Collection of regulogs in Chloroflexi taxonomic group

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

Collection of regulogs in Chloroflexi taxonomic group

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

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.

General statistics
Genomes	5
TF regulogs	30
TF regulons	107
TF binding sites	314
RNA regulogs	17
RNA regulons	65
RNA sites	98

Genomic distribution of regulons
Family	Type	Regulator						Function
ArsR	TF	Caur_3587	2 Caur_3587 Chloroflexus aggregans DSM 9485	2 Caur_3587 Chloroflexus sp. Y-400-fl	2 Caur_3587 Roseiflexus castenholzii DSM 13941	2 Caur_3587 Roseiflexus sp. RS-1	2 Caur_3587 Herpetosiphon aurantiacus ATCC 23779
CRP	TF	HcpR	2 HcpR Chloroflexus aggregans DSM 9485		1 HcpR Roseiflexus castenholzii DSM 13941	1 HcpR Roseiflexus sp. RS-1		Nitrosative stress response
DeoR	TF	RhaR	1 RhaR Chloroflexus aggregans DSM 9485	1 RhaR Chloroflexus sp. Y-400-fl	1 RhaR Roseiflexus castenholzii DSM 13941	1 RhaR Roseiflexus sp. RS-1		Rhamnose utilization
DtxR	TF	FetR	2 FetR Chloroflexus aggregans DSM 9485	5 FetR Chloroflexus sp. Y-400-fl	3 FetR Roseiflexus castenholzii DSM 13941	3 FetR Roseiflexus sp. RS-1		Iron homeostasis
	TF	MntR	2 MntR Chloroflexus aggregans DSM 9485	1 MntR Chloroflexus sp. Y-400-fl	2 MntR Roseiflexus castenholzii DSM 13941	3 MntR Roseiflexus sp. RS-1	1 MntR Herpetosiphon aurantiacus ATCC 23779	Manganese homeostasis
FUR	TF	Zur	5 Zur Chloroflexus aggregans DSM 9485	1 Zur Chloroflexus sp. Y-400-fl	2 Zur Roseiflexus castenholzii DSM 13941	1 Zur Roseiflexus sp. RS-1	8 Zur Herpetosiphon aurantiacus ATCC 23779	Zinc homeostasis
	TF	Zur2			5 Zur2 Roseiflexus castenholzii DSM 13941	5 Zur2 Roseiflexus sp. RS-1		Zinc homeostasis
GntR/Others	TF	Cagg_1084	2 Cagg_1084 Chloroflexus aggregans DSM 9485	2 Cagg_1084 Chloroflexus sp. Y-400-fl
	TF	Cagg_3094	1 Cagg_3094 Chloroflexus aggregans DSM 9485	1 Cagg_3094 Chloroflexus sp. Y-400-fl	1 Cagg_3094 Roseiflexus castenholzii DSM 13941	1 Cagg_3094 Roseiflexus sp. RS-1		Creatinine utilization
	TF	Rcas_2304			1 Rcas_2304 Roseiflexus castenholzii DSM 13941	1 Rcas_2304 Roseiflexus sp. RS-1		Amino acid utilization
	TF	Rcas_3562			1 Rcas_3562 Roseiflexus castenholzii DSM 13941	1 Rcas_3562 Roseiflexus sp. RS-1		Alpha-galactosides utilization
HrcA	TF	HrcA	2 HrcA Chloroflexus aggregans DSM 9485	2 HrcA Chloroflexus sp. Y-400-fl	2 HrcA Roseiflexus castenholzii DSM 13941	2 HrcA Roseiflexus sp. RS-1	2 HrcA Herpetosiphon aurantiacus ATCC 23779	Heat shock response
IclR	TF	MhpR	2 MhpR Chloroflexus aggregans DSM 9485	2 MhpR Chloroflexus sp. Y-400-fl	1 MhpR Roseiflexus castenholzii DSM 13941	1 MhpR Roseiflexus sp. RS-1		Utilization of aromatic compounds
LacI	TF	BfrR	1 BfrR Chloroflexus aggregans DSM 9485	1 BfrR Chloroflexus sp. Y-400-fl				Fructooligosaccharides utilization
	TF	Caur_1157	1 Caur_1157 Chloroflexus aggregans DSM 9485	1 Caur_1157 Chloroflexus sp. Y-400-fl			3 Caur_1157 Herpetosiphon aurantiacus ATCC 23779	Beta-glucosides utilization
	TF	Caur_3448	1 Caur_3448 Chloroflexus aggregans DSM 9485	1 Caur_3448 Chloroflexus sp. Y-400-fl	1 Caur_3448 Roseiflexus castenholzii DSM 13941	1 Caur_3448 Roseiflexus sp. RS-1	1 Caur_3448 Herpetosiphon aurantiacus ATCC 23779	Sugar utilization
	TF	Caur_3866	1 Caur_3866 Chloroflexus aggregans DSM 9485	1 Caur_3866 Chloroflexus sp. Y-400-fl				Beta-glucosides utilization
	TF	KojR	1 KojR Chloroflexus aggregans DSM 9485	1 KojR Chloroflexus sp. Y-400-fl				Kojibiose utilization
	TF	RhmR		1 RhmR Chloroflexus sp. Y-400-fl				Rhamnose oligosaccharides utilization
LexA	TF	LexA	9 LexA Chloroflexus aggregans DSM 9485	9 LexA Chloroflexus sp. Y-400-fl	10 LexA Roseiflexus castenholzii DSM 13941	10 LexA Roseiflexus sp. RS-1	10 LexA Herpetosiphon aurantiacus ATCC 23779	SOS response
LysR	TF	Caur_1779	2 Caur_1779 Chloroflexus aggregans DSM 9485	2 Caur_1779 Chloroflexus sp. Y-400-fl				Energy metabolism
NrdR	TF	NrdR	1 NrdR Chloroflexus aggregans DSM 9485	1 NrdR Chloroflexus sp. Y-400-fl	1 NrdR Roseiflexus castenholzii DSM 13941	1 NrdR Roseiflexus sp. RS-1	1 NrdR Herpetosiphon aurantiacus ATCC 23779	Deoxyribonucleotide biosynthesis
NrtR	TF	NrtR	4 NrtR Chloroflexus aggregans DSM 9485	4 NrtR Chloroflexus sp. Y-400-fl	4 NrtR Roseiflexus castenholzii DSM 13941	4 NrtR Roseiflexus sp. RS-1	4 NrtR Herpetosiphon aurantiacus ATCC 23779	NAD biosynthesis
PadR	TF	ModR	1 ModR Chloroflexus aggregans DSM 9485	2 ModR Chloroflexus sp. Y-400-fl	1 ModR Roseiflexus castenholzii DSM 13941			Molybdenum homeostasis
ROK	TF	NagR		1 NagR Chloroflexus sp. Y-400-fl	1 NagR Roseiflexus castenholzii DSM 13941	1 NagR Roseiflexus sp. RS-1	1 NagR Herpetosiphon aurantiacus ATCC 23779	N-acetylglucosamine utilization
Rex	TF	Rex	11 Rex Chloroflexus aggregans DSM 9485	10 Rex Chloroflexus sp. Y-400-fl	11 Rex Roseiflexus castenholzii DSM 13941	10 Rex Roseiflexus sp. RS-1	4 Rex Herpetosiphon aurantiacus ATCC 23779	Energy metabolism
TetR	TF	AcrR	2 AcrR Chloroflexus aggregans DSM 9485	2 AcrR Chloroflexus sp. Y-400-fl	2 AcrR Roseiflexus castenholzii DSM 13941	1 AcrR Roseiflexus sp. RS-1		Multidrug efflux; Multidrug resistance
	TF	Caur_3401	1 Caur_3401 Chloroflexus aggregans DSM 9485	1 Caur_3401 Chloroflexus sp. Y-400-fl	1 Caur_3401 Roseiflexus castenholzii DSM 13941	1 Caur_3401 Roseiflexus sp. RS-1		Multidrug resistance; Multidrug efflux
TrmB	TF	HpdR	1 HpdR Chloroflexus aggregans DSM 9485	1 HpdR Chloroflexus sp. Y-400-fl			1 HpdR Herpetosiphon aurantiacus ATCC 23779	Tyrosine degradation
[Other]	TF	SufR	1 SufR Chloroflexus aggregans DSM 9485	1 SufR Chloroflexus sp. Y-400-fl	1 SufR Roseiflexus castenholzii DSM 13941	1 SufR Roseiflexus sp. RS-1	1 SufR Herpetosiphon aurantiacus ATCC 23779	Iron-sulfur cluster biogenesis
RF00050	RNA	FMN	2 FMN Chloroflexus aggregans DSM 9485	2 FMN Chloroflexus sp. Y-400-fl	1 FMN Roseiflexus castenholzii DSM 13941	2 FMN Roseiflexus sp. RS-1	1 FMN Herpetosiphon aurantiacus ATCC 23779	Riboflavin biosynthesis
RF00059	RNA	TPP	2 TPP Chloroflexus aggregans DSM 9485	4 TPP Chloroflexus sp. Y-400-fl	3 TPP Roseiflexus castenholzii DSM 13941	4 TPP Roseiflexus sp. RS-1	1 TPP Herpetosiphon aurantiacus ATCC 23779	Thiamine biosynthesis
RF00080	RNA	yybP-ykoY	1 yybP-ykoY Chloroflexus aggregans DSM 9485	1 yybP-ykoY Chloroflexus sp. Y-400-fl	1 yybP-ykoY Roseiflexus castenholzii DSM 13941		2 yybP-ykoY Herpetosiphon aurantiacus ATCC 23779
RF00162	RNA	SAM	3 SAM Chloroflexus aggregans DSM 9485	3 SAM Chloroflexus sp. Y-400-fl	2 SAM Roseiflexus castenholzii DSM 13941	2 SAM Roseiflexus sp. RS-1	4 SAM Herpetosiphon aurantiacus ATCC 23779	Methionine biosynthesis
RF00174	RNA	Cobalamin	2 Cobalamin Chloroflexus aggregans DSM 9485	3 Cobalamin Chloroflexus sp. Y-400-fl	2 Cobalamin Roseiflexus castenholzii DSM 13941	3 Cobalamin Roseiflexus sp. RS-1	3 Cobalamin Herpetosiphon aurantiacus ATCC 23779	Cobalamin biosynthesis
RF00230	RNA	T-box(Gly)	1 T-box(Gly) Chloroflexus aggregans DSM 9485	1 T-box(Gly) Chloroflexus sp. Y-400-fl	1 T-box(Gly) Roseiflexus castenholzii DSM 13941	1 T-box(Gly) Roseiflexus sp. RS-1	1 T-box(Gly) Herpetosiphon aurantiacus ATCC 23779	Amino acid metabolism
	RNA	T-box(Ile)	1 T-box(Ile) Chloroflexus aggregans DSM 9485	1 T-box(Ile) Chloroflexus sp. Y-400-fl	1 T-box(Ile) Roseiflexus castenholzii DSM 13941	1 T-box(Ile) Roseiflexus sp. RS-1	1 T-box(Ile) Herpetosiphon aurantiacus ATCC 23779	Amino acid metabolism
	RNA	T-box(Phe)			1 T-box(Phe) Roseiflexus castenholzii DSM 13941	1 T-box(Phe) Roseiflexus sp. RS-1		Amino acid metabolism
	RNA	T-box(Pro)					1 T-box(Pro) Herpetosiphon aurantiacus ATCC 23779	Amino acid metabolism
	RNA	T-box(Ser)			1 T-box(Ser) Roseiflexus castenholzii DSM 13941		1 T-box(Ser) Herpetosiphon aurantiacus ATCC 23779	Amino acid metabolism
	RNA	T-box(Thr)		1 T-box(Thr) Chloroflexus sp. Y-400-fl	1 T-box(Thr) Roseiflexus castenholzii DSM 13941	1 T-box(Thr) Roseiflexus sp. RS-1	1 T-box(Thr) Herpetosiphon aurantiacus ATCC 23779	Amino acid metabolism
	RNA	T-box(Trp)	1 T-box(Trp) Chloroflexus aggregans DSM 9485	1 T-box(Trp) Chloroflexus sp. Y-400-fl	1 T-box(Trp) Roseiflexus castenholzii DSM 13941	1 T-box(Trp) Roseiflexus sp. RS-1	1 T-box(Trp) Herpetosiphon aurantiacus ATCC 23779	Amino acid metabolism
	RNA	T-box(Val)					1 T-box(Val) Herpetosiphon aurantiacus ATCC 23779	Amino acid metabolism
RF00234	RNA	glmS	1 glmS Chloroflexus aggregans DSM 9485	1 glmS Chloroflexus sp. Y-400-fl	1 glmS Roseiflexus castenholzii DSM 13941	1 glmS Roseiflexus sp. RS-1	1 glmS Herpetosiphon aurantiacus ATCC 23779	Amino sugar metabolism
RF00504	RNA	Glycine			1 Glycine Roseiflexus castenholzii DSM 13941	1 Glycine Roseiflexus sp. RS-1	1 Glycine Herpetosiphon aurantiacus ATCC 23779	Glycine metabolism
RF00515	RNA	PyrR	1 PyrR Chloroflexus aggregans DSM 9485	1 PyrR Chloroflexus sp. Y-400-fl			1 PyrR Herpetosiphon aurantiacus ATCC 23779	Pyrimidine metabolism
RF00557	RNA	L10_leader	1 L10_leader Chloroflexus aggregans DSM 9485	1 L10_leader Chloroflexus sp. Y-400-fl	1 L10_leader Roseiflexus castenholzii DSM 13941	1 L10_leader Roseiflexus sp. RS-1	1 L10_leader Herpetosiphon aurantiacus ATCC 23779	Ribosome biogenesis

Chloroflexus aggregans DSM 9485

Chloroflexus sp. Y-400-fl

Herpetosiphon aurantiacus ATCC 23779

Roseiflexus castenholzii DSM 13941

Roseiflexus sp. RS-1