Collection of regulogs in Psychromonadaceae/Aeromonadales taxonomic group

General statistics
Genomes	6
TF regulogs	56
TF regulons	194
TF binding sites	965
RNA regulogs	3
RNA regulons	16
RNA sites	24

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
Aeromonas hydrophila subsp. hydrophila ATCC 7966	41	239	3	4	44	243
Aeromonas salmonicida subsp. salmonicida A449	37	218	3	4	40	222
Moritella sp. PE36	32	183	3	5	35	188
Psychromonas ingrahamii 37	31	114	2	4	33	118
Psychromonas sp. CNPT3	27	106	2	3	29	109
Tolumonas auensis DSM 9187	26	105	3	4	29	109

Genomic distribution of regulons
Family	Type	Regulator							Function
ArgR	TF	ArgR	7 ArgR Psychromonas ingrahamii 37	4 ArgR Psychromonas sp. CNPT3	5 ArgR Moritella sp. PE36	7 ArgR Aeromonas hydrophila subsp. hydrophila ATCC 7966	7 ArgR Aeromonas salmonicida subsp. salmonicida A449	6 ArgR Tolumonas auensis DSM 9187	Arginine degradation; Arginine biosynthesis
BirA	TF	BirA	2 BirA Psychromonas ingrahamii 37	2 BirA Psychromonas sp. CNPT3	2 BirA Moritella sp. PE36	2 BirA Aeromonas hydrophila subsp. hydrophila ATCC 7966	2 BirA Aeromonas salmonicida subsp. salmonicida A449	2 BirA Tolumonas auensis DSM 9187	Biotin biosynthesis
DeoR	TF	AgaR		2 AgaR Psychromonas sp. CNPT3		2 AgaR Aeromonas hydrophila subsp. hydrophila ATCC 7966			N-acetylgalactosamine utilization
FUR	TF	Fur	3 Fur Psychromonas ingrahamii 37	8 Fur Psychromonas sp. CNPT3	23 Fur Moritella sp. PE36	24 Fur Aeromonas hydrophila subsp. hydrophila ATCC 7966	24 Fur Aeromonas salmonicida subsp. salmonicida A449	8 Fur Tolumonas auensis DSM 9187	Iron homeostasis
	TF	Zur	1 Zur Psychromonas ingrahamii 37	2 Zur Psychromonas sp. CNPT3	5 Zur Moritella sp. PE36	3 Zur Aeromonas hydrophila subsp. hydrophila ATCC 7966	3 Zur Aeromonas salmonicida subsp. salmonicida A449	2 Zur Tolumonas auensis DSM 9187	Zinc homeostasis
Fis	TF	NorR			3 NorR Moritella sp. PE36	2 NorR Aeromonas hydrophila subsp. hydrophila ATCC 7966	2 NorR Aeromonas salmonicida subsp. salmonicida A449		Nitrosative stress response
	TF	NtrC	2 NtrC Psychromonas ingrahamii 37	2 NtrC Psychromonas sp. CNPT3	3 NtrC Moritella sp. PE36	4 NtrC Aeromonas hydrophila subsp. hydrophila ATCC 7966	5 NtrC Aeromonas salmonicida subsp. salmonicida A449	4 NtrC Tolumonas auensis DSM 9187	Nitrogen assimilation
GntR/MocR	TF	AHA_3778				1 AHA_3778 Aeromonas hydrophila subsp. hydrophila ATCC 7966	1 AHA_3778 Aeromonas salmonicida subsp. salmonicida A449
	TF	GabR	1 GabR Psychromonas ingrahamii 37						Gamma-aminobutyrate utilization
	TF	PE36_10153			1 PE36_10153 Moritella sp. PE36				Metabolite transport
	TF	TauR	2 TauR Psychromonas ingrahamii 37						Taurine utilization
	TF	Tola_2572		2 Tola_2572 Psychromonas sp. CNPT3	2 Tola_2572 Moritella sp. PE36			2 Tola_2572 Tolumonas auensis DSM 9187
	TF	Tola_2750				2 Tola_2750 Aeromonas hydrophila subsp. hydrophila ATCC 7966		2 Tola_2750 Tolumonas auensis DSM 9187	Metabolite transport
	TF	YdcR				1 YdcR Aeromonas hydrophila subsp. hydrophila ATCC 7966	1 YdcR Aeromonas salmonicida subsp. salmonicida A449
GntR/Others	TF	FadR	1 FadR Psychromonas ingrahamii 37	1 FadR Psychromonas sp. CNPT3	2 FadR Moritella sp. PE36	3 FadR Aeromonas hydrophila subsp. hydrophila ATCC 7966	3 FadR Aeromonas salmonicida subsp. salmonicida A449		Fatty acid degradation
	TF	HutC	3 HutC Psychromonas ingrahamii 37		2 HutC Moritella sp. PE36	1 HutC Aeromonas hydrophila subsp. hydrophila ATCC 7966	2 HutC Aeromonas salmonicida subsp. salmonicida A449		Histidine utilization
	TF	HypR	2 HypR Psychromonas ingrahamii 37			2 HypR Aeromonas hydrophila subsp. hydrophila ATCC 7966	2 HypR Aeromonas salmonicida subsp. salmonicida A449		Proline and 4-hydrohyproline utilization
	TF	PCNPT3_10213		1 PCNPT3_10213 Psychromonas sp. CNPT3					Multidrug resistance; Multidrug efflux
	TF	PdhR	1 PdhR Psychromonas ingrahamii 37	1 PdhR Psychromonas sp. CNPT3	1 PdhR Moritella sp. PE36	1 PdhR Aeromonas hydrophila subsp. hydrophila ATCC 7966	1 PdhR Aeromonas salmonicida subsp. salmonicida A449	1 PdhR Tolumonas auensis DSM 9187	Pyruvate metabolism
	TF	PhnF	1 PhnF Psychromonas ingrahamii 37						Phosphonate utilization
	TF	PhnR	2 PhnR Psychromonas ingrahamii 37	2 PhnR Psychromonas sp. CNPT3	3 PhnR Moritella sp. PE36	4 PhnR Aeromonas hydrophila subsp. hydrophila ATCC 7966			Phosphonate utilization; 2-aminoethylphosphonate utilization
	TF	PhnR1				2 PhnR1 Aeromonas hydrophila subsp. hydrophila ATCC 7966	2 PhnR1 Aeromonas salmonicida subsp. salmonicida A449		2-aminoethylphosphonate utilization
	TF	PrpR	1 PrpR Psychromonas ingrahamii 37		2 PrpR Moritella sp. PE36				Methylcitrate utilization
	TF	UxuR	4 UxuR Psychromonas ingrahamii 37	2 UxuR Psychromonas sp. CNPT3				4 UxuR Tolumonas auensis DSM 9187	Glucuronate utilization
LacI	TF	EbgR		1 EbgR Psychromonas sp. CNPT3		2 EbgR Aeromonas hydrophila subsp. hydrophila ATCC 7966			Galactosides utilization
	TF	FruR	2 FruR Psychromonas ingrahamii 37	2 FruR Psychromonas sp. CNPT3	2 FruR Moritella sp. PE36	2 FruR Aeromonas hydrophila subsp. hydrophila ATCC 7966	2 FruR Aeromonas salmonicida subsp. salmonicida A449	2 FruR Tolumonas auensis DSM 9187	Fructose utilization
	TF	GntR	3 GntR Psychromonas ingrahamii 37		3 GntR Moritella sp. PE36	3 GntR Aeromonas hydrophila subsp. hydrophila ATCC 7966	3 GntR Aeromonas salmonicida subsp. salmonicida A449	2 GntR Tolumonas auensis DSM 9187	Gluconate utilization
	TF	ManR				3 ManR Aeromonas hydrophila subsp. hydrophila ATCC 7966			Mannose utilization
	TF	RbsR	1 RbsR Psychromonas ingrahamii 37	1 RbsR Psychromonas sp. CNPT3	1 RbsR Moritella sp. PE36	1 RbsR Aeromonas hydrophila subsp. hydrophila ATCC 7966	1 RbsR Aeromonas salmonicida subsp. salmonicida A449	1 RbsR Tolumonas auensis DSM 9187	Ribose utilization
	TF	ScrR				2 ScrR Aeromonas hydrophila subsp. hydrophila ATCC 7966	2 ScrR Aeromonas salmonicida subsp. salmonicida A449	1 ScrR Tolumonas auensis DSM 9187	Sucrose utilization
	TF	SgaR	2 SgaR Psychromonas ingrahamii 37			2 SgaR Aeromonas hydrophila subsp. hydrophila ATCC 7966	2 SgaR Aeromonas salmonicida subsp. salmonicida A449		Ascorbate utilization
	TF	TreR	1 TreR Psychromonas ingrahamii 37			1 TreR Aeromonas hydrophila subsp. hydrophila ATCC 7966	1 TreR Aeromonas salmonicida subsp. salmonicida A449	1 TreR Tolumonas auensis DSM 9187	Trehalose utilization
LexA	TF	LexA	8 LexA Psychromonas ingrahamii 37	11 LexA Psychromonas sp. CNPT3	12 LexA Moritella sp. PE36	11 LexA Aeromonas hydrophila subsp. hydrophila ATCC 7966	10 LexA Aeromonas salmonicida subsp. salmonicida A449	8 LexA Tolumonas auensis DSM 9187	SOS response
LuxR	TF	NarP		2 NarP Psychromonas sp. CNPT3	12 NarP Moritella sp. PE36	16 NarP Aeromonas hydrophila subsp. hydrophila ATCC 7966	15 NarP Aeromonas salmonicida subsp. salmonicida A449		Nitrate and nitrite respiration
LysR	TF	MetR	2 MetR Psychromonas ingrahamii 37		2 MetR Moritella sp. PE36	2 MetR Aeromonas hydrophila subsp. hydrophila ATCC 7966	2 MetR Aeromonas salmonicida subsp. salmonicida A449	2 MetR Tolumonas auensis DSM 9187	Methionine biosynthesis
MerR	TF	CadR-PbrR						1 CadR-PbrR Tolumonas auensis DSM 9187	Lead resistance; Cadmium resistance
	TF	CueR	2 CueR Psychromonas ingrahamii 37	2 CueR Psychromonas sp. CNPT3	3 CueR Moritella sp. PE36	1 CueR Aeromonas hydrophila subsp. hydrophila ATCC 7966	1 CueR Aeromonas salmonicida subsp. salmonicida A449	2 CueR Tolumonas auensis DSM 9187	Copper resistance
	TF	LiuR				7 LiuR Aeromonas hydrophila subsp. hydrophila ATCC 7966	7 LiuR Aeromonas salmonicida subsp. salmonicida A449		Branched-chain amino acid degradation
	TF	MerR	1 MerR Psychromonas ingrahamii 37				1 MerR Aeromonas salmonicida subsp. salmonicida A449		Mercury resistance
	TF	PhrR				1 PhrR Aeromonas hydrophila subsp. hydrophila ATCC 7966	1 PhrR Aeromonas salmonicida subsp. salmonicida A449		Light-dependent DNA repair
	TF	SoxR			1 SoxR Moritella sp. PE36	1 SoxR Aeromonas hydrophila subsp. hydrophila ATCC 7966	1 SoxR Aeromonas salmonicida subsp. salmonicida A449		Superoxide stress response
	TF	ZntR		1 ZntR Psychromonas sp. CNPT3		1 ZntR Aeromonas hydrophila subsp. hydrophila ATCC 7966	1 ZntR Aeromonas salmonicida subsp. salmonicida A449		Zinc resistance
MetJ	TF	MetJ	4 MetJ Psychromonas ingrahamii 37	5 MetJ Psychromonas sp. CNPT3	8 MetJ Moritella sp. PE36	14 MetJ Aeromonas hydrophila subsp. hydrophila ATCC 7966	14 MetJ Aeromonas salmonicida subsp. salmonicida A449	7 MetJ Tolumonas auensis DSM 9187	Methionine metabolism; Methionine biosynthesis
ModE	TF	ModE			1 ModE Moritella sp. PE36			2 ModE Tolumonas auensis DSM 9187	Molybdenum homeostasis
NrdR	TF	NrdR	3 NrdR Psychromonas ingrahamii 37	2 NrdR Psychromonas sp. CNPT3	2 NrdR Moritella sp. PE36	3 NrdR Aeromonas hydrophila subsp. hydrophila ATCC 7966	3 NrdR Aeromonas salmonicida subsp. salmonicida A449	2 NrdR Tolumonas auensis DSM 9187	Deoxyribonucleotide biosynthesis
NrtR	TF	NrtR				2 NrtR Aeromonas hydrophila subsp. hydrophila ATCC 7966	2 NrtR Aeromonas salmonicida subsp. salmonicida A449	2 NrtR Tolumonas auensis DSM 9187	NAD biosynthesis
ROK	TF	NagC	1 NagC Psychromonas ingrahamii 37	2 NagC Psychromonas sp. CNPT3	4 NagC Moritella sp. PE36	3 NagC Aeromonas hydrophila subsp. hydrophila ATCC 7966	3 NagC Aeromonas salmonicida subsp. salmonicida A449	2 NagC Tolumonas auensis DSM 9187	N-acetylglucosamine utilization
RpiR	TF	HexR	11 HexR Psychromonas ingrahamii 37	8 HexR Psychromonas sp. CNPT3	7 HexR Moritella sp. PE36	18 HexR Aeromonas hydrophila subsp. hydrophila ATCC 7966	18 HexR Aeromonas salmonicida subsp. salmonicida A449	6 HexR Tolumonas auensis DSM 9187	Central carbohydrate metabolism
	TF	SiaR		6 SiaR Psychromonas sp. CNPT3					Sialic acid utilization
Rrf2	TF	IscR	2 IscR Psychromonas ingrahamii 37	2 IscR Psychromonas sp. CNPT3	2 IscR Moritella sp. PE36	2 IscR Aeromonas hydrophila subsp. hydrophila ATCC 7966	2 IscR Aeromonas salmonicida subsp. salmonicida A449	2 IscR Tolumonas auensis DSM 9187	Iron-sulfur cluster biogenesis
	TF	NsrR	2 NsrR Psychromonas ingrahamii 37	2 NsrR Psychromonas sp. CNPT3					Nitrosative stress response
TetR	TF	FabR	2 FabR Psychromonas ingrahamii 37		7 FabR Moritella sp. PE36	7 FabR Aeromonas hydrophila subsp. hydrophila ATCC 7966	7 FabR Aeromonas salmonicida subsp. salmonicida A449		Fatty acid biosynthesis
	TF	PsrA			6 PsrA Moritella sp. PE36	4 PsrA Aeromonas hydrophila subsp. hydrophila ATCC 7966	4 PsrA Aeromonas salmonicida subsp. salmonicida A449		Fatty acid degradation
	TF	RutR			4 RutR Moritella sp. PE36				Pyrimidine utilization
TrpR	TF	TrpR		1 TrpR Psychromonas sp. CNPT3	1 TrpR Moritella sp. PE36				Tryptophan biosynthesis
TyrR	TF	TyrR			2 TyrR Moritella sp. PE36	4 TyrR Aeromonas hydrophila subsp. hydrophila ATCC 7966	4 TyrR Aeromonas salmonicida subsp. salmonicida A449	1 TyrR Tolumonas auensis DSM 9187	Aromatic amino acid metabolism
RF00050	RNA	FMN		1 FMN Psychromonas sp. CNPT3	1 FMN Moritella sp. PE36	1 FMN Aeromonas hydrophila subsp. hydrophila ATCC 7966	1 FMN Aeromonas salmonicida subsp. salmonicida A449	1 FMN Tolumonas auensis DSM 9187	Riboflavin biosynthesis
RF00059	RNA	TPP	3 TPP Psychromonas ingrahamii 37	2 TPP Psychromonas sp. CNPT3	3 TPP Moritella sp. PE36	2 TPP Aeromonas hydrophila subsp. hydrophila ATCC 7966	2 TPP Aeromonas salmonicida subsp. salmonicida A449	2 TPP Tolumonas auensis DSM 9187	Thiamine biosynthesis
RF01055	RNA	MOCO_RNA_motif	1 MOCO_RNA_motif Psychromonas ingrahamii 37		1 MOCO_RNA_motif Moritella sp. PE36	1 MOCO_RNA_motif Aeromonas hydrophila subsp. hydrophila ATCC 7966	1 MOCO_RNA_motif Aeromonas salmonicida subsp. salmonicida A449	1 MOCO_RNA_motif Tolumonas auensis DSM 9187	Molybdopterin biosynthesis

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

Collection of regulogs in Psychromonadaceae/Aeromonadales taxonomic group

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