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Standard Name	phnE
Gene Synonym(s)	ECK4096, b4103, JW4064, ECK4097, b4104, JW4065^[1]
Product Desc.	phosphonate/organophosphate ester transporter (pseudogene)^[2]^[3]^[4] Component of alkylphosphonate ABC transporter^[3]^[4]
Product Synonyms(s)	phosphonate/organophosphate ester transporter subunit^[1], membrane component of ABC superfamily^[1], B4103^[3]^[1] , ECK4096, JW4064, b4104
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): phnCDEEFGHIJKLMNOP^[3], OP00283, phnCDE-w4011-phnFGHIJKLMNOP, phnCDE-w4011-phnFGHIJKLMNOPQ, phnCDE-b4103-phnFGHIJKLMNOP
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	phnE
Mnemonic
Synonyms	ECK4096, b4103, JW4064, ECK4097, b4104, JW4065^[1]
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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	93.12 minutes, 93.12 minutes, 93.12 minutes	MG1655: 4320834..4320466 <gbrowseImage> name=NC_000913:4320466..4320834 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4302083..4301265 <gbrowseImage> name=NC_012967:4301265..4302083 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
W3110		W3110: 4327489..4327121 <gbrowseImage> name=NC_007779:4327121..4327489 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
MG1655	93.12 minutes, 93.12 minutes, 93.12 minutes	MG1655: 4321304..4320684 <gbrowseImage> name=NC_000913:4320684..4321304 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse (MG1655)	FASTA Dump
W3110		W3110: 4327959..4327339 <gbrowseImage> name=NC_007779:4327339..4327959 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse (W3110)	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
phnE(del) (Keio:JW4064)	deletion	deletion	PMID:16738554	Shigen CGSC10923^[5]
phnE(del) (Keio:JW4065)	deletion	deletion	PMID:16738554	Shigen CGSC10923^[5]
phnE728(del)::kan			PMID:16738554	CGSC:102334
phnE729(del)::kan			PMID:16738554	CGSC:102336
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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
JW4064	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCTGGCGCTGTTTATCCACAC Primer 2:CCGATAAAGTGCTTACGCAACCG
10H5	Kohara Phage	Genobase	PMID:3038334
12H2	Kohara Phage	Genobase	PMID:3038334
2C12	Kohara Phage	Genobase	PMID:3038334
JW4065	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCCGGATGCGGTGCAAGCACC Primer 2:CCtCTGTGGCAGCACGCCGTAGA
zje-2241::Tn10	Linked marker	CAG18427 = CGSC7481^[5]	est. P1 cotransduction: 59% ^[6]
cadB2231::Tn10	Linked marker	CAG18488 = CGSC7479^[5]	est. P1 cotransduction: 23% ^[6] Synonyms:zjd-2231::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
NCBI (EcoliWiki Page)	GeneID:948625	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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	PhnE
Synonyms	phosphonate/organophosphate ester transporter subunit^[1], membrane component of ABC superfamily^[1], B4103^[3]^[1] , ECK4096, JW4064, b4104
Product description	phosphonate/organophosphate ester transporter (pseudogene)^[2]^[3]^[4] Component of alkylphosphonate ABC transporter^[3]^[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:0005215	transporter activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000515	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-0997	C	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-0997	C	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: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:0005887	integral to plasma membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005769	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005887	integral to plasma membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005769	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006810	transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000515	P	Seeded from EcoCyc (v14.0)	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:0015604	phosphonate transmembrane transporter activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005769	F	Seeded from EcoCyc (v14.0)	complete
	GO:0015716	phosphonate transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005769	P	Seeded from EcoCyc (v14.0)	complete
	GO:0015716	phosphonate transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0918	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000515	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000515	C	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: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:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042916	alkylphosphonate transport	PMID:1846145	IGI: Inferred from Genetic Interaction		P	Seeded from EcoCyc (v14.0)	Missing: with/from
	GO:0042917	alkylphosphonate transmembrane transporter activity	PMID:1846145	IGI: Inferred from Genetic Interaction		F	Seeded from EcoCyc (v14.0)	Missing: with/from
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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	Notes	References	Evidence
Protein	Subunits of alkylphosphonate ABC transporter	could be indirect
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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^[4]
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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 MPDAVQAPYP AYRPEPNMQT ITIAPPKRSW FSLLSWAVVL AVLVVSWQGA EMAPLTLIKD GGNMATFAAD FFPPDFSQWQ DYLTEMAVTL QIAVWGTALA VVLSIPFGLM SAENLVPWWV YQPVRRLMDA CRAINEMVFA MLFVVAVGLG PFAGVLACWR CLSTPPACSP SCFPKRWKRL SPARWKAFAP PVPTSSKRSS TACCHR
Length	206
Mol. Wt	22.796 kDa
pI	8.9 (calculated)
Extinction coefficient	60,960 - 61,835 (calc based on 4 Y, 10 W, and 7 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	87..259	PF00528 Binding-protein-dependent transport system inner membrane component		PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

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

Structures

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

Models

View models at:

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Structure figures

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Notes

The sequence given is for the reactivated version of the protein. In MG1655, the gene is inactivated by an 8bp insertion.

Gene Product Resources

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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)	GeneID:948625	Escherichia coli str. K-12 substr. MG1655
ASAP (EcoliWiki Page)	ASAP:ABE-0013439	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P16683	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948625	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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)
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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)
phnCDEEFGHIJKLMNOP
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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_000913:4320814..4320854 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:b4104 (EcoliWiki Page)	NCBI GEO profiles for phnE
microarray	GenExpDB:b4104 (EcoliWiki Page)	Summary of data for phnE 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 phnE Expression

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

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4104
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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	PHNE	From SHIGELLACYC
E. coli O157	PHNE	From ECOO157CYC
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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00528 Binding-protein-dependent transport system inner membrane component
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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 Makino, K et al. (1991) Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12. J. Bacteriol. 173 2665-72 PubMed
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 ^4.3 ^4.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^5.0 ^5.1 ^5.2 ^5.3 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).

phnE: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 phnE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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