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Expression|

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Standard Name	yphE
Gene Synonym(s)	ECK2544, b2547, JW2531^[1], JW2531
Product Desc.	YphE^[2]^[3]; Component of YphD/YphE/YphF ABC transporter^[2]^[3] Putative ABC transporter ATP-binding protein; function unknown^[4]
Product Synonyms(s)	fused predicted sugar transporter subunits of ABC superfamily: ATP-binding components^[1], B2547^[2]^[1], YphE^[2]^[1] , ECK2544, JW2531, b2547
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yphD^[2]
Regulation/Activity
Quick Links
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Notes

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Predicted yphFEDCB operon. Putative YphDEF ABC transport system.^[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	yphE
Mnemonic	Systematic nomenclature
Synonyms	ECK2544, b2547, JW2531^[1], JW2531
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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	57.65 minutes	MG1655: 2676383..2674872 <gbrowseImage> name=NC_000913:2674872..2676383 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2599060..2597549 <gbrowseImage> name=NC_012967:2597549..2599060 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2560677..2562188 <gbrowseImage> name=NC_012759:2560677..2562188 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2677017..2675506 <gbrowseImage> name=NC_007779:2675506..2677017 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2768148..2766637 <gbrowseImage> name=NC_010473:2766637..2768148 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
ΔyphE (Keio:JW2531)	deletion	deletion	PMID:16738554	Shigen CGSC10016^[5]
ΔyphE721::kan			PMID:16738554	CGSC:105928
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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
JW2531	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTTCACGGCAACAGAGGCAGT Primer 2:CCGTGCACAGACAGAATGGCGGA
6F10	Kohara Phage	Genobase	PMID:3038334
8E12	Kohara Phage	Genobase	PMID:3038334
zfh-208::Tn10	Linked marker	CAG18481 = CGSC7417^[5]	est. P1 cotransduction: 67% ^[6] Synonyms:zff-208::Tn10
nadB51::Tn10	Linked marker	CAG18480 = CGSC7419^[5]	est. P1 cotransduction: 25% ^[6]
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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:G7341	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13466	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003911	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948990	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3239	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008376	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	YphE
Synonyms	fused predicted sugar transporter subunits of ABC superfamily: ATP-binding components^[1], B2547^[2]^[1], YphE^[2]^[1] , ECK2544, JW2531, b2547
Product description	YphE^[2]^[3]; Component of YphD/YphE/YphF ABC transporter^[2]^[3] Putative ABC transporter ATP-binding protein; function unknown^[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:0000166	nucleotide binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003593	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003439	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017871	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	F	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:0016887	ATPase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003439	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016887	ATPase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017871	F	Seeded from EcoCyc (v14.0)	complete
	GO:0017111	nucleoside-triphosphatase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003593	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003674	molecular function	n/a	ND: No biological Data available		F		Missing: reference
	GO:0008150	biological process	n/a	ND: No biological Data available		P		Missing: reference
	GO:0005575	cellular component	n/a	ND: No biological Data available		C		Missing: reference
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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 YphD/YphE/YphF ABC transporter	could be indirect
Protein	groL		PMID:16606699	Experiment(s):EBI-1143218
Protein	sdhA		PMID:16606699	Experiment(s):EBI-1143218
Protein	hscA		PMID:16606699	Experiment(s):EBI-1143218
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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
cytoplasm			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 MFTATEAVPV AKVVAGNKRY PGVVALDNVN FTLNKGEVRA LLGKNGAGKS TLIRMLTGSE RPDSGDIWIG ETRLEGDEAT LTRRAAELGV RAVYQELSLV EGLTVAENLC LGQWPRRNGM IDYLQMAQDA QRCLQALGVD VSPEQLVSTL SPAQKQLVEI ARVMKGEPRV VILDEPTSSL ASAEVELVIS AVKKMSALGV AVIYVSHRME EIRRIASCAT VMRDGQVAGD VMLENTSTHH IVSLMLGRDH VDIAPVAPQE IVDQAVLEVR ALRHKPKLED ISFTLRRGEV LGIAGLLGAG RSELLKAIVG LEEYEQGEIV INGEKITRPD YGDMLKRGIG YTPENRKEAG IIPWLGVDEN TVLTNRQKIS ANGVLQWSTI RRLTEEVMQR MTVKAASSET PIGTLSGGNQ QKVVIGRWVY AASQILLLDE PTRGVDIEAK QQIYRIVREL AAEGKSVVFI SSEVEELPLV CDRILLLQHG TFSQEFHAPV NVDELMSAIL SVH
Length	503
Mol. Wt	55.015 kDa
pI	5.5 (calculated)
Extinction coefficient	40,910 - 41,410 (calc based on 9 Y, 5 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	References
Domain	50..178	PF00005 ABC transporter	PMID:19920124
Domain	302..433	PF00005 ABC transporter	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=yphE 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:16130472	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948990	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008376	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77509	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7341	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13466	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948990	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003911	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3239	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	1.44+/-0.053	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.00198544	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	0^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	0^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)
yphD
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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_000913:2676363..2676403 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:b2547 (EcoliWiki Page)	NCBI GEO profiles for yphE
microarray	GenExpDB:b2547 (EcoliWiki Page)	Summary of data for yphE 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 yphE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7341	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3239	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2547
EcoGene	EcoGene:EG13466	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003911	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008376	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
Drosophila pseudoobscura	YP_026286 (score: 0.230) GA14368-PA (score: 1.000; bootstrap: 87%) GA13367-PA (score: 0.116)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000017727 (score: 1.000; bootstrap: 81%)	From Inparanoid:20070104
Shigella flexneri	YPHE	From SHIGELLACYC
E. coli O157	YPHE	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)	PF00005 ABC transporter
Pfam (EcoliWiki Page)	PF00005 ABC transporter
Superfamily (EcoliWiki Page)	SUPERFAMILY:52540
Superfamily (EcoliWiki Page)	SUPERFAMILY:52540
Panther (EcoliWiki Page)	PTHR24220:SF12
EcoCyc	EcoCyc:G7341	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13466	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003911	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3239	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008376	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 ^2.7 ^2.8 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).

yphE: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 yphE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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