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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	yhbU
Gene Synonym(s)	ECK3146, b3158, JW3127^[1], JW3127
Product Desc.	predicted peptidase (collagenase-like)^[2]^[3] Function unknown, U32 peptidase family^[4]
Product Synonyms(s)	predicted peptidase (collagenase-like)^[1], B3158^[2]^[1], YhbU^[2]^[1] , ECK3146, JW3127, b3158
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yhbU^[2]
Regulation/Activity
Quick Links
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Notes

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AFMB Structural Genomics target No. 32 (http://afmb.cnrs-mrs.fr/article171.html). ydcP, yegQ, yhbU, and yhbV are paralogs.^[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	yhbU
Mnemonic	Systematic nomenclature
Synonyms	ECK3146, b3158, JW3127^[1], JW3127
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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	71.12 minutes	MG1655: 3299507..3300502 <gbrowseImage> name=NC_000913:3299507..3300502 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3236719..3237714 <gbrowseImage> name=NC_012967:3236719..3237714 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3186655..3187650 <gbrowseImage> name=NC_012759:3186655..3187650 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3301340..3302335 <gbrowseImage> name=NC_007779:3301340..3302335 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3397252..3398247 <gbrowseImage> name=NC_010473:3397252..3398247 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
ΔyhbU (Keio:JW3127)	deletion	deletion	PMID:16738554	Shigen CGSC10382^[5]
ΔyhbU771::kan			PMID:16738554	CGSC:105114
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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
JW3127	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGAGCTGCTCTGCCCTGCCGG Primer 2:CCtTGCCATTTACGGTGATATGC
13A9	Kohara Phage	Genobase	PMID:3038334
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[5]	est. P1 cotransduction: % ^[6] Synonyms:zgh-3075::Tn10, zgj-3075::Tn10
sfsB203::Tn10	Linked marker	CAG12072 = CGSC7440^[5]	est. P1 cotransduction: 28% ^[6] Synonyms:zgj-203::Tn10, zha-203::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:G7652	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12790	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004202	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:949115	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2642	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010380	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	YhbU
Synonyms	predicted peptidase (collagenase-like)^[1], B3158^[2]^[1], YhbU^[2]^[1] , ECK3146, JW3127, b3158
Product description	predicted peptidase (collagenase-like)^[2]^[3] Function unknown, U32 peptidase family^[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:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001539	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008233	peptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001539	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008233	peptidase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0645	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0378	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	References	Evidence
Protein	aceE	PMID:15690043	Experiment(s):EBI-881807
Protein	aceF	PMID:15690043	Experiment(s):EBI-881807
Protein	lon	PMID:15690043	Experiment(s):EBI-881807
Protein	lpdA	PMID:15690043	Experiment(s):EBI-881807
Protein	groL	PMID:15690043	Experiment(s):EBI-881807, EBI-889312
Protein	tufA	PMID:15690043	Experiment(s):EBI-881807
Protein	yhbV	PMID:15690043	Experiment(s):EBI-881807
Protein	ddpD	PMID:16606699	Experiment(s):EBI-1144963
Protein	groL	PMID:16606699	Experiment(s):EBI-1144963
Protein	pldA	PMID:16606699	Experiment(s):EBI-1144963
Protein	tufB	PMID:19402753	MALDI(Z-score):20.973798
Protein	groL	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):17.053160
Protein	groS	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):24.918944
Protein	lon	PMID:19402753	MALDI(Z-score):25.435288
Protein	yhbV	PMID:19402753	LCMS(ID Probability):98.1 MALDI(Z-score):38.358142
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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 MELLCPAGNL PALKAAIENG ADAVYIGLKD DTNARHFAGL NFTEKKLQEA VSFVHQHRRK LHIAINTFAH PDGYARWQRA VDMAAQLGAD ALILADLAML EYAAERYPHI ERHVSVQASA TNEEAINFYH RHFDVARVVL PRVLSIHQVK QLARVTPVPL EVFAFGSLCI MSEGRCYLSS YLTGESPNTI GACSPARFVR WQQTPQGLES RLNEVLIDRY QDGENAGYPT LCKGRYLVDG ERYHALEEPT SLNTLELLPE LMAANIASVK IEGRQRSPAY VSQVAKVWRQ AIDRCKADPQ NFVPQSAWME TLGSMSEGTQ TTLGAYHRKW Q
Length	331
Mol. Wt	37.046 kDa
pI	7.1 (calculated)
Extinction coefficient	46,870 - 47,620 (calc based on 13 Y, 5 W, and 6 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	1-15	UniProt Manual:Signal Peptides	UniProt:P45527
Domain	74..331	PF01136 Peptidase family U32		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=yhbU 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:16131050	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:949115	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010380	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P45527	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7652	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12790	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:949115	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004202	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2642	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	E. coli K-12 MG1655	12^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	3^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	3^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)
yhbU
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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_000913:3299487..3299527 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:b3158 (EcoliWiki Page)	NCBI GEO profiles for yhbU
microarray	GenExpDB:b3158 (EcoliWiki Page)	Summary of data for yhbU 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
	GFP Fusion	Intergenic region (3298831..3299149) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ08; Well:A2^[7]
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Notes

Accessions Related to yhbU Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7652	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2642	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3158
EcoGene	EcoGene:EG12790	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004202	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010380	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	YHBU	From SHIGELLACYC
E. coli O157	YHBU	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)	PF01136 Peptidase family U32
EcoCyc	EcoCyc:G7652	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12790	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004202	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2642	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010380	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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

yhbU: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 yhbU Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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