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

Collection of regulogs in Sphingomonadales taxonomic group

General statistics
Genomes 7
TF regulogs 28
TF regulons 108
TF binding sites 416
RNA regulogs 2
RNA regulons 7
RNA sites 7

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
Erythrobacter litoralis HTCC2594 14 56 1 1 15 57
Erythrobacter sp. NAP1 13 61 1 1 14 62
Novosphingobium aromaticivorans DSM 12444 20 66 1 1 21 67
Sphingobium japonicum UT26S 13 57 1 1 14 58
Sphingomonas wittichii RW1 18 50 1 1 19 51
Sphingopyxis alaskensis RB2256 19 90 1 1 20 91
Zymomonas mobilis subsp. mobilis ZM4 11 36 1 1 12 37
Genomic distribution of regulons
Family Type Regulator Function
ArsR TF SahR
3 SahR

Erythrobacter litoralis HTCC2594
3 SahR

Erythrobacter sp. NAP1
3 SahR

Novosphingobium aromaticivorans DSM 12444
3 SahR

Sphingopyxis alaskensis RB2256
3 SahR

Sphingobium japonicum UT26S
4 SahR

Sphingomonas wittichii RW1
4 SahR

Zymomonas mobilis subsp. mobilis ZM4
Methionine metabolism
CRP TF FnrN
5 FnrN

Erythrobacter sp. NAP1
5 FnrN

Novosphingobium aromaticivorans DSM 12444
4 FnrN

Sphingopyxis alaskensis RB2256
3 FnrN

Sphingobium japonicum UT26S
1 FnrN

Sphingomonas wittichii RW1
Oxidative stress response; Nitrogen fixation
TF NnrR
2 NnrR

Sphingomonas wittichii RW1
Denitrification
FUR TF Fur
7 Fur

Erythrobacter litoralis HTCC2594
11 Fur

Erythrobacter sp. NAP1
4 Fur

Novosphingobium aromaticivorans DSM 12444
10 Fur

Sphingopyxis alaskensis RB2256
13 Fur

Sphingobium japonicum UT26S
9 Fur

Sphingomonas wittichii RW1
9 Fur

Zymomonas mobilis subsp. mobilis ZM4
Iron homeostasis
TF Zur
2 Zur

Erythrobacter litoralis HTCC2594
2 Zur

Erythrobacter sp. NAP1
2 Zur

Novosphingobium aromaticivorans DSM 12444
3 Zur

Sphingopyxis alaskensis RB2256
4 Zur

Sphingobium japonicum UT26S
2 Zur

Sphingomonas wittichii RW1
6 Zur

Zymomonas mobilis subsp. mobilis ZM4
Zinc homeostasis
Fis TF NifA
4 NifA

Zymomonas mobilis subsp. mobilis ZM4
Nitrogen fixation
TF NtrC
3 NtrC

Erythrobacter litoralis HTCC2594
3 NtrC

Erythrobacter sp. NAP1
3 NtrC

Novosphingobium aromaticivorans DSM 12444
3 NtrC

Sphingopyxis alaskensis RB2256
3 NtrC

Sphingobium japonicum UT26S
3 NtrC

Sphingomonas wittichii RW1
Nitrogen assimilation
GntR/MocR TF PdxQ2
2 PdxQ2

Sphingomonas wittichii RW1
2 PdxQ2

Zymomonas mobilis subsp. mobilis ZM4
Pyridoxine/pyridoxal homeostasis; Metabolite transport
TF PdxR2
1 PdxR2

Zymomonas mobilis subsp. mobilis ZM4
Pyridoxine/pyridoxal homeostasis
TF Swit_4344
1 Swit_4344

Sphingomonas wittichii RW1
TF YrdX3
2 YrdX3

Sphingomonas wittichii RW1
GntR/Others TF ELI_12480
4 ELI_12480

Erythrobacter litoralis HTCC2594
5 ELI_12480

Erythrobacter sp. NAP1
3 ELI_12480

Novosphingobium aromaticivorans DSM 12444
4 ELI_12480

Sphingopyxis alaskensis RB2256
4 ELI_12480

Sphingobium japonicum UT26S
3 ELI_12480

Sphingomonas wittichii RW1
Multidrug resistance; Multidrug efflux
TF HutC
3 HutC

Sphingopyxis alaskensis RB2256
2 HutC

Sphingomonas wittichii RW1
Histidine utilization
HrcA TF HrcA
1 HrcA

Erythrobacter litoralis HTCC2594
1 HrcA

Erythrobacter sp. NAP1
1 HrcA

Novosphingobium aromaticivorans DSM 12444
1 HrcA

Sphingopyxis alaskensis RB2256
1 HrcA

Sphingobium japonicum UT26S
1 HrcA

Sphingomonas wittichii RW1
1 HrcA

Zymomonas mobilis subsp. mobilis ZM4
Heat shock response
LacI TF BglR
1 BglR

Erythrobacter sp. NAP1
2 BglR

Novosphingobium aromaticivorans DSM 12444
2 BglR

Sphingopyxis alaskensis RB2256
Beta-glucosides utilization
TF MalR
2 MalR

Erythrobacter litoralis HTCC2594
2 MalR

Novosphingobium aromaticivorans DSM 12444
2 MalR

Sphingopyxis alaskensis RB2256
Maltose utilization
TF ScrR
2 ScrR

Erythrobacter litoralis HTCC2594
3 ScrR

Novosphingobium aromaticivorans DSM 12444
Sucrose utilization
LexA TF LexA
10 LexA

Erythrobacter litoralis HTCC2594
10 LexA

Erythrobacter sp. NAP1
10 LexA

Novosphingobium aromaticivorans DSM 12444
8 LexA

Sphingopyxis alaskensis RB2256
10 LexA

Sphingobium japonicum UT26S
9 LexA

Sphingomonas wittichii RW1
3 LexA

Zymomonas mobilis subsp. mobilis ZM4
SOS response
MerR TF CadR-PbrR
1 CadR-PbrR

Erythrobacter litoralis HTCC2594
1 CadR-PbrR

Novosphingobium aromaticivorans DSM 12444
2 CadR-PbrR

Sphingopyxis alaskensis RB2256
1 CadR-PbrR

Sphingobium japonicum UT26S
1 CadR-PbrR

Zymomonas mobilis subsp. mobilis ZM4
Lead resistance; Cadmium resistance
TF CueR
1 CueR

Novosphingobium aromaticivorans DSM 12444
Copper resistance
TF LiuR
7 LiuR

Erythrobacter litoralis HTCC2594
9 LiuR

Erythrobacter sp. NAP1
5 LiuR

Novosphingobium aromaticivorans DSM 12444
18 LiuR

Sphingopyxis alaskensis RB2256
4 LiuR

Sphingobium japonicum UT26S
1 LiuR

Sphingomonas wittichii RW1
Branched-chain amino acid degradation
TF MerR
1 MerR

Novosphingobium aromaticivorans DSM 12444
2 MerR

Sphingopyxis alaskensis RB2256
1 MerR

Sphingomonas wittichii RW1
Mercury resistance
TF SoxR
1 SoxR

Erythrobacter litoralis HTCC2594
1 SoxR

Erythrobacter sp. NAP1
1 SoxR

Novosphingobium aromaticivorans DSM 12444
2 SoxR

Sphingopyxis alaskensis RB2256
Superoxide stress response
TF ZntR
1 ZntR

Sphingopyxis alaskensis RB2256
1 ZntR

Sphingobium japonicum UT26S
Zinc resistance
ModE TF ModE2
1 ModE2

Novosphingobium aromaticivorans DSM 12444
1 ModE2

Sphingomonas wittichii RW1
Molybdenum homeostasis
NrdR TF NrdR
2 NrdR

Erythrobacter litoralis HTCC2594
2 NrdR

Erythrobacter sp. NAP1
1 NrdR

Novosphingobium aromaticivorans DSM 12444
1 NrdR

Sphingopyxis alaskensis RB2256
1 NrdR

Sphingobium japonicum UT26S
2 NrdR

Sphingomonas wittichii RW1
2 NrdR

Zymomonas mobilis subsp. mobilis ZM4
Deoxyribonucleotide biosynthesis
Rrf2 TF IscR
1 IscR

Erythrobacter litoralis HTCC2594
1 IscR

Erythrobacter sp. NAP1
1 IscR

Novosphingobium aromaticivorans DSM 12444
1 IscR

Sphingopyxis alaskensis RB2256
1 IscR

Sphingobium japonicum UT26S
1 IscR

Sphingomonas wittichii RW1
1 IscR

Zymomonas mobilis subsp. mobilis ZM4
Iron-sulfur cluster biogenesis
TF NsrR
2 NsrR

Novosphingobium aromaticivorans DSM 12444
2 NsrR

Sphingopyxis alaskensis RB2256
Nitrosative stress response
RF00059 RNA TPP
1 TPP

Erythrobacter litoralis HTCC2594
1 TPP

Erythrobacter sp. NAP1
1 TPP

Novosphingobium aromaticivorans DSM 12444
1 TPP

Sphingopyxis alaskensis RB2256
1 TPP

Sphingobium japonicum UT26S
1 TPP

Sphingomonas wittichii RW1
1 TPP

Zymomonas mobilis subsp. mobilis ZM4
Thiamine biosynthesis
RF01055 RNA MOCO_RNA_motif