Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes
-- version 4.0 --

Collection of regulogs in Chloroflexi taxonomic group

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

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
Chloroflexus aggregans DSM 9485 25 74 11 16 36 90
Chloroflexus sp. Y-400-fl 26 67 12 20 38 87
Herpetosiphon aurantiacus ATCC 23779 13 49 16 23 29 72
Roseiflexus castenholzii DSM 13941 22 64 14 19 36 83
Roseiflexus sp. RS-1 21 60 12 20 33 80
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