Collection of regulogs in Rhodospirillales taxonomic group

General statistics
Genomes	9
TF regulogs	40
TF regulons	154
TF binding sites	528
RNA regulogs	3
RNA regulons	14
RNA sites	20

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
Acetobacter pasteurianus IFO 3283-01	13	44	2	3	15	47
Azospirillum sp. B510	27	87	1	3	28	90
Gluconacetobacter diazotrophicus PAl 5	18	49	2	2	20	51
Gluconobacter oxydans 621H	10	33	2	3	12	36
Granulibacter bethesdensis CGDNIH1	11	33	1	1	12	34
Magnetospirillum magneticum AMB-1	16	59	1	1	17	60
Magnetospirillum magnetotacticum MS-1	20	75	2	3	22	78
Rhodospirillum centenum SW	17	70	1	2	18	72
Rhodospirillum rubrum ATCC 11170	22	78	2	2	24	80

Genomic distribution of regulons
Family	Type	Regulator										Function
ArsR	TF	SahR	3 SahR Rhodospirillum rubrum ATCC 11170	2 SahR Magnetospirillum magneticum AMB-1	3 SahR Magnetospirillum magnetotacticum MS-1	2 SahR Azospirillum sp. B510	2 SahR Rhodospirillum centenum SW	2 SahR Gluconacetobacter diazotrophicus PAl 5			3 SahR Granulibacter bethesdensis CGDNIH1	Methionine metabolism
CRP	TF	FnrN	2 FnrN Rhodospirillum rubrum ATCC 11170	1 FnrN Magnetospirillum magneticum AMB-1	2 FnrN Magnetospirillum magnetotacticum MS-1	2 FnrN Azospirillum sp. B510	4 FnrN Rhodospirillum centenum SW	2 FnrN Gluconacetobacter diazotrophicus PAl 5	2 FnrN Acetobacter pasteurianus IFO 3283-01	2 FnrN Gluconobacter oxydans 621H		Oxidative stress response; Nitrogen fixation
	TF	NnrR					3 NnrR Rhodospirillum centenum SW					Denitrification
DtxR	TF	MntR				2 MntR Azospirillum sp. B510		2 MntR Gluconacetobacter diazotrophicus PAl 5	2 MntR Acetobacter pasteurianus IFO 3283-01	2 MntR Gluconobacter oxydans 621H		Manganese homeostasis
FUR	TF	Fur	21 Fur Rhodospirillum rubrum ATCC 11170	10 Fur Magnetospirillum magneticum AMB-1	11 Fur Magnetospirillum magnetotacticum MS-1	7 Fur Azospirillum sp. B510	10 Fur Rhodospirillum centenum SW	5 Fur Gluconacetobacter diazotrophicus PAl 5	13 Fur Acetobacter pasteurianus IFO 3283-01	6 Fur Gluconobacter oxydans 621H	7 Fur Granulibacter bethesdensis CGDNIH1	Iron homeostasis
	TF	Irr	2 Irr Rhodospirillum rubrum ATCC 11170	1 Irr Magnetospirillum magneticum AMB-1	4 Irr Magnetospirillum magnetotacticum MS-1	1 Irr Azospirillum sp. B510	4 Irr Rhodospirillum centenum SW					Iron homeostasis
	TF	Zur	1 Zur Rhodospirillum rubrum ATCC 11170	2 Zur Magnetospirillum magneticum AMB-1	3 Zur Magnetospirillum magnetotacticum MS-1	3 Zur Azospirillum sp. B510	3 Zur Rhodospirillum centenum SW	3 Zur Gluconacetobacter diazotrophicus PAl 5	3 Zur Acetobacter pasteurianus IFO 3283-01	5 Zur Gluconobacter oxydans 621H	4 Zur Granulibacter bethesdensis CGDNIH1	Zinc homeostasis
Fis	TF	NifA	6 NifA Rhodospirillum rubrum ATCC 11170	6 NifA Magnetospirillum magneticum AMB-1	6 NifA Magnetospirillum magnetotacticum MS-1	6 NifA Azospirillum sp. B510	5 NifA Rhodospirillum centenum SW	5 NifA Gluconacetobacter diazotrophicus PAl 5				Nitrogen fixation
	TF	NtrC	4 NtrC Rhodospirillum rubrum ATCC 11170	7 NtrC Magnetospirillum magneticum AMB-1	6 NtrC Magnetospirillum magnetotacticum MS-1	7 NtrC Azospirillum sp. B510	4 NtrC Rhodospirillum centenum SW	2 NtrC Gluconacetobacter diazotrophicus PAl 5	1 NtrC Acetobacter pasteurianus IFO 3283-01		2 NtrC Granulibacter bethesdensis CGDNIH1	Nitrogen assimilation
GntR/MocR	TF	OapR							2 OapR Acetobacter pasteurianus IFO 3283-01			Amino acid metabolism
	TF	PdxQ	1 PdxQ Rhodospirillum rubrum ATCC 11170									Pyridoxine/pyridoxal homeostasis
	TF	PdxQ2	4 PdxQ2 Rhodospirillum rubrum ATCC 11170					3 PdxQ2 Gluconacetobacter diazotrophicus PAl 5				Metabolite transport; Pyridoxine/pyridoxal homeostasis
	TF	PdxR	2 PdxR Rhodospirillum rubrum ATCC 11170									Pyridoxine/pyridoxal homeostasis
	TF	PdxW		1 PdxW Magnetospirillum magneticum AMB-1	1 PdxW Magnetospirillum magnetotacticum MS-1							Pyridoxine/pyridoxal homeostasis
	TF	YrdX3						1 YrdX3 Gluconacetobacter diazotrophicus PAl 5	1 YrdX3 Acetobacter pasteurianus IFO 3283-01
GntR/Others	TF	Gdia_0881						2 Gdia_0881 Gluconacetobacter diazotrophicus PAl 5
	TF	HutC	3 HutC Rhodospirillum rubrum ATCC 11170			2 HutC Azospirillum sp. B510	2 HutC Rhodospirillum centenum SW	2 HutC Gluconacetobacter diazotrophicus PAl 5		4 HutC Gluconobacter oxydans 621H		Histidine utilization
	TF	HypR	1 HypR Rhodospirillum rubrum ATCC 11170									Proline and 4-hydrohyproline utilization
	TF	LldR	2 LldR Rhodospirillum rubrum ATCC 11170	3 LldR Magnetospirillum magneticum AMB-1	4 LldR Magnetospirillum magnetotacticum MS-1	2 LldR Azospirillum sp. B510						Lactate utilization
	TF	MdcY		2 MdcY Magnetospirillum magneticum AMB-1	2 MdcY Magnetospirillum magnetotacticum MS-1							Malonate metabolism
	TF	NagQ				4 NagQ Azospirillum sp. B510						N-acetylglucosamine utilization
HrcA	TF	HrcA	1 HrcA Rhodospirillum rubrum ATCC 11170	1 HrcA Magnetospirillum magneticum AMB-1	1 HrcA Magnetospirillum magnetotacticum MS-1	1 HrcA Azospirillum sp. B510	1 HrcA Rhodospirillum centenum SW	1 HrcA Gluconacetobacter diazotrophicus PAl 5	1 HrcA Acetobacter pasteurianus IFO 3283-01	1 HrcA Gluconobacter oxydans 621H	1 HrcA Granulibacter bethesdensis CGDNIH1	Heat shock response
LacI	TF	AZL_a08610				2 AZL_a08610 Azospirillum sp. B510						Sugar utilization
	TF	FruR2	2 FruR2 Rhodospirillum rubrum ATCC 11170			2 FruR2 Azospirillum sp. B510					2 FruR2 Granulibacter bethesdensis CGDNIH1	Fructose utilization
	TF	GntR				2 GntR Azospirillum sp. B510						Gluconate utilization
LexA	TF	LexA	3 LexA Rhodospirillum rubrum ATCC 11170	5 LexA Magnetospirillum magneticum AMB-1	6 LexA Magnetospirillum magnetotacticum MS-1	6 LexA Azospirillum sp. B510	5 LexA Rhodospirillum centenum SW	6 LexA Gluconacetobacter diazotrophicus PAl 5	6 LexA Acetobacter pasteurianus IFO 3283-01	5 LexA Gluconobacter oxydans 621H	5 LexA Granulibacter bethesdensis CGDNIH1	SOS response
MerR	TF	CadR-PbrR	1 CadR-PbrR Rhodospirillum rubrum ATCC 11170		1 CadR-PbrR Magnetospirillum magnetotacticum MS-1	1 CadR-PbrR Azospirillum sp. B510						Lead resistance; Cadmium resistance
	TF	CueR		2 CueR Magnetospirillum magneticum AMB-1	4 CueR Magnetospirillum magnetotacticum MS-1	1 CueR Azospirillum sp. B510						Copper resistance
	TF	LiuR	4 LiuR Rhodospirillum rubrum ATCC 11170			3 LiuR Azospirillum sp. B510	3 LiuR Rhodospirillum centenum SW					Branched-chain amino acid degradation
	TF	SoxR				1 SoxR Azospirillum sp. B510						Superoxide stress response
ModE	TF	ModE		3 ModE Magnetospirillum magneticum AMB-1	3 ModE Magnetospirillum magnetotacticum MS-1							Molybdopterin biosynthesis
	TF	ModE2				1 ModE2 Azospirillum sp. B510	1 ModE2 Rhodospirillum centenum SW					Molybdenum homeostasis
NadQ	TF	NadQ	1 NadQ Rhodospirillum rubrum ATCC 11170		1 NadQ Magnetospirillum magnetotacticum MS-1	1 NadQ Azospirillum sp. B510	1 NadQ Rhodospirillum centenum SW	1 NadQ Gluconacetobacter diazotrophicus PAl 5	1 NadQ Acetobacter pasteurianus IFO 3283-01		1 NadQ Granulibacter bethesdensis CGDNIH1	NAD biosynthesis
NikR	TF	NikR				2 NikR Azospirillum sp. B510						Nickel homeostasis
NrdR	TF	NrdR	2 NrdR Rhodospirillum rubrum ATCC 11170	1 NrdR Magnetospirillum magneticum AMB-1	1 NrdR Magnetospirillum magnetotacticum MS-1	1 NrdR Azospirillum sp. B510	3 NrdR Rhodospirillum centenum SW	2 NrdR Gluconacetobacter diazotrophicus PAl 5	1 NrdR Acetobacter pasteurianus IFO 3283-01	1 NrdR Gluconobacter oxydans 621H	2 NrdR Granulibacter bethesdensis CGDNIH1	Deoxyribonucleotide biosynthesis
Rrf2	TF	IscR	1 IscR Rhodospirillum rubrum ATCC 11170	1 IscR Magnetospirillum magneticum AMB-1	1 IscR Magnetospirillum magnetotacticum MS-1	1 IscR Azospirillum sp. B510	1 IscR Rhodospirillum centenum SW					Iron-sulfur cluster biogenesis
	TF	IscR2	1 IscR2 Rhodospirillum rubrum ATCC 11170			1 IscR2 Azospirillum sp. B510	1 IscR2 Rhodospirillum centenum SW	1 IscR2 Gluconacetobacter diazotrophicus PAl 5	1 IscR2 Acetobacter pasteurianus IFO 3283-01	1 IscR2 Gluconobacter oxydans 621H	1 IscR2 Granulibacter bethesdensis CGDNIH1	Iron-sulfur cluster biogenesis
	TF	NsrR			2 NsrR Magnetospirillum magnetotacticum MS-1			2 NsrR Gluconacetobacter diazotrophicus PAl 5	3 NsrR Acetobacter pasteurianus IFO 3283-01	2 NsrR Gluconobacter oxydans 621H	2 NsrR Granulibacter bethesdensis CGDNIH1	Nitrosative stress response
SdaR	TF	SdaR				1 SdaR Azospirillum sp. B510		2 SdaR Gluconacetobacter diazotrophicus PAl 5				Glycerate utilization
TetR	TF	RutR			1 RutR Magnetospirillum magnetotacticum MS-1							Pyrimidine utilization
RF00050	RNA	FMN	1 FMN Rhodospirillum rubrum ATCC 11170					1 FMN Gluconacetobacter diazotrophicus PAl 5	1 FMN Acetobacter pasteurianus IFO 3283-01	1 FMN Gluconobacter oxydans 621H		Riboflavin biosynthesis
RF00059	RNA	TPP	1 TPP Rhodospirillum rubrum ATCC 11170	1 TPP Magnetospirillum magneticum AMB-1	2 TPP Magnetospirillum magnetotacticum MS-1	3 TPP Azospirillum sp. B510	2 TPP Rhodospirillum centenum SW	1 TPP Gluconacetobacter diazotrophicus PAl 5	2 TPP Acetobacter pasteurianus IFO 3283-01	2 TPP Gluconobacter oxydans 621H	1 TPP Granulibacter bethesdensis CGDNIH1	Thiamine biosynthesis
RF01055	RNA	MOCO_RNA_motif			1 MOCO_RNA_motif Magnetospirillum magnetotacticum MS-1							Molybdopterin biosynthesis

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

Collection of regulogs in Rhodospirillales taxonomic group

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