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Gene |

Product(s) |

Expression|

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Standard Name	nfrA
Gene Synonym(s)	ECK0560, b0568, JW0557^[1], JW0557
Product Desc.	bacteriophage N4 receptor, outer membrane protein^[2]^[3] Outer membrane protein, putative structural receptor for N4 adsorption^[4]
Product Synonyms(s)	bacteriophage N4 receptor, outer membrane subunit^[1], B0568^[2]^[1], NfrA^[2]^[1] , ECK0560, JW0557, b0568
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): nfrBA^[2]
Regulation/Activity
Quick Links
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Notes

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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	nfrA
Mnemonic	N4 (phage) resistant
Synonyms	ECK0560, b0568, JW0557^[1], JW0557
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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	12.66 minutes	MG1655: 590177..587205 <gbrowseImage> name=NC_000913:587205..590177 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 566305..563333 <gbrowseImage> name=NC_012967:563333..566305 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 489965..492937 <gbrowseImage> name=NC_012759:489965..492937 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 590177..587205 <gbrowseImage> name=NC_007779:587205..590177 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 529509..526537 <gbrowseImage> name=NC_010473:526537..529509 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
DH10B		DH10B: 642769..639797 <gbrowseImage> name=NC_010473:639797..642769 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
ΔnfrA (Keio:JW0557)	deletion	deletion	PMID:16738554	Shigen CGSC8683^[5]
ΔnfrA777::kan			PMID:16738554	CGSC:102054
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Notes

The nfr genes were defined by phage N4 resistant mutants ^[6]

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
JW0557	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAGGAGAATAACCTTAATCG Primer 2:CCCCAGTGCACTCCAATGGTGAG
12A1	Kohara Phage	Genobase	PMID:3038334
2F5	Kohara Phage	Genobase	PMID:3038334
purK79::Tn10	Linked marker	CAG12171 = CGSC7342^[5]	est. P1 cotransduction: 24% ^[7] Synonyms:purE79::Tn10
dsbG601::Tn10	Linked marker	CAG12149 = CGSC7346^[5]	est. P1 cotransduction: 11% ^[7] Synonyms:zbd-601::Tn10, zbe-601::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:EG11740	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11740	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001679	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944741	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1691	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001939	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	NfrA
Synonyms	bacteriophage N4 receptor, outer membrane subunit^[1], B0568^[2]^[1], NfrA^[2]^[1] , ECK0560, JW0557, b0568
Product description	bacteriophage N4 receptor, outer membrane protein^[2]^[3] Outer membrane protein, putative structural receptor for N4 adsorption^[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:0005488	binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011990	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0009279	cell outer membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0998	C	Seeded from EcoCyc (v14.0)	complete
	GO:0009279	cell outer membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0040	C	Seeded from EcoCyc (v14.0)	complete
	GO:0009597	detection of virus	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0580	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0046718	entry of virus into host cell	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0580	P	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	gltD	PMID:16606699	Experiment(s):EBI-1137200
Protein	intA	PMID:16606699	Experiment(s):EBI-1137200
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1137200
Protein	hemG	PMID:16606699	Experiment(s):EBI-1137200
Protein	groL	PMID:16606699	Experiment(s):EBI-1137200
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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
outer membrane
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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 MKENNLNRVI GWSGLLLTSL LSTSALADNI GTSAEELGLS DYRHFVIYPR LDKALKAQKN NDEATAIREF EYIHQQVPDN IPLTLYLAEA YRHFGHDDRA RLLLEDQLKR HPGDARLERS LAAIPVEVKS VTTVEELLAQ QKACDAAPTL RCRSEVGQNA LRLAQLPVAR AQLNDATFAA SPEGKTLRTD LLQRAIYLKQ WSQADTLYNE ARQQNTLSAA ERRQWFDVLL AGQLDDRILA LQSQGIFTDP QSYITYATAL AYRGEKARLQ HYLIENKPLF TTDAQEKSWL YLLSKYSANP VQALANYTVQ FADNRQYVVG ATLPVLLKEG QYDAAQKLLA TLPANEMLEE RYAVSVATRN KAEALRLARL LYQQEPANLT RLDQLTWQLM QNEQSREAAD LLLQRYPFQG DARVSQTLMA RLASLLESHP YLATPAKVAI LSKPLPLAEQ RQWQSQLPGI ADNCPAIVRL LGDMSPSYDA AAWNRLAKCY RDTLPGVALY AWLQAEQRQP SAWQHRAVAY QAYQVEDYAT ALAAWQKISL HDMSNEDLLA AANTAQAAGN GAARDRWLQQ AEKRGLGSNA LYWWLHAQRY IPGQPELALN DLTRSINIAP SANAYVARAT IYRQRHNVPA AVSDLRAALE LEPNNSNTQA ALGYALWDSG DIAQSREMLE PAHKGLPDDP ALIRQLAYVN QRLDDMPATQ HYARLVIDDI DNQALITPLT PEQNQQRFNF RRLHEEVGRR WTFSFDSSIG LRSGAMSTAN NNVGGAAPGK SYRSYGQLEA EYRIGRNMLL EGDLLSVYSR VFADTGENGV MMPVKNPMSG TGLRWKPLRD QIFFIAVEQQ LPLNGQNGAS DTMLRASASF FNGGKYSDEW HPNGSGWFAQ NLYLDAAQYI RQDIQAWTAD YRVSWHQKVA NGQTIEPYAH VQDNGYRDKG TQGAQLGGVG VRWNIWTGET HYDAWPHKVS LGVEYQHTFK AINQRNGERN NAFLTIGVHW
Length	990
Mol. Wt	111.31 kDa
pI	3.5 (calculated)
Extinction coefficient	199,050 - 199,550 (calc based on 45 Y, 24 W, and 4 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
motif	1-27	UniProt Manual:Signal Peptides	UniProt:P31600
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<motif_map/>

Structure
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Structures

<beststructure> gene=nfrA taxon=12017 </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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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
NCBI (Protein) (EcoliWiki Page)	GI:16128551	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944741	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001939	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P31600	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11740	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11740	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944741	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001679	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1691	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	1.075+/-0.084	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.005047106	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	50	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	19	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	16	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		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)
nfrBA
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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_000913:590157..590197 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:b0568 (EcoliWiki Page)	NCBI GEO profiles for nfrA
microarray	GenExpDB:b0568 (EcoliWiki Page)	Summary of data for nfrA 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 nfrA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11740	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1691	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0568
EcoGene	EcoGene:EG11740	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001679	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001939	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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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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
Superfamily (EcoliWiki Page)	SUPERFAMILY:48452
Superfamily (EcoliWiki Page)	SUPERFAMILY:48452
EcoCyc	EcoCyc:EG11740	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11740	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001679	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1691	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001939	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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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
↑ Kiino, DR & Rothman-Denes, LB (1989) Genetic analysis of bacteriophage N4 adsorption. J. Bacteriol. 171 4595-602 PubMed
↑ ^7.0 ^7.1 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).

nfrA:On One Page

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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 nfrA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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