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

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