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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	yadE
Gene Synonym(s)	ECK0129, b0130, JW0126^[1], JW0126
Product Desc.	predicted polysaccharide deacetylase lipoprotein^[2]^[3] Polysaccharide deacetylase-like protein, function unknown^[4]
Product Synonyms(s)	predicted polysaccharide deacetylase lipoprotein^[1], B0130^[2]^[1], YadE^[2]^[1] , ECK0129, JW0126, b0130
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yadE^[2]
Regulation/Activity
Quick Links
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Notes

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YadE has a predicted 19 aa signal peptide.Paralogous to pgaB.^[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	yadE
Mnemonic	Systematic nomenclature
Synonyms	ECK0129, b0130, JW0126^[1], JW0126
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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	3.13 minutes	MG1655: 145081..146310 <gbrowseImage> name=NC_000913:145081..146310 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 147884..149113 <gbrowseImage> name=NC_012967:147884..149113 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 145080..146309 <gbrowseImage> name=NC_012759:145080..146309 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 145081..146310 <gbrowseImage> name=NC_007779:145081..146310 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 119185..120414 <gbrowseImage> name=NC_010473:119185..120414 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)

Phenotype: Type

Phenotype: Description

Reference

Availability

Comments

yadE(del) (Keio:JW0126)

deletion

PMID:16738554

Shigen

CGSC8403^[5]

yadE747(del)::kan

PMID:16738554

CGSC:103464

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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
JW0126	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTACAAACAAGCTGTTATTCT Primer 2:CCTCCCTGCGGCTGGTTACTCAC
17C11	Kohara Phage	Genobase	PMID:3038334
11C5	Kohara Phage	Genobase	PMID:3038334
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[5]	est. P1 cotransduction: 4% ^[6] Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).
zad-220::Tn10	Linked marker	CAG12025 = CGSC7326^[5]	est. P1 cotransduction: 89% ^[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:EG11749	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11749	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946536	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001687	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1699	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000457	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	YadE
Synonyms	predicted polysaccharide deacetylase lipoprotein^[1], B0130^[2]^[1], YadE^[2]^[1] , ECK0129, JW0126, b0130
Product description	predicted polysaccharide deacetylase lipoprotein^[2]^[3] Polysaccharide deacetylase-like 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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011330	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005975	carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002509	P	Seeded from EcoCyc (v14.0)	complete
	GO:0005975	carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011330	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002509	F	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 MYKQAVILLL MLFTASVSAA LPARYMQTIE NAAVWAQIGD KMVTVGNIRA GQIIAVEPTA ASYYAFNFGF GKGFIDKGHL EPVQGRQKVE DGLGDLNKPL SNQNLVTWKD TPVYNAPSAG SAPFGVLADN LRYPILHKLK DRLNQTWYQI RIGDRLAYIS ALDAQPDNGL SVLTYHHILR DEENTRFRHT STTTSVRAFN NQMAWLRDRG YATLSMVQLE GYVKNKINLP ARAVVITFDD GLKSVSRYAY PVLKQYGMKA TAFIVTSRIK RHPQKWNPKS LQFMSVSELN EIRDVFDFQS HTHFLHRVDG YRRPILLSRS EHNILFDFAR SRRALAQFNP HVWYLSYPFG GFNDNAVKAA NDAGFHLAVT TMKGKVKPGD NPLLLKRLYI LRTDSLETMS RLVSNQPQG
Length	409
Mol. Wt	46.316 kDa
pI	10.2 (calculated)
Extinction coefficient	59,820 (calc based on 18 Y, 6 W, and 0 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	1-19	UniProt Manual:Signal Peptides	UniProt:P31666
Domain	226..368	PF01522 Polysaccharide deacetylase		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=yadE 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
NCBI (Protein) (EcoliWiki Page)	GI:16128123	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946536	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000457	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P31666	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11749	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11749	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946536	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001687	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1699	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	1.944+/-0.096	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.008136697	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	63	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	14	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	21^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)
yadE
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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_000913:145061..145101 source=MG1655 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:b0130 (EcoliWiki Page)	NCBI GEO profiles for yadE
microarray	GenExpDB:b0130 (EcoliWiki Page)	Summary of data for yadE 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 yadE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11749	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1699	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0130
EcoGene	EcoGene:EG11749	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001687	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000457	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	YADE	From SHIGELLACYC
E. coli O157	YADE	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)	PF01522 Polysaccharide deacetylase
Superfamily (EcoliWiki Page)	SUPERFAMILY:88713
EcoCyc	EcoCyc:EG11749	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11749	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001687	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1699	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000457	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 ^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).

yadE: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 yadE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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