Collection of regulogs in Various betaproteobacteria taxonomic group

General statistics
Genomes	12
TF regulogs	47
TF regulons	158
TF binding sites	425
RNA regulogs	4
RNA regulons	24
RNA sites	31

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
Azoarcus sp. EbN1	13	28	2	3	15	31
Chromobacterium violaceum ATCC 12472	26	91	3	4	29	95
Dechloromonas aromatica RCB	16	58	2	3	18	61
Laribacter hongkongensis HLHK9	16	48	2	2	18	50
Methylobacillus flagellatus KT	12	24	2	4	14	28
Methylophilales bacterium HTCC2181	6	14	2	2	8	16
Methylotenera mobilis JLW8	13	31	2	2	15	33
Neisseria meningitidis MC58	9	29	1	2	10	31
Nitrosomonas europaea ATCC 19718	9	15	2	2	11	17
Nitrosospira multiformis ATCC 25196	7	11	2	2	9	13
Thauera sp. MZ1T	20	54	2	3	22	57
Thiobacillus denitrificans	11	22	2	2	13	24

Genomic distribution of regulons
Family	Type	Regulator													Function
BirA	TF	BirA				1 BirA Nitrosomonas europaea ATCC 19718	2 BirA Nitrosospira multiformis ATCC 25196	2 BirA Thiobacillus denitrificans	2 BirA Chromobacterium violaceum ATCC 12472		2 BirA Laribacter hongkongensis HLHK9	1 BirA Methylobacillus flagellatus KT	2 BirA Methylotenera mobilis JLW8	1 BirA Methylophilales bacterium HTCC2181	Biotin biosynthesis
FUR	TF	Zur	1 Zur Azoarcus sp. EbN1	2 Zur Thauera sp. MZ1T		1 Zur Nitrosomonas europaea ATCC 19718	1 Zur Nitrosospira multiformis ATCC 25196					3 Zur Methylobacillus flagellatus KT			Zinc homeostasis
	TF	Zur2							1 Zur2 Chromobacterium violaceum ATCC 12472	3 Zur2 Neisseria meningitidis MC58	1 Zur2 Laribacter hongkongensis HLHK9				Zinc homeostasis
Fis	TF	NtrC	5 NtrC Azoarcus sp. EbN1	6 NtrC Thauera sp. MZ1T	5 NtrC Dechloromonas aromatica RCB			3 NtrC Thiobacillus denitrificans	3 NtrC Chromobacterium violaceum ATCC 12472		1 NtrC Laribacter hongkongensis HLHK9	2 NtrC Methylobacillus flagellatus KT	5 NtrC Methylotenera mobilis JLW8	3 NtrC Methylophilales bacterium HTCC2181	Nitrogen assimilation
GntR/MocR	TF	CV1517							1 CV1517 Chromobacterium violaceum ATCC 12472
	TF	CV1900							3 CV1900 Chromobacterium violaceum ATCC 12472						Metabolite transport
	TF	CV4096							1 CV4096 Chromobacterium violaceum ATCC 12472
	TF	Daro_1932			1 Daro_1932 Dechloromonas aromatica RCB						1 Daro_1932 Laribacter hongkongensis HLHK9
	TF	EbA483	2 EbA483 Azoarcus sp. EbN1
	TF	GabR		1 GabR Thauera sp. MZ1T											Gamma-aminobutyrate utilization
	TF	Mfla_0336										1 Mfla_0336 Methylobacillus flagellatus KT	1 Mfla_0336 Methylotenera mobilis JLW8
	TF	PdxR		1 PdxR Thauera sp. MZ1T											Pyridoxine/pyridoxal homeostasis
	TF	PdxW		1 PdxW Thauera sp. MZ1T											Pyridoxine/pyridoxal homeostasis
	TF	PdxW2											1 PdxW2 Methylotenera mobilis JLW8		Pyridoxine/pyridoxal homeostasis
	TF	YdcR		2 YdcR Thauera sp. MZ1T	3 YdcR Dechloromonas aromatica RCB			1 YdcR Thiobacillus denitrificans	1 YdcR Chromobacterium violaceum ATCC 12472		1 YdcR Laribacter hongkongensis HLHK9	2 YdcR Methylobacillus flagellatus KT	1 YdcR Methylotenera mobilis JLW8
GntR/Others	TF	GlcC	1 GlcC Azoarcus sp. EbN1			1 GlcC Nitrosomonas europaea ATCC 19718									Glycolate utilization
	TF	HutC							1 HutC Chromobacterium violaceum ATCC 12472						Histidine utilization
	TF	LldR		1 LldR Thauera sp. MZ1T	2 LldR Dechloromonas aromatica RCB				2 LldR Chromobacterium violaceum ATCC 12472	3 LldR Neisseria meningitidis MC58	2 LldR Laribacter hongkongensis HLHK9				Lactate utilization
	TF	MdcY			2 MdcY Dechloromonas aromatica RCB										Malonate metabolism
	TF	MlnR	2 MlnR Azoarcus sp. EbN1	4 MlnR Thauera sp. MZ1T	6 MlnR Dechloromonas aromatica RCB										Malonate metabolism
	TF	NagQ							9 NagQ Chromobacterium violaceum ATCC 12472						N-acetylglucosamine utilization
	TF	PhnF							2 PhnF Chromobacterium violaceum ATCC 12472		2 PhnF Laribacter hongkongensis HLHK9				Phosphonate utilization
	TF	SdhR	4 SdhR Azoarcus sp. EbN1	5 SdhR Thauera sp. MZ1T	5 SdhR Dechloromonas aromatica RCB				2 SdhR Chromobacterium violaceum ATCC 12472		2 SdhR Laribacter hongkongensis HLHK9		2 SdhR Methylotenera mobilis JLW8	2 SdhR Methylophilales bacterium HTCC2181	Tricarboxylic acid cycle
	TF	TreR							1 TreR Chromobacterium violaceum ATCC 12472						Trehalose utilization
HrcA	TF	HrcA	2 HrcA Azoarcus sp. EbN1	2 HrcA Thauera sp. MZ1T	2 HrcA Dechloromonas aromatica RCB	2 HrcA Nitrosomonas europaea ATCC 19718	1 HrcA Nitrosospira multiformis ATCC 25196	2 HrcA Thiobacillus denitrificans	2 HrcA Chromobacterium violaceum ATCC 12472		3 HrcA Laribacter hongkongensis HLHK9	2 HrcA Methylobacillus flagellatus KT	2 HrcA Methylotenera mobilis JLW8	2 HrcA Methylophilales bacterium HTCC2181	Heat shock response
LacI	TF	FruR2							2 FruR2 Chromobacterium violaceum ATCC 12472						Fructose utilization
	TF	GntR							1 GntR Chromobacterium violaceum ATCC 12472						Gluconate utilization
LexA	TF	LexA	1 LexA Azoarcus sp. EbN1	3 LexA Thauera sp. MZ1T	5 LexA Dechloromonas aromatica RCB			3 LexA Thiobacillus denitrificans							SOS response
LysR	TF	MetR				2 MetR Nitrosomonas europaea ATCC 19718	2 MetR Nitrosospira multiformis ATCC 25196	2 MetR Thiobacillus denitrificans	2 MetR Chromobacterium violaceum ATCC 12472	2 MetR Neisseria meningitidis MC58	2 MetR Laribacter hongkongensis HLHK9	2 MetR Methylobacillus flagellatus KT	2 MetR Methylotenera mobilis JLW8		Methionine biosynthesis
MerR	TF	CadR-PbrR		2 CadR-PbrR Thauera sp. MZ1T	2 CadR-PbrR Dechloromonas aromatica RCB				1 CadR-PbrR Chromobacterium violaceum ATCC 12472		1 CadR-PbrR Laribacter hongkongensis HLHK9	1 CadR-PbrR Methylobacillus flagellatus KT			Lead resistance; Cadmium resistance
	TF	CueR		1 CueR Thauera sp. MZ1T				1 CueR Thiobacillus denitrificans					3 CueR Methylotenera mobilis JLW8		Copper resistance
	TF	LiuR	2 LiuR Azoarcus sp. EbN1	6 LiuR Thauera sp. MZ1T	1 LiuR Dechloromonas aromatica RCB				6 LiuR Chromobacterium violaceum ATCC 12472		4 LiuR Laribacter hongkongensis HLHK9				Branched-chain amino acid degradation
	TF	MerR				1 MerR Nitrosomonas europaea ATCC 19718		1 MerR Thiobacillus denitrificans							Mercury resistance
	TF	NmlR								2 NmlR Neisseria meningitidis MC58					Carbonyl stress response
	TF	SoxR							1 SoxR Chromobacterium violaceum ATCC 12472						Superoxide stress response
ModE	TF	ModE			1 ModE Dechloromonas aromatica RCB						1 ModE Laribacter hongkongensis HLHK9				Molybdenum homeostasis
	TF	ModE2										2 ModE2 Methylobacillus flagellatus KT	2 ModE2 Methylotenera mobilis JLW8		Molybdopterin biosynthesis
NadQ	TF	NadQ								2 NadQ Neisseria meningitidis MC58					NAD biosynthesis
NikR	TF	NikR			1 NikR Dechloromonas aromatica RCB		1 NikR Nitrosospira multiformis ATCC 25196								Nickel homeostasis
NrdR	TF	NrdR	1 NrdR Azoarcus sp. EbN1	1 NrdR Thauera sp. MZ1T	1 NrdR Dechloromonas aromatica RCB	1 NrdR Nitrosomonas europaea ATCC 19718	1 NrdR Nitrosospira multiformis ATCC 25196	1 NrdR Thiobacillus denitrificans	3 NrdR Chromobacterium violaceum ATCC 12472	1 NrdR Neisseria meningitidis MC58	3 NrdR Laribacter hongkongensis HLHK9	2 NrdR Methylobacillus flagellatus KT	2 NrdR Methylotenera mobilis JLW8	1 NrdR Methylophilales bacterium HTCC2181	Deoxyribonucleotide biosynthesis
NrtR	TF	NrtR		2 NrtR Thauera sp. MZ1T					2 NrtR Chromobacterium violaceum ATCC 12472						NAD biosynthesis
RpiR	TF	HexR							3 HexR Chromobacterium violaceum ATCC 12472	4 HexR Neisseria meningitidis MC58					Central carbohydrate metabolism
Rrf2	TF	IscR	3 IscR Azoarcus sp. EbN1	2 IscR Thauera sp. MZ1T	2 IscR Dechloromonas aromatica RCB	1 IscR Nitrosomonas europaea ATCC 19718	2 IscR Nitrosospira multiformis ATCC 25196	3 IscR Thiobacillus denitrificans	1 IscR Chromobacterium violaceum ATCC 12472	1 IscR Neisseria meningitidis MC58	1 IscR Laribacter hongkongensis HLHK9	2 IscR Methylobacillus flagellatus KT	1 IscR Methylotenera mobilis JLW8	2 IscR Methylophilales bacterium HTCC2181	Iron-sulfur cluster biogenesis
	TF	NsrR								5 NsrR Neisseria meningitidis MC58					Nitrosative stress response
	TF	NsrR2		2 NsrR2 Thauera sp. MZ1T		2 NsrR2 Nitrosomonas europaea ATCC 19718		1 NsrR2 Thiobacillus denitrificans	4 NsrR2 Chromobacterium violaceum ATCC 12472			1 NsrR2 Methylobacillus flagellatus KT	2 NsrR2 Methylotenera mobilis JLW8		Nitrosative stress response
TetR	TF	PaaR	2 PaaR Azoarcus sp. EbN1	2 PaaR Thauera sp. MZ1T											Phenylacetic acid degradation
	TF	PsrA	1 PsrA Azoarcus sp. EbN1	1 PsrA Thauera sp. MZ1T	3 PsrA Dechloromonas aromatica RCB				10 PsrA Chromobacterium violaceum ATCC 12472		12 PsrA Laribacter hongkongensis HLHK9				Fatty acid degradation
RF00050	RNA	FMN							1 FMN Chromobacterium violaceum ATCC 12472						Riboflavin biosynthesis
RF00059	RNA	TPP	1 TPP Azoarcus sp. EbN1	1 TPP Thauera sp. MZ1T	1 TPP Dechloromonas aromatica RCB	1 TPP Nitrosomonas europaea ATCC 19718	1 TPP Nitrosospira multiformis ATCC 25196	1 TPP Thiobacillus denitrificans	2 TPP Chromobacterium violaceum ATCC 12472	2 TPP Neisseria meningitidis MC58	1 TPP Laribacter hongkongensis HLHK9	3 TPP Methylobacillus flagellatus KT	1 TPP Methylotenera mobilis JLW8	1 TPP Methylophilales bacterium HTCC2181	Thiamine biosynthesis
RF01055	RNA	MOCO_RNA_motif
RF01057	RNA	SAH_riboswitch	2 SAH_riboswitch Azoarcus sp. EbN1	2 SAH_riboswitch Thauera sp. MZ1T	2 SAH_riboswitch Dechloromonas aromatica RCB	1 SAH_riboswitch Nitrosomonas europaea ATCC 19718	1 SAH_riboswitch Nitrosospira multiformis ATCC 25196	1 SAH_riboswitch Thiobacillus denitrificans	1 SAH_riboswitch Chromobacterium violaceum ATCC 12472		1 SAH_riboswitch Laribacter hongkongensis HLHK9	1 SAH_riboswitch Methylobacillus flagellatus KT	1 SAH_riboswitch Methylotenera mobilis JLW8	1 SAH_riboswitch Methylophilales bacterium HTCC2181	Methionine metabolism

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

Collection of regulogs in Various betaproteobacteria taxonomic group

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