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

Collection of regulogs in Rhodospirillales taxonomic group

General statistics
Genomes 9
TF regulogs 40
TF regulons 154
TF binding sites 528
RNA regulogs 3
RNA regulons 14
RNA sites 20

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
Acetobacter pasteurianus IFO 3283-01 13 44 2 3 15 47
Azospirillum sp. B510 27 87 1 3 28 90
Gluconacetobacter diazotrophicus PAl 5 18 49 2 2 20 51
Gluconobacter oxydans 621H 10 33 2 3 12 36
Granulibacter bethesdensis CGDNIH1 11 33 1 1 12 34
Magnetospirillum magneticum AMB-1 16 59 1 1 17 60
Magnetospirillum magnetotacticum MS-1 20 75 2 3 22 78
Rhodospirillum centenum SW 17 70 1 2 18 72
Rhodospirillum rubrum ATCC 11170 22 78 2 2 24 80
Genomic distribution of regulons
Family Type Regulator Function
ArsR TF SahR
3 SahR

Rhodospirillum rubrum ATCC 11170
2 SahR

Magnetospirillum magneticum AMB-1
3 SahR

Magnetospirillum magnetotacticum MS-1
2 SahR

Azospirillum sp. B510
2 SahR

Rhodospirillum centenum SW
2 SahR

Gluconacetobacter diazotrophicus PAl 5
3 SahR

Granulibacter bethesdensis CGDNIH1
Methionine metabolism
CRP TF FnrN
2 FnrN

Rhodospirillum rubrum ATCC 11170
1 FnrN

Magnetospirillum magneticum AMB-1
2 FnrN

Magnetospirillum magnetotacticum MS-1
2 FnrN

Azospirillum sp. B510
4 FnrN

Rhodospirillum centenum SW
2 FnrN

Gluconacetobacter diazotrophicus PAl 5
2 FnrN

Acetobacter pasteurianus IFO 3283-01
2 FnrN

Gluconobacter oxydans 621H
Oxidative stress response; Nitrogen fixation
TF NnrR
3 NnrR

Rhodospirillum centenum SW
Denitrification
DtxR TF MntR
2 MntR

Azospirillum sp. B510
2 MntR

Gluconacetobacter diazotrophicus PAl 5
2 MntR

Acetobacter pasteurianus IFO 3283-01
2 MntR

Gluconobacter oxydans 621H
Manganese homeostasis
FUR TF Fur
21 Fur

Rhodospirillum rubrum ATCC 11170
10 Fur

Magnetospirillum magneticum AMB-1
11 Fur

Magnetospirillum magnetotacticum MS-1
7 Fur

Azospirillum sp. B510
10 Fur

Rhodospirillum centenum SW
5 Fur

Gluconacetobacter diazotrophicus PAl 5
13 Fur

Acetobacter pasteurianus IFO 3283-01
6 Fur

Gluconobacter oxydans 621H
7 Fur

Granulibacter bethesdensis CGDNIH1
Iron homeostasis
TF Irr
2 Irr

Rhodospirillum rubrum ATCC 11170
1 Irr

Magnetospirillum magneticum AMB-1
4 Irr

Magnetospirillum magnetotacticum MS-1
1 Irr

Azospirillum sp. B510
4 Irr

Rhodospirillum centenum SW
Iron homeostasis
TF Zur
1 Zur

Rhodospirillum rubrum ATCC 11170
2 Zur

Magnetospirillum magneticum AMB-1
3 Zur

Magnetospirillum magnetotacticum MS-1
3 Zur

Azospirillum sp. B510
3 Zur

Rhodospirillum centenum SW
3 Zur

Gluconacetobacter diazotrophicus PAl 5
3 Zur

Acetobacter pasteurianus IFO 3283-01
5 Zur

Gluconobacter oxydans 621H
4 Zur

Granulibacter bethesdensis CGDNIH1
Zinc homeostasis
Fis TF NifA
6 NifA

Rhodospirillum rubrum ATCC 11170
6 NifA

Magnetospirillum magneticum AMB-1
6 NifA

Magnetospirillum magnetotacticum MS-1
6 NifA

Azospirillum sp. B510
5 NifA

Rhodospirillum centenum SW
5 NifA

Gluconacetobacter diazotrophicus PAl 5
Nitrogen fixation
TF NtrC
4 NtrC

Rhodospirillum rubrum ATCC 11170
7 NtrC

Magnetospirillum magneticum AMB-1
6 NtrC

Magnetospirillum magnetotacticum MS-1
7 NtrC

Azospirillum sp. B510
4 NtrC

Rhodospirillum centenum SW
2 NtrC

Gluconacetobacter diazotrophicus PAl 5
1 NtrC

Acetobacter pasteurianus IFO 3283-01
2 NtrC

Granulibacter bethesdensis CGDNIH1
Nitrogen assimilation
GntR/MocR TF OapR
2 OapR

Acetobacter pasteurianus IFO 3283-01
Amino acid metabolism
TF PdxQ
1 PdxQ

Rhodospirillum rubrum ATCC 11170
Pyridoxine/pyridoxal homeostasis
TF PdxQ2
4 PdxQ2

Rhodospirillum rubrum ATCC 11170
3 PdxQ2

Gluconacetobacter diazotrophicus PAl 5
Metabolite transport; Pyridoxine/pyridoxal homeostasis
TF PdxR
2 PdxR

Rhodospirillum rubrum ATCC 11170
Pyridoxine/pyridoxal homeostasis
TF PdxW
1 PdxW

Magnetospirillum magneticum AMB-1
1 PdxW

Magnetospirillum magnetotacticum MS-1
Pyridoxine/pyridoxal homeostasis
TF YrdX3
1 YrdX3

Gluconacetobacter diazotrophicus PAl 5
1 YrdX3

Acetobacter pasteurianus IFO 3283-01
GntR/Others TF Gdia_0881
2 Gdia_0881

Gluconacetobacter diazotrophicus PAl 5
TF HutC
3 HutC

Rhodospirillum rubrum ATCC 11170
2 HutC

Azospirillum sp. B510
2 HutC

Rhodospirillum centenum SW
2 HutC

Gluconacetobacter diazotrophicus PAl 5
4 HutC

Gluconobacter oxydans 621H
Histidine utilization
TF HypR
1 HypR

Rhodospirillum rubrum ATCC 11170
Proline and 4-hydrohyproline utilization
TF LldR
2 LldR

Rhodospirillum rubrum ATCC 11170
3 LldR

Magnetospirillum magneticum AMB-1
4 LldR

Magnetospirillum magnetotacticum MS-1
2 LldR

Azospirillum sp. B510
Lactate utilization
TF MdcY
2 MdcY

Magnetospirillum magneticum AMB-1
2 MdcY

Magnetospirillum magnetotacticum MS-1
Malonate metabolism
TF NagQ
4 NagQ

Azospirillum sp. B510
N-acetylglucosamine utilization
HrcA TF HrcA
1 HrcA

Rhodospirillum rubrum ATCC 11170
1 HrcA

Magnetospirillum magneticum AMB-1
1 HrcA

Magnetospirillum magnetotacticum MS-1
1 HrcA

Azospirillum sp. B510
1 HrcA

Rhodospirillum centenum SW
1 HrcA

Gluconacetobacter diazotrophicus PAl 5
1 HrcA

Acetobacter pasteurianus IFO 3283-01
1 HrcA

Gluconobacter oxydans 621H
1 HrcA

Granulibacter bethesdensis CGDNIH1
Heat shock response
LacI TF AZL_a08610
2 AZL_a08610

Azospirillum sp. B510
Sugar utilization
TF FruR2
2 FruR2

Rhodospirillum rubrum ATCC 11170
2 FruR2

Azospirillum sp. B510
2 FruR2

Granulibacter bethesdensis CGDNIH1
Fructose utilization
TF GntR
2 GntR

Azospirillum sp. B510
Gluconate utilization
LexA TF LexA
3 LexA

Rhodospirillum rubrum ATCC 11170
5 LexA

Magnetospirillum magneticum AMB-1
6 LexA

Magnetospirillum magnetotacticum MS-1
6 LexA

Azospirillum sp. B510
5 LexA

Rhodospirillum centenum SW
6 LexA

Gluconacetobacter diazotrophicus PAl 5
6 LexA

Acetobacter pasteurianus IFO 3283-01
5 LexA

Gluconobacter oxydans 621H
5 LexA

Granulibacter bethesdensis CGDNIH1
SOS response
MerR TF CadR-PbrR
1 CadR-PbrR

Rhodospirillum rubrum ATCC 11170
1 CadR-PbrR

Magnetospirillum magnetotacticum MS-1
1 CadR-PbrR

Azospirillum sp. B510
Lead resistance; Cadmium resistance
TF CueR
2 CueR

Magnetospirillum magneticum AMB-1
4 CueR

Magnetospirillum magnetotacticum MS-1
1 CueR

Azospirillum sp. B510
Copper resistance
TF LiuR
4 LiuR

Rhodospirillum rubrum ATCC 11170
3 LiuR

Azospirillum sp. B510
3 LiuR

Rhodospirillum centenum SW
Branched-chain amino acid degradation
TF SoxR
1 SoxR

Azospirillum sp. B510
Superoxide stress response
ModE TF ModE
3 ModE

Magnetospirillum magneticum AMB-1
3 ModE

Magnetospirillum magnetotacticum MS-1
Molybdopterin biosynthesis
TF ModE2
1 ModE2

Azospirillum sp. B510
1 ModE2

Rhodospirillum centenum SW
Molybdenum homeostasis
NadQ TF NadQ
1 NadQ

Rhodospirillum rubrum ATCC 11170
1 NadQ

Magnetospirillum magnetotacticum MS-1
1 NadQ

Azospirillum sp. B510
1 NadQ

Rhodospirillum centenum SW
1 NadQ

Gluconacetobacter diazotrophicus PAl 5
1 NadQ

Acetobacter pasteurianus IFO 3283-01
1 NadQ

Granulibacter bethesdensis CGDNIH1
NAD biosynthesis
NikR TF NikR
2 NikR

Azospirillum sp. B510
Nickel homeostasis
NrdR TF NrdR
2 NrdR

Rhodospirillum rubrum ATCC 11170
1 NrdR

Magnetospirillum magneticum AMB-1
1 NrdR

Magnetospirillum magnetotacticum MS-1
1 NrdR

Azospirillum sp. B510
3 NrdR

Rhodospirillum centenum SW
2 NrdR

Gluconacetobacter diazotrophicus PAl 5
1 NrdR

Acetobacter pasteurianus IFO 3283-01
1 NrdR

Gluconobacter oxydans 621H
2 NrdR

Granulibacter bethesdensis CGDNIH1
Deoxyribonucleotide biosynthesis
Rrf2 TF IscR
1 IscR

Rhodospirillum rubrum ATCC 11170
1 IscR

Magnetospirillum magneticum AMB-1
1 IscR

Magnetospirillum magnetotacticum MS-1
1 IscR

Azospirillum sp. B510
1 IscR

Rhodospirillum centenum SW
Iron-sulfur cluster biogenesis
TF IscR2
1 IscR2

Rhodospirillum rubrum ATCC 11170
1 IscR2

Azospirillum sp. B510
1 IscR2

Rhodospirillum centenum SW
1 IscR2

Gluconacetobacter diazotrophicus PAl 5
1 IscR2

Acetobacter pasteurianus IFO 3283-01
1 IscR2

Gluconobacter oxydans 621H
1 IscR2

Granulibacter bethesdensis CGDNIH1
Iron-sulfur cluster biogenesis
TF NsrR
2 NsrR

Magnetospirillum magnetotacticum MS-1
2 NsrR

Gluconacetobacter diazotrophicus PAl 5
3 NsrR

Acetobacter pasteurianus IFO 3283-01
2 NsrR

Gluconobacter oxydans 621H
2 NsrR

Granulibacter bethesdensis CGDNIH1
Nitrosative stress response
SdaR TF SdaR
1 SdaR

Azospirillum sp. B510
2 SdaR

Gluconacetobacter diazotrophicus PAl 5
Glycerate utilization
TetR TF RutR
1 RutR

Magnetospirillum magnetotacticum MS-1
Pyrimidine utilization
RF00050 RNA FMN
1 FMN

Rhodospirillum rubrum ATCC 11170
1 FMN

Gluconacetobacter diazotrophicus PAl 5
1 FMN

Acetobacter pasteurianus IFO 3283-01
1 FMN

Gluconobacter oxydans 621H
Riboflavin biosynthesis
RF00059 RNA TPP
1 TPP

Rhodospirillum rubrum ATCC 11170
1 TPP

Magnetospirillum magneticum AMB-1
2 TPP

Magnetospirillum magnetotacticum MS-1
3 TPP

Azospirillum sp. B510
2 TPP

Rhodospirillum centenum SW
1 TPP

Gluconacetobacter diazotrophicus PAl 5
2 TPP

Acetobacter pasteurianus IFO 3283-01
2 TPP

Gluconobacter oxydans 621H
1 TPP

Granulibacter bethesdensis CGDNIH1
Thiamine biosynthesis
RF01055 RNA MOCO_RNA_motif
1 MOCO_RNA_motif

Magnetospirillum magnetotacticum MS-1
Molybdopterin biosynthesis