Collection of regulogs in Listeriaceae taxonomic group

General statistics
Genomes	4
TF regulogs	25
TF regulons	94
TF binding sites	361
RNA regulogs	0
RNA regulons	0
RNA sites	0

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
Listeria innocua Clip11262	24	93	0	0	24	93
Listeria monocytogenes EGD-e	24	99	0	0	24	99
Listeria seeligeri serovar 1/2b str. SLCC3954	22	79	0	0	22	79
Listeria welshimeri serovar 6b str. SLCC5334	24	90	0	0	24	90

Genomic distribution of regulons
Family	Type	Regulator					Function
ArgR	TF	ArgR	2 ArgR Listeria monocytogenes EGD-e	2 ArgR Listeria seeligeri serovar 1/2b str. SLCC3954	2 ArgR Listeria welshimeri serovar 6b str. SLCC5334	2 ArgR Listeria innocua Clip11262	Arginine biosynthesis
ArsR	TF	CzrA	1 CzrA Listeria monocytogenes EGD-e	1 CzrA Listeria seeligeri serovar 1/2b str. SLCC3954	1 CzrA Listeria welshimeri serovar 6b str. SLCC5334	1 CzrA Listeria innocua Clip11262	Zinc resistance; Nickel resistance; Copper resistance; Cobalt resistance; Cadmium resistance
BirA	TF	BirA		1 BirA Listeria seeligeri serovar 1/2b str. SLCC3954	1 BirA Listeria welshimeri serovar 6b str. SLCC5334	1 BirA Listeria innocua Clip11262	Biotin biosynthesis
CsoR	TF	CsoR	1 CsoR Listeria monocytogenes EGD-e	1 CsoR Listeria seeligeri serovar 1/2b str. SLCC3954	1 CsoR Listeria welshimeri serovar 6b str. SLCC5334	1 CsoR Listeria innocua Clip11262	Copper resistance
DtxR	TF	MntR	2 MntR Listeria monocytogenes EGD-e	2 MntR Listeria seeligeri serovar 1/2b str. SLCC3954	2 MntR Listeria welshimeri serovar 6b str. SLCC5334	2 MntR Listeria innocua Clip11262	Manganese homeostasis
FUR	TF	Fur	16 Fur Listeria monocytogenes EGD-e	13 Fur Listeria seeligeri serovar 1/2b str. SLCC3954	14 Fur Listeria welshimeri serovar 6b str. SLCC5334	16 Fur Listeria innocua Clip11262	Iron homeostasis
	TF	Zur	4 Zur Listeria monocytogenes EGD-e	4 Zur Listeria seeligeri serovar 1/2b str. SLCC3954	4 Zur Listeria welshimeri serovar 6b str. SLCC5334	4 Zur Listeria innocua Clip11262	Zinc homeostasis
GntR/MocR	TF	PdxR	2 PdxR Listeria monocytogenes EGD-e	2 PdxR Listeria seeligeri serovar 1/2b str. SLCC3954	2 PdxR Listeria welshimeri serovar 6b str. SLCC5334	2 PdxR Listeria innocua Clip11262	Pyridoxine biosynthesis
GntR/Others	TF	GmuR	4 GmuR Listeria monocytogenes EGD-e	4 GmuR Listeria seeligeri serovar 1/2b str. SLCC3954	4 GmuR Listeria welshimeri serovar 6b str. SLCC5334	4 GmuR Listeria innocua Clip11262	Glucomannan utilization
	TF	NagR	4 NagR Listeria monocytogenes EGD-e	4 NagR Listeria seeligeri serovar 1/2b str. SLCC3954	4 NagR Listeria welshimeri serovar 6b str. SLCC5334	4 NagR Listeria innocua Clip11262	N-acetylglucosamine utilization
	TF	TreR	1 TreR Listeria monocytogenes EGD-e	1 TreR Listeria seeligeri serovar 1/2b str. SLCC3954	1 TreR Listeria welshimeri serovar 6b str. SLCC5334	1 TreR Listeria innocua Clip11262	Trehalose utilization
	TF	YhcF	1 YhcF Listeria monocytogenes EGD-e	1 YhcF Listeria seeligeri serovar 1/2b str. SLCC3954	1 YhcF Listeria welshimeri serovar 6b str. SLCC5334	1 YhcF Listeria innocua Clip11262	Multidrug efflux; Multidrug resistance
	TF	YtrA	1 YtrA Listeria monocytogenes EGD-e	1 YtrA Listeria seeligeri serovar 1/2b str. SLCC3954	1 YtrA Listeria welshimeri serovar 6b str. SLCC5334	1 YtrA Listeria innocua Clip11262	Multidrug resistance; Multidrug efflux
HrcA	TF	HrcA	2 HrcA Listeria monocytogenes EGD-e	2 HrcA Listeria seeligeri serovar 1/2b str. SLCC3954	2 HrcA Listeria welshimeri serovar 6b str. SLCC5334	2 HrcA Listeria innocua Clip11262	Heat shock response
LacI	TF	AlsR	2 AlsR Listeria monocytogenes EGD-e		2 AlsR Listeria welshimeri serovar 6b str. SLCC5334		Allose utilization
	TF	BglR	2 BglR Listeria monocytogenes EGD-e	2 BglR Listeria seeligeri serovar 1/2b str. SLCC3954	2 BglR Listeria welshimeri serovar 6b str. SLCC5334	2 BglR Listeria innocua Clip11262	Beta-glucosides utilization
	TF	BglR2	4 BglR2 Listeria monocytogenes EGD-e	4 BglR2 Listeria seeligeri serovar 1/2b str. SLCC3954	4 BglR2 Listeria welshimeri serovar 6b str. SLCC5334	4 BglR2 Listeria innocua Clip11262	Beta-glucosides utilization
	TF	CcpB	1 CcpB Listeria monocytogenes EGD-e	1 CcpB Listeria seeligeri serovar 1/2b str. SLCC3954	1 CcpB Listeria welshimeri serovar 6b str. SLCC5334	1 CcpB Listeria innocua Clip11262
	TF	Lmo0031	2 Lmo0031 Listeria monocytogenes EGD-e			2 Lmo0031 Listeria innocua Clip11262	Sugar utilization
	TF	MdxR	2 MdxR Listeria monocytogenes EGD-e	2 MdxR Listeria seeligeri serovar 1/2b str. SLCC3954	2 MdxR Listeria welshimeri serovar 6b str. SLCC5334	2 MdxR Listeria innocua Clip11262	Maltodextrin utilization; Maltose utilization
	TF	UriR	1 UriR Listeria monocytogenes EGD-e	1 UriR Listeria seeligeri serovar 1/2b str. SLCC3954	1 UriR Listeria welshimeri serovar 6b str. SLCC5334	1 UriR Listeria innocua Clip11262	Nucleoside utilization
	TF	YcjW	3 YcjW Listeria monocytogenes EGD-e		3 YcjW Listeria welshimeri serovar 6b str. SLCC5334	3 YcjW Listeria innocua Clip11262	Sugar utilization
LexA	TF	LexA	12 LexA Listeria monocytogenes EGD-e	10 LexA Listeria seeligeri serovar 1/2b str. SLCC3954	10 LexA Listeria welshimeri serovar 6b str. SLCC5334	12 LexA Listeria innocua Clip11262	SOS response
NrdR	TF	NrdR	2 NrdR Listeria monocytogenes EGD-e	2 NrdR Listeria seeligeri serovar 1/2b str. SLCC3954	2 NrdR Listeria welshimeri serovar 6b str. SLCC5334	2 NrdR Listeria innocua Clip11262	Deoxyribonucleotide biosynthesis
TrpR	TF	HisR	2 HisR Listeria monocytogenes EGD-e	2 HisR Listeria seeligeri serovar 1/2b str. SLCC3954	2 HisR Listeria welshimeri serovar 6b str. SLCC5334	2 HisR Listeria innocua Clip11262	Histidine biosynthesis

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

Collection of regulogs in Listeriaceae taxonomic group

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