Regulog NikR - Desulfovibrionales

Properties
Regulator type:	Transcription factor
Regulator family:	NikR
Regulation mode:	repressor
Biological process:	Nickel homeostasis
Effector:	Nickel ion, (Ni2+)
Phylum:	Proteobacteria/delta
Visualization:
	Allows to visualize regulog content in the context of metabolic pathways

Built upon 16 sites [see more]

Member of regulog collections

By taxonomy - Desulfovibrionales
By trascription factor - NikR
By TF family - NikR
By effector - Nickel ion, (Ni2+)
By pathway - Nickel homeostasis

Statistics of regulated genes
Genome	Genes	Operons
Desulfovibrio vulgaris Hildenborough	4	2
Desulfovibrio vulgaris str. Miyazaki F	4	3
Desulfovibrio desulfuricans G20	9	3
Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774	5	2
Desulfovibrio piger ATCC 29098	5	1
Desulfovibrio salexigens DSM 2638	2	1
Desulfovibrio magneticus RS-1
Lawsonia intracellularis PHE/MN1-00	4	1
Desulfomicrobium baculatum DSM 4028	2	1
Desulfohalobium retbaense DSM 5692

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

CRON 1.
hydA2	Desulfovibrio vulgaris Hildenborough	Desulfovibrio vulgaris str. Miyazaki F	* Desulfovibrio desulfuricans G20 Site: position = -122 score = 5.18421 sequence = GTGGTAG-(13)-ATAGCAC Site: position = -82 score = 7.40833 sequence = GTATTAC-(13)-GTAACAC Gene: Dde_2281: Periplasmic [Fe] hydrogenase large subunit (EC 1.12.7.2)	Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774	Desulfovibrio piger ATCC 29098	Desulfovibrio salexigens DSM 2638 Gene: Desal_1332: Periplasmic [Fe] hydrogenase large subunit (EC 1.12.7.2)	Desulfovibrio magneticus RS-1	Lawsonia intracellularis PHE/MN1-00	Desulfomicrobium baculatum DSM 4028	Desulfohalobium retbaense DSM 5692	Periplasmic [Fe] hydrogenase large subunit (EC 1.12.7.2)
hydB2	Desulfovibrio vulgaris Hildenborough	Desulfovibrio vulgaris str. Miyazaki F	Desulfovibrio desulfuricans G20 Gene: Dde_2280: Periplasmic [Fe] hydrogenase small subunit (EC 1.12.7.2)	Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774	Desulfovibrio piger ATCC 29098	Desulfovibrio salexigens DSM 2638 Gene: Desal_1333: Periplasmic [Fe] hydrogenase small subunit (EC 1.12.7.2)	Desulfovibrio magneticus RS-1	Lawsonia intracellularis PHE/MN1-00	Desulfomicrobium baculatum DSM 4028	Desulfohalobium retbaense DSM 5692	Periplasmic [Fe] hydrogenase small subunit (EC 1.12.7.2)

CRON 2.
nikK	* Desulfovibrio vulgaris Hildenborough Site: position = -83 score = 6.75042 sequence = GTGACAC-(13)-GTGTAAC Gene: DVU2769: Additional periplasmic component NikK of nickel ECF transporter	* Desulfovibrio vulgaris str. Miyazaki F Site: position = -89 score = 6.75042 sequence = GTGACAC-(13)-GTGTAAC Gene: DvMF_2859: Additional periplasmic component NikK of nickel ECF transporter	* Desulfovibrio desulfuricans G20 Site: position = -105 score = 7.30298 sequence = GTGTTAT-(13)-GTAACAC Gene: Dde_1189: Additional periplasmic component NikK of nickel ECF transporter	* Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 Site: position = -93 score = 5.35245 sequence = TTGCTAC-(13)-GTGTAAC Gene: Ddes_1470: Additional periplasmic component NikK of nickel ECF transporter	* Desulfovibrio piger ATCC 29098 Site: position = -134 score = 5.18188 sequence = GTGTAAA-(13)-CTAACGC Gene: DESPIG_00816: Additional periplasmic component NikK of nickel ECF transporter	Desulfovibrio salexigens DSM 2638 Gene: Desal_1883: Additional periplasmic component NikK of nickel ECF transporter	Desulfovibrio magneticus RS-1	Lawsonia intracellularis PHE/MN1-00	Desulfomicrobium baculatum DSM 4028 Gene: Dbac_3139: Additional periplasmic component NikK of nickel ECF transporter	Desulfohalobium retbaense DSM 5692 Gene: Dret_0755: Additional periplasmic component NikK of nickel ECF transporter	Additional periplasmic component NikK of nickel ECF transporter
nikM	* Desulfovibrio vulgaris Hildenborough Site: position = -121 score = 7.30298 sequence = GTGTTAT-(13)-GTAACAC Gene: DVU1058: Substrate-specific component NikM of nickel ECF transporter	Desulfovibrio vulgaris str. Miyazaki F Gene: DvMF_3139: Substrate-specific component NikM of nickel ECF transporter	Desulfovibrio desulfuricans G20 Gene: Dde_1190: Substrate-specific component NikM of nickel ECF transporter	Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 Gene: Ddes_1471: Substrate-specific component NikM of nickel ECF transporter	Desulfovibrio piger ATCC 29098 Gene: DESPIG_00817: Substrate-specific component NikM of nickel ECF transporter	Desulfovibrio salexigens DSM 2638 Gene: Desal_0774: Substrate-specific component NikM of nickel ECF transporter	Desulfovibrio magneticus RS-1	Lawsonia intracellularis PHE/MN1-00 Gene: LI0863: Substrate-specific component NikM of nickel ECF transporter	Desulfomicrobium baculatum DSM 4028 Gene: Dbac_3138: Substrate-specific component NikM of nickel ECF transporter	Desulfohalobium retbaense DSM 5692 Gene: Dret_0756: Substrate-specific component NikM of nickel ECF transporter	Substrate-specific component NikM of nickel ECF transporter
nikL	Desulfovibrio vulgaris Hildenborough	Desulfovibrio vulgaris str. Miyazaki F	Desulfovibrio desulfuricans G20 Gene: Dde_1191: Additional component NikL of nickel ECF transporter	Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 Gene: Ddes_1472: Additional component NikL of nickel ECF transporter	Desulfovibrio piger ATCC 29098 Gene: DESPIG_00818: Additional component NikL of nickel ECF transporter	* Desulfovibrio salexigens DSM 2638 Site: position = -71 score = 6.73655 sequence = GTACCAC-(13)-GTGACAC Gene: Desal_1884: Additional component NikL of nickel ECF transporter	Desulfovibrio magneticus RS-1	Lawsonia intracellularis PHE/MN1-00	Desulfomicrobium baculatum DSM 4028 Gene: Dbac_3137: Additional component NikL of nickel ECF transporter	Desulfohalobium retbaense DSM 5692 Gene: Dret_0757: Additional component NikL of nickel ECF transporter	Additional component NikL of nickel ECF transporter
nikQ	Desulfovibrio vulgaris Hildenborough Gene: DVU1057: Transmembrane component NikQ of energizing module of nickel ECF transporter	Desulfovibrio vulgaris str. Miyazaki F Gene: DvMF_3138: Transmembrane component NikQ of energizing module of nickel ECF transporter	Desulfovibrio desulfuricans G20 Gene: Dde_1192: Transmembrane component NikQ of energizing module of nickel ECF transporter	Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 Gene: Ddes_1473: Transmembrane component NikQ of energizing module of nickel ECF transporter	Desulfovibrio piger ATCC 29098 Gene: DESPIG_00819: Transmembrane component NikQ of energizing module of nickel ECF transporter	Desulfovibrio salexigens DSM 2638 Gene: Desal_3207: Transmembrane component NikQ of energizing module of nickel ECF transporter	Desulfovibrio magneticus RS-1	Lawsonia intracellularis PHE/MN1-00 Gene: LI0862: Transmembrane component NikQ of energizing module of nickel ECF transporter	Desulfomicrobium baculatum DSM 4028 Gene: Dbac_3136: Transmembrane component NikQ of energizing module of nickel ECF transporter	Desulfohalobium retbaense DSM 5692 Gene: Dret_0162: Transmembrane component NikQ of energizing module of nickel ECF transporter	Transmembrane component NikQ of energizing module of nickel ECF transporter
nikO	Desulfovibrio vulgaris Hildenborough Gene: DVU1056: ATPase component NikO of energizing module of nickel ECF transporter	Desulfovibrio vulgaris str. Miyazaki F Gene: DvMF_3137: ATPase component NikO of energizing module of nickel ECF transporter	Desulfovibrio desulfuricans G20 Gene: Dde_1193: ATPase component NikO of energizing module of nickel ECF transporter	Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 Gene: Ddes_1474: ATPase component NikO of energizing module of nickel ECF transporter	Desulfovibrio piger ATCC 29098 Gene: DESPIG_00820: ATPase component NikO of energizing module of nickel ECF transporter	Desulfovibrio salexigens DSM 2638 Gene: Desal_3208: ATPase component NikO of energizing module of nickel ECF transporter	Desulfovibrio magneticus RS-1	Lawsonia intracellularis PHE/MN1-00 Gene: LI0861: ATPase component NikO of energizing module of nickel ECF transporter	Desulfomicrobium baculatum DSM 4028 Gene: Dbac_3135: ATPase component NikO of energizing module of nickel ECF transporter	Desulfohalobium retbaense DSM 5692 Gene: Dret_0161: ATPase component NikO of energizing module of nickel ECF transporter	ATPase component NikO of energizing module of nickel ECF transporter
LI0864	Desulfovibrio vulgaris Hildenborough	Desulfovibrio vulgaris str. Miyazaki F	Desulfovibrio desulfuricans G20	Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774	Desulfovibrio piger ATCC 29098	Desulfovibrio salexigens DSM 2638	Desulfovibrio magneticus RS-1	* Lawsonia intracellularis PHE/MN1-00 Site: position = -98 score = 6.53909 sequence = GTATCAT-(13)-GTATTAC Site: position = -68 score = 5.53091 sequence = ATGATAT-(13)-GTTACAC Gene: LI0864: hypothetical protein	Desulfomicrobium baculatum DSM 4028	Desulfohalobium retbaense DSM 5692	hypothetical protein

CRON 3.
nikA	Desulfovibrio vulgaris Hildenborough	Desulfovibrio vulgaris str. Miyazaki F Gene: DvMF_2402: Nickel ABC transporter, periplasmic nickel-binding protein NikA (TC 3.A.1.5.3)	Desulfovibrio desulfuricans G20	* Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 Site: position = -85 score = 6.97052 sequence = GTGTCAC-(13)-TTGACAC Gene: Ddes_1032: Nickel ABC transporter, periplasmic nickel-binding protein NikA (TC 3.A.1.5.3)	Desulfovibrio piger ATCC 29098	Desulfovibrio salexigens DSM 2638	Desulfovibrio magneticus RS-1 Gene: DMR_12040: Nickel ABC transporter, periplasmic nickel-binding protein NikA (TC 3.A.1.5.3)	Lawsonia intracellularis PHE/MN1-00	Desulfomicrobium baculatum DSM 4028	Desulfohalobium retbaense DSM 5692	Nickel ABC transporter, periplasmic nickel-binding protein NikA (TC 3.A.1.5.3)
nikB	Desulfovibrio vulgaris Hildenborough	Desulfovibrio vulgaris str. Miyazaki F Gene: DvMF_2401: Nickel transport system permease protein NikB (TC 3.A.1.5.3)	Desulfovibrio desulfuricans G20	Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 Gene: Ddes_1031: Nickel transport system permease protein NikB (TC 3.A.1.5.3)	Desulfovibrio piger ATCC 29098	Desulfovibrio salexigens DSM 2638	Desulfovibrio magneticus RS-1 Gene: DMR_12030: Nickel transport system permease protein NikB (TC 3.A.1.5.3)	Lawsonia intracellularis PHE/MN1-00	Desulfomicrobium baculatum DSM 4028	Desulfohalobium retbaense DSM 5692	Nickel transport system permease protein NikB (TC 3.A.1.5.3)
nikC	Desulfovibrio vulgaris Hildenborough	Desulfovibrio vulgaris str. Miyazaki F Gene: DvMF_2400: Nickel transport system permease protein NikC (TC 3.A.1.5.3)	Desulfovibrio desulfuricans G20	Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 Gene: Ddes_1030: Nickel transport system permease protein NikC (TC 3.A.1.5.3)	Desulfovibrio piger ATCC 29098	Desulfovibrio salexigens DSM 2638	Desulfovibrio magneticus RS-1 Gene: DMR_12020: Nickel transport system permease protein NikC (TC 3.A.1.5.3)	Lawsonia intracellularis PHE/MN1-00	Desulfomicrobium baculatum DSM 4028	Desulfohalobium retbaense DSM 5692	Nickel transport system permease protein NikC (TC 3.A.1.5.3)
nikD	Desulfovibrio vulgaris Hildenborough	2 Desulfovibrio vulgaris str. Miyazaki F* Gene: DvMF_2399: Nickel transport ATP-binding protein NikD (TC 3.A.1.5.3) Site: position = -265 score = 5.39099 sequence = GCAACAC-(13)-GTGACCC Gene: DvMF_2398: Nickel transport ATP-binding protein NikD (TC 3.A.1.5.3)	Desulfovibrio desulfuricans G20	Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 Gene: Ddes_1029: Nickel transport ATP-binding protein NikD (TC 3.A.1.5.3)	Desulfovibrio piger ATCC 29098	Desulfovibrio salexigens DSM 2638	2 Desulfovibrio magneticus RS-1 Gene: DMR_12010: Nickel transport ATP-binding protein NikD (TC 3.A.1.5.3) Gene: DMR_12000: Nickel transport ATP-binding protein NikD (TC 3.A.1.5.3)	Lawsonia intracellularis PHE/MN1-00	Desulfomicrobium baculatum DSM 4028	Desulfohalobium retbaense DSM 5692	Nickel transport ATP-binding protein NikD (TC 3.A.1.5.3)

CRON 4.
hysB	Desulfovibrio vulgaris Hildenborough Gene: DVU1917: [Ni/Fe] hydrogenase, group 1, small subunit	* Desulfovibrio vulgaris str. Miyazaki F Site: position = -244 score = 6.80137 sequence = GTAACAC-(13)-ATAACAC Gene: DvMF_0274: [Ni/Fe] hydrogenase, group 1, small subunit	* Desulfovibrio desulfuricans G20 Site: position = -65 score = 5.66554 sequence = GTCTCAG-(13)-GTAAAAC Gene: Dde_2134: [Ni/Fe] hydrogenase, group 1, small subunit	Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774	Desulfovibrio piger ATCC 29098 Gene: DESPIG_00297: [Ni/Fe] hydrogenase, group 1, small subunit	Desulfovibrio salexigens DSM 2638 Gene: Desal_2050: [Ni/Fe] hydrogenase, group 1, small subunit	Desulfovibrio magneticus RS-1	Lawsonia intracellularis PHE/MN1-00	* Desulfomicrobium baculatum DSM 4028 Site: position = -216 score = 6.25979 sequence = GTGTTAT-(13)-GTAACAT Gene: Dbac_1970: [Ni/Fe] hydrogenase, group 1, small subunit	Desulfohalobium retbaense DSM 5692	[Ni/Fe] hydrogenase, group 1, small subunit
hysA	Desulfovibrio vulgaris Hildenborough Gene: DVU1918: [Ni/Fe] hydrogenase, group 1, large subunit; selenocysteine-containing	Desulfovibrio vulgaris str. Miyazaki F Gene: DvMF_0273: [Ni/Fe] hydrogenase, group 1, large subunit; selenocysteine-containing	Desulfovibrio desulfuricans G20 Gene: Dde_2135: [Ni/Fe] hydrogenase, group 1, large subunit; selenocysteine-containing	Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774	Desulfovibrio piger ATCC 29098 Gene: DESPIG_00296: [Ni/Fe] hydrogenase, group 1, large subunit; selenocysteine-containing	Desulfovibrio salexigens DSM 2638 Gene: Desal_2049: [Ni/Fe] hydrogenase, group 1, large subunit; selenocysteine-containing	Desulfovibrio magneticus RS-1	Lawsonia intracellularis PHE/MN1-00	Desulfomicrobium baculatum DSM 4028 Gene: Dbac_1969: [Ni/Fe] hydrogenase, group 1, large subunit; selenocysteine-containing	Desulfohalobium retbaense DSM 5692	[Ni/Fe] hydrogenase, group 1, large subunit; selenocysteine-containing

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 NikR - Desulfovibrionales

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