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

Collection of regulogs in Nocardiaceae taxonomic group

General statistics
Genomes 4
TF regulogs 35
TF regulons 114
TF binding sites 381
RNA regulogs 0
RNA regulons 0
RNA sites 0

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
Nocardia farcinica IFM 10152 24 68 0 0 24 68
Rhodococcus erythropolis PR4 28 82 0 0 28 82
Rhodococcus opacus B4 31 115 0 0 31 115
Rhodococcus sp. RHA1 31 116 0 0 31 116
Genomic distribution of regulons
Family Type Regulator Function
ArgR TF ArgR
2 ArgR

Nocardia farcinica IFM 10152
1 ArgR

Rhodococcus erythropolis PR4
1 ArgR

Rhodococcus sp. RHA1
1 ArgR

Rhodococcus opacus B4
Arginine biosynthesis
ArsR TF ArsR
2 ArsR

Nocardia farcinica IFM 10152
2 ArsR

Rhodococcus erythropolis PR4
1 ArsR

Rhodococcus sp. RHA1
2 ArsR

Rhodococcus opacus B4
Arsenic resistance
CsoR TF CsoR
2 CsoR

Nocardia farcinica IFM 10152
2 CsoR

Rhodococcus erythropolis PR4
1 CsoR

Rhodococcus sp. RHA1
2 CsoR

Rhodococcus opacus B4
Copper resistance
DtxR TF MntR
1 MntR

Nocardia farcinica IFM 10152
3 MntR

Rhodococcus erythropolis PR4
3 MntR

Rhodococcus sp. RHA1
3 MntR

Rhodococcus opacus B4
Manganese homeostasis
FUR TF Zur
5 Zur

Nocardia farcinica IFM 10152
5 Zur

Rhodococcus erythropolis PR4
6 Zur

Rhodococcus sp. RHA1
6 Zur

Rhodococcus opacus B4
Zinc homeostasis
GntR/MocR TF Nfa21130
1 Nfa21130

Nocardia farcinica IFM 10152
1 Nfa21130

Rhodococcus erythropolis PR4
1 Nfa21130

Rhodococcus sp. RHA1
1 Nfa21130

Rhodococcus opacus B4
Metabolite transport
TF PdxQ
3 PdxQ

Rhodococcus erythropolis PR4
Pyridoxine/pyridoxal homeostasis; Metabolite transport
TF PdxQ3
1 PdxQ3

Nocardia farcinica IFM 10152
Pyridoxine/pyridoxal homeostasis
TF PdxR2
1 PdxR2

Nocardia farcinica IFM 10152
1 PdxR2

Rhodococcus erythropolis PR4
1 PdxR2

Rhodococcus sp. RHA1
1 PdxR2

Rhodococcus opacus B4
Pyridoxine/pyridoxal homeostasis
TF PdxR3
2 PdxR3

Nocardia farcinica IFM 10152
2 PdxR3

Rhodococcus erythropolis PR4
3 PdxR3

Rhodococcus sp. RHA1
4 PdxR3

Rhodococcus opacus B4
Pyridoxine/pyridoxal homeostasis
TF RHA1_ro08093
2 RHA1_ro08093

Rhodococcus sp. RHA1
TF TauR
5 TauR

Rhodococcus sp. RHA1
5 TauR

Rhodococcus opacus B4
Taurine utilization
GntR/Others TF AnsR
2 AnsR

Rhodococcus erythropolis PR4
2 AnsR

Rhodococcus sp. RHA1
2 AnsR

Rhodococcus opacus B4
Aspartate utilization; Asparagine degradation
TF DasR
2 DasR

Rhodococcus erythropolis PR4
2 DasR

Rhodococcus sp. RHA1
2 DasR

Rhodococcus opacus B4
N-acetylglucosamine utilization
TF HutC
5 HutC

Nocardia farcinica IFM 10152
3 HutC

Rhodococcus erythropolis PR4
2 HutC

Rhodococcus sp. RHA1
2 HutC

Rhodococcus opacus B4
Histidine utilization
TF IolR
3 IolR

Rhodococcus erythropolis PR4
6 IolR

Rhodococcus sp. RHA1
6 IolR

Rhodococcus opacus B4
Inositol utilization
TF LldR
2 LldR

Rhodococcus erythropolis PR4
2 LldR

Rhodococcus sp. RHA1
2 LldR

Rhodococcus opacus B4
Lactate utilization
TF Mce2R
2 Mce2R

Nocardia farcinica IFM 10152
1 Mce2R

Rhodococcus erythropolis PR4
1 Mce2R

Rhodococcus sp. RHA1
1 Mce2R

Rhodococcus opacus B4
Fatty acid metabolism
TF Nfa20840
1 Nfa20840

Nocardia farcinica IFM 10152
5 Nfa20840

Rhodococcus sp. RHA1
4 Nfa20840

Rhodococcus opacus B4
TF Nfa3720
1 Nfa3720

Nocardia farcinica IFM 10152
1 Nfa3720

Rhodococcus erythropolis PR4
1 Nfa3720

Rhodococcus opacus B4
Multidrug resistance; Multidrug efflux
TF PhnF
3 PhnF

Nocardia farcinica IFM 10152
2 PhnF

Rhodococcus erythropolis PR4
2 PhnF

Rhodococcus sp. RHA1
2 PhnF

Rhodococcus opacus B4
Phosphonate utilization; 2-aminoethylphosphonate utilization
TF RER_29210
1 RER_29210

Rhodococcus erythropolis PR4
1 RER_29210

Rhodococcus sp. RHA1
1 RER_29210

Rhodococcus opacus B4
Multidrug efflux
TF ROP_32700
2 ROP_32700

Rhodococcus sp. RHA1
2 ROP_32700

Rhodococcus opacus B4
HrcA TF HrcA
4 HrcA

Nocardia farcinica IFM 10152
4 HrcA

Rhodococcus erythropolis PR4
4 HrcA

Rhodococcus sp. RHA1
3 HrcA

Rhodococcus opacus B4
Heat shock response
HxlR TF QorR
2 QorR

Rhodococcus erythropolis PR4
2 QorR

Rhodococcus sp. RHA1
2 QorR

Rhodococcus opacus B4
Energy metabolism
IclR TF LtbR
2 LtbR

Nocardia farcinica IFM 10152
2 LtbR

Rhodococcus erythropolis PR4
2 LtbR

Rhodococcus sp. RHA1
2 LtbR

Rhodococcus opacus B4
Leucine biosynthesis
LacI TF RhaR
1 RhaR

Nocardia farcinica IFM 10152
2 RhaR

Rhodococcus sp. RHA1
Rhamnose utilization
LexA TF LexA
6 LexA

Nocardia farcinica IFM 10152
8 LexA

Rhodococcus erythropolis PR4
7 LexA

Rhodococcus sp. RHA1
7 LexA

Rhodococcus opacus B4
SOS response
NrdR TF NrdR
2 NrdR

Nocardia farcinica IFM 10152
1 NrdR

Rhodococcus erythropolis PR4
1 NrdR

Rhodococcus sp. RHA1
1 NrdR

Rhodococcus opacus B4
Deoxyribonucleotide biosynthesis
NrtR TF NrtR
1 NrtR

Rhodococcus opacus B4
NAD biosynthesis
Rex TF Rex
2 Rex

Nocardia farcinica IFM 10152
4 Rex

Rhodococcus erythropolis PR4
8 Rex

Rhodococcus sp. RHA1
8 Rex

Rhodococcus opacus B4
Energy metabolism
TetR TF AcnR
2 AcnR

Nocardia farcinica IFM 10152
2 AcnR

Rhodococcus erythropolis PR4
2 AcnR

Rhodococcus sp. RHA1
2 AcnR

Rhodococcus opacus B4
Tricarboxylic acid cycle
TF AmtR
2 AmtR

Nocardia farcinica IFM 10152
2 AmtR

Rhodococcus erythropolis PR4
1 AmtR

Rhodococcus sp. RHA1
2 AmtR

Rhodococcus opacus B4
Nitrogen metabolism
TF BioQ
4 BioQ

Nocardia farcinica IFM 10152
4 BioQ

Rhodococcus erythropolis PR4
5 BioQ

Rhodococcus sp. RHA1
6 BioQ

Rhodococcus opacus B4
Biotin biosynthesis
TF PaaR
4 PaaR

Nocardia farcinica IFM 10152
3 PaaR

Rhodococcus erythropolis PR4
5 PaaR

Rhodococcus sp. RHA1
4 PaaR

Rhodococcus opacus B4
Phenylacetic acid degradation