Collection of regulogs in Clostridia-3 taxonomic group

General statistics
Genomes	14
TF regulogs	19
TF regulons	190
TF binding sites	686
RNA regulogs	2
RNA regulons	28
RNA sites	56

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 pectinophilus ATCC 43243	14	38	2	2	16	40
Blautia hansenii DSM 20583	12	29	2	5	14	34
Bryantella formatexigens DSM 14469	13	37	2	3	15	40
Clostridiales bacterium 1_7_47_FAA	14	69	2	6	16	75
Clostridium bolteae ATCC BAA-613	15	68	2	4	17	72
Clostridium nexile DSM 1787	14	43	2	5	16	48
Clostridium scindens ATCC 35704	14	46	2	5	16	51
Dorea formicigenerans ATCC 27755	14	45	2	5	16	50
Dorea longicatena DSM 13814	13	53	2	5	15	58
Eubacterium eligens ATCC 27750	14	47	2	2	16	49
Eubacterium rectale ATCC 33656	14	58	2	3	16	61
Roseburia intestinalis L1-82	13	50	2	5	15	55
Ruminococcus gnavus ATCC 29149	15	53	2	4	17	57
Ruminococcus lactaris ATCC 29176	11	50	2	2	13	52

Genomic distribution of regulons
Family	Type	Regulator															Function
ArgR	TF	ArgR	3 ArgR Clostridium bolteae ATCC BAA-613	1 ArgR Clostridium nexile DSM 1787	3 ArgR Clostridiales bacterium 1_7_47_FAA	2 ArgR Clostridium scindens ATCC 35704	3 ArgR Bacteroides pectinophilus ATCC 43243	3 ArgR Blautia hansenii DSM 20583	2 ArgR Bryantella formatexigens DSM 14469	2 ArgR Dorea formicigenerans ATCC 27755	2 ArgR Dorea longicatena DSM 13814	3 ArgR Eubacterium eligens ATCC 27750	3 ArgR Eubacterium rectale ATCC 33656	3 ArgR Roseburia intestinalis L1-82	3 ArgR Ruminococcus gnavus ATCC 29149	3 ArgR Ruminococcus lactaris ATCC 29176	Arginine biosynthesis
ArsR	TF	CzrA	1 CzrA Clostridium bolteae ATCC BAA-613	1 CzrA Clostridium nexile DSM 1787	1 CzrA Clostridiales bacterium 1_7_47_FAA	1 CzrA Clostridium scindens ATCC 35704	1 CzrA Bacteroides pectinophilus ATCC 43243		1 CzrA Bryantella formatexigens DSM 14469		1 CzrA Dorea longicatena DSM 13814	1 CzrA Eubacterium eligens ATCC 27750	1 CzrA Eubacterium rectale ATCC 33656	2 CzrA Roseburia intestinalis L1-82	1 CzrA Ruminococcus gnavus ATCC 29149		Zinc resistance; Nickel resistance; Copper resistance; Cobalt resistance; Cadmium resistance
BirA	TF	BirA	1 BirA Clostridium bolteae ATCC BAA-613	1 BirA Clostridium nexile DSM 1787	1 BirA Clostridiales bacterium 1_7_47_FAA	2 BirA Clostridium scindens ATCC 35704	2 BirA Bacteroides pectinophilus ATCC 43243	1 BirA Blautia hansenii DSM 20583	1 BirA Bryantella formatexigens DSM 14469	1 BirA Dorea formicigenerans ATCC 27755	3 BirA Dorea longicatena DSM 13814	2 BirA Eubacterium eligens ATCC 27750	2 BirA Eubacterium rectale ATCC 33656	2 BirA Roseburia intestinalis L1-82	2 BirA Ruminococcus gnavus ATCC 29149	2 BirA Ruminococcus lactaris ATCC 29176	Biotin biosynthesis
DtxR	TF	DtxR		2 DtxR Clostridium nexile DSM 1787		2 DtxR Clostridium scindens ATCC 35704				1 DtxR Dorea formicigenerans ATCC 27755	1 DtxR Dorea longicatena DSM 13814						Metal homeostasis
	TF	IdeR	7 IdeR Clostridium bolteae ATCC BAA-613	5 IdeR Clostridium nexile DSM 1787	8 IdeR Clostridiales bacterium 1_7_47_FAA	5 IdeR Clostridium scindens ATCC 35704	3 IdeR Bacteroides pectinophilus ATCC 43243	2 IdeR Blautia hansenii DSM 20583	5 IdeR Bryantella formatexigens DSM 14469	1 IdeR Dorea formicigenerans ATCC 27755	4 IdeR Dorea longicatena DSM 13814	4 IdeR Eubacterium eligens ATCC 27750	5 IdeR Eubacterium rectale ATCC 33656	4 IdeR Roseburia intestinalis L1-82	5 IdeR Ruminococcus gnavus ATCC 29149	4 IdeR Ruminococcus lactaris ATCC 29176	Iron homeostasis
FUR	TF	Fur	4 Fur Clostridium bolteae ATCC BAA-613	3 Fur Clostridium nexile DSM 1787	4 Fur Clostridiales bacterium 1_7_47_FAA	4 Fur Clostridium scindens ATCC 35704	3 Fur Bacteroides pectinophilus ATCC 43243			2 Fur Dorea formicigenerans ATCC 27755	5 Fur Dorea longicatena DSM 13814	3 Fur Eubacterium eligens ATCC 27750	3 Fur Eubacterium rectale ATCC 33656	2 Fur Roseburia intestinalis L1-82	1 Fur Ruminococcus gnavus ATCC 29149	5 Fur Ruminococcus lactaris ATCC 29176	Iron homeostasis
GntR/MocR	TF	CLOBOL_00921	2 CLOBOL_00921 Clostridium bolteae ATCC BAA-613
	TF	PdxR	2 PdxR Clostridium bolteae ATCC BAA-613	1 PdxR Clostridium nexile DSM 1787	2 PdxR Clostridiales bacterium 1_7_47_FAA	2 PdxR Clostridium scindens ATCC 35704	1 PdxR Bacteroides pectinophilus ATCC 43243	1 PdxR Blautia hansenii DSM 20583	1 PdxR Bryantella formatexigens DSM 14469	1 PdxR Dorea formicigenerans ATCC 27755	3 PdxR Dorea longicatena DSM 13814	1 PdxR Eubacterium eligens ATCC 27750	1 PdxR Eubacterium rectale ATCC 33656	1 PdxR Roseburia intestinalis L1-82	2 PdxR Ruminococcus gnavus ATCC 29149	2 PdxR Ruminococcus lactaris ATCC 29176	Pyridoxine biosynthesis
GntR/Others	TF	RUMGNA_00848			1 RUMGNA_00848 Clostridiales bacterium 1_7_47_FAA		1 RUMGNA_00848 Bacteroides pectinophilus ATCC 43243					1 RUMGNA_00848 Eubacterium eligens ATCC 27750	2 RUMGNA_00848 Eubacterium rectale ATCC 33656		1 RUMGNA_00848 Ruminococcus gnavus ATCC 29149		Multidrug resistance; Multidrug efflux
	TF	TreR	1 TreR Clostridium bolteae ATCC BAA-613		1 TreR Clostridiales bacterium 1_7_47_FAA												Trehalose utilization
	TF	YhcF		2 YhcF Clostridium nexile DSM 1787		2 YhcF Clostridium scindens ATCC 35704		1 YhcF Blautia hansenii DSM 20583		1 YhcF Dorea formicigenerans ATCC 27755					1 YhcF Ruminococcus gnavus ATCC 29149		Multidrug resistance; Multidrug efflux
	TF	YtrA	1 YtrA Clostridium bolteae ATCC BAA-613		1 YtrA Clostridiales bacterium 1_7_47_FAA		1 YtrA Bacteroides pectinophilus ATCC 43243	1 YtrA Blautia hansenii DSM 20583	1 YtrA Bryantella formatexigens DSM 14469			1 YtrA Eubacterium eligens ATCC 27750	1 YtrA Eubacterium rectale ATCC 33656	1 YtrA Roseburia intestinalis L1-82			Multidrug resistance; Multidrug efflux; Antibiotic resistance
HrcA	TF	HrcA	6 HrcA Clostridium bolteae ATCC BAA-613	6 HrcA Clostridium nexile DSM 1787	5 HrcA Clostridiales bacterium 1_7_47_FAA	6 HrcA Clostridium scindens ATCC 35704	4 HrcA Bacteroides pectinophilus ATCC 43243	4 HrcA Blautia hansenii DSM 20583	6 HrcA Bryantella formatexigens DSM 14469	5 HrcA Dorea formicigenerans ATCC 27755	8 HrcA Dorea longicatena DSM 13814	5 HrcA Eubacterium eligens ATCC 27750	8 HrcA Eubacterium rectale ATCC 33656	5 HrcA Roseburia intestinalis L1-82	6 HrcA Ruminococcus gnavus ATCC 29149	6 HrcA Ruminococcus lactaris ATCC 29176	Heat shock response
LacI	TF	UxuR	4 UxuR Clostridium bolteae ATCC BAA-613		4 UxuR Clostridiales bacterium 1_7_47_FAA		2 UxuR Bacteroides pectinophilus ATCC 43243		2 UxuR Bryantella formatexigens DSM 14469	2 UxuR Dorea formicigenerans ATCC 27755		2 UxuR Eubacterium eligens ATCC 27750		4 UxuR Roseburia intestinalis L1-82	4 UxuR Ruminococcus gnavus ATCC 29149		Glucuronate utilization
LexA	TF	LexA	7 LexA Clostridium bolteae ATCC BAA-613	4 LexA Clostridium nexile DSM 1787	6 LexA Clostridiales bacterium 1_7_47_FAA	4 LexA Clostridium scindens ATCC 35704	3 LexA Bacteroides pectinophilus ATCC 43243	3 LexA Blautia hansenii DSM 20583	4 LexA Bryantella formatexigens DSM 14469	4 LexA Dorea formicigenerans ATCC 27755	3 LexA Dorea longicatena DSM 13814	3 LexA Eubacterium eligens ATCC 27750	5 LexA Eubacterium rectale ATCC 33656	5 LexA Roseburia intestinalis L1-82	5 LexA Ruminococcus gnavus ATCC 29149	5 LexA Ruminococcus lactaris ATCC 29176	SOS response
NiaR	TF	NiaR	1 NiaR Clostridium bolteae ATCC BAA-613	2 NiaR Clostridium nexile DSM 1787		2 NiaR Clostridium scindens ATCC 35704	1 NiaR Bacteroides pectinophilus ATCC 43243	1 NiaR Blautia hansenii DSM 20583	1 NiaR Bryantella formatexigens DSM 14469	1 NiaR Dorea formicigenerans ATCC 27755	2 NiaR Dorea longicatena DSM 13814	1 NiaR Eubacterium eligens ATCC 27750	2 NiaR Eubacterium rectale ATCC 33656	1 NiaR Roseburia intestinalis L1-82	1 NiaR Ruminococcus gnavus ATCC 29149	1 NiaR Ruminococcus lactaris ATCC 29176	NAD biosynthesis
Rex	TF	Rex	11 Rex Clostridium bolteae ATCC BAA-613	4 Rex Clostridium nexile DSM 1787	14 Rex Clostridiales bacterium 1_7_47_FAA	2 Rex Clostridium scindens ATCC 35704	8 Rex Bacteroides pectinophilus ATCC 43243	3 Rex Blautia hansenii DSM 20583	2 Rex Bryantella formatexigens DSM 14469	9 Rex Dorea formicigenerans ATCC 27755	5 Rex Dorea longicatena DSM 13814	10 Rex Eubacterium eligens ATCC 27750	10 Rex Eubacterium rectale ATCC 33656	9 Rex Roseburia intestinalis L1-82	5 Rex Ruminococcus gnavus ATCC 29149	7 Rex Ruminococcus lactaris ATCC 29176	Energy metabolism
Rrf2	TF	IscR		1 IscR Clostridium nexile DSM 1787		1 IscR Clostridium scindens ATCC 35704		1 IscR Blautia hansenii DSM 20583	1 IscR Bryantella formatexigens DSM 14469	1 IscR Dorea formicigenerans ATCC 27755	1 IscR Dorea longicatena DSM 13814		1 IscR Eubacterium rectale ATCC 33656		1 IscR Ruminococcus gnavus ATCC 29149	1 IscR Ruminococcus lactaris ATCC 29176	Iron-sulfur cluster biogenesis
TrpR	TF	HisR	3 HisR Clostridium bolteae ATCC BAA-613	3 HisR Clostridium nexile DSM 1787	3 HisR Clostridiales bacterium 1_7_47_FAA	3 HisR Clostridium scindens ATCC 35704	1 HisR Bacteroides pectinophilus ATCC 43243	2 HisR Blautia hansenii DSM 20583	1 HisR Bryantella formatexigens DSM 14469	3 HisR Dorea formicigenerans ATCC 27755	3 HisR Dorea longicatena DSM 13814	3 HisR Eubacterium eligens ATCC 27750	3 HisR Eubacterium rectale ATCC 33656	2 HisR Roseburia intestinalis L1-82	3 HisR Ruminococcus gnavus ATCC 29149	3 HisR Ruminococcus lactaris ATCC 29176	Histidine biosynthesis
RF00050	RNA	FMN	2 FMN Clostridium bolteae ATCC BAA-613	1 FMN Clostridium nexile DSM 1787	2 FMN Clostridiales bacterium 1_7_47_FAA	2 FMN Clostridium scindens ATCC 35704	1 FMN Bacteroides pectinophilus ATCC 43243	2 FMN Blautia hansenii DSM 20583	1 FMN Bryantella formatexigens DSM 14469	2 FMN Dorea formicigenerans ATCC 27755	2 FMN Dorea longicatena DSM 13814	1 FMN Eubacterium eligens ATCC 27750	2 FMN Eubacterium rectale ATCC 33656	2 FMN Roseburia intestinalis L1-82	1 FMN Ruminococcus gnavus ATCC 29149	1 FMN Ruminococcus lactaris ATCC 29176	Riboflavin biosynthesis
RF00059	RNA	TPP	2 TPP Clostridium bolteae ATCC BAA-613	3 TPP Clostridium nexile DSM 1787	4 TPP Clostridiales bacterium 1_7_47_FAA	3 TPP Clostridium scindens ATCC 35704	1 TPP Bacteroides pectinophilus ATCC 43243	3 TPP Blautia hansenii DSM 20583	2 TPP Bryantella formatexigens DSM 14469	3 TPP Dorea formicigenerans ATCC 27755	3 TPP Dorea longicatena DSM 13814	1 TPP Eubacterium eligens ATCC 27750	1 TPP Eubacterium rectale ATCC 33656	3 TPP Roseburia intestinalis L1-82	3 TPP Ruminococcus gnavus ATCC 29149	1 TPP Ruminococcus lactaris ATCC 29176	Thiamine biosynthesis

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

Collection of regulogs in Clostridia-3 taxonomic group

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