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

Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes -- version 3.2 --

Collection of regulogs in Desulfuromonadales taxonomic group

Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes
-- version 3.2 --