Regulog HypR2 - Rhodobacterales

Properties
Regulator type:	Transcription factor
Regulator family:	GntR/Others
Regulation mode:
Biological process:	Proline and 4-hydrohyproline utilization
Effector:	4-hydroxyproline
Phylum:	Proteobacteria/alpha
Visualization:
	Allows to visualize regulog content in the context of metabolic pathways

Built upon 17 sites [see more]

Member of regulog collections

By taxonomy - Rhodobacterales
By trascription factor - HypR
By TF family - GntR/Others
By effector - 4-hydroxyproline
By pathway - Proline and 4-hydrohyproline utilization

Statistics of regulated genes
Genome	Genes	Operons
Hyphomonas neptunium ATCC 15444
Jannaschia sp. CCS1
Loktanella vestfoldensis SKA53
Oceanicaulis alexandrii HTCC2633
Oceanicola batsensis HTCC2597
Oceanicola granulosus HTCC2516
Paracoccus denitrificans PD1222	3	2
Rhodobacter sphaeroides 2.4.1
Rhodobacterales bacterium HTCC2654
Roseobacter sp. MED193	3	3
Roseovarius nubinhibens ISM	4	3
Roseovarius sp. 217
Silicibacter TM1040	7	4
Silicibacter pomeroyi DSS-3	8	2
Sulfitobacter sp. EE-36

Clusters of co-Regulated Orthologous operoNs (CRONs)
Genes																Function

CRON 1.
hypR2	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516	* Paracoccus denitrificans PD1222 Site: position = -178 score = 4.25769 sequence = TTTCGTATACTATA Gene: Pden_1183: Predicted regulator for proline and hydrohyproline utilization, GntR family	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	Roseobacter sp. MED193	Roseovarius nubinhibens ISM	Roseovarius sp. 217	Silicibacter TM1040	Silicibacter pomeroyi DSS-3	Sulfitobacter sp. EE-36	Predicted regulator for proline and hydrohyproline utilization, GntR family

CRON 2.
hypY	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516	Paracoccus denitrificans PD1222	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	* Roseobacter sp. MED193 Site: position = -39 score = 4.48484 sequence = GATTGGATACAATA Gene: MED193_08463: Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)	Roseovarius nubinhibens ISM	Roseovarius sp. 217	Silicibacter TM1040	Silicibacter pomeroyi DSS-3	Sulfitobacter sp. EE-36	Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)

CRON 3.
hypR2	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516	Paracoccus denitrificans PD1222	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	* Roseobacter sp. MED193 Site: position = -86 score = 4.6297 sequence = TATTGGATCCAATT Gene: MED193_09635: Predicted regulator for proline and hydrohyproline utilization, GntR family	Roseovarius nubinhibens ISM	Roseovarius sp. 217	Silicibacter TM1040	Silicibacter pomeroyi DSS-3	Sulfitobacter sp. EE-36	Predicted regulator for proline and hydrohyproline utilization, GntR family

CRON 4.
hypS	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516 Gene: OG2516_07021: Putative L-lactate/Malate dehydrogenase	3 Paracoccus denitrificans PD1222 Gene: Pden_4855: Putative L-lactate/Malate dehydrogenase Gene: Pden_4866: Putative L-lactate/Malate dehydrogenase Gene: Pden_0941: Putative L-lactate/Malate dehydrogenase	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	Roseobacter sp. MED193	Roseovarius nubinhibens ISM	Roseovarius sp. 217 Gene: ROS217_16560: Putative L-lactate/Malate dehydrogenase	* Silicibacter TM1040 Site: position = -127 score = 4.83735 sequence = TTTTGGATACGTTA Site: position = -41 score = 4.26549 sequence = TGATGTATCCGATA Gene: TM1040_3323: Putative L-lactate/Malate dehydrogenase	Silicibacter pomeroyi DSS-3	Sulfitobacter sp. EE-36	Putative L-lactate/Malate dehydrogenase

CRON 5.
hypH	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516	Paracoccus denitrificans PD1222	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	Roseobacter sp. MED193	* Roseovarius nubinhibens ISM Site: position = -59 score = 5.19986 sequence = TTTTGGATACATTA Gene: ISM_08240: Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) # hydroxy-L-proline-inducible	Roseovarius sp. 217 Gene: ROS217_16585: Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) # hydroxy-L-proline-inducible	Silicibacter TM1040	Silicibacter pomeroyi DSS-3	Sulfitobacter sp. EE-36	Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) # hydroxy-L-proline-inducible

CRON 6.
hypH	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516 Gene: OG2516_08177: Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) # hydroxy-L-proline-inducible	Paracoccus denitrificans PD1222	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	Roseobacter sp. MED193	Roseovarius nubinhibens ISM	Roseovarius sp. 217	* Silicibacter TM1040 Site: position = -55 score = 4.75144 sequence = ATATGTATACATTA Gene: TM1040_3325: Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) # hydroxy-L-proline-inducible	* Silicibacter pomeroyi DSS-3 Site: position = -64 score = 5.19986 sequence = TTTTGGATACATTA Gene: SPOA0260: Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) # hydroxy-L-proline-inducible	Sulfitobacter sp. EE-36	Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) # hydroxy-L-proline-inducible

CRON 7.
hypD	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516 Gene: OG2516_07031: 1-pyrroline-4-hydroxy-2-carboxylate deaminase (EC 3.5.4.22) # predicted	Paracoccus denitrificans PD1222 Gene: Pden_4867: 1-pyrroline-4-hydroxy-2-carboxylate deaminase (EC 3.5.4.22) # predicted	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	* Roseobacter sp. MED193 Site: position = -151 score = 4.6297 sequence = AATTGGATCCAATA Gene: MED193_09625: 1-pyrroline-4-hydroxy-2-carboxylate deaminase (EC 3.5.4.22) # predicted	* Roseovarius nubinhibens ISM Site: position = -165 score = 5.19986 sequence = TTTTGTATCCATTA Gene: ISM_08255: 1-pyrroline-4-hydroxy-2-carboxylate deaminase (EC 3.5.4.22) # predicted	Roseovarius sp. 217 Gene: ROS217_16545: 1-pyrroline-4-hydroxy-2-carboxylate deaminase (EC 3.5.4.22) # predicted	* Silicibacter TM1040 Site: position = -158 score = 5.3043 sequence = TTTTGGATACAAAA Gene: TM1040_3198: 1-pyrroline-4-hydroxy-2-carboxylate deaminase (EC 3.5.4.22) # predicted	* Silicibacter pomeroyi DSS-3 Site: position = -172 score = 4.9554 sequence = TTCTGTATCCAAAA Gene: SPOA0267: 1-pyrroline-4-hydroxy-2-carboxylate deaminase (EC 3.5.4.22) # predicted	Sulfitobacter sp. EE-36	1-pyrroline-4-hydroxy-2-carboxylate deaminase (EC 3.5.4.22) # predicted
hypE	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516 Gene: OG2516_07016: Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)	Paracoccus denitrificans PD1222 Gene: Pden_4859: Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	Roseobacter sp. MED193 Gene: MED193_09620: Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)	Roseovarius nubinhibens ISM	Roseovarius sp. 217 Gene: ROS217_16540: Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)	Silicibacter TM1040 Gene: TM1040_3199: Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)	Silicibacter pomeroyi DSS-3 Gene: SPOA0266: Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)	Sulfitobacter sp. EE-36	Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)
COG4663	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516	Paracoccus denitrificans PD1222	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	Roseobacter sp. MED193	Roseovarius nubinhibens ISM Gene: ISM_10311: TRAP-type C4-dicarboxylate transport system, periplasmic component	Roseovarius sp. 217	Silicibacter TM1040	Silicibacter pomeroyi DSS-3 Gene: SPOA0265: TRAP-type C4-dicarboxylate transport system, periplasmic component	Sulfitobacter sp. EE-36	TRAP-type C4-dicarboxylate transport system, periplasmic component
COG3090	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516	Paracoccus denitrificans PD1222	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	Roseobacter sp. MED193	Roseovarius nubinhibens ISM Gene: ISM_10306: TRAP-type C4-dicarboxylate transport system, small permease component	Roseovarius sp. 217	Silicibacter TM1040	Silicibacter pomeroyi DSS-3 Gene: SPOA0264: TRAP-type C4-dicarboxylate transport system, small permease component	Sulfitobacter sp. EE-36	TRAP-type C4-dicarboxylate transport system, small permease component
COG4664	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516	Paracoccus denitrificans PD1222	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	Roseobacter sp. MED193	Roseovarius nubinhibens ISM Gene: ISM_10301: TRAP-type C4-dicarboxylate transport system, large permease component	Roseovarius sp. 217	Silicibacter TM1040	Silicibacter pomeroyi DSS-3 Gene: SPOA0263: TRAP-type C4-dicarboxylate transport system, large permease component	Sulfitobacter sp. EE-36	TRAP-type C4-dicarboxylate transport system, large permease component
hypO	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516 Gene: OG2516_08202: D-amino acid dehydrogenase (EC 1.4.99.1) family protein in hydroxy-L-proline catabolic cluster	Paracoccus denitrificans PD1222 Gene: Pden_4860: D-amino acid dehydrogenase (EC 1.4.99.1) family protein in hydroxy-L-proline catabolic cluster	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	Roseobacter sp. MED193 Gene: MED193_09610: D-amino acid dehydrogenase (EC 1.4.99.1) family protein in hydroxy-L-proline catabolic cluster	Roseovarius nubinhibens ISM	Roseovarius sp. 217 Gene: ROS217_16535: D-amino acid dehydrogenase (EC 1.4.99.1) family protein in hydroxy-L-proline catabolic cluster	Silicibacter TM1040 Gene: TM1040_3200: D-amino acid dehydrogenase (EC 1.4.99.1) family protein in hydroxy-L-proline catabolic cluster	Silicibacter pomeroyi DSS-3 Gene: SPOA0262: D-amino acid dehydrogenase (EC 1.4.99.1) family protein in hydroxy-L-proline catabolic cluster	Sulfitobacter sp. EE-36	D-amino acid dehydrogenase (EC 1.4.99.1) family protein in hydroxy-L-proline catabolic cluster
hypR2	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516	Paracoccus denitrificans PD1222	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	Roseobacter sp. MED193	* Roseovarius nubinhibens ISM Site: position = -13 score = 5.19986 sequence = TAATGTATCCAAAA Gene: ISM_08245: Predicted regulator for proline and hydrohyproline utilization, GntR family	Roseovarius sp. 217	* Silicibacter TM1040 Site: position = -129 score = 4.26549 sequence = TATCGGATACATCA Site: position = -43 score = 4.83735 sequence = TAACGTATCCAAAA Gene: TM1040_3324: Predicted regulator for proline and hydrohyproline utilization, GntR family	* Silicibacter pomeroyi DSS-3 Site: position = -38 score = 4.12505 sequence = ATCTGTATCCGAAA Gene: SPOA0261: Predicted regulator for proline and hydrohyproline utilization, GntR family	Sulfitobacter sp. EE-36	Predicted regulator for proline and hydrohyproline utilization, GntR family
hypY	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1 Gene: Jann_1529: Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516 Gene: OG2516_07011: Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)	* Paracoccus denitrificans PD1222 Site: position = -50 score = 4.25769 sequence = TATAGTATACGAAA Gene: Pden_1184: Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	Roseobacter sp. MED193	Roseovarius nubinhibens ISM Gene: ISM_08250: Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)	Roseovarius sp. 217 Gene: ROS217_16530: Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)	Silicibacter TM1040 Gene: TM1040_3201: Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)	Silicibacter pomeroyi DSS-3 Gene: SPO0607: Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)	Sulfitobacter sp. EE-36	Proline racemase /4-hydroxyproline epimerase (EC 5.1.1.8)
COG2423	Hyphomonas neptunium ATCC 15444	Jannaschia sp. CCS1	Loktanella vestfoldensis SKA53	Oceanicaulis alexandrii HTCC2633	Oceanicola batsensis HTCC2597	Oceanicola granulosus HTCC2516	Paracoccus denitrificans PD1222 Gene: Pden_1185: Predicted ornithine cyclodeaminase, mu-crystallin homolog	Rhodobacter sphaeroides 2.4.1	Rhodobacterales bacterium HTCC2654	Roseobacter sp. MED193	Roseovarius nubinhibens ISM	Roseovarius sp. 217	Silicibacter TM1040	Silicibacter pomeroyi DSS-3	Sulfitobacter sp. EE-36	Predicted ornithine cyclodeaminase, mu-crystallin homolog

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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Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes -- version 3.2 --

Regulog HypR2 - Rhodobacterales

Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes
-- version 3.2 --