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

Collection of regulogs in Deinococcus-Thermus taxonomic group

General statistics
Genomes 5
TF regulogs 10
TF regulons 29
TF binding sites 83
RNA regulogs 13
RNA regulons 44
RNA sites 64

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
Deinococcus deserti VCD115 6 19 11 17 17 36
Deinococcus geothermalis DSM 11300 6 20 8 11 14 31
Deinococcus radiodurans R1 5 20 8 11 13 31
Thermus aquaticus Y51MC23 5 10 9 13 14 23
Thermus thermophilus HB27 7 14 8 12 15 26
Genomic distribution of regulons
Family Type Regulator Function
ArgR TF ArgR
2 ArgR

Deinococcus geothermalis DSM 11300
3 ArgR

Deinococcus deserti VCD115
2 ArgR

Deinococcus radiodurans R1
3 ArgR

Thermus aquaticus Y51MC23
3 ArgR

Thermus thermophilus HB27
Arginine biosynthesis
BirA TF BirA
1 BirA

Thermus aquaticus Y51MC23
2 BirA

Thermus thermophilus HB27
Biotin biosynthesis
GntR/MocR TF PdxR2
1 PdxR2

Deinococcus deserti VCD115
Pyridoxine/pyridoxal homeostasis
HrcA TF HrcA
2 HrcA

Thermus aquaticus Y51MC23
2 HrcA

Thermus thermophilus HB27
Heat shock response
LacI TF BglR
2 BglR

Deinococcus geothermalis DSM 11300
1 BglR

Deinococcus deserti VCD115
1 BglR

Thermus thermophilus HB27
Beta-glucosides utilization
TF DR2501
3 DR2501

Deinococcus geothermalis DSM 11300
2 DR2501

Deinococcus deserti VCD115
3 DR2501

Deinococcus radiodurans R1
Sugar utilization
NrdR TF NrdR
1 NrdR

Deinococcus geothermalis DSM 11300
2 NrdR

Deinococcus radiodurans R1
2 NrdR

Thermus thermophilus HB27
Deoxyribonucleotide biosynthesis
Rex TF Rex
3 Rex

Deinococcus geothermalis DSM 11300
3 Rex

Deinococcus deserti VCD115
2 Rex

Deinococcus radiodurans R1
1 Rex

Thermus aquaticus Y51MC23
1 Rex

Thermus thermophilus HB27
Energy metabolism
TetR TF PaaR
2 PaaR

Thermus aquaticus Y51MC23
2 PaaR

Thermus thermophilus HB27
Phenylacetic acid degradation
TF PaaR2
8 PaaR2

Deinococcus geothermalis DSM 11300
8 PaaR2

Deinococcus deserti VCD115
10 PaaR2

Deinococcus radiodurans R1
Phenylacetic acid degradation
RF00050 RNA FMN
1 FMN

Deinococcus geothermalis DSM 11300
1 FMN

Deinococcus deserti VCD115
1 FMN

Deinococcus radiodurans R1
1 FMN

Thermus aquaticus Y51MC23
1 FMN

Thermus thermophilus HB27
Riboflavin biosynthesis
RF00059 RNA TPP
2 TPP

Deinococcus geothermalis DSM 11300
2 TPP

Deinococcus deserti VCD115
2 TPP

Deinococcus radiodurans R1
2 TPP

Thermus aquaticus Y51MC23
2 TPP

Thermus thermophilus HB27
Thiamine biosynthesis
RF00080 RNA yybP-ykoY
1 yybP-ykoY

Deinococcus deserti VCD115
2 yybP-ykoY

Thermus aquaticus Y51MC23
2 yybP-ykoY

Thermus thermophilus HB27
RF00162 RNA SAM
2 SAM

Deinococcus geothermalis DSM 11300
3 SAM

Deinococcus deserti VCD115
2 SAM

Deinococcus radiodurans R1
1 SAM

Thermus aquaticus Y51MC23
1 SAM

Thermus thermophilus HB27
Methionine biosynthesis
RF00174 RNA Cobalamin
2 Cobalamin

Deinococcus geothermalis DSM 11300
2 Cobalamin

Deinococcus deserti VCD115
2 Cobalamin

Deinococcus radiodurans R1
3 Cobalamin

Thermus aquaticus Y51MC23
3 Cobalamin

Thermus thermophilus HB27
Cobalamin biosynthesis
RF00230 RNA T-box(Gly)
1 T-box(Gly)

Deinococcus geothermalis DSM 11300
1 T-box(Gly)

Deinococcus deserti VCD115
1 T-box(Gly)

Deinococcus radiodurans R1
Amino acid metabolism
RNA T-box(Ile)
1 T-box(Ile)

Deinococcus geothermalis DSM 11300
1 T-box(Ile)

Deinococcus deserti VCD115
1 T-box(Ile)

Deinococcus radiodurans R1
1 T-box(Ile)

Thermus aquaticus Y51MC23
1 T-box(Ile)

Thermus thermophilus HB27
Amino acid metabolism
RNA T-box(Val)
1 T-box(Val)

Deinococcus deserti VCD115
1 T-box(Val)

Deinococcus radiodurans R1
Amino acid metabolism
RF00234 RNA glmS
1 glmS

Deinococcus geothermalis DSM 11300
1 glmS

Deinococcus deserti VCD115
1 glmS

Deinococcus radiodurans R1
Amino sugar metabolism
RF00515 RNA PyrR
1 PyrR

Thermus aquaticus Y51MC23
1 PyrR

Thermus thermophilus HB27
Pyrimidine metabolism
RF00557 RNA L10_leader
1 L10_leader

Deinococcus geothermalis DSM 11300
1 L10_leader

Deinococcus deserti VCD115
1 L10_leader

Thermus aquaticus Y51MC23
1 L10_leader

Thermus thermophilus HB27
Ribosome biogenesis
RF01051 RNA GEMM_RNA_motif
3 GEMM_RNA_motif

Deinococcus deserti VCD115
Second messenger response
RF01055 RNA MOCO_RNA_motif
1 MOCO_RNA_motif

Thermus aquaticus Y51MC23
Molybdopterin biosynthesis; Molybdenum homeostasis