Collection of regulogs in Oceanospirillales/Alteromonadales taxonomic group

General statistics
Genomes	12
TF regulogs	72
TF regulons	247
TF binding sites	876
RNA regulogs	3
RNA regulons	16
RNA sites	29

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
Alcanivorax borkumensis SK2	15	45	0	0	15	45
Cellvibrio japonicus Ueda107	18	49	1	2	19	51
Chromohalobacter salexigens DSM 3043	30	109	1	2	31	111
Hahella chejuensis KCTC 2396	34	103	2	3	36	106
Marinobacter aqueolei	21	92	1	2	22	94
Marinobacter sp. ELB17	23	84	1	2	24	86
Marinomonas sp. MWYL1	28	106	2	4	30	110
Oceanobacter sp. RED65	11	41	1	2	12	43
Oceanospirillum sp. MED92	16	50	1	1	17	51
Reinekea sp. MED297	23	99	3	4	26	103
Saccharophagus degradans 2-40	16	53	1	3	17	56
Teredinibacter turnerae T7901	12	45	2	4	14	49

Genomic distribution of regulons
Family	Type	Regulator													Function
ArsR	TF	SahR	1 SahR Hahella chejuensis KCTC 2396	2 SahR Marinobacter aqueolei	2 SahR Marinobacter sp. ELB17	1 SahR Oceanobacter sp. RED65			2 SahR Saccharophagus degradans 2-40	2 SahR Teredinibacter turnerae T7901	2 SahR Cellvibrio japonicus Ueda107		2 SahR Reinekea sp. MED297	1 SahR Alcanivorax borkumensis SK2	Methionine metabolism
BirA	TF	BirA	2 BirA Hahella chejuensis KCTC 2396	2 BirA Marinobacter aqueolei	3 BirA Marinobacter sp. ELB17	1 BirA Oceanobacter sp. RED65		2 BirA Marinomonas sp. MWYL1	2 BirA Saccharophagus degradans 2-40	2 BirA Teredinibacter turnerae T7901	2 BirA Cellvibrio japonicus Ueda107	1 BirA Chromohalobacter salexigens DSM 3043	2 BirA Reinekea sp. MED297	2 BirA Alcanivorax borkumensis SK2	Biotin biosynthesis
FUR	TF	Zur	7 Zur Hahella chejuensis KCTC 2396	2 Zur Marinobacter aqueolei	4 Zur Marinobacter sp. ELB17	1 Zur Oceanobacter sp. RED65	6 Zur Oceanospirillum sp. MED92	4 Zur Marinomonas sp. MWYL1	3 Zur Saccharophagus degradans 2-40	3 Zur Teredinibacter turnerae T7901	3 Zur Cellvibrio japonicus Ueda107	4 Zur Chromohalobacter salexigens DSM 3043	3 Zur Reinekea sp. MED297	2 Zur Alcanivorax borkumensis SK2	Zinc homeostasis
Fis	TF	NorR	4 NorR Hahella chejuensis KCTC 2396					2 NorR Marinomonas sp. MWYL1		2 NorR Teredinibacter turnerae T7901		2 NorR Chromohalobacter salexigens DSM 3043			Nitrosative stress response
	TF	NtrC	4 NtrC Hahella chejuensis KCTC 2396	4 NtrC Marinobacter aqueolei	4 NtrC Marinobacter sp. ELB17	4 NtrC Oceanobacter sp. RED65	3 NtrC Oceanospirillum sp. MED92	3 NtrC Marinomonas sp. MWYL1	4 NtrC Saccharophagus degradans 2-40	5 NtrC Teredinibacter turnerae T7901	3 NtrC Cellvibrio japonicus Ueda107	4 NtrC Chromohalobacter salexigens DSM 3043	3 NtrC Reinekea sp. MED297	5 NtrC Alcanivorax borkumensis SK2	Nitrogen assimilation
GntR/MocR	TF	Csal_1101										2 Csal_1101 Chromohalobacter salexigens DSM 3043			Metabolite transport
	TF	EutR										2 EutR Chromohalobacter salexigens DSM 3043			Ectoine utilization
	TF	HCH_03332	1 HCH_03332 Hahella chejuensis KCTC 2396
	TF	MED92_15328					1 MED92_15328 Oceanospirillum sp. MED92	1 MED92_15328 Marinomonas sp. MWYL1
	TF	Mmwyl1_0258						1 Mmwyl1_0258 Marinomonas sp. MWYL1
	TF	Mmwyl1_0910	1 Mmwyl1_0910 Hahella chejuensis KCTC 2396					1 Mmwyl1_0910 Marinomonas sp. MWYL1							Metabolite transport
	TF	Mmwyl1_4437						1 Mmwyl1_4437 Marinomonas sp. MWYL1
	TF	PdxQ	1 PdxQ Hahella chejuensis KCTC 2396												Pyridoxine/pyridoxal homeostasis
	TF	PdxQ3										1 PdxQ3 Chromohalobacter salexigens DSM 3043			Metabolite transport; Pyridoxine/pyridoxal homeostasis
	TF	PdxW		1 PdxW Marinobacter aqueolei			1 PdxW Oceanospirillum sp. MED92								Pyridoxine/pyridoxal homeostasis
	TF	PdxW2										1 PdxW2 Chromohalobacter salexigens DSM 3043			Pyridoxine/pyridoxal homeostasis
	TF	TERTU_3902								1 TERTU_3902 Teredinibacter turnerae T7901					Multidrug efflux
	TF	TauR					1 TauR Oceanospirillum sp. MED92					2 TauR Chromohalobacter salexigens DSM 3043			Taurine utilization
	TF	YdcR	1 YdcR Hahella chejuensis KCTC 2396								1 YdcR Cellvibrio japonicus Ueda107
	TF	YjiR	1 YjiR Hahella chejuensis KCTC 2396				1 YjiR Oceanospirillum sp. MED92	1 YjiR Marinomonas sp. MWYL1					1 YjiR Reinekea sp. MED297		Metabolite transport
	TF	YjiR2	1 YjiR2 Hahella chejuensis KCTC 2396	1 YjiR2 Marinobacter aqueolei	1 YjiR2 Marinobacter sp. ELB17				1 YjiR2 Saccharophagus degradans 2-40		1 YjiR2 Cellvibrio japonicus Ueda107				Metabolite transport
GntR/Others	TF	CJA_0601									1 CJA_0601 Cellvibrio japonicus Ueda107				Hypothetical ABC transporter
	TF	CJA_1242									1 CJA_1242 Cellvibrio japonicus Ueda107			1 CJA_1242 Alcanivorax borkumensis SK2
	TF	CJA_2253									1 CJA_2253 Cellvibrio japonicus Ueda107				Alkanesulfonates utilization
	TF	Csal_1739										3 Csal_1739 Chromohalobacter salexigens DSM 3043
	TF	Csal_3199			2 Csal_3199 Marinobacter sp. ELB17							3 Csal_3199 Chromohalobacter salexigens DSM 3043			Glycolate utilization; Lactate utilization
	TF	DgoR										1 DgoR Chromohalobacter salexigens DSM 3043			Galactonate utilization
	TF	GlcC		2 GlcC Marinobacter aqueolei	2 GlcC Marinobacter sp. ELB17		2 GlcC Oceanospirillum sp. MED92								Glycolate utilization
	TF	HpxS			3 HpxS Marinobacter sp. ELB17			1 HpxS Marinomonas sp. MWYL1				3 HpxS Chromohalobacter salexigens DSM 3043			Allantoin utilization
	TF	HutC	1 HutC Hahella chejuensis KCTC 2396					4 HutC Marinomonas sp. MWYL1					2 HutC Reinekea sp. MED297		Histidine utilization
	TF	HypR	3 HypR Hahella chejuensis KCTC 2396									3 HypR Chromohalobacter salexigens DSM 3043			Proline and 4-hydrohyproline utilization
	TF	LldR		2 LldR Marinobacter aqueolei	2 LldR Marinobacter sp. ELB17			2 LldR Marinomonas sp. MWYL1				4 LldR Chromohalobacter salexigens DSM 3043			Lactate utilization
	TF	NagQ	2 NagQ Hahella chejuensis KCTC 2396					2 NagQ Marinomonas sp. MWYL1					5 NagQ Reinekea sp. MED297		N-acetylglucosamine utilization
	TF	PdhR	1 PdhR Hahella chejuensis KCTC 2396				1 PdhR Oceanospirillum sp. MED92								Pyruvate metabolism
	TF	PhnF		2 PhnF Marinobacter aqueolei											Phosphonate utilization
	TF	PhnR	4 PhnR Hahella chejuensis KCTC 2396												Phosphonate utilization; 2-aminoethylphosphonate utilization
	TF	PrpR	1 PrpR Hahella chejuensis KCTC 2396	2 PrpR Marinobacter aqueolei	1 PrpR Marinobacter sp. ELB17	1 PrpR Oceanobacter sp. RED65	2 PrpR Oceanospirillum sp. MED92	1 PrpR Marinomonas sp. MWYL1				2 PrpR Chromohalobacter salexigens DSM 3043	2 PrpR Reinekea sp. MED297	1 PrpR Alcanivorax borkumensis SK2	Methylcitrate utilization
	TF	RspR										1 RspR Chromohalobacter salexigens DSM 3043			L-gulonate utilization
	TF	Sde_3525							1 Sde_3525 Saccharophagus degradans 2-40						Multidrug resistance; Multidrug efflux
	TF	UxuR						3 UxuR Marinomonas sp. MWYL1							Glucuronate utilization
	TF	VanR						2 VanR Marinomonas sp. MWYL1				2 VanR Chromohalobacter salexigens DSM 3043			Vanillate utilization
HrcA	TF	HrcA												2 HrcA Alcanivorax borkumensis SK2	Heat shock response
LacI	TF	Csal_3216										2 Csal_3216 Chromohalobacter salexigens DSM 3043			Sugar utilization
	TF	FruR										5 FruR Chromohalobacter salexigens DSM 3043	2 FruR Reinekea sp. MED297		Fructose utilization
	TF	GntR	1 GntR Hahella chejuensis KCTC 2396					1 GntR Marinomonas sp. MWYL1				3 GntR Chromohalobacter salexigens DSM 3043			Gluconate utilization
	TF	IolR	1 IolR Hahella chejuensis KCTC 2396												Inositol utilization
	TF	NagR							4 NagR Saccharophagus degradans 2-40	3 NagR Teredinibacter turnerae T7901	7 NagR Cellvibrio japonicus Ueda107				N-acetylglucosamine utilization
	TF	ScrR							2 ScrR Saccharophagus degradans 2-40						Sucrose utilization
	TF	XltR	2 XltR Hahella chejuensis KCTC 2396					2 XltR Marinomonas sp. MWYL1							Xylitol utilization
LexA	TF	LexA	7 LexA Hahella chejuensis KCTC 2396	9 LexA Marinobacter aqueolei	7 LexA Marinobacter sp. ELB17	7 LexA Oceanobacter sp. RED65	8 LexA Oceanospirillum sp. MED92	11 LexA Marinomonas sp. MWYL1	8 LexA Saccharophagus degradans 2-40	8 LexA Teredinibacter turnerae T7901	4 LexA Cellvibrio japonicus Ueda107	4 LexA Chromohalobacter salexigens DSM 3043	9 LexA Reinekea sp. MED297	6 LexA Alcanivorax borkumensis SK2	SOS response
LysR	TF	MetR	2 MetR Hahella chejuensis KCTC 2396	2 MetR Marinobacter aqueolei	2 MetR Marinobacter sp. ELB17	3 MetR Oceanobacter sp. RED65	2 MetR Oceanospirillum sp. MED92	2 MetR Marinomonas sp. MWYL1	2 MetR Saccharophagus degradans 2-40	2 MetR Teredinibacter turnerae T7901	2 MetR Cellvibrio japonicus Ueda107	3 MetR Chromohalobacter salexigens DSM 3043	2 MetR Reinekea sp. MED297	2 MetR Alcanivorax borkumensis SK2	Methionine biosynthesis
MerR	TF	CadR-PbrR	1 CadR-PbrR Hahella chejuensis KCTC 2396	7 CadR-PbrR Marinobacter aqueolei	1 CadR-PbrR Marinobacter sp. ELB17		1 CadR-PbrR Oceanospirillum sp. MED92		1 CadR-PbrR Saccharophagus degradans 2-40		1 CadR-PbrR Cellvibrio japonicus Ueda107			1 CadR-PbrR Alcanivorax borkumensis SK2	Lead resistance; Cadmium resistance
	TF	CueR							3 CueR Saccharophagus degradans 2-40		4 CueR Cellvibrio japonicus Ueda107				Copper resistance
	TF	LiuR	2 LiuR Hahella chejuensis KCTC 2396	4 LiuR Marinobacter aqueolei	4 LiuR Marinobacter sp. ELB17		3 LiuR Oceanospirillum sp. MED92						3 LiuR Reinekea sp. MED297	2 LiuR Alcanivorax borkumensis SK2	Branched-chain amino acid degradation
	TF	MerR		3 MerR Marinobacter aqueolei	2 MerR Marinobacter sp. ELB17										Mercury resistance
	TF	SoxR	1 SoxR Hahella chejuensis KCTC 2396					1 SoxR Marinomonas sp. MWYL1					1 SoxR Reinekea sp. MED297		Superoxide stress response
	TF	ZntR					1 ZntR Oceanospirillum sp. MED92	1 ZntR Marinomonas sp. MWYL1				1 ZntR Chromohalobacter salexigens DSM 3043	1 ZntR Reinekea sp. MED297		Zinc resistance
ModE	TF	FdsR			2 FdsR Marinobacter sp. ELB17										Formate oxydation
	TF	ModE	1 ModE Hahella chejuensis KCTC 2396					1 ModE Marinomonas sp. MWYL1							Molybdenum homeostasis
NrdR	TF	NrdR	2 NrdR Hahella chejuensis KCTC 2396	2 NrdR Marinobacter aqueolei	2 NrdR Marinobacter sp. ELB17	1 NrdR Oceanobacter sp. RED65	1 NrdR Oceanospirillum sp. MED92	1 NrdR Marinomonas sp. MWYL1	2 NrdR Saccharophagus degradans 2-40	2 NrdR Teredinibacter turnerae T7901	1 NrdR Cellvibrio japonicus Ueda107	1 NrdR Chromohalobacter salexigens DSM 3043	2 NrdR Reinekea sp. MED297	1 NrdR Alcanivorax borkumensis SK2	Deoxyribonucleotide biosynthesis
NrtR	TF	NrtR	4 NrtR Hahella chejuensis KCTC 2396		2 NrtR Marinobacter sp. ELB17										NAD biosynthesis
ROK	TF	NagC											5 NagC Reinekea sp. MED297		N-acetylglucosamine utilization
RpiR	TF	EutR										2 EutR Chromohalobacter salexigens DSM 3043			Ethanolamine utilization
	TF	HexR						10 HexR Marinomonas sp. MWYL1				8 HexR Chromohalobacter salexigens DSM 3043	14 HexR Reinekea sp. MED297		Central carbohydrate metabolism
	TF	HexR2	4 HexR2 Hahella chejuensis KCTC 2396	4 HexR2 Marinobacter aqueolei	4 HexR2 Marinobacter sp. ELB17										Central carbohydrate metabolism
Rrf2	TF	IscR	3 IscR Hahella chejuensis KCTC 2396	4 IscR Marinobacter aqueolei	3 IscR Marinobacter sp. ELB17	3 IscR Oceanobacter sp. RED65	3 IscR Oceanospirillum sp. MED92	3 IscR Marinomonas sp. MWYL1	4 IscR Saccharophagus degradans 2-40	3 IscR Teredinibacter turnerae T7901	4 IscR Cellvibrio japonicus Ueda107	2 IscR Chromohalobacter salexigens DSM 3043	4 IscR Reinekea sp. MED297	4 IscR Alcanivorax borkumensis SK2	Iron-sulfur cluster biogenesis
	TF	NsrR							1 NsrR Saccharophagus degradans 2-40		2 NsrR Cellvibrio japonicus Ueda107		2 NsrR Reinekea sp. MED297	2 NsrR Alcanivorax borkumensis SK2	Nitrosative stress response
TetR	TF	FabR	1 FabR Hahella chejuensis KCTC 2396	5 FabR Marinobacter aqueolei	2 FabR Marinobacter sp. ELB17										Fatty acid biosynthesis
	TF	FabR2	2 FabR2 Hahella chejuensis KCTC 2396	1 FabR2 Marinobacter aqueolei									2 FabR2 Reinekea sp. MED297		Fatty acid biosynthesis
	TF	PsrA	7 PsrA Hahella chejuensis KCTC 2396	8 PsrA Marinobacter aqueolei	7 PsrA Marinobacter sp. ELB17	4 PsrA Oceanobacter sp. RED65			2 PsrA Saccharophagus degradans 2-40			11 PsrA Chromohalobacter salexigens DSM 3043	9 PsrA Reinekea sp. MED297	4 PsrA Alcanivorax borkumensis SK2	Fatty acid degradation
	TF	RutR	4 RutR Hahella chejuensis KCTC 2396		3 RutR Marinobacter sp. ELB17	3 RutR Oceanobacter sp. RED65		5 RutR Marinomonas sp. MWYL1		3 RutR Teredinibacter turnerae T7901	3 RutR Cellvibrio japonicus Ueda107	2 RutR Chromohalobacter salexigens DSM 3043	3 RutR Reinekea sp. MED297		Pyrimidine utilization
TrpR	TF	TrpR						1 TrpR Marinomonas sp. MWYL1					1 TrpR Reinekea sp. MED297		Tryptophan biosynthesis
RF00050	RNA	FMN	1 FMN Hahella chejuensis KCTC 2396					2 FMN Marinomonas sp. MWYL1					1 FMN Reinekea sp. MED297		Riboflavin biosynthesis
RF00059	RNA	TPP	2 TPP Hahella chejuensis KCTC 2396	2 TPP Marinobacter aqueolei	2 TPP Marinobacter sp. ELB17	2 TPP Oceanobacter sp. RED65	1 TPP Oceanospirillum sp. MED92	2 TPP Marinomonas sp. MWYL1	3 TPP Saccharophagus degradans 2-40	3 TPP Teredinibacter turnerae T7901	2 TPP Cellvibrio japonicus Ueda107	2 TPP Chromohalobacter salexigens DSM 3043	2 TPP Reinekea sp. MED297		Thiamine biosynthesis
RF01055	RNA	MOCO_RNA_motif								1 MOCO_RNA_motif Teredinibacter turnerae T7901			1 MOCO_RNA_motif Reinekea sp. MED297		Molybdopterin biosynthesis; Molybdenum homeostasis

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

Collection of regulogs in Oceanospirillales/Alteromonadales taxonomic group

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