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

Collection of regulogs in Psychromonadaceae/Aeromonadales taxonomic group

General statistics
Genomes 6
TF regulogs 56
TF regulons 194
TF binding sites 965
RNA regulogs 3
RNA regulons 16
RNA sites 24

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
Aeromonas hydrophila subsp. hydrophila ATCC 7966 41 239 3 4 44 243
Aeromonas salmonicida subsp. salmonicida A449 37 218 3 4 40 222
Moritella sp. PE36 32 183 3 5 35 188
Psychromonas ingrahamii 37 31 114 2 4 33 118
Psychromonas sp. CNPT3 27 106 2 3 29 109
Tolumonas auensis DSM 9187 26 105 3 4 29 109
Genomic distribution of regulons
Family Type Regulator Function
ArgR TF ArgR
7 ArgR

Psychromonas ingrahamii 37
4 ArgR

Psychromonas sp. CNPT3
5 ArgR

Moritella sp. PE36
7 ArgR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
7 ArgR

Aeromonas salmonicida subsp. salmonicida A449
6 ArgR

Tolumonas auensis DSM 9187
Arginine degradation; Arginine biosynthesis
BirA TF BirA
2 BirA

Psychromonas ingrahamii 37
2 BirA

Psychromonas sp. CNPT3
2 BirA

Moritella sp. PE36
2 BirA

Aeromonas hydrophila subsp. hydrophila ATCC 7966
2 BirA

Aeromonas salmonicida subsp. salmonicida A449
2 BirA

Tolumonas auensis DSM 9187
Biotin biosynthesis
DeoR TF AgaR
2 AgaR

Psychromonas sp. CNPT3
2 AgaR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
N-acetylgalactosamine utilization
FUR TF Fur
3 Fur

Psychromonas ingrahamii 37
8 Fur

Psychromonas sp. CNPT3
23 Fur

Moritella sp. PE36
24 Fur

Aeromonas hydrophila subsp. hydrophila ATCC 7966
24 Fur

Aeromonas salmonicida subsp. salmonicida A449
8 Fur

Tolumonas auensis DSM 9187
Iron homeostasis
TF Zur
1 Zur

Psychromonas ingrahamii 37
2 Zur

Psychromonas sp. CNPT3
5 Zur

Moritella sp. PE36
3 Zur

Aeromonas hydrophila subsp. hydrophila ATCC 7966
3 Zur

Aeromonas salmonicida subsp. salmonicida A449
2 Zur

Tolumonas auensis DSM 9187
Zinc homeostasis
Fis TF NorR
3 NorR

Moritella sp. PE36
2 NorR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
2 NorR

Aeromonas salmonicida subsp. salmonicida A449
Nitrosative stress response
TF NtrC
2 NtrC

Psychromonas ingrahamii 37
2 NtrC

Psychromonas sp. CNPT3
3 NtrC

Moritella sp. PE36
4 NtrC

Aeromonas hydrophila subsp. hydrophila ATCC 7966
5 NtrC

Aeromonas salmonicida subsp. salmonicida A449
4 NtrC

Tolumonas auensis DSM 9187
Nitrogen assimilation
GntR/MocR TF AHA_3778
1 AHA_3778

Aeromonas hydrophila subsp. hydrophila ATCC 7966
1 AHA_3778

Aeromonas salmonicida subsp. salmonicida A449
TF GabR
1 GabR

Psychromonas ingrahamii 37
Gamma-aminobutyrate utilization
TF PE36_10153
1 PE36_10153

Moritella sp. PE36
Metabolite transport
TF TauR
2 TauR

Psychromonas ingrahamii 37
Taurine utilization
TF Tola_2572
2 Tola_2572

Psychromonas sp. CNPT3
2 Tola_2572

Moritella sp. PE36
2 Tola_2572

Tolumonas auensis DSM 9187
TF Tola_2750
2 Tola_2750

Aeromonas hydrophila subsp. hydrophila ATCC 7966
2 Tola_2750

Tolumonas auensis DSM 9187
Metabolite transport
TF YdcR
1 YdcR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
1 YdcR

Aeromonas salmonicida subsp. salmonicida A449
GntR/Others TF FadR
1 FadR

Psychromonas ingrahamii 37
1 FadR

Psychromonas sp. CNPT3
2 FadR

Moritella sp. PE36
3 FadR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
3 FadR

Aeromonas salmonicida subsp. salmonicida A449
Fatty acid degradation
TF HutC
3 HutC

Psychromonas ingrahamii 37
2 HutC

Moritella sp. PE36
1 HutC

Aeromonas hydrophila subsp. hydrophila ATCC 7966
2 HutC

Aeromonas salmonicida subsp. salmonicida A449
Histidine utilization
TF HypR
2 HypR

Psychromonas ingrahamii 37
2 HypR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
2 HypR

Aeromonas salmonicida subsp. salmonicida A449
Proline and 4-hydrohyproline utilization
TF PCNPT3_10213
1 PCNPT3_10213

Psychromonas sp. CNPT3
Multidrug resistance; Multidrug efflux
TF PdhR
1 PdhR

Psychromonas ingrahamii 37
1 PdhR

Psychromonas sp. CNPT3
1 PdhR

Moritella sp. PE36
1 PdhR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
1 PdhR

Aeromonas salmonicida subsp. salmonicida A449
1 PdhR

Tolumonas auensis DSM 9187
Pyruvate metabolism
TF PhnF
1 PhnF

Psychromonas ingrahamii 37
Phosphonate utilization
TF PhnR
2 PhnR

Psychromonas ingrahamii 37
2 PhnR

Psychromonas sp. CNPT3
3 PhnR

Moritella sp. PE36
4 PhnR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
Phosphonate utilization; 2-aminoethylphosphonate utilization
TF PhnR1
2 PhnR1

Aeromonas hydrophila subsp. hydrophila ATCC 7966
2 PhnR1

Aeromonas salmonicida subsp. salmonicida A449
2-aminoethylphosphonate utilization
TF PrpR
1 PrpR

Psychromonas ingrahamii 37
2 PrpR

Moritella sp. PE36
Methylcitrate utilization
TF UxuR
4 UxuR

Psychromonas ingrahamii 37
2 UxuR

Psychromonas sp. CNPT3
4 UxuR

Tolumonas auensis DSM 9187
Glucuronate utilization
LacI TF EbgR
1 EbgR

Psychromonas sp. CNPT3
2 EbgR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
Galactosides utilization
TF FruR
2 FruR

Psychromonas ingrahamii 37
2 FruR

Psychromonas sp. CNPT3
2 FruR

Moritella sp. PE36
2 FruR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
2 FruR

Aeromonas salmonicida subsp. salmonicida A449
2 FruR

Tolumonas auensis DSM 9187
Fructose utilization
TF GntR
3 GntR

Psychromonas ingrahamii 37
3 GntR

Moritella sp. PE36
3 GntR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
3 GntR

Aeromonas salmonicida subsp. salmonicida A449
2 GntR

Tolumonas auensis DSM 9187
Gluconate utilization
TF ManR
3 ManR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
Mannose utilization
TF RbsR
1 RbsR

Psychromonas ingrahamii 37
1 RbsR

Psychromonas sp. CNPT3
1 RbsR

Moritella sp. PE36
1 RbsR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
1 RbsR

Aeromonas salmonicida subsp. salmonicida A449
1 RbsR

Tolumonas auensis DSM 9187
Ribose utilization
TF ScrR
2 ScrR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
2 ScrR

Aeromonas salmonicida subsp. salmonicida A449
1 ScrR

Tolumonas auensis DSM 9187
Sucrose utilization
TF SgaR
2 SgaR

Psychromonas ingrahamii 37
2 SgaR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
2 SgaR

Aeromonas salmonicida subsp. salmonicida A449
Ascorbate utilization
TF TreR
1 TreR

Psychromonas ingrahamii 37
1 TreR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
1 TreR

Aeromonas salmonicida subsp. salmonicida A449
1 TreR

Tolumonas auensis DSM 9187
Trehalose utilization
LexA TF LexA
8 LexA

Psychromonas ingrahamii 37
11 LexA

Psychromonas sp. CNPT3
12 LexA

Moritella sp. PE36
11 LexA

Aeromonas hydrophila subsp. hydrophila ATCC 7966
10 LexA

Aeromonas salmonicida subsp. salmonicida A449
8 LexA

Tolumonas auensis DSM 9187
SOS response
LuxR TF NarP
2 NarP

Psychromonas sp. CNPT3
12 NarP

Moritella sp. PE36
16 NarP

Aeromonas hydrophila subsp. hydrophila ATCC 7966
15 NarP

Aeromonas salmonicida subsp. salmonicida A449
Nitrate and nitrite respiration
LysR TF MetR
2 MetR

Psychromonas ingrahamii 37
2 MetR

Moritella sp. PE36
2 MetR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
2 MetR

Aeromonas salmonicida subsp. salmonicida A449
2 MetR

Tolumonas auensis DSM 9187
Methionine biosynthesis
MerR TF CadR-PbrR
1 CadR-PbrR

Tolumonas auensis DSM 9187
Lead resistance; Cadmium resistance
TF CueR
2 CueR

Psychromonas ingrahamii 37
2 CueR

Psychromonas sp. CNPT3
3 CueR

Moritella sp. PE36
1 CueR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
1 CueR

Aeromonas salmonicida subsp. salmonicida A449
2 CueR

Tolumonas auensis DSM 9187
Copper resistance
TF LiuR
7 LiuR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
7 LiuR

Aeromonas salmonicida subsp. salmonicida A449
Branched-chain amino acid degradation
TF MerR
1 MerR

Psychromonas ingrahamii 37
1 MerR

Aeromonas salmonicida subsp. salmonicida A449
Mercury resistance
TF PhrR
1 PhrR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
1 PhrR

Aeromonas salmonicida subsp. salmonicida A449
Light-dependent DNA repair
TF SoxR
1 SoxR

Moritella sp. PE36
1 SoxR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
1 SoxR

Aeromonas salmonicida subsp. salmonicida A449
Superoxide stress response
TF ZntR
1 ZntR

Psychromonas sp. CNPT3
1 ZntR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
1 ZntR

Aeromonas salmonicida subsp. salmonicida A449
Zinc resistance
MetJ TF MetJ
4 MetJ

Psychromonas ingrahamii 37
5 MetJ

Psychromonas sp. CNPT3
8 MetJ

Moritella sp. PE36
14 MetJ

Aeromonas hydrophila subsp. hydrophila ATCC 7966
14 MetJ

Aeromonas salmonicida subsp. salmonicida A449
7 MetJ

Tolumonas auensis DSM 9187
Methionine metabolism; Methionine biosynthesis
ModE TF ModE
1 ModE

Moritella sp. PE36
2 ModE

Tolumonas auensis DSM 9187
Molybdenum homeostasis
NrdR TF NrdR
3 NrdR

Psychromonas ingrahamii 37
2 NrdR

Psychromonas sp. CNPT3
2 NrdR

Moritella sp. PE36
3 NrdR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
3 NrdR

Aeromonas salmonicida subsp. salmonicida A449
2 NrdR

Tolumonas auensis DSM 9187
Deoxyribonucleotide biosynthesis
NrtR TF NrtR
2 NrtR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
2 NrtR

Aeromonas salmonicida subsp. salmonicida A449
2 NrtR

Tolumonas auensis DSM 9187
NAD biosynthesis
ROK TF NagC
1 NagC

Psychromonas ingrahamii 37
2 NagC

Psychromonas sp. CNPT3
4 NagC

Moritella sp. PE36
3 NagC

Aeromonas hydrophila subsp. hydrophila ATCC 7966
3 NagC

Aeromonas salmonicida subsp. salmonicida A449
2 NagC

Tolumonas auensis DSM 9187
N-acetylglucosamine utilization
RpiR TF HexR
11 HexR

Psychromonas ingrahamii 37
8 HexR

Psychromonas sp. CNPT3
7 HexR

Moritella sp. PE36
18 HexR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
18 HexR

Aeromonas salmonicida subsp. salmonicida A449
6 HexR

Tolumonas auensis DSM 9187
Central carbohydrate metabolism
TF SiaR
6 SiaR

Psychromonas sp. CNPT3
Sialic acid utilization
Rrf2 TF IscR
2 IscR

Psychromonas ingrahamii 37
2 IscR

Psychromonas sp. CNPT3
2 IscR

Moritella sp. PE36
2 IscR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
2 IscR

Aeromonas salmonicida subsp. salmonicida A449
2 IscR

Tolumonas auensis DSM 9187
Iron-sulfur cluster biogenesis
TF NsrR
2 NsrR

Psychromonas ingrahamii 37
2 NsrR

Psychromonas sp. CNPT3
Nitrosative stress response
TetR TF FabR
2 FabR

Psychromonas ingrahamii 37
7 FabR

Moritella sp. PE36
7 FabR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
7 FabR

Aeromonas salmonicida subsp. salmonicida A449
Fatty acid biosynthesis
TF PsrA
6 PsrA

Moritella sp. PE36
4 PsrA

Aeromonas hydrophila subsp. hydrophila ATCC 7966
4 PsrA

Aeromonas salmonicida subsp. salmonicida A449
Fatty acid degradation
TF RutR
4 RutR

Moritella sp. PE36
Pyrimidine utilization
TrpR TF TrpR
1 TrpR

Psychromonas sp. CNPT3
1 TrpR

Moritella sp. PE36
Tryptophan biosynthesis
TyrR TF TyrR
2 TyrR

Moritella sp. PE36
4 TyrR

Aeromonas hydrophila subsp. hydrophila ATCC 7966
4 TyrR

Aeromonas salmonicida subsp. salmonicida A449
1 TyrR

Tolumonas auensis DSM 9187
Aromatic amino acid metabolism
RF00050 RNA FMN
1 FMN

Psychromonas sp. CNPT3
1 FMN

Moritella sp. PE36
1 FMN

Aeromonas hydrophila subsp. hydrophila ATCC 7966
1 FMN

Aeromonas salmonicida subsp. salmonicida A449
1 FMN

Tolumonas auensis DSM 9187
Riboflavin biosynthesis
RF00059 RNA TPP
3 TPP

Psychromonas ingrahamii 37
2 TPP

Psychromonas sp. CNPT3
3 TPP

Moritella sp. PE36
2 TPP

Aeromonas hydrophila subsp. hydrophila ATCC 7966
2 TPP

Aeromonas salmonicida subsp. salmonicida A449
2 TPP

Tolumonas auensis DSM 9187
Thiamine biosynthesis
RF01055 RNA MOCO_RNA_motif
1 MOCO_RNA_motif

Psychromonas ingrahamii 37
1 MOCO_RNA_motif

Moritella sp. PE36
1 MOCO_RNA_motif

Aeromonas hydrophila subsp. hydrophila ATCC 7966
1 MOCO_RNA_motif

Aeromonas salmonicida subsp. salmonicida A449
1 MOCO_RNA_motif

Tolumonas auensis DSM 9187
Molybdopterin biosynthesis