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

Collection of regulogs in Thermotogales taxonomic group

General statistics
Genomes 11
TF regulogs 34
TF regulons 245
TF binding sites 648
RNA regulogs 13
RNA regulons 74
RNA sites 88

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
Fervidobacterium nodosum Rt17-B1 14 34 5 8 19 42
Petrotoga mobilis SJ95 11 23 9 9 20 32
Thermosipho africanus TCF52B 17 40 7 10 24 50
Thermosipho melanesiensis BI429 15 30 8 13 23 43
Thermotoga lettingae TMO 23 42 9 12 32 54
Thermotoga maritima MSB8 31 92 6 6 37 98
Thermotoga naphthophila RKU-10 33 92 6 6 39 98
Thermotoga neapolitana DSM 4359 31 83 7 7 38 90
Thermotoga petrophila RKU-1 31 95 6 6 37 101
Thermotoga sp. RQ2 29 95 6 6 35 101
Thermotogales bacterium TBF 19.5.1 10 22 5 5 15 27
Genomic distribution of regulons
Family Type Regulator Function
ArgR TF ArgR
2 ArgR

Thermotoga maritima MSB8
2 ArgR

Thermotoga sp. RQ2
2 ArgR

Thermotoga neapolitana DSM 4359
2 ArgR

Thermotoga petrophila RKU-1
2 ArgR

Thermotoga naphthophila RKU-10
Arginine biosynthesis
CRP TF HcpR
2 HcpR

Thermotoga maritima MSB8
2 HcpR

Thermotoga sp. RQ2
1 HcpR

Thermotoga neapolitana DSM 4359
2 HcpR

Thermotoga petrophila RKU-1
2 HcpR

Thermotoga naphthophila RKU-10
2 HcpR

Thermotoga lettingae TMO
2 HcpR

Thermosipho africanus TCF52B
1 HcpR

Thermosipho melanesiensis BI429
2 HcpR

Fervidobacterium nodosum Rt17-B1
2 HcpR

Petrotoga mobilis SJ95
2 HcpR

Thermotogales bacterium TBF 19.5.1
Nitrosative stress response
DeoR TF FruR
1 FruR

Thermotoga sp. RQ2
1 FruR

Thermotoga naphthophila RKU-10
Fructose utilization
TF RhaR
3 RhaR

Thermotoga maritima MSB8
3 RhaR

Thermotoga neapolitana DSM 4359
3 RhaR

Thermotoga petrophila RKU-1
3 RhaR

Thermotoga naphthophila RKU-10
Rhamnose utilization; Rhamnose oligosaccharides utilization
FUR TF Fur
5 Fur

Thermotoga maritima MSB8
4 Fur

Thermotoga sp. RQ2
2 Fur

Thermotoga neapolitana DSM 4359
4 Fur

Thermotoga petrophila RKU-1
3 Fur

Thermotoga naphthophila RKU-10
1 Fur

Thermotoga lettingae TMO
3 Fur

Thermosipho africanus TCF52B
1 Fur

Thermosipho melanesiensis BI429
1 Fur

Fervidobacterium nodosum Rt17-B1
1 Fur

Thermotogales bacterium TBF 19.5.1
Iron homeostasis
TF Zur
1 Zur

Thermotoga maritima MSB8
1 Zur

Thermotoga sp. RQ2
1 Zur

Thermotoga neapolitana DSM 4359
1 Zur

Thermotoga petrophila RKU-1
1 Zur

Thermotoga naphthophila RKU-10
1 Zur

Thermosipho africanus TCF52B
1 Zur

Thermosipho melanesiensis BI429
1 Zur

Fervidobacterium nodosum Rt17-B1
1 Zur

Petrotoga mobilis SJ95
Zinc homeostasis
GntR/Others TF AraR
3 AraR

Thermotoga maritima MSB8
5 AraR

Thermotoga sp. RQ2
2 AraR

Thermotoga neapolitana DSM 4359
5 AraR

Thermotoga petrophila RKU-1
3 AraR

Thermotoga naphthophila RKU-10
2 AraR

Thermotoga lettingae TMO
Arabinose utilization
TF THA_1503
1 THA_1503

Thermotoga lettingae TMO
1 THA_1503

Thermosipho africanus TCF52B
1 THA_1503

Thermosipho melanesiensis BI429
1 THA_1503

Fervidobacterium nodosum Rt17-B1
1 THA_1503

Petrotoga mobilis SJ95
1 THA_1503

Thermotogales bacterium TBF 19.5.1
Multidrug resistance; Multidrug efflux
TF TM0766
1 TM0766

Thermotoga maritima MSB8
1 TM0766

Thermotoga sp. RQ2
1 TM0766

Thermotoga neapolitana DSM 4359
1 TM0766

Thermotoga petrophila RKU-1
1 TM0766

Thermotoga naphthophila RKU-10
1 TM0766

Thermotoga lettingae TMO
1 TM0766

Thermosipho africanus TCF52B
1 TM0766

Thermosipho melanesiensis BI429
1 TM0766

Fervidobacterium nodosum Rt17-B1
Hypothetical ABC transporter
TF UxaR
4 UxaR

Thermotoga maritima MSB8
5 UxaR

Thermotoga sp. RQ2
3 UxaR

Thermotoga neapolitana DSM 4359
3 UxaR

Thermotoga petrophila RKU-1
3 UxaR

Thermotoga naphthophila RKU-10
Galacturonate utilization; Pectin utilization
HrcA TF HrcA
4 HrcA

Thermotoga maritima MSB8
4 HrcA

Thermotoga sp. RQ2
5 HrcA

Thermotoga neapolitana DSM 4359
5 HrcA

Thermotoga petrophila RKU-1
5 HrcA

Thermotoga naphthophila RKU-10
3 HrcA

Thermotoga lettingae TMO
4 HrcA

Thermosipho africanus TCF52B
4 HrcA

Thermosipho melanesiensis BI429
6 HrcA

Fervidobacterium nodosum Rt17-B1
4 HrcA

Petrotoga mobilis SJ95
3 HrcA

Thermotogales bacterium TBF 19.5.1
Heat shock response
IclR TF KdgR
6 KdgR

Thermotoga maritima MSB8
4 KdgR

Thermotoga sp. RQ2
4 KdgR

Thermotoga neapolitana DSM 4359
6 KdgR

Thermotoga petrophila RKU-1
6 KdgR

Thermotoga naphthophila RKU-10
Glucuronate utilization
LacI TF CelR
7 CelR

Thermotoga maritima MSB8
7 CelR

Thermotoga sp. RQ2
5 CelR

Thermotoga neapolitana DSM 4359
5 CelR

Thermotoga petrophila RKU-1
5 CelR

Thermotoga naphthophila RKU-10
1 CelR

Thermotoga lettingae TMO
1 CelR

Fervidobacterium nodosum Rt17-B1
Cellobiose utilization
TF GalR
2 GalR

Thermotoga maritima MSB8
2 GalR

Thermotoga sp. RQ2
1 GalR

Thermotoga neapolitana DSM 4359
2 GalR

Thermotoga petrophila RKU-1
2 GalR

Thermotoga naphthophila RKU-10
3 GalR

Thermotoga lettingae TMO
1 GalR

Thermosipho africanus TCF52B
2 GalR

Fervidobacterium nodosum Rt17-B1
1 GalR

Petrotoga mobilis SJ95
Galactosides utilization
TF GloR
2 GloR

Thermotoga maritima MSB8
2 GloR

Thermotoga sp. RQ2
2 GloR

Thermotoga naphthophila RKU-10
1 GloR

Thermotoga lettingae TMO
1 GloR

Petrotoga mobilis SJ95
Fucose-glucose oligosaccharide utilization
TF RbsR
1 RbsR

Thermotoga maritima MSB8
1 RbsR

Thermotoga neapolitana DSM 4359
1 RbsR

Thermotoga petrophila RKU-1
1 RbsR

Thermotoga naphthophila RKU-10
1 RbsR

Thermotoga lettingae TMO
1 RbsR

Thermosipho africanus TCF52B
1 RbsR

Petrotoga mobilis SJ95
1 RbsR

Thermotogales bacterium TBF 19.5.1
Ribose utilization
TF UgpR
1 UgpR

Thermotoga maritima MSB8
1 UgpR

Thermotoga neapolitana DSM 4359
1 UgpR

Thermotoga petrophila RKU-1
1 UgpR

Thermotoga naphthophila RKU-10
1 UgpR

Thermotoga lettingae TMO
1 UgpR

Thermosipho africanus TCF52B
1 UgpR

Thermosipho melanesiensis BI429
Possibly alpha-mannosides utilization
NiaR TF NiaR
2 NiaR

Thermotoga maritima MSB8
2 NiaR

Thermotoga sp. RQ2
2 NiaR

Thermotoga neapolitana DSM 4359
2 NiaR

Thermotoga petrophila RKU-1
2 NiaR

Thermotoga naphthophila RKU-10
1 NiaR

Thermotoga lettingae TMO
1 NiaR

Thermosipho africanus TCF52B
1 NiaR

Thermosipho melanesiensis BI429
NAD biosynthesis
NrdR TF NrdR
4 NrdR

Thermotoga maritima MSB8
4 NrdR

Thermotoga sp. RQ2
4 NrdR

Thermotoga neapolitana DSM 4359
4 NrdR

Thermotoga petrophila RKU-1
4 NrdR

Thermotoga naphthophila RKU-10
2 NrdR

Thermotoga lettingae TMO
1 NrdR

Thermosipho africanus TCF52B
1 NrdR

Thermosipho melanesiensis BI429
2 NrdR

Fervidobacterium nodosum Rt17-B1
2 NrdR

Petrotoga mobilis SJ95
2 NrdR

Thermotogales bacterium TBF 19.5.1
Deoxyribonucleotide biosynthesis
OmpR TF PhoB
1 PhoB

Thermotoga maritima MSB8
1 PhoB

Thermotoga sp. RQ2
1 PhoB

Thermotoga neapolitana DSM 4359
1 PhoB

Thermotoga petrophila RKU-1
1 PhoB

Thermotoga naphthophila RKU-10
1 PhoB

Thermotoga lettingae TMO
1 PhoB

Thermosipho africanus TCF52B
1 PhoB

Thermosipho melanesiensis BI429
1 PhoB

Fervidobacterium nodosum Rt17-B1
1 PhoB

Petrotoga mobilis SJ95
1 PhoB

Thermotogales bacterium TBF 19.5.1
Phosphate metabolism
TF ZnuR
1 ZnuR

Thermotoga maritima MSB8
1 ZnuR

Thermotoga sp. RQ2
1 ZnuR

Thermotoga neapolitana DSM 4359
1 ZnuR

Thermotoga petrophila RKU-1
1 ZnuR

Thermotoga naphthophila RKU-10
Zinc homeostasis
ROK TF BglR
1 BglR

Thermotoga maritima MSB8
1 BglR

Thermotoga sp. RQ2
1 BglR

Thermotoga neapolitana DSM 4359
1 BglR

Thermotoga petrophila RKU-1
1 BglR

Thermotoga naphthophila RKU-10
2 BglR

Thermotoga lettingae TMO
Beta-glucosides utilization
TF ChiR
1 ChiR

Thermotoga maritima MSB8
1 ChiR

Thermotoga sp. RQ2
1 ChiR

Thermotoga neapolitana DSM 4359
1 ChiR

Thermotoga petrophila RKU-1
1 ChiR

Thermotoga naphthophila RKU-10
1 ChiR

Thermotoga lettingae TMO
1 ChiR

Thermosipho africanus TCF52B
1 ChiR

Thermosipho melanesiensis BI429
Chitobiose utilization
TF GluR
2 GluR

Thermotoga sp. RQ2
2 GluR

Thermotoga neapolitana DSM 4359
1 GluR

Thermotoga petrophila RKU-1
2 GluR

Thermotoga naphthophila RKU-10
Glucose utilization; Trehalose utilization
TF IolR
1 IolR

Thermotoga maritima MSB8
1 IolR

Thermotoga neapolitana DSM 4359
1 IolR

Thermotoga petrophila RKU-1
1 IolR

Thermotoga naphthophila RKU-10
Inositol utilization
TF ManR
2 ManR

Thermotoga maritima MSB8
2 ManR

Thermotoga sp. RQ2
1 ManR

Thermotoga neapolitana DSM 4359
1 ManR

Thermotoga petrophila RKU-1
1 ManR

Thermotoga naphthophila RKU-10
Mannan and beta-mannosides utilization
TF TreR
1 TreR

Thermotoga maritima MSB8
2 TreR

Thermotoga sp. RQ2
2 TreR

Thermotoga neapolitana DSM 4359
2 TreR

Thermotoga petrophila RKU-1
2 TreR

Thermotoga naphthophila RKU-10
1 TreR

Thermotoga lettingae TMO
2 TreR

Thermosipho africanus TCF52B
2 TreR

Thermosipho melanesiensis BI429
2 TreR

Fervidobacterium nodosum Rt17-B1
2 TreR

Thermotogales bacterium TBF 19.5.1
Trehalose utilization
TF XylR
7 XylR

Thermotoga maritima MSB8
8 XylR

Thermotoga sp. RQ2
8 XylR

Thermotoga neapolitana DSM 4359
7 XylR

Thermotoga petrophila RKU-1
7 XylR

Thermotoga naphthophila RKU-10
2 XylR

Thermotoga lettingae TMO
Xylose utilization
Rex TF Rex
12 Rex

Thermotoga maritima MSB8
13 Rex

Thermotoga sp. RQ2
11 Rex

Thermotoga neapolitana DSM 4359
13 Rex

Thermotoga petrophila RKU-1
12 Rex

Thermotoga naphthophila RKU-10
5 Rex

Thermotoga lettingae TMO
7 Rex

Thermosipho africanus TCF52B
7 Rex

Thermosipho melanesiensis BI429
7 Rex

Fervidobacterium nodosum Rt17-B1
4 Rex

Petrotoga mobilis SJ95
4 Rex

Thermotogales bacterium TBF 19.5.1
Energy metabolism
TF Rex1
1 Rex1

Thermotoga maritima MSB8
1 Rex1

Thermotoga sp. RQ2
1 Rex1

Thermotoga neapolitana DSM 4359
1 Rex1

Thermotoga petrophila RKU-1
1 Rex1

Thermotoga naphthophila RKU-10
1 Rex1

Thermotoga lettingae TMO
1 Rex1

Thermosipho africanus TCF52B
1 Rex1

Thermosipho melanesiensis BI429
2 Rex1

Fervidobacterium nodosum Rt17-B1
Energy metabolism
RpiR TF UctR
1 UctR

Thermotoga maritima MSB8
1 UctR

Thermotoga sp. RQ2
1 UctR

Thermotoga neapolitana DSM 4359
1 UctR

Thermotoga petrophila RKU-1
1 UctR

Thermotoga naphthophila RKU-10
Sugar utilization
TF UgtR
1 UgtR

Thermotoga maritima MSB8
1 UgtR

Thermotoga sp. RQ2
1 UgtR

Thermotoga neapolitana DSM 4359
1 UgtR

Thermotoga petrophila RKU-1
1 UgtR

Thermotoga naphthophila RKU-10
1 UgtR

Thermotoga lettingae TMO
1 UgtR

Petrotoga mobilis SJ95
1 UgtR

Thermotogales bacterium TBF 19.5.1
Sugar utilization
TetR TF TM1030
1 TM1030

Thermotoga maritima MSB8
1 TM1030

Thermotoga sp. RQ2
1 TM1030

Thermotoga neapolitana DSM 4359
1 TM1030

Thermotoga petrophila RKU-1
1 TM1030

Thermotoga naphthophila RKU-10
1 TM1030

Thermotoga lettingae TMO
Multidrug resistance
XRE TF PuuR
1 PuuR

Thermotoga maritima MSB8
1 PuuR

Thermotoga sp. RQ2
1 PuuR

Thermotoga neapolitana DSM 4359
1 PuuR

Thermotoga petrophila RKU-1
1 PuuR

Thermotoga naphthophila RKU-10
1 PuuR

Thermotoga lettingae TMO
1 PuuR

Thermosipho africanus TCF52B
1 PuuR

Thermosipho melanesiensis BI429
1 PuuR

Fervidobacterium nodosum Rt17-B1
Spermidine biosynthesis
RF00050 RNA FMN
1 FMN

Thermotoga maritima MSB8
1 FMN

Thermotoga sp. RQ2
1 FMN

Thermotoga neapolitana DSM 4359
1 FMN

Thermotoga petrophila RKU-1
1 FMN

Thermotoga naphthophila RKU-10
1 FMN

Thermosipho melanesiensis BI429
1 FMN

Fervidobacterium nodosum Rt17-B1
1 FMN

Thermotogales bacterium TBF 19.5.1
Riboflavin biosynthesis
RF00059 RNA TPP
1 TPP

Thermotoga maritima MSB8
1 TPP

Thermotoga sp. RQ2
1 TPP

Thermotoga neapolitana DSM 4359
1 TPP

Thermotoga petrophila RKU-1
1 TPP

Thermotoga naphthophila RKU-10
2 TPP

Thermotoga lettingae TMO
2 TPP

Thermosipho africanus TCF52B
3 TPP

Thermosipho melanesiensis BI429
2 TPP

Fervidobacterium nodosum Rt17-B1
1 TPP

Petrotoga mobilis SJ95
1 TPP

Thermotogales bacterium TBF 19.5.1
Thiamine biosynthesis
RF00080 RNA yybP-ykoY
1 yybP-ykoY

Petrotoga mobilis SJ95
RF00162 RNA SAM
1 SAM

Petrotoga mobilis SJ95
Methionine biosynthesis
RF00167 RNA Purine
1 Purine

Thermotoga lettingae TMO
1 Purine

Petrotoga mobilis SJ95
Purine metabolism
RF00168 RNA Lysine
1 Lysine

Thermotoga maritima MSB8
1 Lysine

Thermotoga sp. RQ2
1 Lysine

Thermotoga neapolitana DSM 4359
1 Lysine

Thermotoga petrophila RKU-1
1 Lysine

Thermotoga naphthophila RKU-10
1 Lysine

Thermosipho africanus TCF52B
1 Lysine

Thermosipho melanesiensis BI429
1 Lysine

Petrotoga mobilis SJ95
1 Lysine

Thermotogales bacterium TBF 19.5.1
Lysine biosynthesis
RF00174 RNA Cobalamin
1 Cobalamin

Thermotoga maritima MSB8
1 Cobalamin

Thermotoga sp. RQ2
1 Cobalamin

Thermotoga neapolitana DSM 4359
1 Cobalamin

Thermotoga petrophila RKU-1
1 Cobalamin

Thermotoga naphthophila RKU-10
3 Cobalamin

Thermotoga lettingae TMO
3 Cobalamin

Thermosipho africanus TCF52B
4 Cobalamin

Thermosipho melanesiensis BI429
3 Cobalamin

Fervidobacterium nodosum Rt17-B1
1 Cobalamin

Petrotoga mobilis SJ95
1 Cobalamin

Thermotogales bacterium TBF 19.5.1
Cobalamin biosynthesis
RF00513 RNA Trp_leader
1 Trp_leader

Thermotoga lettingae TMO
1 Trp_leader

Thermosipho africanus TCF52B
1 Trp_leader

Thermosipho melanesiensis BI429
Tryptophan biosynthesis
RF00514 RNA His_leader
1 His_leader

Thermotoga lettingae TMO
Histidine biosynthesis
RF00557 RNA L10_leader
1 L10_leader

Thermotoga maritima MSB8
1 L10_leader

Thermotoga sp. RQ2
1 L10_leader

Thermotoga neapolitana DSM 4359
1 L10_leader

Thermotoga petrophila RKU-1
1 L10_leader

Thermotoga naphthophila RKU-10
1 L10_leader

Thermotoga lettingae TMO
1 L10_leader

Thermosipho africanus TCF52B
1 L10_leader

Thermosipho melanesiensis BI429
1 L10_leader

Fervidobacterium nodosum Rt17-B1
1 L10_leader

Petrotoga mobilis SJ95
1 L10_leader

Thermotogales bacterium TBF 19.5.1
Ribosome biogenesis
RF00558 RNA L20_leader
1 L20_leader

Thermotoga maritima MSB8
1 L20_leader

Thermotoga sp. RQ2
1 L20_leader

Thermotoga neapolitana DSM 4359
1 L20_leader

Thermotoga petrophila RKU-1
1 L20_leader

Thermotoga naphthophila RKU-10
1 L20_leader

Thermotoga lettingae TMO
1 L20_leader

Thermosipho africanus TCF52B
1 L20_leader

Thermosipho melanesiensis BI429
1 L20_leader

Fervidobacterium nodosum Rt17-B1
1 L20_leader

Petrotoga mobilis SJ95
Ribosome biogenesis
RF00559 RNA L21_leader
1 L21_leader

Thermotoga neapolitana DSM 4359
1 L21_leader

Thermotoga lettingae TMO
1 L21_leader

Thermosipho africanus TCF52B
1 L21_leader

Thermosipho melanesiensis BI429
Ribosome biogenesis
RF01055 RNA MOCO_RNA_motif
1 MOCO_RNA_motif

Thermotoga lettingae TMO
1 MOCO_RNA_motif

Petrotoga mobilis SJ95
Molybdopterin biosynthesis; Molybdenum homeostasis