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

Collection of regulogs in Frankineae/Propionibacterineae/Pseudonocardiaceae taxonomic group

General statistics
Genomes 9
TF regulogs 29
TF regulons 123
TF binding sites 421
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
Acidothermus cellulolyticus 11B 9 43 0 0 9 43
Actinosynnema mirum DSM 43827 14 71 0 0 14 71
Frankia sp. CcI3 8 25 0 0 8 25
Frankia sp. EAN1pec 11 34 0 0 11 34
Nakamurella multipartita DSM 44233 19 57 0 0 19 57
Nocardioides sp. JS614 13 28 0 0 13 28
Propionibacterium acnes KPA171202 10 40 0 0 10 40
Saccharomonospora viridis DSM 43017 14 39 0 0 14 39
Saccharopolyspora erythraea NRRL 2338 25 84 0 0 25 84
Genomic distribution of regulons
Family Type Regulator Function
ArgR TF ArgR
2 ArgR

Actinosynnema mirum DSM 43827
2 ArgR

Saccharopolyspora erythraea NRRL 2338
2 ArgR

Saccharomonospora viridis DSM 43017
1 ArgR

Nakamurella multipartita DSM 44233
1 ArgR

Frankia sp. EAN1pec
1 ArgR

Frankia sp. CcI3
1 ArgR

Acidothermus cellulolyticus 11B
2 ArgR

Propionibacterium acnes KPA171202
1 ArgR

Nocardioides sp. JS614
Arginine biosynthesis
FUR TF Zur
7 Zur

Actinosynnema mirum DSM 43827
3 Zur

Saccharopolyspora erythraea NRRL 2338
1 Zur

Saccharomonospora viridis DSM 43017
3 Zur

Nakamurella multipartita DSM 44233
2 Zur

Frankia sp. EAN1pec
4 Zur

Propionibacterium acnes KPA171202
1 Zur

Nocardioides sp. JS614
Zinc homeostasis
GntR/MocR TF PdxQ
2 PdxQ

Saccharopolyspora erythraea NRRL 2338
Pyridoxine/pyridoxal homeostasis; Metabolite transport
TF PdxR
1 PdxR

Propionibacterium acnes KPA171202
Pyridoxine biosynthesis
TF PdxR2
2 PdxR2

Actinosynnema mirum DSM 43827
2 PdxR2

Saccharopolyspora erythraea NRRL 2338
1 PdxR2

Saccharomonospora viridis DSM 43017
1 PdxR2

Nakamurella multipartita DSM 44233
1 PdxR2

Nocardioides sp. JS614
Pyridoxine biosynthesis
TF PdxR3
1 PdxR3

Saccharopolyspora erythraea NRRL 2338
1 PdxR3

Nakamurella multipartita DSM 44233
1 PdxR3

Nocardioides sp. JS614
Pyridoxine biosynthesis
TF SACE_6928
2 SACE_6928

Saccharopolyspora erythraea NRRL 2338
1 SACE_6928

Nakamurella multipartita DSM 44233
Metabolite transport
GntR/Others TF Amir_6997
4 Amir_6997

Actinosynnema mirum DSM 43827
2 Amir_6997

Saccharopolyspora erythraea NRRL 2338
2 Amir_6997

Nakamurella multipartita DSM 44233
1 Amir_6997

Nocardioides sp. JS614
TF AnsR
1 AnsR

Saccharopolyspora erythraea NRRL 2338
2 AnsR

Nakamurella multipartita DSM 44233
Aspartate utilization; Asparagine degradation
TF DasR
15 DasR

Actinosynnema mirum DSM 43827
13 DasR

Saccharopolyspora erythraea NRRL 2338
5 DasR

Saccharomonospora viridis DSM 43017
2 DasR

Nakamurella multipartita DSM 44233
9 DasR

Acidothermus cellulolyticus 11B
3 DasR

Propionibacterium acnes KPA171202
1 DasR

Nocardioides sp. JS614
N-acetylglucosamine utilization
TF IolR
7 IolR

Saccharopolyspora erythraea NRRL 2338
7 IolR

Nakamurella multipartita DSM 44233
4 IolR

Acidothermus cellulolyticus 11B
8 IolR

Propionibacterium acnes KPA171202
Inositol utilization
TF LldR
2 LldR

Actinosynnema mirum DSM 43827
2 LldR

Saccharopolyspora erythraea NRRL 2338
5 LldR

Nakamurella multipartita DSM 44233
2 LldR

Propionibacterium acnes KPA171202
Lactate utilization
TF LndYR
1 LndYR

Actinosynnema mirum DSM 43827
1 LndYR

Saccharopolyspora erythraea NRRL 2338
1 LndYR

Saccharomonospora viridis DSM 43017
2 LndYR

Nakamurella multipartita DSM 44233
1 LndYR

Frankia sp. EAN1pec
Antibiotic resistance
TF Mce2R
1 Mce2R

Nocardioides sp. JS614
Fatty acid metabolism
TF PhnF
2 PhnF

Saccharopolyspora erythraea NRRL 2338
Phosphonate utilization
TF SACE_5794
4 SACE_5794

Saccharopolyspora erythraea NRRL 2338
TF SACE_6121
1 SACE_6121

Saccharopolyspora erythraea NRRL 2338
1 SACE_6121

Saccharomonospora viridis DSM 43017
1 SACE_6121

Frankia sp. EAN1pec
Multidrug efflux
TF Svir_39240
1 Svir_39240

Saccharomonospora viridis DSM 43017
1 Svir_39240

Nakamurella multipartita DSM 44233
Multidrug resistance; Multidrug efflux
HrcA TF HrcA
3 HrcA

Actinosynnema mirum DSM 43827
2 HrcA

Saccharopolyspora erythraea NRRL 2338
3 HrcA

Saccharomonospora viridis DSM 43017
5 HrcA

Nakamurella multipartita DSM 44233
6 HrcA

Frankia sp. EAN1pec
4 HrcA

Frankia sp. CcI3
5 HrcA

Acidothermus cellulolyticus 11B
3 HrcA

Propionibacterium acnes KPA171202
4 HrcA

Nocardioides sp. JS614
Heat shock response
HxlR TF QorR
2 QorR

Saccharopolyspora erythraea NRRL 2338
2 QorR

Frankia sp. EAN1pec
2 QorR

Frankia sp. CcI3
Energy metabolism
IclR TF LtbR
2 LtbR

Actinosynnema mirum DSM 43827
2 LtbR

Saccharopolyspora erythraea NRRL 2338
2 LtbR

Saccharomonospora viridis DSM 43017
2 LtbR

Nakamurella multipartita DSM 44233
2 LtbR

Frankia sp. EAN1pec
2 LtbR

Frankia sp. CcI3
2 LtbR

Acidothermus cellulolyticus 11B
2 LtbR

Nocardioides sp. JS614
Leucine biosynthesis
LacI TF RhaR
3 RhaR

Actinosynnema mirum DSM 43827
4 RhaR

Saccharopolyspora erythraea NRRL 2338
Rhamnose utilization
LexA TF LexA
8 LexA

Actinosynnema mirum DSM 43827
4 LexA

Saccharopolyspora erythraea NRRL 2338
5 LexA

Saccharomonospora viridis DSM 43017
6 LexA

Nakamurella multipartita DSM 44233
9 LexA

Frankia sp. EAN1pec
8 LexA

Frankia sp. CcI3
5 LexA

Acidothermus cellulolyticus 11B
1 LexA

Propionibacterium acnes KPA171202
5 LexA

Nocardioides sp. JS614
SOS response
NrdR TF NrdR
2 NrdR

Actinosynnema mirum DSM 43827
2 NrdR

Saccharopolyspora erythraea NRRL 2338
2 NrdR

Saccharomonospora viridis DSM 43017
1 NrdR

Nakamurella multipartita DSM 44233
1 NrdR

Frankia sp. EAN1pec
1 NrdR

Frankia sp. CcI3
1 NrdR

Acidothermus cellulolyticus 11B
3 NrdR

Propionibacterium acnes KPA171202
1 NrdR

Nocardioides sp. JS614
Deoxyribonucleotide biosynthesis
NrtR TF NrtR
3 NrtR

Frankia sp. EAN1pec
1 NrtR

Frankia sp. CcI3
NAD biosynthesis
Rex TF Rex
4 Rex

Actinosynnema mirum DSM 43827
3 Rex

Saccharopolyspora erythraea NRRL 2338
3 Rex

Saccharomonospora viridis DSM 43017
3 Rex

Nakamurella multipartita DSM 44233
2 Rex

Frankia sp. EAN1pec
2 Rex

Frankia sp. CcI3
3 Rex

Acidothermus cellulolyticus 11B
3 Rex

Nocardioides sp. JS614
Energy metabolism
TetR TF AcnR
3 AcnR

Actinosynnema mirum DSM 43827
2 AcnR

Saccharopolyspora erythraea NRRL 2338
3 AcnR

Saccharomonospora viridis DSM 43017
1 AcnR

Nakamurella multipartita DSM 44233
Tricarboxylic acid cycle
TF BioQ
2 BioQ

Saccharopolyspora erythraea NRRL 2338
5 BioQ

Propionibacterium acnes KPA171202
3 BioQ

Nocardioides sp. JS614
Biotin biosynthesis
TF PaaR
2 PaaR

Saccharopolyspora erythraea NRRL 2338
3 PaaR

Saccharomonospora viridis DSM 43017
2 PaaR

Nakamurella multipartita DSM 44233
2 PaaR

Acidothermus cellulolyticus 11B
Phenylacetic acid degradation