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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	ydeK
Gene Synonym(s)	ECK1503, b1510, JW1503, orfT^[1]
Product Desc.	predicted lipoprotein^[2]^[3] Putative OM autotransporter adhesin, function unknown; AidA homolog^[4]
Product Synonyms(s)	predicted lipoprotein^[1], B1510^[2]^[1], YdeK^[2]^[1], OrfT^[2]^[1]
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ydeK^[2]
Regulation/Activity
Quick Links
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Notes

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Probable false positive lipoprotein prediction, Cys not conserved in other autotransporters.^[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	ydeK
Mnemonic
Synonyms	ECK1503, b1510, JW1503, orfT^[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	34.32 minutes	MG1655: 1596110..1592133 <gbrowseImage> name=NC_000913:1592133..1596110 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 1484192..1488169 <gbrowseImage> name=NC_012759:1484192..1488169 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1599800..1595823 <gbrowseImage> name=NC_007779:1595823..1599800 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1685735..1681758 <gbrowseImage> name=NC_010473:1681758..1685735 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
ΔydeK (Keio:JW1503)	deletion	deletion	PMID:16738554	Shigen CGSC9301^[5]
ΔydeK731::kan			PMID:16738554	CGSC:104224
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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
JW1503	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATAGAATCTATCGCGTGAT Primer 2:CCGCGACGCAGTGCCCCCCCC
2A9	Kohara Phage	Genobase	PMID:3038334
5F9	Kohara Phage	Genobase	PMID:3038334
zdd-235::Tn10	Linked marker	CAG18461 = CGSC7378^[5]	est. P1 cotransduction: 6% ^[6] Synonyms:zdc-235::Tn10
zdi-925::Tn10	Linked marker	CAG12151 = CGSC7385^[5]	est. P1 cotransduction: % ^[6] Synonyms:zdh-925::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:EG11780	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11780	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001714	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1728	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005037	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	YdeK
Synonyms	predicted lipoprotein^[1], B1510^[2]^[1], YdeK^[2]^[1], OrfT^[2]^[1]
Product description	predicted lipoprotein^[2]^[3] Putative OM autotransporter adhesin, function unknown; AidA homolog^[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: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: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:0031225	anchored to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9901	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	Notes	References	Evidence
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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
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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 MNRIYRVIWN CTLQVFQACS ELTRRAGKTS TVNLRKSSGL TTKFSRLTLG VLLALSGSAS GASLEVDNDQ ITNIDTDVAY DAYLVGWYGT GVLNILAGGN ASLTTITTSV IGANEDSEGT VNVLGGTWRL YDSGNNARPL NVGQSGTGTL NIKQKGHVDG GYLRLGSSTG GVGTVNVEGE DSVLTTELFE IGSYGTGSLN ITDKGYVTSS IVAILGYQAG SNGQVVVEKG GEWLIKNNDS SIEFQIGNQG TGEATIREGG LVTAENTIIG GNATGIGTLN VQDQDSVITV RRLYNGYFGN GTVNISNNGL INNKEYSLVG VQDGSHGVVN VTDKGHWNFL GTGEAFRYIY IGDAGDGELN VSSEGKVDSG IITAGMKETG TGNITVKDKN SVITNLGTNL GYDGHGEMNI SNQGLVVSNG GSSLGYGETG VGNVSITTGG MWEVNKNVYT TIGVAGVGNL NISDGGKFVS QNITFLGDKA SGIGTLNLMD ATSSFDTVGI NVGNFGSGIV NVSNGATLNS TGYGFIGGNA SGKGIVNIST DSLWNLKTSS TNAQLLQVGV LGTGELNITT GGIVKARDTQ IALNDKSKGD VRVDGQNSLL ETFNMYVGTS GTGTLTLTNN GTLNVEGGEV YLGVFEPAVG TLNIGAAHGE AAADAGFITN ATKVEFGLGE GVFVFNHTNN SDAGYQVDML ITGDDKDGKV IHDAGHTVFN AGNTYSGKTL VNDGLLTIAS HTADGVTGMG SSEVTIANPG TLDILASTNS AGDYTLTNAL KGDGLMRVQL SSSDKMFGFT HATGTEFAGV AQLKDSTFTL ERDNTAALTH AMLQSDSENT TSVKVGEQSI GGLAMNGGTI IFDTDIPAAT LAEGYISVDT LVVGAGDYTW KGRNYQVNGT GDVLIDVPKP WNDPMANNPL TTLNLLEHDD SHVGVQLVKA QTVIGSGGSL TLRDLQGDEV EADKTLHIAQ NGTVVAEGDY GFRLTTAPGN GLYVNYGLKA LNIHGGQKLT LAEHGGAYGA TADMSAKIGG EGDLAINTVR QVSLSNGQND YQGATYVQMG TLRTDADGAL GNTRELNISN AAIVDLNGST QTVETFTGQM GSTVLFKEGA LTVNKGGISQ GELTGGGNLN VTGGTLAIEG LNARYNALTS ISPNAEVSLD NTQGLGRGNI ANDGLLTLKN VTGELRNSIS GKGIVSATAR TDVELDGDNS RFVGQFNIDT GSALSVNEQK NLGDASVINN GLLTISTERS WAMTHSISGS GDVTKLGTGI LTLNNDSAAY QGTTDIVGGE IAFGSDSAIN MASQHINIHN SGVMSGNVTT AGDMNVMPGG GTACR
Length	1,325
Mol. Wt	136.515 kDa
pI	4.5 (calculated)
Extinction coefficient	105,660 - 106,035 (calc based on 34 Y, 10 W, and 3 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	1-18	UniProt Manual:Signal Peptides	UniProt:P32051
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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=ydeK 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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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:EG11780	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11780	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001714	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1728	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005037	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)
ydeK
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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_000913:1596090..1596130 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:b1510 (EcoliWiki Page)	NCBI GEO profiles for ydeK
microarray	GenExpDB:b1510 (EcoliWiki Page)	Summary of data for ydeK 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 ydeK Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11780	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1728	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1510
EcoGene	EcoGene:EG11780	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001714	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005037	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
Caenorhabditis briggsae	WBGene00027619 (score: 1.000; bootstrap: 51%)	From Inparanoid:20070104
Mus musculus	MGI:3644391 (score: 1.000; bootstrap: 52%) MGI:3645846 (score: 0.077) MGI:3647315 (score: 0.070)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000041626 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	YDEK	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
EcoCyc	EcoCyc:EG11780	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11780	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001714	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1728	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005037	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 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 ^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).

ydeK: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 ydeK Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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