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

Collection of regulogs in Clostridia-1 taxonomic group

General statistics
Genomes 8
TF regulogs 33
TF regulons 160
TF binding sites 961
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
Clostridium acetobutylicum ATCC 824 20 215 0 0 20 215
Clostridium beijerincki NCIMB 8052 29 193 0 0 29 193
Clostridium botulinum A str. ATCC 3502 22 105 0 0 22 105
Clostridium butyricum 5521 22 138 0 0 22 138
Clostridium kluyveri DSM 555 14 52 0 0 14 52
Clostridium novyi NT 19 91 0 0 19 91
Clostridium perfringens ATCC 13124 19 96 0 0 19 96
Clostridium tetani E88 15 71 0 0 15 71
Genomic distribution of regulons
Family Type Regulator Function
ArgR TF ArgR
8 ArgR

Clostridium acetobutylicum ATCC 824
3 ArgR

Clostridium butyricum 5521
2 ArgR

Clostridium beijerincki NCIMB 8052
3 ArgR

Clostridium botulinum A str. ATCC 3502
3 ArgR

Clostridium kluyveri DSM 555
6 ArgR

Clostridium novyi NT
3 ArgR

Clostridium perfringens ATCC 13124
2 ArgR

Clostridium tetani E88
Arginine biosynthesis
ArsR TF CzrA
1 CzrA

Clostridium acetobutylicum ATCC 824
1 CzrA

Clostridium butyricum 5521
1 CzrA

Clostridium beijerincki NCIMB 8052
1 CzrA

Clostridium botulinum A str. ATCC 3502
1 CzrA

Clostridium kluyveri DSM 555
1 CzrA

Clostridium novyi NT
1 CzrA

Clostridium perfringens ATCC 13124
Zinc resistance; Nickel resistance; Copper resistance; Cobalt resistance; Cadmium resistance
BirA TF BirA
4 BirA

Clostridium acetobutylicum ATCC 824
3 BirA

Clostridium butyricum 5521
2 BirA

Clostridium beijerincki NCIMB 8052
1 BirA

Clostridium botulinum A str. ATCC 3502
3 BirA

Clostridium kluyveri DSM 555
2 BirA

Clostridium novyi NT
3 BirA

Clostridium tetani E88
Biotin biosynthesis
CRP TF HcpR
6 HcpR

Clostridium acetobutylicum ATCC 824
1 HcpR

Clostridium butyricum 5521
4 HcpR

Clostridium beijerincki NCIMB 8052
5 HcpR

Clostridium botulinum A str. ATCC 3502
3 HcpR

Clostridium kluyveri DSM 555
3 HcpR

Clostridium novyi NT
2 HcpR

Clostridium perfringens ATCC 13124
7 HcpR

Clostridium tetani E88
Nitrosative stress response
DtxR TF MntR
1 MntR

Clostridium acetobutylicum ATCC 824
2 MntR

Clostridium beijerincki NCIMB 8052
2 MntR

Clostridium novyi NT
Manganese homeostasis
FUR TF Zur
5 Zur

Clostridium acetobutylicum ATCC 824
4 Zur

Clostridium butyricum 5521
6 Zur

Clostridium beijerincki NCIMB 8052
4 Zur

Clostridium botulinum A str. ATCC 3502
5 Zur

Clostridium kluyveri DSM 555
4 Zur

Clostridium novyi NT
6 Zur

Clostridium perfringens ATCC 13124
3 Zur

Clostridium tetani E88
Zinc homeostasis
GntR/MocR TF CBY_0654
2 CBY_0654

Clostridium butyricum 5521
2 CBY_0654

Clostridium botulinum A str. ATCC 3502
TF PdxQ
1 PdxQ

Clostridium beijerincki NCIMB 8052
1 PdxQ

Clostridium botulinum A str. ATCC 3502
Pyridoxine/pyridoxal homeostasis
TF YcxD
1 YcxD

Clostridium beijerincki NCIMB 8052
1 YcxD

Clostridium botulinum A str. ATCC 3502
Multidrug efflux
TF YdfD/YisV
1 YdfD/YisV

Clostridium beijerincki NCIMB 8052
1 YdfD/YisV

Clostridium kluyveri DSM 555
Metabolite transport
GntR/Others TF AgaR
4 AgaR

Clostridium butyricum 5521
3 AgaR

Clostridium beijerincki NCIMB 8052
5 AgaR

Clostridium novyi NT
2 AgaR

Clostridium perfringens ATCC 13124
N-acetylgalactosamine utilization
TF AraR
7 AraR

Clostridium acetobutylicum ATCC 824
6 AraR

Clostridium beijerincki NCIMB 8052
Arabinose utilization
TF CBO1205
1 CBO1205

Clostridium botulinum A str. ATCC 3502
2 CBO1205

Clostridium tetani E88
Multidrug efflux; Macrolides efflux
TF Cbei_4343
1 Cbei_4343

Clostridium beijerincki NCIMB 8052
2 Cbei_4343

Clostridium botulinum A str. ATCC 3502
1 Cbei_4343

Clostridium kluyveri DSM 555
1 Cbei_4343

Clostridium novyi NT
1 Cbei_4343

Clostridium perfringens ATCC 13124
1 Cbei_4343

Clostridium tetani E88
Multidrug resistance; Multidrug efflux
TF NagR
1 NagR

Clostridium acetobutylicum ATCC 824
1 NagR

Clostridium botulinum A str. ATCC 3502
1 NagR

Clostridium perfringens ATCC 13124
N-acetylglucosamine utilization
TF TreR
1 TreR

Clostridium beijerincki NCIMB 8052
1 TreR

Clostridium botulinum A str. ATCC 3502
2 TreR

Clostridium perfringens ATCC 13124
Trehalose utilization
TF YhcF
2 YhcF

Clostridium acetobutylicum ATCC 824
1 YhcF

Clostridium butyricum 5521
1 YhcF

Clostridium beijerincki NCIMB 8052
1 YhcF

Clostridium botulinum A str. ATCC 3502
2 YhcF

Clostridium kluyveri DSM 555
1 YhcF

Clostridium novyi NT
1 YhcF

Clostridium perfringens ATCC 13124
Multidrug resistance; Multidrug efflux
TF YtrA
1 YtrA

Clostridium butyricum 5521
1 YtrA

Clostridium beijerincki NCIMB 8052
1 YtrA

Clostridium botulinum A str. ATCC 3502
1 YtrA

Clostridium novyi NT
1 YtrA

Clostridium tetani E88
Multidrug resistance; Multidrug efflux; Antibiotic resistance
HrcA TF HrcA
3 HrcA

Clostridium acetobutylicum ATCC 824
2 HrcA

Clostridium butyricum 5521
2 HrcA

Clostridium beijerincki NCIMB 8052
3 HrcA

Clostridium botulinum A str. ATCC 3502
3 HrcA

Clostridium kluyveri DSM 555
2 HrcA

Clostridium novyi NT
3 HrcA

Clostridium perfringens ATCC 13124
2 HrcA

Clostridium tetani E88
Heat shock response
LacI TF CcpA
92 CcpA

Clostridium acetobutylicum ATCC 824
54 CcpA

Clostridium butyricum 5521
74 CcpA

Clostridium beijerincki NCIMB 8052
40 CcpA

Clostridium botulinum A str. ATCC 3502
13 CcpA

Clostridium kluyveri DSM 555
21 CcpA

Clostridium novyi NT
28 CcpA

Clostridium perfringens ATCC 13124
20 CcpA

Clostridium tetani E88
Carbohydrate metabolism
TF ExuR
7 ExuR

Clostridium acetobutylicum ATCC 824
3 ExuR

Clostridium butyricum 5521
1 ExuR

Clostridium beijerincki NCIMB 8052
Galacturonate utilization
TF MalR1
1 MalR1

Clostridium butyricum 5521
1 MalR1

Clostridium beijerincki NCIMB 8052
1 MalR1

Clostridium novyi NT
1 MalR1

Clostridium perfringens ATCC 13124
Maltose utilization; Maltodextrin utilization
TF MalR2
3 MalR2

Clostridium butyricum 5521
3 MalR2

Clostridium beijerincki NCIMB 8052
2 MalR2

Clostridium botulinum A str. ATCC 3502
1 MalR2

Clostridium perfringens ATCC 13124
Maltose utilization; Maltodextrin utilization
TF RbsR
1 RbsR

Clostridium butyricum 5521
1 RbsR

Clostridium novyi NT
1 RbsR

Clostridium perfringens ATCC 13124
1 RbsR

Clostridium tetani E88
Ribose utilization
TF ScrR
1 ScrR

Clostridium beijerincki NCIMB 8052
1 ScrR

Clostridium perfringens ATCC 13124
Sucrose utilization
LexA TF LexA
3 LexA

Clostridium acetobutylicum ATCC 824
4 LexA

Clostridium butyricum 5521
5 LexA

Clostridium beijerincki NCIMB 8052
2 LexA

Clostridium botulinum A str. ATCC 3502
2 LexA

Clostridium kluyveri DSM 555
3 LexA

Clostridium novyi NT
4 LexA

Clostridium perfringens ATCC 13124
2 LexA

Clostridium tetani E88
SOS response
NiaR TF NiaR
1 NiaR

Clostridium acetobutylicum ATCC 824
2 NiaR

Clostridium butyricum 5521
2 NiaR

Clostridium beijerincki NCIMB 8052
2 NiaR

Clostridium botulinum A str. ATCC 3502
2 NiaR

Clostridium kluyveri DSM 555
2 NiaR

Clostridium novyi NT
2 NiaR

Clostridium tetani E88
NAD biosynthesis
NrtR TF NrtR
2 NrtR

Clostridium acetobutylicum ATCC 824
1 NrtR

Clostridium beijerincki NCIMB 8052
NAD biosynthesis
ROK TF XylR
4 XylR

Clostridium acetobutylicum ATCC 824
3 XylR

Clostridium butyricum 5521
9 XylR

Clostridium beijerincki NCIMB 8052
Xylose utilization
Rex TF Rex
7 Rex

Clostridium acetobutylicum ATCC 824
11 Rex

Clostridium butyricum 5521
11 Rex

Clostridium beijerincki NCIMB 8052
8 Rex

Clostridium botulinum A str. ATCC 3502
2 Rex

Clostridium kluyveri DSM 555
9 Rex

Clostridium novyi NT
8 Rex

Clostridium perfringens ATCC 13124
11 Rex

Clostridium tetani E88
Energy metabolism
Rrf2 TF CymR
6 CymR

Clostridium acetobutylicum ATCC 824
2 CymR

Clostridium butyricum 5521
4 CymR

Clostridium beijerincki NCIMB 8052
2 CymR

Clostridium botulinum A str. ATCC 3502
1 CymR

Clostridium tetani E88
Cysteine metabolism
TF IscR
2 IscR

Clostridium acetobutylicum ATCC 824
1 IscR

Clostridium butyricum 5521
2 IscR

Clostridium beijerincki NCIMB 8052
1 IscR

Clostridium botulinum A str. ATCC 3502
2 IscR

Clostridium kluyveri DSM 555
1 IscR

Clostridium novyi NT
4 IscR

Clostridium perfringens ATCC 13124
1 IscR

Clostridium tetani E88
Iron-sulfur cluster biogenesis
SdaR TF SdaR
1 SdaR

Clostridium acetobutylicum ATCC 824
1 SdaR

Clostridium butyricum 5521
1 SdaR

Clostridium beijerincki NCIMB 8052
1 SdaR

Clostridium novyi NT
1 SdaR

Clostridium perfringens ATCC 13124
Glycerate utilization