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

Regulog TPP - Comamonadaceae

Properties
Regulator type: RNA regulatory element
Name: TPP
RFAM: RF00059
Regulation mode:
Biological process: Thiamine biosynthesis
Effector: Thiamine pyrophosphate
Phylum: Proteobacteria/Beta
Member of regulog collections
Statistics of regulated genes
Genome Genes Operons
Acidovorax avenae subsp. citrulli AAC00-1 11 3
Acidovorax sp. JS42 5 2
Comamonas testosteroni KF-1 8 3
Delftia acidovorans SPH-1 11 3
Polaromonas naphthalenivorans CJ2 1 1
Polaromonas sp. JS666 3 2
Rhodoferax ferrireducens DSM 15236 12 4
Variovorax paradoxus S110 2 2
Verminephrobacter eiseniae EF01-2 1 1
Methylibium petroleiphilum PM1 6 2
Leptothrix cholodnii SP-6 6 2
Clusters of co-Regulated Orthologous operoNs (CRONs)
Genes Function
 
CRON 1.
PF04443
*
Acidovorax avenae subsp. citrulli AAC00-1

Site:
position = -185
score = 50.47
sequence = CCGCAACGCTCCGGG...

Gene: Aave_4517: Acyl-protein synthetase, LuxE
 
Acidovorax sp. JS42
*
Comamonas testosteroni KF-1

Site:
position = -163
score = 48.67
sequence = GCGCCGCGCTCCGGG...

Gene: CtesDRAFT_2085: Acyl-protein synthetase, LuxE
*
Delftia acidovorans SPH-1

Site:
position = -160
score = 45.65
sequence = GCCCTCCGCTCCGGG...

Gene: Daci_4530: Acyl-protein synthetase, LuxE
 
Polaromonas naphthalenivorans CJ2
 
Polaromonas sp. JS666
 
Rhodoferax ferrireducens DSM 15236
 
Variovorax paradoxus S110
 
Verminephrobacter eiseniae EF01-2
 
Methylibium petroleiphilum PM1
 
Leptothrix cholodnii SP-6
Acyl-protein synthetase, LuxE
PF05893
 
Acidovorax avenae subsp. citrulli AAC00-1

Gene: Aave_4516: putative acyl-CoA reductase
 
Acidovorax sp. JS42
 
Comamonas testosteroni KF-1

Gene: CtesDRAFT_2084: putative acyl-CoA reductase
 
Delftia acidovorans SPH-1

Gene: Daci_4529: putative acyl-CoA reductase
 
Polaromonas naphthalenivorans CJ2
 
Polaromonas sp. JS666
 
Rhodoferax ferrireducens DSM 15236
 
Variovorax paradoxus S110
 
Verminephrobacter eiseniae EF01-2
 
Methylibium petroleiphilum PM1
 
Leptothrix cholodnii SP-6
putative acyl-CoA reductase
thiZ
 
Acidovorax avenae subsp. citrulli AAC00-1

Gene: Aave_4515: Hydroxymethylpyrimidine ABC transporter, ATPase component
 
Acidovorax sp. JS42
 
Comamonas testosteroni KF-1

Gene: CtesDRAFT_2083: Hydroxymethylpyrimidine ABC transporter, ATPase component
 
Delftia acidovorans SPH-1

Gene: Daci_4528: Hydroxymethylpyrimidine ABC transporter, ATPase component
 
Polaromonas naphthalenivorans CJ2
 
Polaromonas sp. JS666
 
Rhodoferax ferrireducens DSM 15236
 
Variovorax paradoxus S110
 
Verminephrobacter eiseniae EF01-2
 
Methylibium petroleiphilum PM1
 
Leptothrix cholodnii SP-6
Hydroxymethylpyrimidine ABC transporter, ATPase component
thiX
 
Acidovorax avenae subsp. citrulli AAC00-1

Gene: Aave_4514: Hydroxymethylpyrimidine ABC transporter, transmembrane component
 
Acidovorax sp. JS42
 
Comamonas testosteroni KF-1

Gene: CtesDRAFT_2082: Hydroxymethylpyrimidine ABC transporter, transmembrane component
 
Delftia acidovorans SPH-1

Gene: Daci_4527: Hydroxymethylpyrimidine ABC transporter, transmembrane component
 
Polaromonas naphthalenivorans CJ2
 
Polaromonas sp. JS666
 
Rhodoferax ferrireducens DSM 15236
 
Variovorax paradoxus S110
 
Verminephrobacter eiseniae EF01-2
 
Methylibium petroleiphilum PM1
 
Leptothrix cholodnii SP-6
Hydroxymethylpyrimidine ABC transporter, transmembrane component
thiY
 
Acidovorax avenae subsp. citrulli AAC00-1

Gene: Aave_4513: Hydroxymethylpyrimidine ABC transporter, substrate-binding component
 
Acidovorax sp. JS42
 
Comamonas testosteroni KF-1

Gene: CtesDRAFT_2081: Hydroxymethylpyrimidine ABC transporter, substrate-binding component
 
Delftia acidovorans SPH-1

Gene: Daci_4526: Hydroxymethylpyrimidine ABC transporter, substrate-binding component
 
Polaromonas naphthalenivorans CJ2
 
Polaromonas sp. JS666
 
Rhodoferax ferrireducens DSM 15236
 
Variovorax paradoxus S110
 
Verminephrobacter eiseniae EF01-2
 
Methylibium petroleiphilum PM1
 
Leptothrix cholodnii SP-6
Hydroxymethylpyrimidine ABC transporter, substrate-binding component
oarX
 
Acidovorax avenae subsp. citrulli AAC00-1

Gene: Aave_4512: Thiamin-related 3-oxoacyl-[acyl-carrier protein] reductase OarX
 
Acidovorax sp. JS42
 
Comamonas testosteroni KF-1

Gene: CtesDRAFT_2080: Thiamin-related 3-oxoacyl-[acyl-carrier protein] reductase OarX
 
Delftia acidovorans SPH-1

Gene: Daci_4525: Thiamin-related 3-oxoacyl-[acyl-carrier protein] reductase OarX
 
Polaromonas naphthalenivorans CJ2
 
Polaromonas sp. JS666
 
Rhodoferax ferrireducens DSM 15236
 
Variovorax paradoxus S110
 
Verminephrobacter eiseniae EF01-2
 
Methylibium petroleiphilum PM1
 
Leptothrix cholodnii SP-6
Thiamin-related 3-oxoacyl-[acyl-carrier protein] reductase OarX
 
CRON 2.
thiM
 
Acidovorax avenae subsp. citrulli AAC00-1
 
Acidovorax sp. JS42
 
Comamonas testosteroni KF-1
 
Delftia acidovorans SPH-1
 
Polaromonas naphthalenivorans CJ2
 
Polaromonas sp. JS666
*
Rhodoferax ferrireducens DSM 15236

Site:
position = -137
score = 60.4
sequence = CCGTGCTTGCTAGAG...

Gene: Rfer_2472: Hydroxyethylthiazole kinase (EC 2.7.1.50)
 
Variovorax paradoxus S110
 
Verminephrobacter eiseniae EF01-2
 
Methylibium petroleiphilum PM1
 
Leptothrix cholodnii SP-6

Gene: Lcho_2206: Hydroxyethylthiazole kinase (EC 2.7.1.50)
Hydroxyethylthiazole kinase (EC 2.7.1.50)
thiE
 
Acidovorax avenae subsp. citrulli AAC00-1
 
Acidovorax sp. JS42
 
Comamonas testosteroni KF-1
 
Delftia acidovorans SPH-1
 
Polaromonas naphthalenivorans CJ2
 
Polaromonas sp. JS666
 
Rhodoferax ferrireducens DSM 15236

Gene: Rfer_2471: Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
 
Variovorax paradoxus S110
 
Verminephrobacter eiseniae EF01-2
 
Methylibium petroleiphilum PM1
 
Leptothrix cholodnii SP-6

Gene: Lcho_2205: Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
thiD
 
Acidovorax avenae subsp. citrulli AAC00-1

Gene: Aave_3067: Phosphomethylpyrimidine kinase (EC 2.7.4.7)
 
Acidovorax sp. JS42

Gene: Ajs_1787: Phosphomethylpyrimidine kinase (EC 2.7.4.7)
 
Comamonas testosteroni KF-1

Gene: CtesDRAFT_0937: Phosphomethylpyrimidine kinase (EC 2.7.4.7)
 
Delftia acidovorans SPH-1

Gene: Daci_3294: Phosphomethylpyrimidine kinase (EC 2.7.4.7)
 
Polaromonas naphthalenivorans CJ2

Gene: Pnap_2435: Phosphomethylpyrimidine kinase (EC 2.7.4.7)
 
Polaromonas sp. JS666

Gene: Bpro_2331: Phosphomethylpyrimidine kinase (EC 2.7.4.7)
 
Rhodoferax ferrireducens DSM 15236

Gene: Rfer_2470: Phosphomethylpyrimidine kinase (EC 2.7.4.7)
 
Variovorax paradoxus S110

Gene: Vapar_2399: Phosphomethylpyrimidine kinase (EC 2.7.4.7)
 
Verminephrobacter eiseniae EF01-2

Gene: Veis_4315: Phosphomethylpyrimidine kinase (EC 2.7.4.7)
 
Methylibium petroleiphilum PM1
 
Leptothrix cholodnii SP-6

Gene: Lcho_2204: Phosphomethylpyrimidine kinase (EC 2.7.4.7)
Phosphomethylpyrimidine kinase (EC 2.7.4.7)
 
CRON 3.
omp_thi
 
Acidovorax avenae subsp. citrulli AAC00-1
 
Acidovorax sp. JS42
 
Comamonas testosteroni KF-1
 
Delftia acidovorans SPH-1
 
Polaromonas naphthalenivorans CJ2
 
Polaromonas sp. JS666
 
Rhodoferax ferrireducens DSM 15236
 
Variovorax paradoxus S110
 
Verminephrobacter eiseniae EF01-2
*
Methylibium petroleiphilum PM1

Site:
position = -180
score = 50.66
sequence = CGACACCAGCTAGGG...

Gene: Mpe_A1495: Predicted thiamin-specific outer membrane transporter, TonB-dependent
 
Leptothrix cholodnii SP-6
Predicted thiamin-specific outer membrane transporter, TonB-dependent
 
CRON 4.
thiB
 
Acidovorax avenae subsp. citrulli AAC00-1
 
Acidovorax sp. JS42
 
Comamonas testosteroni KF-1
 
Delftia acidovorans SPH-1
 
Polaromonas naphthalenivorans CJ2
 
Polaromonas sp. JS666
*
Rhodoferax ferrireducens DSM 15236

Site:
position = -140
score = 54.92
sequence = GCGAGTTCACCGGGG...

Gene: Rfer_3246: Thiamin ABC transporter, substrate-binding component
 
Variovorax paradoxus S110
 
Verminephrobacter eiseniae EF01-2
 
Methylibium petroleiphilum PM1
 
Leptothrix cholodnii SP-6
Thiamin ABC transporter, substrate-binding component
thiP
 
Acidovorax avenae subsp. citrulli AAC00-1
 
Acidovorax sp. JS42
 
Comamonas testosteroni KF-1
 
Delftia acidovorans SPH-1
 
Polaromonas naphthalenivorans CJ2
 
Polaromonas sp. JS666
 
Rhodoferax ferrireducens DSM 15236

Gene: Rfer_3245: Thiamin ABC transporter, permease protein
 
Variovorax paradoxus S110
 
Verminephrobacter eiseniae EF01-2
 
Methylibium petroleiphilum PM1
 
Leptothrix cholodnii SP-6
Thiamin ABC transporter, permease protein
thiQ
 
Acidovorax avenae subsp. citrulli AAC00-1
 
Acidovorax sp. JS42
 
Comamonas testosteroni KF-1
 
Delftia acidovorans SPH-1
 
Polaromonas naphthalenivorans CJ2
 
Polaromonas sp. JS666
 
Rhodoferax ferrireducens DSM 15236

Gene: Rfer_3244: Thiamin ABC transporter, ATP-binding protein
 
Variovorax paradoxus S110
 
Verminephrobacter eiseniae EF01-2
 
Methylibium petroleiphilum PM1
 
Leptothrix cholodnii SP-6
Thiamin ABC transporter, ATP-binding protein
 
CRON 5.
cytX
 
Acidovorax avenae subsp. citrulli AAC00-1
 
Acidovorax sp. JS42
*
Comamonas testosteroni KF-1

Site:
position = -213
score = 32.17
sequence = GCAGCAATGCTGGGG...

Gene: CtesDRAFT_0940: Predicted hydroxymethylpyrimidine transporter CytX
 
Delftia acidovorans SPH-1
 
Polaromonas naphthalenivorans CJ2

Gene: Pnap_2434: Predicted hydroxymethylpyrimidine transporter CytX
*
Polaromonas sp. JS666

Site:
position = -171
score = 35.44
sequence = GTGCATCCGCTGGGA...

Gene: Bpro_2332: Predicted hydroxymethylpyrimidine transporter CytX
*
Rhodoferax ferrireducens DSM 15236

Site:
position = -187
score = 54.35
sequence = CATTTCGCTAGGGGT...

Gene: Rfer_2463: Predicted hydroxymethylpyrimidine transporter CytX
*
Variovorax paradoxus S110

Site:
position = -185
score = 48.93
sequence = GCACCACCGCTAGGG...

Gene: Vapar_2400: Predicted hydroxymethylpyrimidine transporter CytX
 
Verminephrobacter eiseniae EF01-2
 
Methylibium petroleiphilum PM1
*
Leptothrix cholodnii SP-6

Site:
position = -151
score = 50.75
sequence = TTCCTTGCTGGGGGT...

Gene: Lcho_2203: Predicted hydroxymethylpyrimidine transporter CytX
Predicted hydroxymethylpyrimidine transporter CytX
thiO
*
Acidovorax avenae subsp. citrulli AAC00-1

Site:
position = -170
score = 52.71
sequence = GGACGAAACAGGGGT...

Gene: Aave_3068: Glycine oxidase ThiO (EC 1.4.3.19)
*
Acidovorax sp. JS42

Site:
position = -184
score = 53.28
sequence = ACGGACGAAACAGGG...

Gene: Ajs_1786: Glycine oxidase ThiO (EC 1.4.3.19)
 
Comamonas testosteroni KF-1

Gene: CtesDRAFT_0936: Glycine oxidase ThiO (EC 1.4.3.19)
*
Delftia acidovorans SPH-1

Site:
position = -79
score = 23.39
sequence = TGCCGCGCAGCGCCC...

Gene: Daci_3293: Glycine oxidase ThiO (EC 1.4.3.19)
 
Polaromonas naphthalenivorans CJ2

Gene: Pnap_0020: Glycine oxidase ThiO (EC 1.4.3.19)
 
Polaromonas sp. JS666

Gene: Bpro_0038: Glycine oxidase ThiO (EC 1.4.3.19)
 
Rhodoferax ferrireducens DSM 15236

Gene: Rfer_2464: Glycine oxidase ThiO (EC 1.4.3.19)
 
Variovorax paradoxus S110

Gene: Vapar_2398: Glycine oxidase ThiO (EC 1.4.3.19)
 
Verminephrobacter eiseniae EF01-2

Gene: Veis_4314: Glycine oxidase ThiO (EC 1.4.3.19)
 
Methylibium petroleiphilum PM1

Gene: Mpe_A1609: Glycine oxidase ThiO (EC 1.4.3.19)
 
Leptothrix cholodnii SP-6

Gene: Lcho_2431: Glycine oxidase ThiO (EC 1.4.3.19)
Glycine oxidase ThiO (EC 1.4.3.19)
thiS
 
Acidovorax avenae subsp. citrulli AAC00-1

Gene: Aave_3069: Sulfur carrier protein ThiS
 
Acidovorax sp. JS42

Gene: Ajs_1785: Sulfur carrier protein ThiS
 
Comamonas testosteroni KF-1

Gene: CtesDRAFT_0935: Sulfur carrier protein ThiS
 
Delftia acidovorans SPH-1

Gene: Daci_3292: Sulfur carrier protein ThiS
 
Polaromonas naphthalenivorans CJ2

Gene: Pnap_0021: Sulfur carrier protein ThiS
 
Polaromonas sp. JS666
 
Rhodoferax ferrireducens DSM 15236

Gene: Rfer_2465: Sulfur carrier protein ThiS
 
Variovorax paradoxus S110

Gene: Vapar_2397: Sulfur carrier protein ThiS
 
Verminephrobacter eiseniae EF01-2

Gene: Veis_4313: Sulfur carrier protein ThiS
 
Methylibium petroleiphilum PM1

Gene: Mpe_A1608: Sulfur carrier protein ThiS
 
Leptothrix cholodnii SP-6

Gene: Lcho_2432: Sulfur carrier protein ThiS
Sulfur carrier protein ThiS
thiG
 
Acidovorax avenae subsp. citrulli AAC00-1

Gene: Aave_3070: Thiazole biosynthesis protein ThiG
 
Acidovorax sp. JS42

Gene: Ajs_1784: Thiazole biosynthesis protein ThiG
 
Comamonas testosteroni KF-1

Gene: CtesDRAFT_0934: Thiazole biosynthesis protein ThiG
 
Delftia acidovorans SPH-1

Gene: Daci_3291: Thiazole biosynthesis protein ThiG
 
Polaromonas naphthalenivorans CJ2

Gene: Pnap_0022: Thiazole biosynthesis protein ThiG
 
Polaromonas sp. JS666

Gene: Bpro_0040: Thiazole biosynthesis protein ThiG
 
Rhodoferax ferrireducens DSM 15236

Gene: Rfer_2466: Thiazole biosynthesis protein ThiG
 
Variovorax paradoxus S110

Gene: Vapar_2396: Thiazole biosynthesis protein ThiG
 
Verminephrobacter eiseniae EF01-2

Gene: Veis_4312: Thiazole biosynthesis protein ThiG
 
Methylibium petroleiphilum PM1

Gene: Mpe_A1607: Thiazole biosynthesis protein ThiG
 
Leptothrix cholodnii SP-6

Gene: Lcho_2433: Thiazole biosynthesis protein ThiG
Thiazole biosynthesis protein ThiG
thiE
 
Acidovorax avenae subsp. citrulli AAC00-1

Gene: Aave_3071: Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
 
Acidovorax sp. JS42

Gene: Ajs_1783: Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
 
Comamonas testosteroni KF-1

Gene: CtesDRAFT_0933: Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
 
Delftia acidovorans SPH-1

Gene: Daci_3290: Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
 
Polaromonas naphthalenivorans CJ2

Gene: Pnap_0023: Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
 
Polaromonas sp. JS666

Gene: Bpro_0041: Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
 
Rhodoferax ferrireducens DSM 15236

Gene: Rfer_2467: Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
 
Variovorax paradoxus S110

Gene: Vapar_2395: Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
 
Verminephrobacter eiseniae EF01-2

Gene: Veis_4311: Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
 
Methylibium petroleiphilum PM1
 
Leptothrix cholodnii SP-6
Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
thiC
*
Acidovorax avenae subsp. citrulli AAC00-1

Site:
position = -292
score = 53.99
sequence = CGCCTGCTCCGGGGT...

Gene: Aave_0829: Thiamin biosynthesis protein ThiC
*
Acidovorax sp. JS42

Site:
position = -212
score = 54.83
sequence = CGGCCCCGCTCCGGG...

Gene: Ajs_3661: Thiamin biosynthesis protein ThiC
*
Comamonas testosteroni KF-1

Site:
position = -346
score = 57.98
sequence = ATGCAGCTCCGGGGT...

Gene: CtesDRAFT_0498: Thiamin biosynthesis protein ThiC
*
Delftia acidovorans SPH-1

Site:
position = -390
score = 54.36
sequence = GCTCTGCTCCGGGGT...

Gene: Daci_2313: Thiamin biosynthesis protein ThiC
*
Polaromonas naphthalenivorans CJ2

Site:
position = -204
score = 75.86
sequence = GCAGCTTGTCGGGGT...

Gene: Pnap_0019: Thiamin biosynthesis protein ThiC
*
Polaromonas sp. JS666

Site:
position = -182
score = 75.41
sequence = AAAGCTTGTCGGGGT...

Gene: Bpro_0037: Thiamin biosynthesis protein ThiC
*
Rhodoferax ferrireducens DSM 15236

Site:
position = -197
score = 60.84
sequence = CGCCCTGCCCGGGGT...

Gene: Rfer_1708: Thiamin biosynthesis protein ThiC
*
Variovorax paradoxus S110

Site:
position = -196
score = 60.02
sequence = AGTCCCCGCTCCGGG...

Gene: Vapar_4728: Thiamin biosynthesis protein ThiC
*
Verminephrobacter eiseniae EF01-2

Site:
position = -224
score = 54.33
sequence = GGCCGCTGCTCCGGG...

Gene: Veis_1523: Thiamin biosynthesis protein ThiC
*
Methylibium petroleiphilum PM1

Site:
position = -178
score = 56.76
sequence = GAGCACTGCTCCGGG...

Gene: Mpe_A1610: Thiamin biosynthesis protein ThiC
*
Leptothrix cholodnii SP-6

Site:
position = -214
score = 44.31
sequence = CTCCCGCTCCGGGGT...

Gene: Lcho_2430: Thiamin biosynthesis protein ThiC
Thiamin biosynthesis protein ThiC
thiDE
 
Acidovorax avenae subsp. citrulli AAC00-1
 
Acidovorax sp. JS42
 
Comamonas testosteroni KF-1
 
Delftia acidovorans SPH-1
 
Polaromonas naphthalenivorans CJ2
 
Polaromonas sp. JS666
 
Rhodoferax ferrireducens DSM 15236
 
Variovorax paradoxus S110
 
Verminephrobacter eiseniae EF01-2
 
Methylibium petroleiphilum PM1

Gene: Mpe_A1606: Phosphomethylpyrimidine kinase (EC 2.7.4.7) / Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
 
Leptothrix cholodnii SP-6

Gene: Lcho_2434: Phosphomethylpyrimidine kinase (EC 2.7.4.7) / Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
Phosphomethylpyrimidine kinase (EC 2.7.4.7) / Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3)
Bluish color - the gene is in regulated operon. Different regulated operons are shown in different shades of blue.
Red color - the gene is in non-regulated operon.
Gray color - the orthologous gene is absent.
The star symbol - the TFBS is located in upstream region of this gene.
The number - the numeber of homologs (shown only if it is greater than one).
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