Collection of regulogs in Bacteroidaceae taxonomic group

General statistics
Genomes	11
TF regulogs	38
TF regulons	223
TF binding sites	704
RNA regulogs	2
RNA regulons	22
RNA sites	84

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
Bacteroides cellulosilyticus DSM 14838	24	65	2	10	26	75
Bacteroides coprophilus DSM 18228	9	20	2	4	11	24
Bacteroides dorei DSM 17855	19	68	2	9	21	77
Bacteroides eggerthii DSM 20697	18	64	2	5	20	69
Bacteroides fragilis NCTC 9343	15	52	2	9	17	61
Bacteroides ovatus ATCC 8483	30	88	2	9	32	97
Bacteroides plebeius DSM 17135	20	51	2	5	22	56
Bacteroides stercoris ATCC 43183	16	55	2	7	18	62
Bacteroides thetaiotaomicron VPI-5482	36	109	2	9	38	118
Bacteroides uniformis ATCC 8492	17	60	2	7	19	67
Bacteroides vulgatus ATCC 8482	19	72	2	10	21	82

Genomic distribution of regulons
Family	Type	Regulator												Function
AraC	TF	RhaR	1 RhaR Bacteroides thetaiotaomicron VPI-5482	1 RhaR Bacteroides vulgatus ATCC 8482		1 RhaR Bacteroides dorei DSM 17855	1 RhaR Bacteroides eggerthii DSM 20697		1 RhaR Bacteroides uniformis ATCC 8492	1 RhaR Bacteroides cellulosilyticus DSM 14838		1 RhaR Bacteroides ovatus ATCC 8483	1 RhaR Bacteroides stercoris ATCC 43183	Rhamnose utilization
ArgR	TF	ArgR	1 ArgR Bacteroides thetaiotaomicron VPI-5482	1 ArgR Bacteroides vulgatus ATCC 8482	1 ArgR Bacteroides coprophilus DSM 18228	1 ArgR Bacteroides dorei DSM 17855	1 ArgR Bacteroides eggerthii DSM 20697	1 ArgR Bacteroides fragilis NCTC 9343	1 ArgR Bacteroides uniformis ATCC 8492	1 ArgR Bacteroides cellulosilyticus DSM 14838	1 ArgR Bacteroides plebeius DSM 17135	1 ArgR Bacteroides ovatus ATCC 8483	1 ArgR Bacteroides stercoris ATCC 43183	Arginine biosynthesis
CRP	TF	Crp	13 Crp Bacteroides thetaiotaomicron VPI-5482	10 Crp Bacteroides vulgatus ATCC 8482	3 Crp Bacteroides coprophilus DSM 18228	10 Crp Bacteroides dorei DSM 17855	11 Crp Bacteroides eggerthii DSM 20697	11 Crp Bacteroides fragilis NCTC 9343	12 Crp Bacteroides uniformis ATCC 8492	11 Crp Bacteroides cellulosilyticus DSM 14838	4 Crp Bacteroides plebeius DSM 17135	11 Crp Bacteroides ovatus ATCC 8483	9 Crp Bacteroides stercoris ATCC 43183
	TF	HcpR	1 HcpR Bacteroides thetaiotaomicron VPI-5482	2 HcpR Bacteroides vulgatus ATCC 8482	3 HcpR Bacteroides coprophilus DSM 18228	2 HcpR Bacteroides dorei DSM 17855		2 HcpR Bacteroides fragilis NCTC 9343	2 HcpR Bacteroides uniformis ATCC 8492	2 HcpR Bacteroides cellulosilyticus DSM 14838	3 HcpR Bacteroides plebeius DSM 17135	1 HcpR Bacteroides ovatus ATCC 8483		Nitrosative stress response
	TF	NrfR	1 NrfR Bacteroides thetaiotaomicron VPI-5482					1 NrfR Bacteroides fragilis NCTC 9343	1 NrfR Bacteroides uniformis ATCC 8492	1 NrfR Bacteroides cellulosilyticus DSM 14838	1 NrfR Bacteroides plebeius DSM 17135	1 NrfR Bacteroides ovatus ATCC 8483		Nitrate and nitrite respiration
FUR	TF	Fur	1 Fur Bacteroides thetaiotaomicron VPI-5482	1 Fur Bacteroides vulgatus ATCC 8482	1 Fur Bacteroides coprophilus DSM 18228	1 Fur Bacteroides dorei DSM 17855	1 Fur Bacteroides eggerthii DSM 20697	1 Fur Bacteroides fragilis NCTC 9343	1 Fur Bacteroides uniformis ATCC 8492	1 Fur Bacteroides cellulosilyticus DSM 14838	1 Fur Bacteroides plebeius DSM 17135	1 Fur Bacteroides ovatus ATCC 8483	1 Fur Bacteroides stercoris ATCC 43183	Iron homeostasis
	TF	PerR	3 PerR Bacteroides thetaiotaomicron VPI-5482	7 PerR Bacteroides vulgatus ATCC 8482	6 PerR Bacteroides coprophilus DSM 18228	7 PerR Bacteroides dorei DSM 17855	4 PerR Bacteroides eggerthii DSM 20697	3 PerR Bacteroides fragilis NCTC 9343	5 PerR Bacteroides uniformis ATCC 8492	4 PerR Bacteroides cellulosilyticus DSM 14838	5 PerR Bacteroides plebeius DSM 17135	3 PerR Bacteroides ovatus ATCC 8483	4 PerR Bacteroides stercoris ATCC 43183	Peroxide stress response; Oxidative stress response
	TF	Zur	3 Zur Bacteroides thetaiotaomicron VPI-5482	3 Zur Bacteroides vulgatus ATCC 8482	2 Zur Bacteroides coprophilus DSM 18228	3 Zur Bacteroides dorei DSM 17855	2 Zur Bacteroides eggerthii DSM 20697	1 Zur Bacteroides fragilis NCTC 9343	2 Zur Bacteroides uniformis ATCC 8492	3 Zur Bacteroides cellulosilyticus DSM 14838	1 Zur Bacteroides plebeius DSM 17135	3 Zur Bacteroides ovatus ATCC 8483	2 Zur Bacteroides stercoris ATCC 43183	Zinc homeostasis
GntR/MocR	TF	BACOVA_03038										1 BACOVA_03038 Bacteroides ovatus ATCC 8483
GntR/Others	TF	FucR	1 FucR Bacteroides thetaiotaomicron VPI-5482	1 FucR Bacteroides vulgatus ATCC 8482		1 FucR Bacteroides dorei DSM 17855		2 FucR Bacteroides fragilis NCTC 9343		1 FucR Bacteroides cellulosilyticus DSM 14838	1 FucR Bacteroides plebeius DSM 17135	1 FucR Bacteroides ovatus ATCC 8483		Fucose utilization
	TF	GalR	2 GalR Bacteroides thetaiotaomicron VPI-5482					1 GalR Bacteroides fragilis NCTC 9343						Galactose utilization
	TF	ManR	3 ManR Bacteroides thetaiotaomicron VPI-5482				3 ManR Bacteroides eggerthii DSM 20697					3 ManR Bacteroides ovatus ATCC 8483		Mannose utilization; Mannosides utilization
LacI	TF	KdgR	4 KdgR Bacteroides thetaiotaomicron VPI-5482	4 KdgR Bacteroides vulgatus ATCC 8482		3 KdgR Bacteroides dorei DSM 17855	4 KdgR Bacteroides eggerthii DSM 20697	4 KdgR Bacteroides fragilis NCTC 9343	4 KdgR Bacteroides uniformis ATCC 8492	3 KdgR Bacteroides cellulosilyticus DSM 14838	3 KdgR Bacteroides plebeius DSM 17135	4 KdgR Bacteroides ovatus ATCC 8483	4 KdgR Bacteroides stercoris ATCC 43183	Glucuronate utilization; Galacturonate utilization
	TF	LgoR	3 LgoR Bacteroides thetaiotaomicron VPI-5482	2 LgoR Bacteroides vulgatus ATCC 8482		2 LgoR Bacteroides dorei DSM 17855	1 LgoR Bacteroides eggerthii DSM 20697			3 LgoR Bacteroides cellulosilyticus DSM 14838		2 LgoR Bacteroides ovatus ATCC 8483		L-galactose utilization
	TF	MalR					6 MalR Bacteroides eggerthii DSM 20697	4 MalR Bacteroides fragilis NCTC 9343	7 MalR Bacteroides uniformis ATCC 8492	4 MalR Bacteroides cellulosilyticus DSM 14838			7 MalR Bacteroides stercoris ATCC 43183	Maltose utilization
	TF	UxaR	2 UxaR Bacteroides thetaiotaomicron VPI-5482				2 UxaR Bacteroides eggerthii DSM 20697		2 UxaR Bacteroides uniformis ATCC 8492	2 UxaR Bacteroides cellulosilyticus DSM 14838		2 UxaR Bacteroides ovatus ATCC 8483	2 UxaR Bacteroides stercoris ATCC 43183	Glucuronate utilization; Galacturonate utilization
	TF	UxuR	1 UxuR Bacteroides thetaiotaomicron VPI-5482								1 UxuR Bacteroides plebeius DSM 17135	1 UxuR Bacteroides ovatus ATCC 8483		Glucuronate utilization
NrtR	TF	AraR	4 AraR Bacteroides thetaiotaomicron VPI-5482	1 AraR Bacteroides vulgatus ATCC 8482		1 AraR Bacteroides dorei DSM 17855	2 AraR Bacteroides eggerthii DSM 20697		2 AraR Bacteroides uniformis ATCC 8492	2 AraR Bacteroides cellulosilyticus DSM 14838	3 AraR Bacteroides plebeius DSM 17135	2 AraR Bacteroides ovatus ATCC 8483		Arabinose utilization
	TF	XylR	2 XylR Bacteroides thetaiotaomicron VPI-5482	4 XylR Bacteroides vulgatus ATCC 8482		4 XylR Bacteroides dorei DSM 17855	2 XylR Bacteroides eggerthii DSM 20697	1 XylR Bacteroides fragilis NCTC 9343	1 XylR Bacteroides uniformis ATCC 8492	2 XylR Bacteroides cellulosilyticus DSM 14838	1 XylR Bacteroides plebeius DSM 17135	2 XylR Bacteroides ovatus ATCC 8483	2 XylR Bacteroides stercoris ATCC 43183	Xylose utilization
ROK	TF	NanR	3 NanR Bacteroides thetaiotaomicron VPI-5482	5 NanR Bacteroides vulgatus ATCC 8482	2 NanR Bacteroides coprophilus DSM 18228	4 NanR Bacteroides dorei DSM 17855	4 NanR Bacteroides eggerthii DSM 20697	7 NanR Bacteroides fragilis NCTC 9343	5 NanR Bacteroides uniformis ATCC 8492	2 NanR Bacteroides cellulosilyticus DSM 14838	5 NanR Bacteroides plebeius DSM 17135	4 NanR Bacteroides ovatus ATCC 8483	5 NanR Bacteroides stercoris ATCC 43183	Sialic acid utilization; N-acetylglucosamine utilization
[Other]	TF	HTCS_Aga-1	3 HTCS_Aga-1 Bacteroides thetaiotaomicron VPI-5482											Arabinogalactan utilization
	TF	HTCS_Ara-1	2 HTCS_Ara-1 Bacteroides thetaiotaomicron VPI-5482	2 HTCS_Ara-1 Bacteroides vulgatus ATCC 8482		2 HTCS_Ara-1 Bacteroides dorei DSM 17855	2 HTCS_Ara-1 Bacteroides eggerthii DSM 20697			1 HTCS_Ara-1 Bacteroides cellulosilyticus DSM 14838	2 HTCS_Ara-1 Bacteroides plebeius DSM 17135			Arabinan utilization
	TF	HTCS_Ara-2	3 HTCS_Ara-2 Bacteroides thetaiotaomicron VPI-5482	1 HTCS_Ara-2 Bacteroides vulgatus ATCC 8482		1 HTCS_Ara-2 Bacteroides dorei DSM 17855				1 HTCS_Ara-2 Bacteroides cellulosilyticus DSM 14838	2 HTCS_Ara-2 Bacteroides plebeius DSM 17135	3 HTCS_Ara-2 Bacteroides ovatus ATCC 8483		Arabinan utilization
	TF	HTCS_Fru	4 HTCS_Fru Bacteroides thetaiotaomicron VPI-5482	2 HTCS_Fru Bacteroides vulgatus ATCC 8482	1 HTCS_Fru Bacteroides coprophilus DSM 18228	1 HTCS_Fru Bacteroides dorei DSM 17855		2 HTCS_Fru Bacteroides fragilis NCTC 9343	2 HTCS_Fru Bacteroides uniformis ATCC 8492	3 HTCS_Fru Bacteroides cellulosilyticus DSM 14838	2 HTCS_Fru Bacteroides plebeius DSM 17135	3 HTCS_Fru Bacteroides ovatus ATCC 8483	2 HTCS_Fru Bacteroides stercoris ATCC 43183	Fructosides utilization; Fructose utilization
	TF	HTCS_Hep	3 HTCS_Hep Bacteroides thetaiotaomicron VPI-5482				2 HTCS_Hep Bacteroides eggerthii DSM 20697					3 HTCS_Hep Bacteroides ovatus ATCC 8483	2 HTCS_Hep Bacteroides stercoris ATCC 43183	Heparin utilization
	TF	HTCS_Hya	2 HTCS_Hya Bacteroides thetaiotaomicron VPI-5482				2 HTCS_Hya Bacteroides eggerthii DSM 20697		1 HTCS_Hya Bacteroides uniformis ATCC 8492	2 HTCS_Hya Bacteroides cellulosilyticus DSM 14838	1 HTCS_Hya Bacteroides plebeius DSM 17135	2 HTCS_Hya Bacteroides ovatus ATCC 8483	3 HTCS_Hya Bacteroides stercoris ATCC 43183	Hyaluronan utilization; Chondroitin sulphate utilization
	TF	HTCS_Man-1	2 HTCS_Man-1 Bacteroides thetaiotaomicron VPI-5482									1 HTCS_Man-1 Bacteroides ovatus ATCC 8483		Alpha-mannans utilization
	TF	HTCS_Man-2	1 HTCS_Man-2 Bacteroides thetaiotaomicron VPI-5482											Alpha-mannans utilization
	TF	HTCS_Man-3	4 HTCS_Man-3 Bacteroides thetaiotaomicron VPI-5482					1 HTCS_Man-3 Bacteroides fragilis NCTC 9343		2 HTCS_Man-3 Bacteroides cellulosilyticus DSM 14838				Alpha-mannans utilization
	TF	HTCS_Ogl-1	1 HTCS_Ogl-1 Bacteroides thetaiotaomicron VPI-5482											O-glycans utilization
	TF	HTCS_Ogl-2	2 HTCS_Ogl-2 Bacteroides thetaiotaomicron VPI-5482											O-glycans utilization
	TF	HTCS_Pga	1 HTCS_Pga Bacteroides thetaiotaomicron VPI-5482							1 HTCS_Pga Bacteroides cellulosilyticus DSM 14838		1 HTCS_Pga Bacteroides ovatus ATCC 8483		Pectic galactan utilization
	TF	HTCS_Rgu-1	5 HTCS_Rgu-1 Bacteroides thetaiotaomicron VPI-5482	4 HTCS_Rgu-1 Bacteroides vulgatus ATCC 8482		4 HTCS_Rgu-1 Bacteroides dorei DSM 17855	3 HTCS_Rgu-1 Bacteroides eggerthii DSM 20697			3 HTCS_Rgu-1 Bacteroides cellulosilyticus DSM 14838	2 HTCS_Rgu-1 Bacteroides plebeius DSM 17135	3 HTCS_Rgu-1 Bacteroides ovatus ATCC 8483	2 HTCS_Rgu-1 Bacteroides stercoris ATCC 43183	Rhamnogalacturonides utilization
	TF	HTCS_Rgu-2	8 HTCS_Rgu-2 Bacteroides thetaiotaomicron VPI-5482	8 HTCS_Rgu-2 Bacteroides vulgatus ATCC 8482		8 HTCS_Rgu-2 Bacteroides dorei DSM 17855					6 HTCS_Rgu-2 Bacteroides plebeius DSM 17135	8 HTCS_Rgu-2 Bacteroides ovatus ATCC 8483		Rhamnogalacturonides utilization
	TF	SusR	2 SusR Bacteroides thetaiotaomicron VPI-5482	2 SusR Bacteroides vulgatus ATCC 8482	1 SusR Bacteroides coprophilus DSM 18228	2 SusR Bacteroides dorei DSM 17855					2 SusR Bacteroides plebeius DSM 17135	2 SusR Bacteroides ovatus ATCC 8483		Starch utilization
	TF	SusR2	1 SusR2 Bacteroides thetaiotaomicron VPI-5482						1 SusR2 Bacteroides uniformis ATCC 8492	1 SusR2 Bacteroides cellulosilyticus DSM 14838		1 SusR2 Bacteroides ovatus ATCC 8483	1 SusR2 Bacteroides stercoris ATCC 43183	Starch utilization
	TF	SusR3	1 SusR3 Bacteroides thetaiotaomicron VPI-5482									1 SusR3 Bacteroides ovatus ATCC 8483		Polysaccharides utilization
	TF	SusR4	1 SusR4 Bacteroides thetaiotaomicron VPI-5482									1 SusR4 Bacteroides ovatus ATCC 8483		Polysaccharides utilization
RF00059	RNA	TPP	3 TPP Bacteroides thetaiotaomicron VPI-5482	1 TPP Bacteroides vulgatus ATCC 8482	1 TPP Bacteroides coprophilus DSM 18228	1 TPP Bacteroides dorei DSM 17855	2 TPP Bacteroides eggerthii DSM 20697	2 TPP Bacteroides fragilis NCTC 9343	2 TPP Bacteroides uniformis ATCC 8492	2 TPP Bacteroides cellulosilyticus DSM 14838	1 TPP Bacteroides plebeius DSM 17135	2 TPP Bacteroides ovatus ATCC 8483	2 TPP Bacteroides stercoris ATCC 43183	Thiamine biosynthesis
RF00174	RNA	Cobalamin	6 Cobalamin Bacteroides thetaiotaomicron VPI-5482	9 Cobalamin Bacteroides vulgatus ATCC 8482	3 Cobalamin Bacteroides coprophilus DSM 18228	8 Cobalamin Bacteroides dorei DSM 17855	3 Cobalamin Bacteroides eggerthii DSM 20697	7 Cobalamin Bacteroides fragilis NCTC 9343	5 Cobalamin Bacteroides uniformis ATCC 8492	8 Cobalamin Bacteroides cellulosilyticus DSM 14838	4 Cobalamin Bacteroides plebeius DSM 17135	7 Cobalamin Bacteroides ovatus ATCC 8483	5 Cobalamin Bacteroides stercoris ATCC 43183	Cobalamin biosynthesis

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

Collection of regulogs in Bacteroidaceae taxonomic group

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