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

Collection of regulogs in Alteromonadales taxonomic group

General statistics
Genomes 9
TF regulogs 50
TF regulons 231
TF binding sites 1215
RNA regulogs 3
RNA regulons 13
RNA sites 17

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
Alteromonadales bacterium TW-7 26 158 1 1 27 159
Alteromonas macleodii 'Deep ecotype' 26 136 2 3 28 139
Colwellia psychrerythraea 34H 34 185 2 3 36 188
Glaciecola sp. HTCC2999 19 83 1 1 20 84
Idiomarina baltica OS145 21 82 1 1 22 83
Idiomarina loihiensis L2TR 19 97 1 2 20 99
Pseudoalteromonas atlantica T6c 28 163 2 3 30 166
Pseudoalteromonas haloplanktis TAC125 26 134 2 2 28 136
Pseudoalteromonas tunicata D2 32 177 1 1 33 178
Genomic distribution of regulons
Family Type Regulator Function
ArgR TF ArgR
3 ArgR

Pseudoalteromonas atlantica T6c
4 ArgR

Alteromonas macleodii 'Deep ecotype'
3 ArgR

Glaciecola sp. HTCC2999
5 ArgR

Colwellia psychrerythraea 34H
5 ArgR

Alteromonadales bacterium TW-7
4 ArgR

Pseudoalteromonas haloplanktis TAC125
5 ArgR

Pseudoalteromonas tunicata D2
4 ArgR

Idiomarina baltica OS145
5 ArgR

Idiomarina loihiensis L2TR
Arginine biosynthesis; Arginine degradation
BirA TF BirA
2 BirA

Pseudoalteromonas atlantica T6c
2 BirA

Alteromonas macleodii 'Deep ecotype'
2 BirA

Glaciecola sp. HTCC2999
2 BirA

Colwellia psychrerythraea 34H
2 BirA

Alteromonadales bacterium TW-7
1 BirA

Pseudoalteromonas haloplanktis TAC125
2 BirA

Pseudoalteromonas tunicata D2
2 BirA

Idiomarina baltica OS145
2 BirA

Idiomarina loihiensis L2TR
Biotin biosynthesis
FUR TF Fur
17 Fur

Pseudoalteromonas atlantica T6c
10 Fur

Alteromonas macleodii 'Deep ecotype'
4 Fur

Glaciecola sp. HTCC2999
10 Fur

Colwellia psychrerythraea 34H
16 Fur

Alteromonadales bacterium TW-7
15 Fur

Pseudoalteromonas haloplanktis TAC125
20 Fur

Pseudoalteromonas tunicata D2
10 Fur

Idiomarina baltica OS145
18 Fur

Idiomarina loihiensis L2TR
Iron homeostasis
TF Zur
7 Zur

Pseudoalteromonas atlantica T6c
5 Zur

Alteromonas macleodii 'Deep ecotype'
2 Zur

Glaciecola sp. HTCC2999
4 Zur

Colwellia psychrerythraea 34H
6 Zur

Alteromonadales bacterium TW-7
3 Zur

Pseudoalteromonas haloplanktis TAC125
4 Zur

Pseudoalteromonas tunicata D2
2 Zur

Idiomarina baltica OS145
3 Zur

Idiomarina loihiensis L2TR
Zinc homeostasis
Fis TF NorR
2 NorR

Pseudoalteromonas atlantica T6c
2 NorR

Colwellia psychrerythraea 34H
2 NorR

Pseudoalteromonas haloplanktis TAC125
2 NorR

Pseudoalteromonas tunicata D2
Nitrosative stress response
TF NtrC
3 NtrC

Pseudoalteromonas atlantica T6c
3 NtrC

Alteromonas macleodii 'Deep ecotype'
3 NtrC

Glaciecola sp. HTCC2999
3 NtrC

Colwellia psychrerythraea 34H
3 NtrC

Alteromonadales bacterium TW-7
3 NtrC

Pseudoalteromonas haloplanktis TAC125
3 NtrC

Pseudoalteromonas tunicata D2
2 NtrC

Idiomarina baltica OS145
3 NtrC

Idiomarina loihiensis L2TR
Nitrogen assimilation
GntR/MocR TF CPS_3393
1 CPS_3393

Colwellia psychrerythraea 34H
Metabolite transport
TF CPS_4612
1 CPS_4612

Colwellia psychrerythraea 34H
1 CPS_4612

Pseudoalteromonas haloplanktis TAC125
1 CPS_4612

Pseudoalteromonas tunicata D2
Metabolite transport
TF PTD2_03046
2 PTD2_03046

Pseudoalteromonas tunicata D2
Metabolite transport
TF PdxW
1 PdxW

Colwellia psychrerythraea 34H
1 PdxW

Pseudoalteromonas tunicata D2
Pyridoxine/pyridoxal homeostasis
GntR/Others TF CPS_0449
1 CPS_0449

Colwellia psychrerythraea 34H
1 CPS_0449

Pseudoalteromonas tunicata D2
Multidrug resistance; Multidrug efflux
TF FadR
5 FadR

Pseudoalteromonas atlantica T6c
6 FadR

Alteromonas macleodii 'Deep ecotype'
4 FadR

Glaciecola sp. HTCC2999
3 FadR

Colwellia psychrerythraea 34H
6 FadR

Alteromonadales bacterium TW-7
5 FadR

Pseudoalteromonas haloplanktis TAC125
5 FadR

Pseudoalteromonas tunicata D2
2 FadR

Idiomarina baltica OS145
3 FadR

Idiomarina loihiensis L2TR
Fatty acid degradation
TF HutC
2 HutC

Pseudoalteromonas atlantica T6c
2 HutC

Alteromonas macleodii 'Deep ecotype'
5 HutC

Colwellia psychrerythraea 34H
2 HutC

Alteromonadales bacterium TW-7
2 HutC

Pseudoalteromonas haloplanktis TAC125
2 HutC

Pseudoalteromonas tunicata D2
2 HutC

Idiomarina baltica OS145
3 HutC

Idiomarina loihiensis L2TR
Histidine utilization
TF HypR
5 HypR

Colwellia psychrerythraea 34H
6 HypR

Alteromonadales bacterium TW-7
6 HypR

Pseudoalteromonas tunicata D2
Proline and 4-hydrohyproline utilization
TF PdhR
1 PdhR

Pseudoalteromonas atlantica T6c
1 PdhR

Alteromonas macleodii 'Deep ecotype'
2 PdhR

Glaciecola sp. HTCC2999
2 PdhR

Colwellia psychrerythraea 34H
2 PdhR

Alteromonadales bacterium TW-7
3 PdhR

Pseudoalteromonas haloplanktis TAC125
2 PdhR

Pseudoalteromonas tunicata D2
1 PdhR

Idiomarina baltica OS145
1 PdhR

Idiomarina loihiensis L2TR
Pyruvate metabolism
TF PrpR
1 PrpR

Pseudoalteromonas atlantica T6c
1 PrpR

Alteromonas macleodii 'Deep ecotype'
1 PrpR

Glaciecola sp. HTCC2999
4 PrpR

Colwellia psychrerythraea 34H
1 PrpR

Alteromonadales bacterium TW-7
1 PrpR

Pseudoalteromonas haloplanktis TAC125
1 PrpR

Pseudoalteromonas tunicata D2
1 PrpR

Idiomarina baltica OS145
1 PrpR

Idiomarina loihiensis L2TR
Methylcitrate utilization
TF VanR
5 VanR

Pseudoalteromonas atlantica T6c
Vanillate utilization
HrcA TF HrcA
1 HrcA

Pseudoalteromonas haloplanktis TAC125
1 HrcA

Pseudoalteromonas tunicata D2
Heat shock response
LacI TF BglR
2 BglR

Alteromonas macleodii 'Deep ecotype'
4 BglR

Glaciecola sp. HTCC2999
4 BglR

Colwellia psychrerythraea 34H
6 BglR

Alteromonadales bacterium TW-7
3 BglR

Pseudoalteromonas tunicata D2
3 BglR

Idiomarina baltica OS145
Beta-glucosides utilization
TF GalR
4 GalR

Alteromonas macleodii 'Deep ecotype'
2 GalR

Pseudoalteromonas haloplanktis TAC125
Galactose utilization
TF GntR
3 GntR

Pseudoalteromonas haloplanktis TAC125
Gluconate utilization
TF MalR
7 MalR

Pseudoalteromonas atlantica T6c
6 MalR

Alteromonas macleodii 'Deep ecotype'
4 MalR

Glaciecola sp. HTCC2999
7 MalR

Colwellia psychrerythraea 34H
6 MalR

Alteromonadales bacterium TW-7
4 MalR

Pseudoalteromonas haloplanktis TAC125
5 MalR

Pseudoalteromonas tunicata D2
Maltose utilization; Maltodextrin utilization
TF ManR1
3 ManR1

Colwellia psychrerythraea 34H
1 ManR1

Alteromonadales bacterium TW-7
2 ManR1

Pseudoalteromonas tunicata D2
Mannosides utilization; Mannose utilization
TF ManR2
3 ManR2

Pseudoalteromonas atlantica T6c
Mannosides utilization; Mannose utilization
TF NagR
11 NagR

Colwellia psychrerythraea 34H
3 NagR

Alteromonadales bacterium TW-7
9 NagR

Pseudoalteromonas tunicata D2
N-acetylglucosamine utilization
TF Patl_0292
2 Patl_0292

Pseudoalteromonas atlantica T6c
TF ScrR
4 ScrR

Pseudoalteromonas atlantica T6c
5 ScrR

Alteromonas macleodii 'Deep ecotype'
5 ScrR

Glaciecola sp. HTCC2999
3 ScrR

Alteromonadales bacterium TW-7
3 ScrR

Pseudoalteromonas tunicata D2
Sucrose utilization
TF Sde_0506
2 Sde_0506

Pseudoalteromonas atlantica T6c
2 Sde_0506

Alteromonas macleodii 'Deep ecotype'
Sugar utilization
TF TreR
3 TreR

Pseudoalteromonas atlantica T6c
4 TreR

Colwellia psychrerythraea 34H
3 TreR

Pseudoalteromonas tunicata D2
Trehalose utilization
LexA TF LexA
11 LexA

Pseudoalteromonas atlantica T6c
10 LexA

Alteromonas macleodii 'Deep ecotype'
9 LexA

Glaciecola sp. HTCC2999
12 LexA

Colwellia psychrerythraea 34H
11 LexA

Alteromonadales bacterium TW-7
12 LexA

Pseudoalteromonas haloplanktis TAC125
11 LexA

Pseudoalteromonas tunicata D2
5 LexA

Idiomarina baltica OS145
6 LexA

Idiomarina loihiensis L2TR
SOS response
LysR TF MetR
2 MetR

Colwellia psychrerythraea 34H
4 MetR

Alteromonadales bacterium TW-7
4 MetR

Pseudoalteromonas haloplanktis TAC125
3 MetR

Pseudoalteromonas tunicata D2
Methionine biosynthesis
MarR TF HmgS
2 HmgS

Alteromonadales bacterium TW-7
2 HmgS

Pseudoalteromonas haloplanktis TAC125
2 HmgS

Pseudoalteromonas tunicata D2
Tyrosine degradation
MerR TF CadR-PbrR
1 CadR-PbrR

Pseudoalteromonas atlantica T6c
1 CadR-PbrR

Glaciecola sp. HTCC2999
1 CadR-PbrR

Pseudoalteromonas haloplanktis TAC125
3 CadR-PbrR

Idiomarina baltica OS145
3 CadR-PbrR

Idiomarina loihiensis L2TR
Lead resistance; Cadmium resistance
TF CueR
1 CueR

Colwellia psychrerythraea 34H
Copper resistance
TF LiuR
4 LiuR

Pseudoalteromonas atlantica T6c
5 LiuR

Alteromonas macleodii 'Deep ecotype'
5 LiuR

Colwellia psychrerythraea 34H
10 LiuR

Alteromonadales bacterium TW-7
9 LiuR

Pseudoalteromonas haloplanktis TAC125
9 LiuR

Pseudoalteromonas tunicata D2
4 LiuR

Idiomarina baltica OS145
3 LiuR

Idiomarina loihiensis L2TR
Branched-chain amino acid degradation
TF MerR
4 MerR

Alteromonas macleodii 'Deep ecotype'
1 MerR

Idiomarina baltica OS145
1 MerR

Idiomarina loihiensis L2TR
Mercury resistance
TF NmlR
1 NmlR

Colwellia psychrerythraea 34H
Carbonyl stress response
TF SoxR
1 SoxR

Pseudoalteromonas atlantica T6c
1 SoxR

Alteromonadales bacterium TW-7
1 SoxR

Pseudoalteromonas tunicata D2
Superoxide stress response
MetJ TF MetJ
7 MetJ

Pseudoalteromonas atlantica T6c
6 MetJ

Alteromonas macleodii 'Deep ecotype'
6 MetJ

Glaciecola sp. HTCC2999
9 MetJ

Colwellia psychrerythraea 34H
8 MetJ

Alteromonadales bacterium TW-7
9 MetJ

Pseudoalteromonas haloplanktis TAC125
12 MetJ

Pseudoalteromonas tunicata D2
6 MetJ

Idiomarina baltica OS145
7 MetJ

Idiomarina loihiensis L2TR
Methionine metabolism; Methionine biosynthesis
NrdR TF NrdR
1 NrdR

Pseudoalteromonas atlantica T6c
2 NrdR

Alteromonas macleodii 'Deep ecotype'
1 NrdR

Glaciecola sp. HTCC2999
2 NrdR

Colwellia psychrerythraea 34H
1 NrdR

Alteromonadales bacterium TW-7
1 NrdR

Pseudoalteromonas haloplanktis TAC125
1 NrdR

Pseudoalteromonas tunicata D2
1 NrdR

Idiomarina baltica OS145
2 NrdR

Idiomarina loihiensis L2TR
Deoxyribonucleotide biosynthesis
RpiR TF HexR
9 HexR

Pseudoalteromonas atlantica T6c
10 HexR

Alteromonas macleodii 'Deep ecotype'
6 HexR

Glaciecola sp. HTCC2999
4 HexR

Colwellia psychrerythraea 34H
2 HexR

Idiomarina baltica OS145
Central carbohydrate metabolism
Rrf2 TF IscR
3 IscR

Pseudoalteromonas atlantica T6c
3 IscR

Alteromonas macleodii 'Deep ecotype'
3 IscR

Glaciecola sp. HTCC2999
4 IscR

Colwellia psychrerythraea 34H
4 IscR

Alteromonadales bacterium TW-7
4 IscR

Pseudoalteromonas haloplanktis TAC125
4 IscR

Pseudoalteromonas tunicata D2
3 IscR

Idiomarina baltica OS145
5 IscR

Idiomarina loihiensis L2TR
Iron-sulfur cluster biogenesis
TF NsrR
2 NsrR

Pseudoalteromonas haloplanktis TAC125
Nitrosative stress response
TetR TF FabR
4 FabR

Pseudoalteromonas atlantica T6c
4 FabR

Alteromonas macleodii 'Deep ecotype'
4 FabR

Glaciecola sp. HTCC2999
2 FabR

Colwellia psychrerythraea 34H
8 FabR

Alteromonadales bacterium TW-7
7 FabR

Pseudoalteromonas haloplanktis TAC125
5 FabR

Pseudoalteromonas tunicata D2
3 FabR

Idiomarina baltica OS145
4 FabR

Idiomarina loihiensis L2TR
Fatty acid biosynthesis
TF PsrA
3 PsrA

Alteromonas macleodii 'Deep ecotype'
8 PsrA

Colwellia psychrerythraea 34H
6 PsrA

Idiomarina baltica OS145
7 PsrA

Idiomarina loihiensis L2TR
Fatty acid degradation
TF RutR
7 RutR

Pseudoalteromonas atlantica T6c
6 RutR

Alteromonas macleodii 'Deep ecotype'
3 RutR

Colwellia psychrerythraea 34H
2 RutR

Alteromonadales bacterium TW-7
Pyrimidine utilization
TF RutR2
2 RutR2

Alteromonas macleodii 'Deep ecotype'
Pyrimidine utilization
TyrR TF MdeR
2 MdeR

Colwellia psychrerythraea 34H
Methionine metabolism
TF TyrR1
4 TyrR1

Pseudoalteromonas atlantica T6c
3 TyrR1

Alteromonas macleodii 'Deep ecotype'
2 TyrR1

Glaciecola sp. HTCC2999
3 TyrR1

Colwellia psychrerythraea 34H
4 TyrR1

Alteromonadales bacterium TW-7
4 TyrR1

Pseudoalteromonas haloplanktis TAC125
4 TyrR1

Pseudoalteromonas tunicata D2
Aromatic amino acid metabolism
TF TyrR2
3 TyrR2

Idiomarina baltica OS145
2 TyrR2

Idiomarina loihiensis L2TR
Tyrosine degradation; Aromatic amino acid metabolism
RF00050 RNA FMN
1 FMN

Pseudoalteromonas haloplanktis TAC125
Riboflavin biosynthesis
RF00059 RNA TPP
2 TPP

Pseudoalteromonas atlantica T6c
2 TPP

Alteromonas macleodii 'Deep ecotype'
1 TPP

Glaciecola sp. HTCC2999
2 TPP

Colwellia psychrerythraea 34H
1 TPP

Alteromonadales bacterium TW-7
1 TPP

Pseudoalteromonas haloplanktis TAC125
1 TPP

Pseudoalteromonas tunicata D2
1 TPP

Idiomarina baltica OS145
2 TPP

Idiomarina loihiensis L2TR
RF01055 RNA MOCO_RNA_motif
1 MOCO_RNA_motif

Pseudoalteromonas atlantica T6c
1 MOCO_RNA_motif

Alteromonas macleodii 'Deep ecotype'
1 MOCO_RNA_motif

Colwellia psychrerythraea 34H
Molybdenum homeostasis; Molybdopterin biosynthesis