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

Collection of regulogs in Desulfuromonadales taxonomic group

General statistics
Genomes 9
TF regulogs 19
TF regulons 111
TF binding sites 354
RNA regulogs 3
RNA regulons 18
RNA sites 41

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
Desulfuromonas acetoxidans DSM 684 9 30 3 6 12 36
Geobacter lovleyi SZ 11 39 1 2 12 41
Geobacter metallireducens GS-15 11 38 2 5 13 43
Geobacter sp. FRC-32 12 39 1 5 13 44
Geobacter sp. M21 16 48 2 4 18 52
Geobacter sulfurreducens PCA 14 48 2 3 16 51
Geobacter uraniumreducens Rf4 15 48 2 5 17 53
Pelobacter carbinolicus str. DSM 2380 11 26 3 8 14 34
Pelobacter propionicus DSM 2379 12 38 2 3 14 41
Genomic distribution of regulons
Family Type Regulator Function
ArsR TF SahR
1 SahR

Geobacter uraniumreducens Rf4
1 SahR

Geobacter sp. FRC-32
1 SahR

Geobacter sp. M21
1 SahR

Geobacter lovleyi SZ
1 SahR

Pelobacter propionicus DSM 2379
1 SahR

Pelobacter carbinolicus str. DSM 2380
Methionine metabolism
BirA TF BirA
2 BirA

Geobacter metallireducens GS-15
2 BirA

Geobacter sulfurreducens PCA
2 BirA

Geobacter uraniumreducens Rf4
2 BirA

Geobacter sp. FRC-32
2 BirA

Geobacter sp. M21
2 BirA

Geobacter lovleyi SZ
1 BirA

Pelobacter propionicus DSM 2379
2 BirA

Pelobacter carbinolicus str. DSM 2380
Biotin biosynthesis
CRP TF HcpR
7 HcpR

Geobacter metallireducens GS-15
7 HcpR

Geobacter sulfurreducens PCA
7 HcpR

Geobacter uraniumreducens Rf4
4 HcpR

Geobacter sp. FRC-32
6 HcpR

Geobacter sp. M21
5 HcpR

Geobacter lovleyi SZ
4 HcpR

Pelobacter propionicus DSM 2379
1 HcpR

Pelobacter carbinolicus str. DSM 2380
1 HcpR

Desulfuromonas acetoxidans DSM 684
Nitrosative stress response
FUR TF Fur
4 Fur

Geobacter metallireducens GS-15
4 Fur

Geobacter sulfurreducens PCA
3 Fur

Geobacter uraniumreducens Rf4
4 Fur

Geobacter sp. FRC-32
5 Fur

Geobacter sp. M21
3 Fur

Geobacter lovleyi SZ
6 Fur

Pelobacter propionicus DSM 2379
4 Fur

Pelobacter carbinolicus str. DSM 2380
3 Fur

Desulfuromonas acetoxidans DSM 684
Iron homeostasis
TF Zur
1 Zur

Geobacter sulfurreducens PCA
1 Zur

Geobacter uraniumreducens Rf4
1 Zur

Geobacter sp. FRC-32
1 Zur

Geobacter sp. M21
Zinc homeostasis
Fis TF NtrC
5 NtrC

Geobacter metallireducens GS-15
5 NtrC

Geobacter sulfurreducens PCA
4 NtrC

Geobacter uraniumreducens Rf4
5 NtrC

Geobacter sp. FRC-32
4 NtrC

Geobacter sp. M21
3 NtrC

Geobacter lovleyi SZ
5 NtrC

Pelobacter propionicus DSM 2379
3 NtrC

Pelobacter carbinolicus str. DSM 2380
5 NtrC

Desulfuromonas acetoxidans DSM 684
Nitrogen assimilation
GntR/MocR TF Gbem_0803
1 Gbem_0803

Geobacter sulfurreducens PCA
1 Gbem_0803

Geobacter uraniumreducens Rf4
1 Gbem_0803

Geobacter sp. FRC-32
1 Gbem_0803

Geobacter sp. M21
2 Gbem_0803

Pelobacter carbinolicus str. DSM 2380
TF PdxQ
1 PdxQ

Desulfuromonas acetoxidans DSM 684
Pyridoxine/pyridoxal homeostasis
TF PdxW
2 PdxW

Geobacter sp. M21
Pyridoxine/pyridoxal homeostasis
GntR/Others TF LldR
2 LldR

Geobacter sulfurreducens PCA
3 LldR

Geobacter uraniumreducens Rf4
2 LldR

Geobacter sp. M21
4 LldR

Pelobacter propionicus DSM 2379
Lactate utilization
TF PrpR
1 PrpR

Geobacter metallireducens GS-15
1 PrpR

Geobacter sp. FRC-32
1 PrpR

Geobacter sp. M21
Methylcitrate utilization
TF SdhR2
9 SdhR2

Geobacter metallireducens GS-15
9 SdhR2

Geobacter sulfurreducens PCA
9 SdhR2

Geobacter uraniumreducens Rf4
9 SdhR2

Geobacter sp. FRC-32
9 SdhR2

Geobacter sp. M21
9 SdhR2

Geobacter lovleyi SZ
3 SdhR2

Pelobacter propionicus DSM 2379
9 SdhR2

Desulfuromonas acetoxidans DSM 684
Tricarboxylic acid cycle
HrcA TF HrcA
3 HrcA

Geobacter metallireducens GS-15
3 HrcA

Geobacter sulfurreducens PCA
3 HrcA

Geobacter uraniumreducens Rf4
3 HrcA

Geobacter sp. FRC-32
3 HrcA

Geobacter sp. M21
4 HrcA

Geobacter lovleyi SZ
4 HrcA

Pelobacter propionicus DSM 2379
3 HrcA

Pelobacter carbinolicus str. DSM 2380
3 HrcA

Desulfuromonas acetoxidans DSM 684
Heat shock response
LexA TF LexA
1 LexA

Geobacter metallireducens GS-15
2 LexA

Geobacter sulfurreducens PCA
2 LexA

Geobacter uraniumreducens Rf4
1 LexA

Geobacter sp. M21
2 LexA

Geobacter lovleyi SZ
2 LexA

Pelobacter carbinolicus str. DSM 2380
SOS response
MerR TF CadR-PbrR
1 CadR-PbrR

Pelobacter propionicus DSM 2379
Lead resistance; Cadmium resistance
ModE TF ModE
1 ModE

Geobacter sulfurreducens PCA
1 ModE

Geobacter uraniumreducens Rf4
1 ModE

Geobacter sp. M21
1 ModE

Geobacter lovleyi SZ
2 ModE

Pelobacter propionicus DSM 2379
3 ModE

Pelobacter carbinolicus str. DSM 2380
1 ModE

Desulfuromonas acetoxidans DSM 684
Molybdenum homeostasis
NikR TF NikR
1 NikR

Geobacter metallireducens GS-15
1 NikR

Geobacter sulfurreducens PCA
2 NikR

Geobacter uraniumreducens Rf4
1 NikR

Geobacter sp. M21
1 NikR

Geobacter lovleyi SZ
1 NikR

Pelobacter propionicus DSM 2379
Nickel homeostasis
NrdR TF NrdR
1 NrdR

Geobacter metallireducens GS-15
1 NrdR

Geobacter sulfurreducens PCA
1 NrdR

Geobacter uraniumreducens Rf4
1 NrdR

Geobacter sp. FRC-32
1 NrdR

Geobacter sp. M21
2 NrdR

Geobacter lovleyi SZ
1 NrdR

Pelobacter propionicus DSM 2379
1 NrdR

Pelobacter carbinolicus str. DSM 2380
3 NrdR

Desulfuromonas acetoxidans DSM 684
Deoxyribonucleotide biosynthesis
Rrf2 TF IscR
2 IscR

Geobacter metallireducens GS-15
2 IscR

Geobacter sulfurreducens PCA
1 IscR

Geobacter uraniumreducens Rf4
1 IscR

Geobacter sp. FRC-32
1 IscR

Pelobacter carbinolicus str. DSM 2380
1 IscR

Desulfuromonas acetoxidans DSM 684
Iron-sulfur cluster biogenesis
RF00050 RNA FMN
1 FMN

Pelobacter propionicus DSM 2379
1 FMN

Pelobacter carbinolicus str. DSM 2380
1 FMN

Desulfuromonas acetoxidans DSM 684
Riboflavin biosynthesis
RF00059 RNA TPP
2 TPP

Geobacter metallireducens GS-15
2 TPP

Geobacter sulfurreducens PCA
2 TPP

Geobacter uraniumreducens Rf4
1 TPP

Geobacter sp. M21
2 TPP

Geobacter lovleyi SZ
2 TPP

Pelobacter propionicus DSM 2379
2 TPP

Pelobacter carbinolicus str. DSM 2380
2 TPP

Desulfuromonas acetoxidans DSM 684
Thiamine biosynthesis
RF01055 RNA MOCO_RNA_motif
3 MOCO_RNA_motif

Geobacter metallireducens GS-15
1 MOCO_RNA_motif

Geobacter sulfurreducens PCA
3 MOCO_RNA_motif

Geobacter uraniumreducens Rf4
4 MOCO_RNA_motif

Geobacter sp. FRC-32
3 MOCO_RNA_motif

Geobacter sp. M21
5 MOCO_RNA_motif

Pelobacter carbinolicus str. DSM 2380
3 MOCO_RNA_motif

Desulfuromonas acetoxidans DSM 684
Molybdopterin biosynthesis; Tungsten homeostasis; Molybdenum homeostasis