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On One Page

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Gene |

Product(s) |

Expression|

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Quickview

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Standard Name	napD
Gene Synonym(s)	ECK2199, b2207, JW2195, yojF^[1], yojF
Product Desc.	NapD protein^[2]^[3] Twin-arginine signal-peptide-binding chaperone for NapA^[4]
Product Synonyms(s)	assembly protein for periplasmic nitrate reductase^[1], B2207^[2]^[1], YojF^[2]^[1], NapD^[2]^[1] , ECK2199, JW2195, yojF, b2207
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): napFDAGHBC^[2], napFDAGHBC-ccmABCDEFGH^[2], aeg-46.5
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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Nap has a strong anti-transport actvity in vitro, but is essential for NapA activity and transport in vivo.^[4]

Gene

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Nomenclature

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

Standard name	napD
Mnemonic	NitrAte reductase, periplasmic
Synonyms	ECK2199, b2207, JW2195, yojF^[1], yojF
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Notes

Location(s) and DNA Sequence

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<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	49.59 minutes, 49.59 minutes	MG1655: 2301035..2300772 <gbrowseImage> name=NC_000913:2300772..2301035 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2253002..2252739 <gbrowseImage> name=NC_012967:2252739..2253002 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2186577..2186840 <gbrowseImage> name=NC_012759:2186577..2186840 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2306347..2306084 <gbrowseImage> name=NC_007779:2306084..2306347 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2392023..2391760 <gbrowseImage> name=NC_010473:2391760..2392023 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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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
ΔnapD (Keio:JW2195)	deletion	deletion	PMID:16738554	Shigen
napD::Tn5KAN-I-SceI (FB20702)	Insertion at nt 154 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20702	contains pKD46
napD::Tn5KAN-I-SceI (FB20703)	Insertion at nt 154 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20703	does not contain pKD46
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Notes

Genetic Interactions

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

Genetic Resources

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

Resource	Resource Type	Source	Notes/Reference
JW2195	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCACACTAACTGGCAAGTTTG Primer 2:CCTGGTGTTTCCTCACCTTGCTC
19D1	Kohara Phage	Genobase	PMID:3038334
22A6	Kohara Phage	Genobase	PMID:3038334
zbd-3104::Tn10	Linked marker	CAG12021 = CGSC7344^[5]	est. P1 cotransduction: % ^[6] Synonyms:zbc-3105::Tn10, zbd-3105::Tn10
napA722::Tn10	Linked marker	CAG12098 = CGSC7400^[5]	est. P1 cotransduction: 98% ^[6] Synonyms:zeg-722, zei-722::Tn10
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Notes

Accessions in Other Databases

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12143	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12143	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002044	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945187	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2064	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007291	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

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

Standard name	NapD
Synonyms	assembly protein for periplasmic nitrate reductase^[1], B2207^[2]^[1], YojF^[2]^[1], NapD^[2]^[1] , ECK2199, JW2195, yojF, b2207
Product description	NapD protein^[2]^[3] Twin-arginine signal-peptide-binding chaperone for NapA^[4]
EC number (for enzymes)
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Notes

Function

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<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:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	References	Evidence
Protein	pta	PMID:15690043	Experiment(s):EBI-886362, EBI-892823
Protein	aceF	PMID:15690043	Experiment(s):EBI-892823
Protein	groL	PMID:15690043	Experiment(s):EBI-892823
Protein	rplW	PMID:15690043	Experiment(s):EBI-892823
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1142158
Protein	aspS	PMID:16606699	Experiment(s):EBI-1142158
Protein	yahO	PMID:16606699	Experiment(s):EBI-1142158
Protein	greB	PMID:16606699	Experiment(s):EBI-1142158
Protein	yecF	PMID:16606699	Experiment(s):EBI-1142158
Protein	nuoG	PMID:16606699	Experiment(s):EBI-1142158
Protein	htpG	PMID:16606699	Experiment(s):EBI-1142158
Protein	uvrY	PMID:16606699	Experiment(s):EBI-1142158
Protein	rplB	PMID:16606699	Experiment(s):EBI-1142158
Protein	nudI	PMID:16606699	Experiment(s):EBI-1142158
Protein	yfjM	PMID:16606699	Experiment(s):EBI-1142158
Protein	rpsB	PMID:16606699	Experiment(s):EBI-1142158
Protein	yqhH	PMID:16606699	Experiment(s):EBI-1142158
Protein	groS	PMID:19402753	LCMS(ID Probability):99.6
Protein	groL	PMID:19402753	LCMS(ID Probability):99.6
Protein	pta	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):28.433911
Protein	yacL	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplW	PMID:19402753	LCMS(ID Probability):99.6
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Notes

Localization

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

Compartment	Description	Evidence	Reference/Source	Notes
plasma membrane			From EcoCyc^[3]
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Notes

Structure and Physical Properties

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<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 MHTNWQVCSL VVQAKSERIS DISTQLNAFP GCEVAVSDAP SGQLIVVVEA EDSETLIQTI ESVRNVEGVL AVSLVYHQQE EQGEETP
Length	87
Mol. Wt	9.467 kDa
pI	4.0 (calculated)
Extinction coefficient	6,990 - 7,240 (calc based on 1 Y, 1 W, and 2 C residues)
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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
Domain	3..82	PF03927 NapD protein		PMID:19920124
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<motif_map/>

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

Structures

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

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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

Resource type	Source	Notes/Reference
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Accessions in Other Databases

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

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16130144	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945187	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007291	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A9I5	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12143	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12143	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945187	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002044	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2064	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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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

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	Ecoli K-12	1.045+/-0.019	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	28^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	8^a	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	0^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
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)
napFDAGHBC
napFDAGHBC-ccmABCDEFGH
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Figure courtesy of RegulonDB

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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

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<protect><gbrowseImage> name=NC_000913:2301015..2301055 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

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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

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

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b2207 (EcoliWiki Page)	NCBI GEO profiles for napD
microarray	GenExpDB:b2207 (EcoliWiki Page)	Summary of data for napD from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to napD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12143	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2064	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2207
EcoGene	EcoGene:EG12143	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002044	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007291	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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

Organism	Homologs (Statistics)	Comments
Shigella flexneri	NAPD	From SHIGELLACYC
E. coli O157	NAPD	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF03927 NapD protein
EcoCyc	EcoCyc:EG12143	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12143	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002044	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2064	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007291	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 ^2.9 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 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 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).

napD:On One Page

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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 napD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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