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

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