8 LexA Jannaschia sp. CCS1	9 LexA Rhodobacterales bacterium HTCC2654	8 LexA Oceanicola granulosus HTCC2516	7 LexA Loktanella vestfoldensis SKA53	8 LexA Oceanicola batsensis HTCC2597	7 LexA Roseovarius nubinhibens ISM	9 LexA Roseovarius sp. 217	9 LexA Sulfitobacter sp. EE-36	7 LexA Silicibacter TM1040	6 LexA Silicibacter pomeroyi DSS-3	9 LexA Roseobacter sp. MED193	7 LexA Hyphomonas neptunium ATCC 15444	6 LexA Oceanicaulis alexandrii HTCC2633	SOS response
LysR	TF	MetR	3 MetR Rhodobacter sphaeroides 2.4.1	2 MetR Paracoccus denitrificans PD1222	1 MetR Jannaschia sp. CCS1	3 MetR Rhodobacterales bacterium HTCC2654	2 MetR Oceanicola granulosus HTCC2516	3 MetR Loktanella vestfoldensis SKA53	2 MetR Oceanicola batsensis HTCC2597	2 MetR Roseovarius nubinhibens ISM	3 MetR Roseovarius sp. 217	2 MetR Sulfitobacter sp. EE-36	3 MetR Silicibacter TM1040	2 MetR Silicibacter pomeroyi DSS-3	2 MetR Roseobacter sp. MED193			Methionine biosynthesis
MerR	TF	CadR-PbrR	1 CadR-PbrR Rhodobacter sphaeroides 2.4.1	2 CadR-PbrR Paracoccus denitrificans PD1222		5 CadR-PbrR Rhodobacterales bacterium HTCC2654	1 CadR-PbrR Oceanicola granulosus HTCC2516		6 CadR-PbrR Oceanicola batsensis HTCC2597	4 CadR-PbrR Roseovarius nubinhibens ISM	5 CadR-PbrR Roseovarius sp. 217	1 CadR-PbrR Sulfitobacter sp. EE-36	1 CadR-PbrR Silicibacter TM1040		5 CadR-PbrR Roseobacter sp. MED193	1 CadR-PbrR Hyphomonas neptunium ATCC 15444		Lead resistance; Cadmium resistance
	TF	CueR	2 CueR Rhodobacter sphaeroides 2.4.1		1 CueR Jannaschia sp. CCS1	2 CueR Rhodobacterales bacterium HTCC2654			2 CueR Oceanicola batsensis HTCC2597	2 CueR Roseovarius nubinhibens ISM	5 CueR Roseovarius sp. 217	1 CueR Sulfitobacter sp. EE-36		1 CueR Silicibacter pomeroyi DSS-3	2 CueR Roseobacter sp. MED193			Copper resistance
	TF	LiuR	1 LiuR Rhodobacter sphaeroides 2.4.1	1 LiuR Paracoccus denitrificans PD1222	1 LiuR Jannaschia sp. CCS1	1 LiuR Rhodobacterales bacterium HTCC2654		1 LiuR Loktanella vestfoldensis SKA53	1 LiuR Oceanicola batsensis HTCC2597	1 LiuR Roseovarius nubinhibens ISM	1 LiuR Roseovarius sp. 217		1 LiuR Silicibacter TM1040	1 LiuR Silicibacter pomeroyi DSS-3	1 LiuR Roseobacter sp. MED193	6 LiuR Hyphomonas neptunium ATCC 15444	1 LiuR Oceanicaulis alexandrii HTCC2633	Branched-chain amino acid degradation
	TF	MerR														1 MerR Hyphomonas neptunium ATCC 15444		Mercury resistance
	TF	SoxR					2 SoxR Oceanicola granulosus HTCC2516			2 SoxR Roseovarius nubinhibens ISM		2 SoxR Sulfitobacter sp. EE-36	3 SoxR Silicibacter TM1040	2 SoxR Silicibacter pomeroyi DSS-3	3 SoxR Roseobacter sp. MED193	2 SoxR Hyphomonas neptunium ATCC 15444	2 SoxR Oceanicaulis alexandrii HTCC2633	Superoxide stress response
ModE	TF	ModE	3 ModE Rhodobacter sphaeroides 2.4.1															Molybdopterin biosynthesis
	TF	ModE2		1 ModE2 Paracoccus denitrificans PD1222		1 ModE2 Rhodobacterales bacterium HTCC2654					1 ModE2 Roseovarius sp. 217			1 ModE2 Silicibacter pomeroyi DSS-3				Molybdenum homeostasis
NadQ	TF	NadQ														2 NadQ Hyphomonas neptunium ATCC 15444	2 NadQ Oceanicaulis alexandrii HTCC2633	NAD biosynthesis
NikR	TF	NikR	1 NikR Rhodobacter sphaeroides 2.4.1					1 NikR Loktanella vestfoldensis SKA53										Nickel homeostasis
NrdR	TF	NrdR	1 NrdR Rhodobacter sphaeroides 2.4.1	1 NrdR Paracoccus denitrificans PD1222	1 NrdR Jannaschia sp. CCS1	1 NrdR Rhodobacterales bacterium HTCC2654	1 NrdR Oceanicola granulosus HTCC2516	1 NrdR Loktanella vestfoldensis SKA53	1 NrdR Oceanicola batsensis HTCC2597	1 NrdR Roseovarius nubinhibens ISM	1 NrdR Roseovarius sp. 217	1 NrdR Sulfitobacter sp. EE-36	1 NrdR Silicibacter TM1040	1 NrdR Silicibacter pomeroyi DSS-3	1 NrdR Roseobacter sp. MED193	2 NrdR Hyphomonas neptunium ATCC 15444	2 NrdR Oceanicaulis alexandrii HTCC2633	Deoxyribonucleotide biosynthesis
NrtR	TF	NrtR													1 NrtR Roseobacter sp. MED193			NAD biosynthesis
OmpR	TF	Chvl	1 Chvl Rhodobacter sphaeroides 2.4.1			1 Chvl Rhodobacterales bacterium HTCC2654	1 Chvl Oceanicola granulosus HTCC2516		1 Chvl Oceanicola batsensis HTCC2597	1 Chvl Roseovarius nubinhibens ISM		1 Chvl Sulfitobacter sp. EE-36	1 Chvl Silicibacter TM1040	1 Chvl Silicibacter pomeroyi DSS-3	1 Chvl Roseobacter sp. MED193
RpiR	TF	EutR	2 EutR Rhodobacter sphaeroides 2.4.1	2 EutR Paracoccus denitrificans PD1222				2 EutR Loktanella vestfoldensis SKA53	2 EutR Oceanicola batsensis HTCC2597	2 EutR Roseovarius nubinhibens ISM	2 EutR Roseovarius sp. 217	2 EutR Sulfitobacter sp. EE-36	2 EutR Silicibacter TM1040	2 EutR Silicibacter pomeroyi DSS-3	2 EutR Roseobacter sp. MED193			Ethanolamine utilization
Rrf2	TF	IscR	8 IscR Rhodobacter sphaeroides 2.4.1	6 IscR Paracoccus denitrificans PD1222	10 IscR Jannaschia sp. CCS1	6 IscR Rhodobacterales bacterium HTCC2654	2 IscR Oceanicola granulosus HTCC2516	9 IscR Loktanella vestfoldensis SKA53	9 IscR Oceanicola batsensis HTCC2597	9 IscR Roseovarius nubinhibens ISM	8 IscR Roseovarius sp. 217	12 IscR Sulfitobacter sp. EE-36	7 IscR Silicibacter TM1040	5 IscR Silicibacter pomeroyi DSS-3	8 IscR Roseobacter sp. MED193		1 IscR Oceanicaulis alexandrii HTCC2633	Iron-sulfur cluster biogenesis; Iron homeostasis
	TF	NsrR		4 NsrR Paracoccus denitrificans PD1222					2 NsrR Oceanicola batsensis HTCC2597		4 NsrR Roseovarius sp. 217			3 NsrR Silicibacter pomeroyi DSS-3		2 NsrR Hyphomonas neptunium ATCC 15444		Nitrosative stress response
TetR	TF	PaaR		4 PaaR Paracoccus denitrificans PD1222		2 PaaR Rhodobacterales bacterium HTCC2654							2 PaaR Silicibacter TM1040	3 PaaR Silicibacter pomeroyi DSS-3	2 PaaR Roseobacter sp. MED193			Phenylacetic acid degradation
	TF	RutR	4 RutR Rhodobacter sphaeroides 2.4.1	1 RutR Paracoccus denitrificans PD1222	5 RutR Jannaschia sp. CCS1	6 RutR Rhodobacterales bacterium HTCC2654	4 RutR Oceanicola granulosus HTCC2516	4 RutR Loktanella vestfoldensis SKA53	3 RutR Oceanicola batsensis HTCC2597	4 RutR Roseovarius nubinhibens ISM	4 RutR Roseovarius sp. 217	3 RutR Sulfitobacter sp. EE-36	6 RutR Silicibacter TM1040	7 RutR Silicibacter pomeroyi DSS-3	8 RutR Roseobacter sp. MED193			Pyrimidine utilization
[Other]	TF	PpsR	12 PpsR Rhodobacter sphaeroides 2.4.1		12 PpsR Jannaschia sp. CCS1			10 PpsR Loktanella vestfoldensis SKA53			9 PpsR Roseovarius sp. 217							Photosynthesis
RF00050	RNA	FMN		1 FMN Paracoccus denitrificans PD1222						1 FMN Roseovarius nubinhibens ISM		1 FMN Sulfitobacter sp. EE-36	2 FMN Silicibacter TM1040	1 FMN Silicibacter pomeroyi DSS-3	1 FMN Roseobacter sp. MED193			Riboflavin biosynthesis
RF00059	RNA	TPP	2 TPP Rhodobacter sphaeroides 2.4.1	3 TPP Paracoccus denitrificans PD1222	1 TPP Jannaschia sp. CCS1	2 TPP Rhodobacterales bacterium HTCC2654	2 TPP Oceanicola granulosus HTCC2516	1 TPP Loktanella vestfoldensis SKA53	4 TPP Oceanicola batsensis HTCC2597	2 TPP Roseovarius nubinhibens ISM	3 TPP Roseovarius sp. 217	2 TPP Sulfitobacter sp. EE-36	3 TPP Silicibacter TM1040	1 TPP Silicibacter pomeroyi DSS-3	2 TPP Roseobacter sp. MED193	1 TPP Hyphomonas neptunium ATCC 15444	1 TPP Oceanicaulis alexandrii HTCC2633	Thiamine biosynthesis
RF00080	RNA	yybP-ykoY														1 yybP-ykoY Hyphomonas neptunium ATCC 15444
RF00114	RNA	S15	1 S15 Rhodobacter sphaeroides 2.4.1		1 S15 Jannaschia sp. CCS1			1 S15 Loktanella vestfoldensis SKA53		1 S15 Roseovarius nubinhibens ISM	1 S15 Roseovarius sp. 217	1 S15 Sulfitobacter sp. EE-36	1 S15 Silicibacter TM1040		1 S15 Roseobacter sp. MED193		1 S15 Oceanicaulis alexandrii HTCC2633	Ribosome biogenesis
RF00174	RNA	Cobalamin	6 Cobalamin Rhodobacter sphaeroides 2.4.1	10 Cobalamin Paracoccus denitrificans PD1222	2 Cobalamin Jannaschia sp. CCS1	1 Cobalamin Rhodobacterales bacterium HTCC2654	1 Cobalamin Oceanicola granulosus HTCC2516	1 Cobalamin Loktanella vestfoldensis SKA53	1 Cobalamin Oceanicola batsensis HTCC2597	4 Cobalamin Roseovarius nubinhibens ISM	2 Cobalamin Roseovarius sp. 217	4 Cobalamin Sulfitobacter sp. EE-36	6 Cobalamin Silicibacter TM1040	3 Cobalamin Silicibacter pomeroyi DSS-3	4 Cobalamin Roseobacter sp. MED193	2 Cobalamin Hyphomonas neptunium ATCC 15444	1 Cobalamin Oceanicaulis alexandrii HTCC2633	Cobalamin biosynthesis
RF00442	RNA	ykkC-yxkD	1 ykkC-yxkD Rhodobacter sphaeroides 2.4.1	1 ykkC-yxkD Paracoccus denitrificans PD1222		1 ykkC-yxkD Rhodobacterales bacterium HTCC2654												Multidrug resistance
RF00504	RNA	Glycine	1 Glycine Rhodobacter sphaeroides 2.4.1	2 Glycine Paracoccus denitrificans PD1222	1 Glycine Jannaschia sp. CCS1	1 Glycine Rhodobacterales bacterium HTCC2654	1 Glycine Oceanicola granulosus HTCC2516	1 Glycine Loktanella vestfoldensis SKA53	1 Glycine Oceanicola batsensis HTCC2597	1 Glycine Roseovarius nubinhibens ISM	1 Glycine Roseovarius sp. 217	1 Glycine Sulfitobacter sp. EE-36	1 Glycine Silicibacter TM1040		2 Glycine Roseobacter sp. MED193	1 Glycine Hyphomonas neptunium ATCC 15444	1 Glycine Oceanicaulis alexandrii HTCC2633	Glycine metabolism
RF00517	RNA	serC	1 serC Rhodobacter sphaeroides 2.4.1	1 serC Paracoccus denitrificans PD1222	1 serC Jannaschia sp. CCS1	1 serC Rhodobacterales bacterium HTCC2654	1 serC Oceanicola granulosus HTCC2516	1 serC Loktanella vestfoldensis SKA53	1 serC Oceanicola batsensis HTCC2597	1 serC Roseovarius nubinhibens ISM	1 serC Roseovarius sp. 217	1 serC Sulfitobacter sp. EE-36	1 serC Silicibacter TM1040	1 serC Silicibacter pomeroyi DSS-3	1 serC Roseobacter sp. MED193	1 serC Hyphomonas neptunium ATCC 15444		Serine biosynthesis
RF00521	RNA	SAM_alpha	1 SAM_alpha Rhodobacter sphaeroides 2.4.1		1 SAM_alpha Jannaschia sp. CCS1	1 SAM_alpha Rhodobacterales bacterium HTCC2654	1 SAM_alpha Oceanicola granulosus HTCC2516	1 SAM_alpha Loktanella vestfoldensis SKA53	1 SAM_alpha Oceanicola batsensis HTCC2597	1 SAM_alpha Roseovarius nubinhibens ISM	1 SAM_alpha Roseovarius sp. 217	1 SAM_alpha Sulfitobacter sp. EE-36	1 SAM_alpha Silicibacter TM1040	1 SAM_alpha Silicibacter pomeroyi DSS-3	1 SAM_alpha Roseobacter sp. MED193	1 SAM_alpha Hyphomonas neptunium ATCC 15444	1 SAM_alpha Oceanicaulis alexandrii HTCC2633	Methionine biosynthesis
RF00522	RNA	PreQ1									1 PreQ1 Roseovarius sp. 217							Queuosine biosynthesis
RF01055	RNA	MOCO_RNA_motif														1 MOCO_RNA_motif Hyphomonas neptunium ATCC 15444		Molybdopterin biosynthesis; Molybdenum homeostasis
RF01068	RNA	mini-ykkC			1 mini-ykkC Jannaschia sp. CCS1	1 mini-ykkC Rhodobacterales bacterium HTCC2654			2 mini-ykkC Oceanicola batsensis HTCC2597	1 mini-ykkC Roseovarius nubinhibens ISM	1 mini-ykkC Roseovarius sp. 217	1 mini-ykkC Sulfitobacter sp. EE-36	1 mini-ykkC Silicibacter TM1040			1 mini-ykkC Hyphomonas neptunium ATCC 15444	1 mini-ykkC Oceanicaulis alexandrii HTCC2633	Multidrug resistance
RF01727	RNA	SAM-SAH	1 SAM-SAH Rhodobacter sphaeroides 2.4.1	1 SAM-SAH Paracoccus denitrificans PD1222	1 SAM-SAH Jannaschia sp. CCS1	1 SAM-SAH Rhodobacterales bacterium HTCC2654	1 SAM-SAH Oceanicola granulosus HTCC2516	1 SAM-SAH Loktanella vestfoldensis SKA53	1 SAM-SAH Oceanicola batsensis HTCC2597	1 SAM-SAH Roseovarius nubinhibens ISM	1 SAM-SAH Roseovarius sp. 217	1 SAM-SAH Sulfitobacter sp. EE-36	1 SAM-SAH Silicibacter TM1040	1 SAM-SAH Silicibacter pomeroyi DSS-3	1 SAM-SAH Roseobacter sp. MED193			Methionine metabolism

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

Collection of regulogs in Rhodobacterales taxonomic group

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