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

Collection of regulogs in Clostridia-2 taxonomic group

General statistics
Genomes 3
TF regulogs 19
TF regulons 40
TF binding sites 254
RNA regulogs 1
RNA regulons 3
RNA sites 8

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 bartlettii DSM 16795 10 53 1 3 11 56
Clostridium difficile 630 19 156 1 3 20 159
Clostridium hiranonis DSM 13275 11 45 1 2 12 47
Genomic distribution of regulons
Family Type Regulator Function
BirA TF BirA
2 BirA

Clostridium difficile 630
1 BirA

Clostridium bartlettii DSM 16795
1 BirA

Clostridium hiranonis DSM 13275
Biotin biosynthesis
CRP TF HcpR
2 HcpR

Clostridium difficile 630
Nitrosative stress response
FUR TF Fur
9 Fur

Clostridium difficile 630
5 Fur

Clostridium bartlettii DSM 16795
3 Fur

Clostridium hiranonis DSM 13275
Iron homeostasis
GntR/MocR TF CD2285
3 CD2285

Clostridium difficile 630
TF CD3353
1 CD3353

Clostridium difficile 630
GntR/Others TF AgaR
3 AgaR

Clostridium difficile 630
N-acetylgalactosamine utilization
TF CD0652
2 CD0652

Clostridium difficile 630
1 CD0652

Clostridium hiranonis DSM 13275
Multidrug resistance; Multidrug efflux
TF CD1503
1 CD1503

Clostridium difficile 630
1 CD1503

Clostridium bartlettii DSM 16795
1 CD1503

Clostridium hiranonis DSM 13275
Multidrug resistance; Multidrug efflux
TF NagR
1 NagR

Clostridium difficile 630
1 NagR

Clostridium hiranonis DSM 13275
N-acetylglucosamine utilization
TF TreR
2 TreR

Clostridium difficile 630
Trehalose utilization
TF YhcF
3 YhcF

Clostridium difficile 630
1 YhcF

Clostridium bartlettii DSM 16795
3 YhcF

Clostridium hiranonis DSM 13275
Multidrug resistance; Multidrug efflux
HrcA TF HrcA
2 HrcA

Clostridium difficile 630
3 HrcA

Clostridium bartlettii DSM 16795
2 HrcA

Clostridium hiranonis DSM 13275
Heat shock response
LacI TF CD0683
2 CD0683

Clostridium difficile 630
TF CcpA
59 CcpA

Clostridium difficile 630
11 CcpA

Clostridium bartlettii DSM 16795
13 CcpA

Clostridium hiranonis DSM 13275
Carbon catabolism; Carbohydrate metabolism
LexA TF LexA
4 LexA

Clostridium difficile 630
3 LexA

Clostridium bartlettii DSM 16795
4 LexA

Clostridium hiranonis DSM 13275
SOS response
NiaR TF NiaR
2 NiaR

Clostridium difficile 630
3 NiaR

Clostridium bartlettii DSM 16795
NAD biosynthesis
ROK TF XylR
3 XylR

Clostridium difficile 630
Xylose utilization
Rex TF Rex
9 Rex

Clostridium difficile 630
9 Rex

Clostridium bartlettii DSM 16795
4 Rex

Clostridium hiranonis DSM 13275
Energy metabolism
Rrf2 TF IscR
1 IscR

Clostridium difficile 630
1 IscR

Clostridium bartlettii DSM 16795
1 IscR

Clostridium hiranonis DSM 13275
Iron-sulfur cluster biogenesis
RF00050 RNA FMN
3 FMN

Clostridium difficile 630
3 FMN

Clostridium bartlettii DSM 16795
2 FMN

Clostridium hiranonis DSM 13275
Riboflavin biosynthesis