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

Collection of regulogs in Chlorobiales taxonomic group

General statistics
Genomes 11
TF regulogs 5
TF regulons 46
TF binding sites 69
RNA regulogs 6
RNA regulons 45
RNA sites 73

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
Chlorobaculum parvum NCIB 8327 5 6 4 6 9 12
Chlorobium chlorochromatii CaD3 4 5 3 3 7 8
Chlorobium ferrooxidans DSM 13031 4 5 3 4 7 9
Chlorobium limicola DSM 245 5 7 5 8 10 15
Chlorobium phaeobacteroides BS1 4 5 4 5 8 10
Chlorobium phaeobacteroides DSM 266 5 10 4 4 9 14
Chloroherpeton thalassium ATCC 35110 3 6 6 12 9 18
Pelodictyon luteolum DSM 273 4 5 4 7 8 12
Pelodictyon phaeoclathratiforme BU-1 4 6 4 6 8 12
Prosthecochloris aestuarii DSM 271 4 7 4 11 8 18
Prosthecochloris vibrioformis DSM 265 4 7 4 7 8 14
Genomic distribution of regulons
Family Type Regulator Function
ArgR TF ArgR
1 ArgR

Chlorobaculum parvum NCIB 8327
1 ArgR

Chlorobium chlorochromatii CaD3
1 ArgR

Chlorobium ferrooxidans DSM 13031
1 ArgR

Chlorobium limicola DSM 245
1 ArgR

Chlorobium phaeobacteroides BS1
1 ArgR

Chlorobium phaeobacteroides DSM 266
1 ArgR

Chloroherpeton thalassium ATCC 35110
1 ArgR

Pelodictyon luteolum DSM 273
1 ArgR

Pelodictyon phaeoclathratiforme BU-1
2 ArgR

Prosthecochloris aestuarii DSM 271
1 ArgR

Prosthecochloris vibrioformis DSM 265
Arginine biosynthesis
BirA TF BirA
1 BirA

Chlorobaculum parvum NCIB 8327
1 BirA

Chlorobium chlorochromatii CaD3
1 BirA

Chlorobium ferrooxidans DSM 13031
1 BirA

Chlorobium limicola DSM 245
1 BirA

Chlorobium phaeobacteroides BS1
1 BirA

Chlorobium phaeobacteroides DSM 266
1 BirA

Pelodictyon luteolum DSM 273
1 BirA

Pelodictyon phaeoclathratiforme BU-1
1 BirA

Prosthecochloris aestuarii DSM 271
1 BirA

Prosthecochloris vibrioformis DSM 265
Biotin biosynthesis
HrcA TF HrcA
1 HrcA

Chlorobaculum parvum NCIB 8327
1 HrcA

Chlorobium chlorochromatii CaD3
1 HrcA

Chlorobium limicola DSM 245
1 HrcA

Chlorobium phaeobacteroides BS1
1 HrcA

Chlorobium phaeobacteroides DSM 266
1 HrcA

Chloroherpeton thalassium ATCC 35110
1 HrcA

Pelodictyon luteolum DSM 273
1 HrcA

Pelodictyon phaeoclathratiforme BU-1
1 HrcA

Prosthecochloris aestuarii DSM 271
1 HrcA

Prosthecochloris vibrioformis DSM 265
Heat shock response
ModE TF ModE
2 ModE

Chlorobaculum parvum NCIB 8327
2 ModE

Chlorobium chlorochromatii CaD3
1 ModE

Chlorobium ferrooxidans DSM 13031
2 ModE

Chlorobium limicola DSM 245
3 ModE

Chlorobium phaeobacteroides DSM 266
2 ModE

Chloroherpeton thalassium ATCC 35110
2 ModE

Pelodictyon luteolum DSM 273
2 ModE

Pelodictyon phaeoclathratiforme BU-1
2 ModE

Prosthecochloris aestuarii DSM 271
3 ModE

Prosthecochloris vibrioformis DSM 265
Molybdopterin biosynthesis
NikR TF NikR
1 NikR

Chlorobaculum parvum NCIB 8327
1 NikR

Chlorobium ferrooxidans DSM 13031
1 NikR

Chlorobium limicola DSM 245
1 NikR

Chlorobium phaeobacteroides BS1
1 NikR

Chlorobium phaeobacteroides DSM 266
Nickel homeostasis
RF00050 RNA FMN
1 FMN

Chlorobium limicola DSM 245
1 FMN

Chloroherpeton thalassium ATCC 35110
Riboflavin biosynthesis
RF00059 RNA TPP
1 TPP

Chlorobaculum parvum NCIB 8327
1 TPP

Chlorobium limicola DSM 245
1 TPP

Chlorobium phaeobacteroides BS1
1 TPP

Chlorobium phaeobacteroides DSM 266
2 TPP

Chloroherpeton thalassium ATCC 35110
1 TPP

Pelodictyon luteolum DSM 273
1 TPP

Pelodictyon phaeoclathratiforme BU-1
2 TPP

Prosthecochloris aestuarii DSM 271
1 TPP

Prosthecochloris vibrioformis DSM 265
Thiamine biosynthesis
RF00162 RNA SAM
1 SAM

Chlorobaculum parvum NCIB 8327
1 SAM

Chlorobium chlorochromatii CaD3
2 SAM

Chlorobium ferrooxidans DSM 13031
1 SAM

Chlorobium limicola DSM 245
1 SAM

Chlorobium phaeobacteroides BS1
1 SAM

Chlorobium phaeobacteroides DSM 266
1 SAM

Chloroherpeton thalassium ATCC 35110
2 SAM

Pelodictyon luteolum DSM 273
2 SAM

Pelodictyon phaeoclathratiforme BU-1
1 SAM

Prosthecochloris aestuarii DSM 271
1 SAM

Prosthecochloris vibrioformis DSM 265
Methionine biosynthesis
RF00174 RNA Cobalamin
3 Cobalamin

Chlorobaculum parvum NCIB 8327
1 Cobalamin

Chlorobium chlorochromatii CaD3
1 Cobalamin

Chlorobium ferrooxidans DSM 13031
4 Cobalamin

Chlorobium limicola DSM 245
2 Cobalamin

Chlorobium phaeobacteroides BS1
1 Cobalamin

Chlorobium phaeobacteroides DSM 266
6 Cobalamin

Chloroherpeton thalassium ATCC 35110
3 Cobalamin

Pelodictyon luteolum DSM 273
2 Cobalamin

Pelodictyon phaeoclathratiforme BU-1
7 Cobalamin

Prosthecochloris aestuarii DSM 271
4 Cobalamin

Prosthecochloris vibrioformis DSM 265
Cobalamin biosynthesis
RF01055 RNA MOCO_RNA_motif
1 MOCO_RNA_motif

Chloroherpeton thalassium ATCC 35110
Molybdopterin biosynthesis; Molybdenum homeostasis
RF01724 RNA SAM-Chlorobi
1 SAM-Chlorobi

Chlorobaculum parvum NCIB 8327
1 SAM-Chlorobi

Chlorobium chlorochromatii CaD3
1 SAM-Chlorobi

Chlorobium ferrooxidans DSM 13031
1 SAM-Chlorobi

Chlorobium limicola DSM 245
1 SAM-Chlorobi

Chlorobium phaeobacteroides BS1
1 SAM-Chlorobi

Chlorobium phaeobacteroides DSM 266
1 SAM-Chlorobi

Chloroherpeton thalassium ATCC 35110
1 SAM-Chlorobi

Pelodictyon luteolum DSM 273
1 SAM-Chlorobi

Pelodictyon phaeoclathratiforme BU-1
1 SAM-Chlorobi

Prosthecochloris aestuarii DSM 271
1 SAM-Chlorobi

Prosthecochloris vibrioformis DSM 265
Methionine metabolism