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

Collection of regulogs in Bacteroidaceae taxonomic group

General statistics
Genomes 11
TF regulogs 38
TF regulons 223
TF binding sites 704
RNA regulogs 2
RNA regulons 22
RNA sites 84

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
Bacteroides cellulosilyticus DSM 14838 24 65 2 10 26 75
Bacteroides coprophilus DSM 18228 9 20 2 4 11 24
Bacteroides dorei DSM 17855 19 68 2 9 21 77
Bacteroides eggerthii DSM 20697 18 64 2 5 20 69
Bacteroides fragilis NCTC 9343 15 52 2 9 17 61
Bacteroides ovatus ATCC 8483 30 88 2 9 32 97
Bacteroides plebeius DSM 17135 20 51 2 5 22 56
Bacteroides stercoris ATCC 43183 16 55 2 7 18 62
Bacteroides thetaiotaomicron VPI-5482 36 109 2 9 38 118
Bacteroides uniformis ATCC 8492 17 60 2 7 19 67
Bacteroides vulgatus ATCC 8482 19 72 2 10 21 82
Genomic distribution of regulons
Family Type Regulator Function
AraC TF RhaR
1 RhaR

Bacteroides thetaiotaomicron VPI-5482
1 RhaR

Bacteroides vulgatus ATCC 8482
1 RhaR

Bacteroides dorei DSM 17855
1 RhaR

Bacteroides eggerthii DSM 20697
1 RhaR

Bacteroides uniformis ATCC 8492
1 RhaR

Bacteroides cellulosilyticus DSM 14838
1 RhaR

Bacteroides ovatus ATCC 8483
1 RhaR

Bacteroides stercoris ATCC 43183
Rhamnose utilization
ArgR TF ArgR
1 ArgR

Bacteroides thetaiotaomicron VPI-5482
1 ArgR

Bacteroides vulgatus ATCC 8482
1 ArgR

Bacteroides coprophilus DSM 18228
1 ArgR

Bacteroides dorei DSM 17855
1 ArgR

Bacteroides eggerthii DSM 20697
1 ArgR

Bacteroides fragilis NCTC 9343
1 ArgR

Bacteroides uniformis ATCC 8492
1 ArgR

Bacteroides cellulosilyticus DSM 14838
1 ArgR

Bacteroides plebeius DSM 17135
1 ArgR

Bacteroides ovatus ATCC 8483
1 ArgR

Bacteroides stercoris ATCC 43183
Arginine biosynthesis
CRP TF Crp
13 Crp

Bacteroides thetaiotaomicron VPI-5482
10 Crp

Bacteroides vulgatus ATCC 8482
3 Crp

Bacteroides coprophilus DSM 18228
10 Crp

Bacteroides dorei DSM 17855
11 Crp

Bacteroides eggerthii DSM 20697
11 Crp

Bacteroides fragilis NCTC 9343
12 Crp

Bacteroides uniformis ATCC 8492
11 Crp

Bacteroides cellulosilyticus DSM 14838
4 Crp

Bacteroides plebeius DSM 17135
11 Crp

Bacteroides ovatus ATCC 8483
9 Crp

Bacteroides stercoris ATCC 43183
TF HcpR
1 HcpR

Bacteroides thetaiotaomicron VPI-5482
2 HcpR

Bacteroides vulgatus ATCC 8482
3 HcpR

Bacteroides coprophilus DSM 18228
2 HcpR

Bacteroides dorei DSM 17855
2 HcpR

Bacteroides fragilis NCTC 9343
2 HcpR

Bacteroides uniformis ATCC 8492
2 HcpR

Bacteroides cellulosilyticus DSM 14838
3 HcpR

Bacteroides plebeius DSM 17135
1 HcpR

Bacteroides ovatus ATCC 8483
Nitrosative stress response
TF NrfR
1 NrfR

Bacteroides thetaiotaomicron VPI-5482
1 NrfR

Bacteroides fragilis NCTC 9343
1 NrfR

Bacteroides uniformis ATCC 8492
1 NrfR

Bacteroides cellulosilyticus DSM 14838
1 NrfR

Bacteroides plebeius DSM 17135
1 NrfR

Bacteroides ovatus ATCC 8483
Nitrate and nitrite respiration
FUR TF Fur
1 Fur

Bacteroides thetaiotaomicron VPI-5482
1 Fur

Bacteroides vulgatus ATCC 8482
1 Fur

Bacteroides coprophilus DSM 18228
1 Fur

Bacteroides dorei DSM 17855
1 Fur

Bacteroides eggerthii DSM 20697
1 Fur

Bacteroides fragilis NCTC 9343
1 Fur

Bacteroides uniformis ATCC 8492
1 Fur

Bacteroides cellulosilyticus DSM 14838
1 Fur

Bacteroides plebeius DSM 17135
1 Fur

Bacteroides ovatus ATCC 8483
1 Fur

Bacteroides stercoris ATCC 43183
Iron homeostasis
TF PerR
3 PerR

Bacteroides thetaiotaomicron VPI-5482
7 PerR

Bacteroides vulgatus ATCC 8482
6 PerR

Bacteroides coprophilus DSM 18228
7 PerR

Bacteroides dorei DSM 17855
4 PerR

Bacteroides eggerthii DSM 20697
3 PerR

Bacteroides fragilis NCTC 9343
5 PerR

Bacteroides uniformis ATCC 8492
4 PerR

Bacteroides cellulosilyticus DSM 14838
5 PerR

Bacteroides plebeius DSM 17135
3 PerR

Bacteroides ovatus ATCC 8483
4 PerR

Bacteroides stercoris ATCC 43183
Peroxide stress response; Oxidative stress response
TF Zur
3 Zur

Bacteroides thetaiotaomicron VPI-5482
3 Zur

Bacteroides vulgatus ATCC 8482
2 Zur

Bacteroides coprophilus DSM 18228
3 Zur

Bacteroides dorei DSM 17855
2 Zur

Bacteroides eggerthii DSM 20697
1 Zur

Bacteroides fragilis NCTC 9343
2 Zur

Bacteroides uniformis ATCC 8492
3 Zur

Bacteroides cellulosilyticus DSM 14838
1 Zur

Bacteroides plebeius DSM 17135
3 Zur

Bacteroides ovatus ATCC 8483
2 Zur

Bacteroides stercoris ATCC 43183
Zinc homeostasis
GntR/MocR TF BACOVA_03038
1 BACOVA_03038

Bacteroides ovatus ATCC 8483
GntR/Others TF FucR
1 FucR

Bacteroides thetaiotaomicron VPI-5482
1 FucR

Bacteroides vulgatus ATCC 8482
1 FucR

Bacteroides dorei DSM 17855
2 FucR

Bacteroides fragilis NCTC 9343
1 FucR

Bacteroides cellulosilyticus DSM 14838
1 FucR

Bacteroides plebeius DSM 17135
1 FucR

Bacteroides ovatus ATCC 8483
Fucose utilization
TF GalR
2 GalR

Bacteroides thetaiotaomicron VPI-5482
1 GalR

Bacteroides fragilis NCTC 9343
Galactose utilization
TF ManR
3 ManR

Bacteroides thetaiotaomicron VPI-5482
3 ManR

Bacteroides eggerthii DSM 20697
3 ManR

Bacteroides ovatus ATCC 8483
Mannose utilization; Mannosides utilization
LacI TF KdgR
4 KdgR

Bacteroides thetaiotaomicron VPI-5482
4 KdgR

Bacteroides vulgatus ATCC 8482
3 KdgR

Bacteroides dorei DSM 17855
4 KdgR

Bacteroides eggerthii DSM 20697
4 KdgR

Bacteroides fragilis NCTC 9343
4 KdgR

Bacteroides uniformis ATCC 8492
3 KdgR

Bacteroides cellulosilyticus DSM 14838
3 KdgR

Bacteroides plebeius DSM 17135
4 KdgR

Bacteroides ovatus ATCC 8483
4 KdgR

Bacteroides stercoris ATCC 43183
Glucuronate utilization; Galacturonate utilization
TF LgoR
3 LgoR

Bacteroides thetaiotaomicron VPI-5482
2 LgoR

Bacteroides vulgatus ATCC 8482
2 LgoR

Bacteroides dorei DSM 17855
1 LgoR

Bacteroides eggerthii DSM 20697
3 LgoR

Bacteroides cellulosilyticus DSM 14838
2 LgoR

Bacteroides ovatus ATCC 8483
L-galactose utilization
TF MalR
6 MalR

Bacteroides eggerthii DSM 20697
4 MalR

Bacteroides fragilis NCTC 9343
7 MalR

Bacteroides uniformis ATCC 8492
4 MalR

Bacteroides cellulosilyticus DSM 14838
7 MalR

Bacteroides stercoris ATCC 43183
Maltose utilization
TF UxaR
2 UxaR

Bacteroides thetaiotaomicron VPI-5482
2 UxaR

Bacteroides eggerthii DSM 20697
2 UxaR

Bacteroides uniformis ATCC 8492
2 UxaR

Bacteroides cellulosilyticus DSM 14838
2 UxaR

Bacteroides ovatus ATCC 8483
2 UxaR

Bacteroides stercoris ATCC 43183
Glucuronate utilization; Galacturonate utilization
TF UxuR
1 UxuR

Bacteroides thetaiotaomicron VPI-5482
1 UxuR

Bacteroides plebeius DSM 17135
1 UxuR

Bacteroides ovatus ATCC 8483
Glucuronate utilization
NrtR TF AraR
4 AraR

Bacteroides thetaiotaomicron VPI-5482
1 AraR

Bacteroides vulgatus ATCC 8482
1 AraR

Bacteroides dorei DSM 17855
2 AraR

Bacteroides eggerthii DSM 20697
2 AraR

Bacteroides uniformis ATCC 8492
2 AraR

Bacteroides cellulosilyticus DSM 14838
3 AraR

Bacteroides plebeius DSM 17135
2 AraR

Bacteroides ovatus ATCC 8483
Arabinose utilization
TF XylR
2 XylR

Bacteroides thetaiotaomicron VPI-5482
4 XylR

Bacteroides vulgatus ATCC 8482
4 XylR

Bacteroides dorei DSM 17855
2 XylR

Bacteroides eggerthii DSM 20697
1 XylR

Bacteroides fragilis NCTC 9343
1 XylR

Bacteroides uniformis ATCC 8492
2 XylR

Bacteroides cellulosilyticus DSM 14838
1 XylR

Bacteroides plebeius DSM 17135
2 XylR

Bacteroides ovatus ATCC 8483
2 XylR

Bacteroides stercoris ATCC 43183
Xylose utilization
ROK TF NanR
3 NanR

Bacteroides thetaiotaomicron VPI-5482
5 NanR

Bacteroides vulgatus ATCC 8482
2 NanR

Bacteroides coprophilus DSM 18228
4 NanR

Bacteroides dorei DSM 17855
4 NanR

Bacteroides eggerthii DSM 20697
7 NanR

Bacteroides fragilis NCTC 9343
5 NanR

Bacteroides uniformis ATCC 8492
2 NanR

Bacteroides cellulosilyticus DSM 14838
5 NanR

Bacteroides plebeius DSM 17135
4 NanR

Bacteroides ovatus ATCC 8483
5 NanR

Bacteroides stercoris ATCC 43183
Sialic acid utilization; N-acetylglucosamine utilization
[Other] TF HTCS_Aga-1
3 HTCS_Aga-1

Bacteroides thetaiotaomicron VPI-5482
Arabinogalactan utilization
TF HTCS_Ara-1
2 HTCS_Ara-1

Bacteroides thetaiotaomicron VPI-5482
2 HTCS_Ara-1

Bacteroides vulgatus ATCC 8482
2 HTCS_Ara-1

Bacteroides dorei DSM 17855
2 HTCS_Ara-1

Bacteroides eggerthii DSM 20697
1 HTCS_Ara-1

Bacteroides cellulosilyticus DSM 14838
2 HTCS_Ara-1

Bacteroides plebeius DSM 17135
Arabinan utilization
TF HTCS_Ara-2
3 HTCS_Ara-2

Bacteroides thetaiotaomicron VPI-5482
1 HTCS_Ara-2

Bacteroides vulgatus ATCC 8482
1 HTCS_Ara-2

Bacteroides dorei DSM 17855
1 HTCS_Ara-2

Bacteroides cellulosilyticus DSM 14838
2 HTCS_Ara-2

Bacteroides plebeius DSM 17135
3 HTCS_Ara-2

Bacteroides ovatus ATCC 8483
Arabinan utilization
TF HTCS_Fru
4 HTCS_Fru

Bacteroides thetaiotaomicron VPI-5482
2 HTCS_Fru

Bacteroides vulgatus ATCC 8482
1 HTCS_Fru

Bacteroides coprophilus DSM 18228
1 HTCS_Fru

Bacteroides dorei DSM 17855
2 HTCS_Fru

Bacteroides fragilis NCTC 9343
2 HTCS_Fru

Bacteroides uniformis ATCC 8492
3 HTCS_Fru

Bacteroides cellulosilyticus DSM 14838
2 HTCS_Fru

Bacteroides plebeius DSM 17135
3 HTCS_Fru

Bacteroides ovatus ATCC 8483
2 HTCS_Fru

Bacteroides stercoris ATCC 43183
Fructosides utilization; Fructose utilization
TF HTCS_Hep
3 HTCS_Hep

Bacteroides thetaiotaomicron VPI-5482
2 HTCS_Hep

Bacteroides eggerthii DSM 20697
3 HTCS_Hep

Bacteroides ovatus ATCC 8483
2 HTCS_Hep

Bacteroides stercoris ATCC 43183
Heparin utilization
TF HTCS_Hya
2 HTCS_Hya

Bacteroides thetaiotaomicron VPI-5482
2 HTCS_Hya

Bacteroides eggerthii DSM 20697
1 HTCS_Hya

Bacteroides uniformis ATCC 8492
2 HTCS_Hya

Bacteroides cellulosilyticus DSM 14838
1 HTCS_Hya

Bacteroides plebeius DSM 17135
2 HTCS_Hya

Bacteroides ovatus ATCC 8483
3 HTCS_Hya

Bacteroides stercoris ATCC 43183
Hyaluronan utilization; Chondroitin sulphate utilization
TF HTCS_Man-1
2 HTCS_Man-1

Bacteroides thetaiotaomicron VPI-5482
1 HTCS_Man-1

Bacteroides ovatus ATCC 8483
Alpha-mannans utilization
TF HTCS_Man-2
1 HTCS_Man-2

Bacteroides thetaiotaomicron VPI-5482
Alpha-mannans utilization
TF HTCS_Man-3
4 HTCS_Man-3

Bacteroides thetaiotaomicron VPI-5482
1 HTCS_Man-3

Bacteroides fragilis NCTC 9343
2 HTCS_Man-3

Bacteroides cellulosilyticus DSM 14838
Alpha-mannans utilization
TF HTCS_Ogl-1
1 HTCS_Ogl-1

Bacteroides thetaiotaomicron VPI-5482
O-glycans utilization
TF HTCS_Ogl-2
2 HTCS_Ogl-2

Bacteroides thetaiotaomicron VPI-5482
O-glycans utilization
TF HTCS_Pga
1 HTCS_Pga

Bacteroides thetaiotaomicron VPI-5482
1 HTCS_Pga

Bacteroides cellulosilyticus DSM 14838
1 HTCS_Pga

Bacteroides ovatus ATCC 8483
Pectic galactan utilization
TF HTCS_Rgu-1
5 HTCS_Rgu-1

Bacteroides thetaiotaomicron VPI-5482
4 HTCS_Rgu-1

Bacteroides vulgatus ATCC 8482
4 HTCS_Rgu-1

Bacteroides dorei DSM 17855
3 HTCS_Rgu-1

Bacteroides eggerthii DSM 20697
3 HTCS_Rgu-1

Bacteroides cellulosilyticus DSM 14838
2 HTCS_Rgu-1

Bacteroides plebeius DSM 17135
3 HTCS_Rgu-1

Bacteroides ovatus ATCC 8483
2 HTCS_Rgu-1

Bacteroides stercoris ATCC 43183
Rhamnogalacturonides utilization
TF HTCS_Rgu-2
8 HTCS_Rgu-2

Bacteroides thetaiotaomicron VPI-5482
8 HTCS_Rgu-2

Bacteroides vulgatus ATCC 8482
8 HTCS_Rgu-2

Bacteroides dorei DSM 17855
6 HTCS_Rgu-2

Bacteroides plebeius DSM 17135
8 HTCS_Rgu-2

Bacteroides ovatus ATCC 8483
Rhamnogalacturonides utilization
TF SusR
2 SusR

Bacteroides thetaiotaomicron VPI-5482
2 SusR

Bacteroides vulgatus ATCC 8482
1 SusR

Bacteroides coprophilus DSM 18228
2 SusR

Bacteroides dorei DSM 17855
2 SusR

Bacteroides plebeius DSM 17135
2 SusR

Bacteroides ovatus ATCC 8483
Starch utilization
TF SusR2
1 SusR2

Bacteroides thetaiotaomicron VPI-5482
1 SusR2

Bacteroides uniformis ATCC 8492
1 SusR2

Bacteroides cellulosilyticus DSM 14838
1 SusR2

Bacteroides ovatus ATCC 8483
1 SusR2

Bacteroides stercoris ATCC 43183
Starch utilization
TF SusR3
1 SusR3

Bacteroides thetaiotaomicron VPI-5482
1 SusR3

Bacteroides ovatus ATCC 8483
Polysaccharides utilization
TF SusR4
1 SusR4

Bacteroides thetaiotaomicron VPI-5482
1 SusR4

Bacteroides ovatus ATCC 8483
Polysaccharides utilization
RF00059 RNA TPP
3 TPP

Bacteroides thetaiotaomicron VPI-5482
1 TPP

Bacteroides vulgatus ATCC 8482
1 TPP

Bacteroides coprophilus DSM 18228
1 TPP

Bacteroides dorei DSM 17855
2 TPP

Bacteroides eggerthii DSM 20697
2 TPP

Bacteroides fragilis NCTC 9343
2 TPP

Bacteroides uniformis ATCC 8492
2 TPP

Bacteroides cellulosilyticus DSM 14838
1 TPP

Bacteroides plebeius DSM 17135
2 TPP

Bacteroides ovatus ATCC 8483
2 TPP

Bacteroides stercoris ATCC 43183
Thiamine biosynthesis
RF00174 RNA Cobalamin
6 Cobalamin

Bacteroides thetaiotaomicron VPI-5482
9 Cobalamin

Bacteroides vulgatus ATCC 8482
3 Cobalamin

Bacteroides coprophilus DSM 18228
8 Cobalamin

Bacteroides dorei DSM 17855
3 Cobalamin

Bacteroides eggerthii DSM 20697
7 Cobalamin

Bacteroides fragilis NCTC 9343
5 Cobalamin

Bacteroides uniformis ATCC 8492
8 Cobalamin

Bacteroides cellulosilyticus DSM 14838
4 Cobalamin

Bacteroides plebeius DSM 17135
7 Cobalamin

Bacteroides ovatus ATCC 8483
5 Cobalamin

Bacteroides stercoris ATCC 43183
Cobalamin biosynthesis