{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Standard Name	nikA
Gene Synonym(s)	ECK3460, b3476, JW3441, hydC, hydD^[1], hydD
Product Desc.	NikA^[2]^[3]; Component of nickel ABC transporter^[2]^[3] Nickel-binding, heme-binding periplasmic protein; Tar-dependent Ni-repellant chemosensor; Fnr-dependent^[4]
Product Synonyms(s)	nickel transporter subunit^[1], periplasmic-binding component of ABC superfamily^[1], B3476^[2]^[1], HydD^[2]^[1], HydC^[2]^[1], NikA^[2]^[1] , ECK3460, hydC, hydD, JW3441, b3476
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): nikABCDER^[2]
Regulation/Activity
Quick Links
edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]

NikA binds hemin and protoporphyrin IX (Shepherd, 2007). Mutants display nickel-remediated formate hydrogen-lyase, hydrogenase, and hydrogenase-related fumarase defects.^[4]

Gene

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]

See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	nikA
Mnemonic	Nickel
Synonyms	ECK3460, b3476, JW3441, hydC, hydD^[1], hydD
edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]

<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	77.84 minutes	MG1655: 3611690..3613264 <gbrowseImage> name=NC_000913:3611690..3613264 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3544355..3545929 <gbrowseImage> name=NC_012967:3544355..3545929 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3500184..3501758 <gbrowseImage> name=NC_012759:3500184..3501758 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4026748..4025174 <gbrowseImage> name=NC_007779:4025174..4026748 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3709435..3711009 <gbrowseImage> name=NC_010473:3709435..3711009 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
edit table

</protect>

Notes

Sequence Features

[back to top]

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	3611756	Edman degradation	PMID:7867647
edit table

Notes

Alleles and Phenotypes

[back to top]

See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Reference	Availability	Comments
ΔnikA (Keio:JW3441)	deletion	deletion	PMID:16738554	Shigen CGSC10553^[5]
nikA::Tn5KAN-I-SceI (FB21228)	Insertion at nt 943 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21228	contains pKD46
ΔnikA730::kan			PMID:16738554	CGSC:102068
edit table

Notes

Genetic Interactions

[back to top]

Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]

See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW3441	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCTCTCCACACTCCGCCGCAC Primer 2:CCAGGTTTCACCGGTTTAATCTG
5F2	Kohara Phage	Genobase	PMID:3038334
7H7	Kohara Phage	Genobase	PMID:3038334
zhg-50::Tn10	Linked marker	CAG18450 = CGSC7450^[5]	est. P1 cotransduction: 47% ^[6] Synonyms:zhf-50::Tn10, zhf-5::Tn10
zic-4901::Tn10	Linked marker	CAG18492 = CGSC7457^[5]	est. P1 cotransduction: % ^[6]
edit table

Notes

Accessions in Other Databases

[back to top]

See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG12075	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12075	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001981	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947981	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2000	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011354	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Product(s)

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	NikA
Synonyms	nickel transporter subunit^[1], periplasmic-binding component of ABC superfamily^[1], B3476^[2]^[1], HydD^[2]^[1], HydC^[2]^[1], NikA^[2]^[1] , ECK3460, hydC, hydD, JW3441, b3476
Product description	NikA^[2]^[3]; Component of nickel ABC transporter^[2]^[3] Nickel-binding, heme-binding periplasmic protein; Tar-dependent Ni-repellant chemosensor; Fnr-dependent^[4]
EC number (for enzymes)
edit table

Notes

Function

[back to top]

<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0005215	transporter activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000914	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006810	transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000914	P	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	PMID:7867647	IDA: Inferred from Direct Assay		C		complete
	GO:0006810	transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016151	nickel ion binding	PMID:7867647	IDA: Inferred from Direct Assay		F		complete
	GO:0016151	nickel ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0533	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0574	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0200	C	Seeded from EcoCyc (v14.0)	complete
	GO:0020037	heme binding	PMID:17411076	IDA: Inferred from Direct Assay		F		complete
	GO:0046914	transition metal ion binding	PMID:7867647	IDA: Inferred from Direct Assay		F		complete
	GO:0050919	negative chemotaxis	PMID:7867647	IMP: Inferred from Mutant Phenotype		P	involved in nickel sensing	complete
edit table

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
Protein	Subunits of nickel ABC transporter	could be indirect
Protein	tufA		PMID:15690043	Experiment(s):EBI-893211
edit table

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Evidence	Reference/Source
Periplasm	PMID:7867647	EchoLocation:nikA
periplasm		From EcoCyc^[3]
edit table

Notes

Structure and Physical Properties

[back to top]

<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MLSTLRRTLF ALLACASFIV HAAAPDEITT AWPVNVGPLN PHLYTPNQMF AQSMVYEPLV KYQADGSVIP WLAKSWTHSE DGKTWTFTLR DDVKFSNGEP FDAEAAAENF RAVLDNRQRH AWLELANQIV DVKALSKTEL QITLKSAYYP FLQELALPRP FRFIAPSQFK NHETMNGIKA PIGTGPWILQ ESKLNQYDVF VRNENYWGEK PAIKKITFNV IPDPTTRAVA FETGDIDLLY GNEGLLPLDT FARFSQNPAY HTQLSQPIET VMLALNTAKA PTNELAVREA LNYAVNKKSL IDNALYGTQQ VADTLFAPSV PYANLGLKPS QYDPQKAKAL LEKAGWTLPA GKDIREKNGQ PLRIELSFIG TDALSKSMAE IIQADMRQIG ADVSLIGEEE SSIYARQRDG RFGMIFHRTW GAPYDPHAFL SSMRVPSHAD FQAQQGLADK PLIDKEIGEV LATHDETQRQ ALYRDILTRL HDEAVYLPIS YISMMVVSKP ELGNIPYAPI ATEIPFEQIK PVKP
Length	524
Mol. Wt	58.72 kDa
pI	6.0 (calculated)
Extinction coefficient	77,810 - 77,935 (calc based on 19 Y, 9 W, and 1 C residues)
edit table

Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
motif	1-22	UniProt Manual:Signal Peptides	UniProt:P33590
Domain	67..441	PF00496 Bacterial extracellular solute-binding proteins, family 5 Middle		PMID:19920124
edit table

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=nikA taxon=562,83333 </beststructure>

Models

View models at:

edit table

</protect>

Structure figures

</protect>

Notes

Gene Product Resources

[back to top]

See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]

See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16131348	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947981	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011354	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P33590	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12075	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12075	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947981	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001981	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2000	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Expression

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

[back to top]

See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MG1655	30	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	10	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	22^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
nikABCDER
edit table

Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

[back to top]

<protect><gbrowseImage> name=NC_000913:3611670..3611710 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

[back to top]

<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
edit table

Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b3476 (EcoliWiki Page)	NCBI GEO profiles for nikA
microarray	GenExpDB:b3476 (EcoliWiki Page)	Summary of data for nikA from multiple microarray studies
edit table

Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
edit table

Notes

Accessions Related to nikA Expression

[back to top]

See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG12075	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2000	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3476
EcoGene	EcoGene:EG12075	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001981	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011354	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Evolution

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]

See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000026819 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000030908 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	NIKA	From SHIGELLACYC
E. coli O157	NIKA	From ECOO157CYC
edit table

Do-It-Yourself Web Tools

Notes

Families

[back to top]

See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:53850
Pfam (EcoliWiki Page)	PF00496 Bacterial extracellular solute-binding proteins, family 5 Middle
EcoCyc	EcoCyc:EG12075	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12075	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001981	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2000	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011354	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

References

[back to top]

See Help:References for how to manage references in EcoliWiki.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 ^1.12 ^1.13 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 ^2.12 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

nikA:On One Page

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to nikA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search