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

Collection of regulogs in Oceanospirillales/Alteromonadales taxonomic group

General statistics
Genomes 12
TF regulogs 72
TF regulons 247
TF binding sites 876
RNA regulogs 3
RNA regulons 16
RNA sites 29

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
Alcanivorax borkumensis SK2 15 45 0 0 15 45
Cellvibrio japonicus Ueda107 18 49 1 2 19 51
Chromohalobacter salexigens DSM 3043 30 109 1 2 31 111
Hahella chejuensis KCTC 2396 34 103 2 3 36 106
Marinobacter aqueolei 21 92 1 2 22 94
Marinobacter sp. ELB17 23 84 1 2 24 86
Marinomonas sp. MWYL1 28 106 2 4 30 110
Oceanobacter sp. RED65 11 41 1 2 12 43
Oceanospirillum sp. MED92 16 50 1 1 17 51
Reinekea sp. MED297 23 99 3 4 26 103
Saccharophagus degradans 2-40 16 53 1 3 17 56
Teredinibacter turnerae T7901 12 45 2 4 14 49
Genomic distribution of regulons
Family Type Regulator Function
ArsR TF SahR
1 SahR

Hahella chejuensis KCTC 2396
2 SahR

Marinobacter aqueolei
2 SahR

Marinobacter sp. ELB17
1 SahR

Oceanobacter sp. RED65
2 SahR

Saccharophagus degradans 2-40
2 SahR

Teredinibacter turnerae T7901
2 SahR

Cellvibrio japonicus Ueda107
2 SahR

Reinekea sp. MED297
1 SahR

Alcanivorax borkumensis SK2
Methionine metabolism
BirA TF BirA
2 BirA

Hahella chejuensis KCTC 2396
2 BirA

Marinobacter aqueolei
3 BirA

Marinobacter sp. ELB17
1 BirA

Oceanobacter sp. RED65
2 BirA

Marinomonas sp. MWYL1
2 BirA

Saccharophagus degradans 2-40
2 BirA

Teredinibacter turnerae T7901
2 BirA

Cellvibrio japonicus Ueda107
1 BirA

Chromohalobacter salexigens DSM 3043
2 BirA

Reinekea sp. MED297
2 BirA

Alcanivorax borkumensis SK2
Biotin biosynthesis
FUR TF Zur
7 Zur

Hahella chejuensis KCTC 2396
2 Zur

Marinobacter aqueolei
4 Zur

Marinobacter sp. ELB17
1 Zur

Oceanobacter sp. RED65
6 Zur

Oceanospirillum sp. MED92
4 Zur

Marinomonas sp. MWYL1
3 Zur

Saccharophagus degradans 2-40
3 Zur

Teredinibacter turnerae T7901
3 Zur

Cellvibrio japonicus Ueda107
4 Zur

Chromohalobacter salexigens DSM 3043
3 Zur

Reinekea sp. MED297
2 Zur

Alcanivorax borkumensis SK2
Zinc homeostasis
Fis TF NorR
4 NorR

Hahella chejuensis KCTC 2396
2 NorR

Marinomonas sp. MWYL1
2 NorR

Teredinibacter turnerae T7901
2 NorR

Chromohalobacter salexigens DSM 3043
Nitrosative stress response
TF NtrC
4 NtrC

Hahella chejuensis KCTC 2396
4 NtrC

Marinobacter aqueolei
4 NtrC

Marinobacter sp. ELB17
4 NtrC

Oceanobacter sp. RED65
3 NtrC

Oceanospirillum sp. MED92
3 NtrC

Marinomonas sp. MWYL1
4 NtrC

Saccharophagus degradans 2-40
5 NtrC

Teredinibacter turnerae T7901
3 NtrC

Cellvibrio japonicus Ueda107
4 NtrC

Chromohalobacter salexigens DSM 3043
3 NtrC

Reinekea sp. MED297
5 NtrC

Alcanivorax borkumensis SK2
Nitrogen assimilation
GntR/MocR TF Csal_1101
2 Csal_1101

Chromohalobacter salexigens DSM 3043
Metabolite transport
TF EutR
2 EutR

Chromohalobacter salexigens DSM 3043
Ectoine utilization
TF HCH_03332
1 HCH_03332

Hahella chejuensis KCTC 2396
TF MED92_15328
1 MED92_15328

Oceanospirillum sp. MED92
1 MED92_15328

Marinomonas sp. MWYL1
TF Mmwyl1_0258
1 Mmwyl1_0258

Marinomonas sp. MWYL1
TF Mmwyl1_0910
1 Mmwyl1_0910

Hahella chejuensis KCTC 2396
1 Mmwyl1_0910

Marinomonas sp. MWYL1
Metabolite transport
TF Mmwyl1_4437
1 Mmwyl1_4437

Marinomonas sp. MWYL1
TF PdxQ
1 PdxQ

Hahella chejuensis KCTC 2396
Pyridoxine/pyridoxal homeostasis
TF PdxQ3
1 PdxQ3

Chromohalobacter salexigens DSM 3043
Metabolite transport; Pyridoxine/pyridoxal homeostasis
TF PdxW
1 PdxW

Marinobacter aqueolei
1 PdxW

Oceanospirillum sp. MED92
Pyridoxine/pyridoxal homeostasis
TF PdxW2
1 PdxW2

Chromohalobacter salexigens DSM 3043
Pyridoxine/pyridoxal homeostasis
TF TERTU_3902
1 TERTU_3902

Teredinibacter turnerae T7901
Multidrug efflux
TF TauR
1 TauR

Oceanospirillum sp. MED92
2 TauR

Chromohalobacter salexigens DSM 3043
Taurine utilization
TF YdcR
1 YdcR

Hahella chejuensis KCTC 2396
1 YdcR

Cellvibrio japonicus Ueda107
TF YjiR
1 YjiR

Hahella chejuensis KCTC 2396
1 YjiR

Oceanospirillum sp. MED92
1 YjiR

Marinomonas sp. MWYL1
1 YjiR

Reinekea sp. MED297
Metabolite transport
TF YjiR2
1 YjiR2

Hahella chejuensis KCTC 2396
1 YjiR2

Marinobacter aqueolei
1 YjiR2

Marinobacter sp. ELB17
1 YjiR2

Saccharophagus degradans 2-40
1 YjiR2

Cellvibrio japonicus Ueda107
Metabolite transport
GntR/Others TF CJA_0601
1 CJA_0601

Cellvibrio japonicus Ueda107
Hypothetical ABC transporter
TF CJA_1242
1 CJA_1242

Cellvibrio japonicus Ueda107
1 CJA_1242

Alcanivorax borkumensis SK2
TF CJA_2253
1 CJA_2253

Cellvibrio japonicus Ueda107
Alkanesulfonates utilization
TF Csal_1739
3 Csal_1739

Chromohalobacter salexigens DSM 3043
TF Csal_3199
2 Csal_3199

Marinobacter sp. ELB17
3 Csal_3199

Chromohalobacter salexigens DSM 3043
Glycolate utilization; Lactate utilization
TF DgoR
1 DgoR

Chromohalobacter salexigens DSM 3043
Galactonate utilization
TF GlcC
2 GlcC

Marinobacter aqueolei
2 GlcC

Marinobacter sp. ELB17
2 GlcC

Oceanospirillum sp. MED92
Glycolate utilization
TF HpxS
3 HpxS

Marinobacter sp. ELB17
1 HpxS

Marinomonas sp. MWYL1
3 HpxS

Chromohalobacter salexigens DSM 3043
Allantoin utilization
TF HutC
1 HutC

Hahella chejuensis KCTC 2396
4 HutC

Marinomonas sp. MWYL1
2 HutC

Reinekea sp. MED297
Histidine utilization
TF HypR
3 HypR

Hahella chejuensis KCTC 2396
3 HypR

Chromohalobacter salexigens DSM 3043
Proline and 4-hydrohyproline utilization
TF LldR
2 LldR

Marinobacter aqueolei
2 LldR

Marinobacter sp. ELB17
2 LldR

Marinomonas sp. MWYL1
4 LldR

Chromohalobacter salexigens DSM 3043
Lactate utilization
TF NagQ
2 NagQ

Hahella chejuensis KCTC 2396
2 NagQ

Marinomonas sp. MWYL1
5 NagQ

Reinekea sp. MED297
N-acetylglucosamine utilization
TF PdhR
1 PdhR

Hahella chejuensis KCTC 2396
1 PdhR

Oceanospirillum sp. MED92
Pyruvate metabolism
TF PhnF
2 PhnF

Marinobacter aqueolei
Phosphonate utilization
TF PhnR
4 PhnR

Hahella chejuensis KCTC 2396
Phosphonate utilization; 2-aminoethylphosphonate utilization
TF PrpR
1 PrpR

Hahella chejuensis KCTC 2396
2 PrpR

Marinobacter aqueolei
1 PrpR

Marinobacter sp. ELB17
1 PrpR

Oceanobacter sp. RED65
2 PrpR

Oceanospirillum sp. MED92
1 PrpR

Marinomonas sp. MWYL1
2 PrpR

Chromohalobacter salexigens DSM 3043
2 PrpR

Reinekea sp. MED297
1 PrpR

Alcanivorax borkumensis SK2
Methylcitrate utilization
TF RspR
1 RspR

Chromohalobacter salexigens DSM 3043
L-gulonate utilization
TF Sde_3525
1 Sde_3525

Saccharophagus degradans 2-40
Multidrug resistance; Multidrug efflux
TF UxuR
3 UxuR

Marinomonas sp. MWYL1
Glucuronate utilization
TF VanR
2 VanR

Marinomonas sp. MWYL1
2 VanR

Chromohalobacter salexigens DSM 3043
Vanillate utilization
HrcA TF HrcA
2 HrcA

Alcanivorax borkumensis SK2
Heat shock response
LacI TF Csal_3216
2 Csal_3216

Chromohalobacter salexigens DSM 3043
Sugar utilization
TF FruR
5 FruR

Chromohalobacter salexigens DSM 3043
2 FruR

Reinekea sp. MED297
Fructose utilization
TF GntR
1 GntR

Hahella chejuensis KCTC 2396
1 GntR

Marinomonas sp. MWYL1
3 GntR

Chromohalobacter salexigens DSM 3043
Gluconate utilization
TF IolR
1 IolR

Hahella chejuensis KCTC 2396
Inositol utilization
TF NagR
4 NagR

Saccharophagus degradans 2-40
3 NagR

Teredinibacter turnerae T7901
7 NagR

Cellvibrio japonicus Ueda107
N-acetylglucosamine utilization
TF ScrR
2 ScrR

Saccharophagus degradans 2-40
Sucrose utilization
TF XltR
2 XltR

Hahella chejuensis KCTC 2396
2 XltR

Marinomonas sp. MWYL1
Xylitol utilization
LexA TF LexA
7 LexA

Hahella chejuensis KCTC 2396
9 LexA

Marinobacter aqueolei
7 LexA

Marinobacter sp. ELB17
7 LexA

Oceanobacter sp. RED65
8 LexA

Oceanospirillum sp. MED92
11 LexA

Marinomonas sp. MWYL1
8 LexA

Saccharophagus degradans 2-40
8 LexA

Teredinibacter turnerae T7901
4 LexA

Cellvibrio japonicus Ueda107
4 LexA

Chromohalobacter salexigens DSM 3043
9 LexA

Reinekea sp. MED297
6 LexA

Alcanivorax borkumensis SK2
SOS response
LysR TF MetR
2 MetR

Hahella chejuensis KCTC 2396
2 MetR

Marinobacter aqueolei
2 MetR

Marinobacter sp. ELB17
3 MetR

Oceanobacter sp. RED65
2 MetR

Oceanospirillum sp. MED92
2 MetR

Marinomonas sp. MWYL1
2 MetR

Saccharophagus degradans 2-40
2 MetR

Teredinibacter turnerae T7901
2 MetR

Cellvibrio japonicus Ueda107
3 MetR

Chromohalobacter salexigens DSM 3043
2 MetR

Reinekea sp. MED297
2 MetR

Alcanivorax borkumensis SK2
Methionine biosynthesis
MerR TF CadR-PbrR
1 CadR-PbrR

Hahella chejuensis KCTC 2396
7 CadR-PbrR

Marinobacter aqueolei
1 CadR-PbrR

Marinobacter sp. ELB17
1 CadR-PbrR

Oceanospirillum sp. MED92
1 CadR-PbrR

Saccharophagus degradans 2-40
1 CadR-PbrR

Cellvibrio japonicus Ueda107
1 CadR-PbrR

Alcanivorax borkumensis SK2
Lead resistance; Cadmium resistance
TF CueR
3 CueR

Saccharophagus degradans 2-40
4 CueR

Cellvibrio japonicus Ueda107
Copper resistance
TF LiuR
2 LiuR

Hahella chejuensis KCTC 2396
4 LiuR

Marinobacter aqueolei
4 LiuR

Marinobacter sp. ELB17
3 LiuR

Oceanospirillum sp. MED92
3 LiuR

Reinekea sp. MED297
2 LiuR

Alcanivorax borkumensis SK2
Branched-chain amino acid degradation
TF MerR
3 MerR

Marinobacter aqueolei
2 MerR

Marinobacter sp. ELB17
Mercury resistance
TF SoxR
1 SoxR

Hahella chejuensis KCTC 2396
1 SoxR

Marinomonas sp. MWYL1
1 SoxR

Reinekea sp. MED297
Superoxide stress response
TF ZntR
1 ZntR

Oceanospirillum sp. MED92
1 ZntR

Marinomonas sp. MWYL1
1 ZntR

Chromohalobacter salexigens DSM 3043
1 ZntR

Reinekea sp. MED297
Zinc resistance
ModE TF FdsR
2 FdsR

Marinobacter sp. ELB17
Formate oxydation
TF ModE
1 ModE

Hahella chejuensis KCTC 2396
1 ModE

Marinomonas sp. MWYL1
Molybdenum homeostasis
NrdR TF NrdR
2 NrdR

Hahella chejuensis KCTC 2396
2 NrdR

Marinobacter aqueolei
2 NrdR

Marinobacter sp. ELB17
1 NrdR

Oceanobacter sp. RED65
1 NrdR

Oceanospirillum sp. MED92
1 NrdR

Marinomonas sp. MWYL1
2 NrdR

Saccharophagus degradans 2-40
2 NrdR

Teredinibacter turnerae T7901
1 NrdR

Cellvibrio japonicus Ueda107
1 NrdR

Chromohalobacter salexigens DSM 3043
2 NrdR

Reinekea sp. MED297
1 NrdR

Alcanivorax borkumensis SK2
Deoxyribonucleotide biosynthesis
NrtR TF NrtR
4 NrtR

Hahella chejuensis KCTC 2396
2 NrtR

Marinobacter sp. ELB17
NAD biosynthesis
ROK TF NagC
5 NagC

Reinekea sp. MED297
N-acetylglucosamine utilization
RpiR TF EutR
2 EutR

Chromohalobacter salexigens DSM 3043
Ethanolamine utilization
TF HexR
10 HexR

Marinomonas sp. MWYL1
8 HexR

Chromohalobacter salexigens DSM 3043
14 HexR

Reinekea sp. MED297
Central carbohydrate metabolism
TF HexR2
4 HexR2

Hahella chejuensis KCTC 2396
4 HexR2

Marinobacter aqueolei
4 HexR2

Marinobacter sp. ELB17
Central carbohydrate metabolism
Rrf2 TF IscR
3 IscR

Hahella chejuensis KCTC 2396
4 IscR

Marinobacter aqueolei
3 IscR

Marinobacter sp. ELB17
3 IscR

Oceanobacter sp. RED65
3 IscR

Oceanospirillum sp. MED92
3 IscR

Marinomonas sp. MWYL1
4 IscR

Saccharophagus degradans 2-40
3 IscR

Teredinibacter turnerae T7901
4 IscR

Cellvibrio japonicus Ueda107
2 IscR

Chromohalobacter salexigens DSM 3043
4 IscR

Reinekea sp. MED297
4 IscR

Alcanivorax borkumensis SK2
Iron-sulfur cluster biogenesis
TF NsrR
1 NsrR

Saccharophagus degradans 2-40
2 NsrR

Cellvibrio japonicus Ueda107
2 NsrR

Reinekea sp. MED297
2 NsrR

Alcanivorax borkumensis SK2
Nitrosative stress response
TetR TF FabR
1 FabR

Hahella chejuensis KCTC 2396
5 FabR

Marinobacter aqueolei
2 FabR

Marinobacter sp. ELB17
Fatty acid biosynthesis
TF FabR2
2 FabR2

Hahella chejuensis KCTC 2396
1 FabR2

Marinobacter aqueolei
2 FabR2

Reinekea sp. MED297
Fatty acid biosynthesis
TF PsrA
7 PsrA

Hahella chejuensis KCTC 2396
8 PsrA

Marinobacter aqueolei
7 PsrA

Marinobacter sp. ELB17
4 PsrA

Oceanobacter sp. RED65
2 PsrA

Saccharophagus degradans 2-40
11 PsrA

Chromohalobacter salexigens DSM 3043
9 PsrA

Reinekea sp. MED297
4 PsrA

Alcanivorax borkumensis SK2
Fatty acid degradation
TF RutR
4 RutR

Hahella chejuensis KCTC 2396
3 RutR

Marinobacter sp. ELB17
3 RutR

Oceanobacter sp. RED65
5 RutR

Marinomonas sp. MWYL1
3 RutR

Teredinibacter turnerae T7901
3 RutR

Cellvibrio japonicus Ueda107
2 RutR

Chromohalobacter salexigens DSM 3043
3 RutR

Reinekea sp. MED297
Pyrimidine utilization
TrpR TF TrpR
1 TrpR

Marinomonas sp. MWYL1
1 TrpR

Reinekea sp. MED297
Tryptophan biosynthesis
RF00050 RNA FMN
1 FMN

Hahella chejuensis KCTC 2396
2 FMN

Marinomonas sp. MWYL1
1 FMN

Reinekea sp. MED297
Riboflavin biosynthesis
RF00059 RNA TPP
2 TPP

Hahella chejuensis KCTC 2396
2 TPP

Marinobacter aqueolei
2 TPP

Marinobacter sp. ELB17
2 TPP

Oceanobacter sp. RED65
1 TPP

Oceanospirillum sp. MED92
2 TPP

Marinomonas sp. MWYL1
3 TPP

Saccharophagus degradans 2-40
3 TPP

Teredinibacter turnerae T7901
2 TPP

Cellvibrio japonicus Ueda107
2 TPP

Chromohalobacter salexigens DSM 3043
2 TPP

Reinekea sp. MED297
Thiamine biosynthesis
RF01055 RNA MOCO_RNA_motif
1 MOCO_RNA_motif

Teredinibacter turnerae T7901
1 MOCO_RNA_motif

Reinekea sp. MED297
Molybdopterin biosynthesis; Molybdenum homeostasis