Collection of regulogs in Xanthomonadales taxonomic group

General statistics
Genomes	4
TF regulogs	42
TF regulons	106
TF binding sites	301
RNA regulogs	4
RNA regulons	10
RNA sites	11

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
Stenotrophomonas maltophilia K279a	33	95	3	4	36	99
Xanthomonas axonopodis pv. citri str. 306	30	88	3	3	33	91
Xanthomonas campestris pv. campestris str. ATCC 33913	31	90	3	3	34	93
Xylella fastidiosa 9a5c	12	28	1	1	13	29

Genomic distribution of regulons
Family	Type	Regulator					Function
ArsR	TF	SamR	5 SamR Xylella fastidiosa 9a5c	4 SamR Xanthomonas axonopodis pv. citri str. 306	4 SamR Xanthomonas campestris pv. campestris str. ATCC 33913	4 SamR Stenotrophomonas maltophilia K279a	Methionine metabolism
BirA	TF	BirA		2 BirA Xanthomonas axonopodis pv. citri str. 306	2 BirA Xanthomonas campestris pv. campestris str. ATCC 33913	1 BirA Stenotrophomonas maltophilia K279a	Biotin biosynthesis
DeoR	TF	AgaR				2 AgaR Stenotrophomonas maltophilia K279a	N-acetylgalactosamine utilization
DtxR	TF	MntR	2 MntR Xylella fastidiosa 9a5c	2 MntR Xanthomonas axonopodis pv. citri str. 306	2 MntR Xanthomonas campestris pv. campestris str. ATCC 33913	2 MntR Stenotrophomonas maltophilia K279a	Manganese homeostasis
FUR	TF	Fur	5 Fur Xylella fastidiosa 9a5c	11 Fur Xanthomonas axonopodis pv. citri str. 306	11 Fur Xanthomonas campestris pv. campestris str. ATCC 33913	17 Fur Stenotrophomonas maltophilia K279a	Iron homeostasis
	TF	Zur	3 Zur Xylella fastidiosa 9a5c	4 Zur Xanthomonas axonopodis pv. citri str. 306	4 Zur Xanthomonas campestris pv. campestris str. ATCC 33913	3 Zur Stenotrophomonas maltophilia K279a	Zinc homeostasis
Fis	TF	NtrC	2 NtrC Xylella fastidiosa 9a5c	2 NtrC Xanthomonas axonopodis pv. citri str. 306	2 NtrC Xanthomonas campestris pv. campestris str. ATCC 33913	2 NtrC Stenotrophomonas maltophilia K279a	Nitrogen assimilation
GntR/MocR	TF	PdxR2				2 PdxR2 Stenotrophomonas maltophilia K279a	Pyridoxine/pyridoxal homeostasis
	TF	Smlt0590				1 Smlt0590 Stenotrophomonas maltophilia K279a
	TF	Smlt1075				1 Smlt1075 Stenotrophomonas maltophilia K279a
	TF	XAC0737		1 XAC0737 Xanthomonas axonopodis pv. citri str. 306	1 XAC0737 Xanthomonas campestris pv. campestris str. ATCC 33913		Metabolite transport
	TF	YrdX3				1 YrdX3 Stenotrophomonas maltophilia K279a
GntR/Others	TF	HutC		2 HutC Xanthomonas axonopodis pv. citri str. 306	2 HutC Xanthomonas campestris pv. campestris str. ATCC 33913	2 HutC Stenotrophomonas maltophilia K279a	Histidine utilization
	TF	LldR				1 LldR Stenotrophomonas maltophilia K279a	Lactate utilization
	TF	MlnR		1 MlnR Xanthomonas axonopodis pv. citri str. 306	1 MlnR Xanthomonas campestris pv. campestris str. ATCC 33913	1 MlnR Stenotrophomonas maltophilia K279a	Malonate metabolism
	TF	NagQ		1 NagQ Xanthomonas axonopodis pv. citri str. 306	1 NagQ Xanthomonas campestris pv. campestris str. ATCC 33913		N-acetylglucosamine utilization
	TF	VanR		2 VanR Xanthomonas axonopodis pv. citri str. 306	2 VanR Xanthomonas campestris pv. campestris str. ATCC 33913		Vanillate utilization
	TF	XAC1548		2 XAC1548 Xanthomonas axonopodis pv. citri str. 306	2 XAC1548 Xanthomonas campestris pv. campestris str. ATCC 33913	2 XAC1548 Stenotrophomonas maltophilia K279a	Multidrug resistance; Multidrug efflux
HrcA	TF	HrcA	1 HrcA Xylella fastidiosa 9a5c	1 HrcA Xanthomonas axonopodis pv. citri str. 306	1 HrcA Xanthomonas campestris pv. campestris str. ATCC 33913	1 HrcA Stenotrophomonas maltophilia K279a	Heat shock response
LacI	TF	FruR2		2 FruR2 Xanthomonas axonopodis pv. citri str. 306	2 FruR2 Xanthomonas campestris pv. campestris str. ATCC 33913	2 FruR2 Stenotrophomonas maltophilia K279a	Fructose utilization
	TF	MalR		5 MalR Xanthomonas axonopodis pv. citri str. 306	5 MalR Xanthomonas campestris pv. campestris str. ATCC 33913	4 MalR Stenotrophomonas maltophilia K279a	Maltodextrin utilization; Maltose utilization
	TF	ManR		3 ManR Xanthomonas axonopodis pv. citri str. 306	3 ManR Xanthomonas campestris pv. campestris str. ATCC 33913	3 ManR Stenotrophomonas maltophilia K279a	Mannosides utilization; Mannose utilization
	TF	NagR	2 NagR Xylella fastidiosa 9a5c	5 NagR Xanthomonas axonopodis pv. citri str. 306	6 NagR Xanthomonas campestris pv. campestris str. ATCC 33913	4 NagR Stenotrophomonas maltophilia K279a	N-acetylglucosamine utilization
	TF	SuxR		2 SuxR Xanthomonas axonopodis pv. citri str. 306	2 SuxR Xanthomonas campestris pv. campestris str. ATCC 33913		Sucrose utilization
	TF	XCC2209		7 XCC2209 Xanthomonas axonopodis pv. citri str. 306	7 XCC2209 Xanthomonas campestris pv. campestris str. ATCC 33913	6 XCC2209 Stenotrophomonas maltophilia K279a	Sugar utilization
	TF	XCC4129		1 XCC4129 Xanthomonas axonopodis pv. citri str. 306	1 XCC4129 Xanthomonas campestris pv. campestris str. ATCC 33913		Sugar utilization
LexA	TF	LexA	2 LexA Xylella fastidiosa 9a5c	1 LexA Xanthomonas axonopodis pv. citri str. 306	2 LexA Xanthomonas campestris pv. campestris str. ATCC 33913	2 LexA Stenotrophomonas maltophilia K279a	SOS response
	TF	LexA2		1 LexA2 Xanthomonas axonopodis pv. citri str. 306	1 LexA2 Xanthomonas campestris pv. campestris str. ATCC 33913		SOS response
LysR	TF	GulR			2 GulR Xanthomonas campestris pv. campestris str. ATCC 33913		Galactarate utilization; Glucarate utilization
	TF	MetR		2 MetR Xanthomonas axonopodis pv. citri str. 306	2 MetR Xanthomonas campestris pv. campestris str. ATCC 33913	2 MetR Stenotrophomonas maltophilia K279a	Methionine biosynthesis
MerR	TF	CueR				2 CueR Stenotrophomonas maltophilia K279a	Copper resistance
	TF	MerR				1 MerR Stenotrophomonas maltophilia K279a	Mercury resistance
	TF	NmlR				1 NmlR Stenotrophomonas maltophilia K279a	Carbonyl stress response
	TF	SoxR		3 SoxR Xanthomonas axonopodis pv. citri str. 306	2 SoxR Xanthomonas campestris pv. campestris str. ATCC 33913	5 SoxR Stenotrophomonas maltophilia K279a	Superoxide stress response
	TF	ZntR				1 ZntR Stenotrophomonas maltophilia K279a	Zinc resistance
NrdR	TF	NrdR	1 NrdR Xylella fastidiosa 9a5c	1 NrdR Xanthomonas axonopodis pv. citri str. 306	1 NrdR Xanthomonas campestris pv. campestris str. ATCC 33913	2 NrdR Stenotrophomonas maltophilia K279a	Deoxyribonucleotide biosynthesis
Rrf2	TF	IscR	1 IscR Xylella fastidiosa 9a5c	1 IscR Xanthomonas axonopodis pv. citri str. 306	1 IscR Xanthomonas campestris pv. campestris str. ATCC 33913	1 IscR Stenotrophomonas maltophilia K279a	Iron-sulfur cluster biogenesis
SdaR	TF	SdaR		1 SdaR Xanthomonas axonopodis pv. citri str. 306	1 SdaR Xanthomonas campestris pv. campestris str. ATCC 33913		Glycerate utilization
TetR	TF	FabR		2 FabR Xanthomonas axonopodis pv. citri str. 306	2 FabR Xanthomonas campestris pv. campestris str. ATCC 33913	2 FabR Stenotrophomonas maltophilia K279a	Fatty acid biosynthesis
	TF	PsrA		2 PsrA Xanthomonas axonopodis pv. citri str. 306	2 PsrA Xanthomonas campestris pv. campestris str. ATCC 33913	3 PsrA Stenotrophomonas maltophilia K279a	Fatty acid degradation
TrpR	TF	HisR	2 HisR Xylella fastidiosa 9a5c	2 HisR Xanthomonas axonopodis pv. citri str. 306	2 HisR Xanthomonas campestris pv. campestris str. ATCC 33913	2 HisR Stenotrophomonas maltophilia K279a	Histidine biosynthesis
	TF	TrpR	1 TrpR Xylella fastidiosa 9a5c				Tryptophan biosynthesis
RF00050	RNA	FMN		1 FMN Xanthomonas axonopodis pv. citri str. 306	1 FMN Xanthomonas campestris pv. campestris str. ATCC 33913	1 FMN Stenotrophomonas maltophilia K279a	Riboflavin biosynthesis
RF00059	RNA	TPP	1 TPP Xylella fastidiosa 9a5c	1 TPP Xanthomonas axonopodis pv. citri str. 306	1 TPP Xanthomonas campestris pv. campestris str. ATCC 33913	2 TPP Stenotrophomonas maltophilia K279a	Thiamine biosynthesis
RF01055	RNA	MOCO_RNA_motif
RF01057	RNA	SAH_riboswitch		1 SAH_riboswitch Xanthomonas axonopodis pv. citri str. 306	1 SAH_riboswitch Xanthomonas campestris pv. campestris str. ATCC 33913	1 SAH_riboswitch Stenotrophomonas maltophilia K279a	Methionine metabolism

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

Collection of regulogs in Xanthomonadales taxonomic group

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