Collection of regulogs in Alteromonadales taxonomic group

General statistics
Genomes	9
TF regulogs	50
TF regulons	231
TF binding sites	1215
RNA regulogs	3
RNA regulons	13
RNA sites	17

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
Alteromonadales bacterium TW-7	26	158	1	1	27	159
Alteromonas macleodii 'Deep ecotype'	26	136	2	3	28	139
Colwellia psychrerythraea 34H	34	185	2	3	36	188
Glaciecola sp. HTCC2999	19	83	1	1	20	84
Idiomarina baltica OS145	21	82	1	1	22	83
Idiomarina loihiensis L2TR	19	97	1	2	20	99
Pseudoalteromonas atlantica T6c	28	163	2	3	30	166
Pseudoalteromonas haloplanktis TAC125	26	134	2	2	28	136
Pseudoalteromonas tunicata D2	32	177	1	1	33	178

Genomic distribution of regulons
Family	Type	Regulator										Function
ArgR	TF	ArgR	3 ArgR Pseudoalteromonas atlantica T6c	4 ArgR Alteromonas macleodii 'Deep ecotype'	3 ArgR Glaciecola sp. HTCC2999	5 ArgR Colwellia psychrerythraea 34H	5 ArgR Alteromonadales bacterium TW-7	4 ArgR Pseudoalteromonas haloplanktis TAC125	5 ArgR Pseudoalteromonas tunicata D2	4 ArgR Idiomarina baltica OS145	5 ArgR Idiomarina loihiensis L2TR	Arginine biosynthesis; Arginine degradation
BirA	TF	BirA	2 BirA Pseudoalteromonas atlantica T6c	2 BirA Alteromonas macleodii 'Deep ecotype'	2 BirA Glaciecola sp. HTCC2999	2 BirA Colwellia psychrerythraea 34H	2 BirA Alteromonadales bacterium TW-7	1 BirA Pseudoalteromonas haloplanktis TAC125	2 BirA Pseudoalteromonas tunicata D2	2 BirA Idiomarina baltica OS145	2 BirA Idiomarina loihiensis L2TR	Biotin biosynthesis
FUR	TF	Fur	17 Fur Pseudoalteromonas atlantica T6c	10 Fur Alteromonas macleodii 'Deep ecotype'	4 Fur Glaciecola sp. HTCC2999	10 Fur Colwellia psychrerythraea 34H	16 Fur Alteromonadales bacterium TW-7	15 Fur Pseudoalteromonas haloplanktis TAC125	20 Fur Pseudoalteromonas tunicata D2	10 Fur Idiomarina baltica OS145	18 Fur Idiomarina loihiensis L2TR	Iron homeostasis
	TF	Zur	7 Zur Pseudoalteromonas atlantica T6c	5 Zur Alteromonas macleodii 'Deep ecotype'	2 Zur Glaciecola sp. HTCC2999	4 Zur Colwellia psychrerythraea 34H	6 Zur Alteromonadales bacterium TW-7	3 Zur Pseudoalteromonas haloplanktis TAC125	4 Zur Pseudoalteromonas tunicata D2	2 Zur Idiomarina baltica OS145	3 Zur Idiomarina loihiensis L2TR	Zinc homeostasis
Fis	TF	NorR	2 NorR Pseudoalteromonas atlantica T6c			2 NorR Colwellia psychrerythraea 34H		2 NorR Pseudoalteromonas haloplanktis TAC125	2 NorR Pseudoalteromonas tunicata D2			Nitrosative stress response
	TF	NtrC	3 NtrC Pseudoalteromonas atlantica T6c	3 NtrC Alteromonas macleodii 'Deep ecotype'	3 NtrC Glaciecola sp. HTCC2999	3 NtrC Colwellia psychrerythraea 34H	3 NtrC Alteromonadales bacterium TW-7	3 NtrC Pseudoalteromonas haloplanktis TAC125	3 NtrC Pseudoalteromonas tunicata D2	2 NtrC Idiomarina baltica OS145	3 NtrC Idiomarina loihiensis L2TR	Nitrogen assimilation
GntR/MocR	TF	CPS_3393				1 CPS_3393 Colwellia psychrerythraea 34H						Metabolite transport
	TF	CPS_4612				1 CPS_4612 Colwellia psychrerythraea 34H		1 CPS_4612 Pseudoalteromonas haloplanktis TAC125	1 CPS_4612 Pseudoalteromonas tunicata D2			Metabolite transport
	TF	PTD2_03046							2 PTD2_03046 Pseudoalteromonas tunicata D2			Metabolite transport
	TF	PdxW				1 PdxW Colwellia psychrerythraea 34H			1 PdxW Pseudoalteromonas tunicata D2			Pyridoxine/pyridoxal homeostasis
GntR/Others	TF	CPS_0449				1 CPS_0449 Colwellia psychrerythraea 34H			1 CPS_0449 Pseudoalteromonas tunicata D2			Multidrug resistance; Multidrug efflux
	TF	FadR	5 FadR Pseudoalteromonas atlantica T6c	6 FadR Alteromonas macleodii 'Deep ecotype'	4 FadR Glaciecola sp. HTCC2999	3 FadR Colwellia psychrerythraea 34H	6 FadR Alteromonadales bacterium TW-7	5 FadR Pseudoalteromonas haloplanktis TAC125	5 FadR Pseudoalteromonas tunicata D2	2 FadR Idiomarina baltica OS145	3 FadR Idiomarina loihiensis L2TR	Fatty acid degradation
	TF	HutC	2 HutC Pseudoalteromonas atlantica T6c	2 HutC Alteromonas macleodii 'Deep ecotype'		5 HutC Colwellia psychrerythraea 34H	2 HutC Alteromonadales bacterium TW-7	2 HutC Pseudoalteromonas haloplanktis TAC125	2 HutC Pseudoalteromonas tunicata D2	2 HutC Idiomarina baltica OS145	3 HutC Idiomarina loihiensis L2TR	Histidine utilization
	TF	HypR				5 HypR Colwellia psychrerythraea 34H	6 HypR Alteromonadales bacterium TW-7		6 HypR Pseudoalteromonas tunicata D2			Proline and 4-hydrohyproline utilization
	TF	PdhR	1 PdhR Pseudoalteromonas atlantica T6c	1 PdhR Alteromonas macleodii 'Deep ecotype'	2 PdhR Glaciecola sp. HTCC2999	2 PdhR Colwellia psychrerythraea 34H	2 PdhR Alteromonadales bacterium TW-7	3 PdhR Pseudoalteromonas haloplanktis TAC125	2 PdhR Pseudoalteromonas tunicata D2	1 PdhR Idiomarina baltica OS145	1 PdhR Idiomarina loihiensis L2TR	Pyruvate metabolism
	TF	PrpR	1 PrpR Pseudoalteromonas atlantica T6c	1 PrpR Alteromonas macleodii 'Deep ecotype'	1 PrpR Glaciecola sp. HTCC2999	4 PrpR Colwellia psychrerythraea 34H	1 PrpR Alteromonadales bacterium TW-7	1 PrpR Pseudoalteromonas haloplanktis TAC125	1 PrpR Pseudoalteromonas tunicata D2	1 PrpR Idiomarina baltica OS145	1 PrpR Idiomarina loihiensis L2TR	Methylcitrate utilization
	TF	VanR	5 VanR Pseudoalteromonas atlantica T6c									Vanillate utilization
HrcA	TF	HrcA						1 HrcA Pseudoalteromonas haloplanktis TAC125	1 HrcA Pseudoalteromonas tunicata D2			Heat shock response
LacI	TF	BglR		2 BglR Alteromonas macleodii 'Deep ecotype'	4 BglR Glaciecola sp. HTCC2999	4 BglR Colwellia psychrerythraea 34H	6 BglR Alteromonadales bacterium TW-7		3 BglR Pseudoalteromonas tunicata D2	3 BglR Idiomarina baltica OS145		Beta-glucosides utilization
	TF	GalR		4 GalR Alteromonas macleodii 'Deep ecotype'				2 GalR Pseudoalteromonas haloplanktis TAC125				Galactose utilization
	TF	GntR						3 GntR Pseudoalteromonas haloplanktis TAC125				Gluconate utilization
	TF	MalR	7 MalR Pseudoalteromonas atlantica T6c	6 MalR Alteromonas macleodii 'Deep ecotype'	4 MalR Glaciecola sp. HTCC2999	7 MalR Colwellia psychrerythraea 34H	6 MalR Alteromonadales bacterium TW-7	4 MalR Pseudoalteromonas haloplanktis TAC125	5 MalR Pseudoalteromonas tunicata D2			Maltose utilization; Maltodextrin utilization
	TF	ManR1				3 ManR1 Colwellia psychrerythraea 34H	1 ManR1 Alteromonadales bacterium TW-7		2 ManR1 Pseudoalteromonas tunicata D2			Mannosides utilization; Mannose utilization
	TF	ManR2	3 ManR2 Pseudoalteromonas atlantica T6c									Mannosides utilization; Mannose utilization
	TF	NagR				11 NagR Colwellia psychrerythraea 34H	3 NagR Alteromonadales bacterium TW-7		9 NagR Pseudoalteromonas tunicata D2			N-acetylglucosamine utilization
	TF	Patl_0292	2 Patl_0292 Pseudoalteromonas atlantica T6c
	TF	ScrR	4 ScrR Pseudoalteromonas atlantica T6c	5 ScrR Alteromonas macleodii 'Deep ecotype'	5 ScrR Glaciecola sp. HTCC2999		3 ScrR Alteromonadales bacterium TW-7		3 ScrR Pseudoalteromonas tunicata D2			Sucrose utilization
	TF	Sde_0506	2 Sde_0506 Pseudoalteromonas atlantica T6c	2 Sde_0506 Alteromonas macleodii 'Deep ecotype'								Sugar utilization
	TF	TreR	3 TreR Pseudoalteromonas atlantica T6c			4 TreR Colwellia psychrerythraea 34H			3 TreR Pseudoalteromonas tunicata D2			Trehalose utilization
LexA	TF	LexA	11 LexA Pseudoalteromonas atlantica T6c	10 LexA Alteromonas macleodii 'Deep ecotype'	9 LexA Glaciecola sp. HTCC2999	12 LexA Colwellia psychrerythraea 34H	11 LexA Alteromonadales bacterium TW-7	12 LexA Pseudoalteromonas haloplanktis TAC125	11 LexA Pseudoalteromonas tunicata D2	5 LexA Idiomarina baltica OS145	6 LexA Idiomarina loihiensis L2TR	SOS response
LysR	TF	MetR				2 MetR Colwellia psychrerythraea 34H	4 MetR Alteromonadales bacterium TW-7	4 MetR Pseudoalteromonas haloplanktis TAC125	3 MetR Pseudoalteromonas tunicata D2			Methionine biosynthesis
MarR	TF	HmgS					2 HmgS Alteromonadales bacterium TW-7	2 HmgS Pseudoalteromonas haloplanktis TAC125	2 HmgS Pseudoalteromonas tunicata D2			Tyrosine degradation
MerR	TF	CadR-PbrR	1 CadR-PbrR Pseudoalteromonas atlantica T6c		1 CadR-PbrR Glaciecola sp. HTCC2999			1 CadR-PbrR Pseudoalteromonas haloplanktis TAC125		3 CadR-PbrR Idiomarina baltica OS145	3 CadR-PbrR Idiomarina loihiensis L2TR	Lead resistance; Cadmium resistance
	TF	CueR				1 CueR Colwellia psychrerythraea 34H						Copper resistance
	TF	LiuR	4 LiuR Pseudoalteromonas atlantica T6c	5 LiuR Alteromonas macleodii 'Deep ecotype'		5 LiuR Colwellia psychrerythraea 34H	10 LiuR Alteromonadales bacterium TW-7	9 LiuR Pseudoalteromonas haloplanktis TAC125	9 LiuR Pseudoalteromonas tunicata D2	4 LiuR Idiomarina baltica OS145	3 LiuR Idiomarina loihiensis L2TR	Branched-chain amino acid degradation
	TF	MerR		4 MerR Alteromonas macleodii 'Deep ecotype'						1 MerR Idiomarina baltica OS145	1 MerR Idiomarina loihiensis L2TR	Mercury resistance
	TF	NmlR				1 NmlR Colwellia psychrerythraea 34H						Carbonyl stress response
	TF	SoxR	1 SoxR Pseudoalteromonas atlantica T6c				1 SoxR Alteromonadales bacterium TW-7		1 SoxR Pseudoalteromonas tunicata D2			Superoxide stress response
MetJ	TF	MetJ	7 MetJ Pseudoalteromonas atlantica T6c	6 MetJ Alteromonas macleodii 'Deep ecotype'	6 MetJ Glaciecola sp. HTCC2999	9 MetJ Colwellia psychrerythraea 34H	8 MetJ Alteromonadales bacterium TW-7	9 MetJ Pseudoalteromonas haloplanktis TAC125	12 MetJ Pseudoalteromonas tunicata D2	6 MetJ Idiomarina baltica OS145	7 MetJ Idiomarina loihiensis L2TR	Methionine metabolism; Methionine biosynthesis
NrdR	TF	NrdR	1 NrdR Pseudoalteromonas atlantica T6c	2 NrdR Alteromonas macleodii 'Deep ecotype'	1 NrdR Glaciecola sp. HTCC2999	2 NrdR Colwellia psychrerythraea 34H	1 NrdR Alteromonadales bacterium TW-7	1 NrdR Pseudoalteromonas haloplanktis TAC125	1 NrdR Pseudoalteromonas tunicata D2	1 NrdR Idiomarina baltica OS145	2 NrdR Idiomarina loihiensis L2TR	Deoxyribonucleotide biosynthesis
RpiR	TF	HexR	9 HexR Pseudoalteromonas atlantica T6c	10 HexR Alteromonas macleodii 'Deep ecotype'	6 HexR Glaciecola sp. HTCC2999	4 HexR Colwellia psychrerythraea 34H				2 HexR Idiomarina baltica OS145		Central carbohydrate metabolism
Rrf2	TF	IscR	3 IscR Pseudoalteromonas atlantica T6c	3 IscR Alteromonas macleodii 'Deep ecotype'	3 IscR Glaciecola sp. HTCC2999	4 IscR Colwellia psychrerythraea 34H	4 IscR Alteromonadales bacterium TW-7	4 IscR Pseudoalteromonas haloplanktis TAC125	4 IscR Pseudoalteromonas tunicata D2	3 IscR Idiomarina baltica OS145	5 IscR Idiomarina loihiensis L2TR	Iron-sulfur cluster biogenesis
	TF	NsrR						2 NsrR Pseudoalteromonas haloplanktis TAC125				Nitrosative stress response
TetR	TF	FabR	4 FabR Pseudoalteromonas atlantica T6c	4 FabR Alteromonas macleodii 'Deep ecotype'	4 FabR Glaciecola sp. HTCC2999	2 FabR Colwellia psychrerythraea 34H	8 FabR Alteromonadales bacterium TW-7	7 FabR Pseudoalteromonas haloplanktis TAC125	5 FabR Pseudoalteromonas tunicata D2	3 FabR Idiomarina baltica OS145	4 FabR Idiomarina loihiensis L2TR	Fatty acid biosynthesis
	TF	PsrA		3 PsrA Alteromonas macleodii 'Deep ecotype'		8 PsrA Colwellia psychrerythraea 34H				6 PsrA Idiomarina baltica OS145	7 PsrA Idiomarina loihiensis L2TR	Fatty acid degradation
	TF	RutR	7 RutR Pseudoalteromonas atlantica T6c	6 RutR Alteromonas macleodii 'Deep ecotype'		3 RutR Colwellia psychrerythraea 34H	2 RutR Alteromonadales bacterium TW-7					Pyrimidine utilization
	TF	RutR2		2 RutR2 Alteromonas macleodii 'Deep ecotype'								Pyrimidine utilization
TyrR	TF	MdeR				2 MdeR Colwellia psychrerythraea 34H						Methionine metabolism
	TF	TyrR1	4 TyrR1 Pseudoalteromonas atlantica T6c	3 TyrR1 Alteromonas macleodii 'Deep ecotype'	2 TyrR1 Glaciecola sp. HTCC2999	3 TyrR1 Colwellia psychrerythraea 34H	4 TyrR1 Alteromonadales bacterium TW-7	4 TyrR1 Pseudoalteromonas haloplanktis TAC125	4 TyrR1 Pseudoalteromonas tunicata D2			Aromatic amino acid metabolism
	TF	TyrR2								3 TyrR2 Idiomarina baltica OS145	2 TyrR2 Idiomarina loihiensis L2TR	Tyrosine degradation; Aromatic amino acid metabolism
RF00050	RNA	FMN						1 FMN Pseudoalteromonas haloplanktis TAC125				Riboflavin biosynthesis
RF00059	RNA	TPP	2 TPP Pseudoalteromonas atlantica T6c	2 TPP Alteromonas macleodii 'Deep ecotype'	1 TPP Glaciecola sp. HTCC2999	2 TPP Colwellia psychrerythraea 34H	1 TPP Alteromonadales bacterium TW-7	1 TPP Pseudoalteromonas haloplanktis TAC125	1 TPP Pseudoalteromonas tunicata D2	1 TPP Idiomarina baltica OS145	2 TPP Idiomarina loihiensis L2TR
RF01055	RNA	MOCO_RNA_motif	1 MOCO_RNA_motif Pseudoalteromonas atlantica T6c	1 MOCO_RNA_motif Alteromonas macleodii 'Deep ecotype'		1 MOCO_RNA_motif Colwellia psychrerythraea 34H						Molybdenum homeostasis; Molybdopterin biosynthesis

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

Collection of regulogs in Alteromonadales taxonomic group

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