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Standard Name	yfhR
Gene Synonym(s)	ECK2531, b2534, JW2518^[1], JW2518
Product Desc.	predicted peptidase^[2]^[3] Function unknown, S9 peptidase family^[4]
Product Synonyms(s)	predicted peptidase^[1], B2534^[2]^[1], YfhR^[2]^[1] , ECK2531, JW2518, b2534
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yfhR^[2]
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	yfhR
Mnemonic	Systematic nomenclature
Synonyms	ECK2531, b2534, JW2518^[1], JW2518
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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	57.38 minutes, 57.38 minutes	MG1655: 2662385..2663266 <gbrowseImage> name=NC_000913:2662385..2663266 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2585062..2585943 <gbrowseImage> name=NC_012967:2585062..2585943 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2548190..2549071 <gbrowseImage> name=NC_012759:2548190..2549071 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2663019..2663900 <gbrowseImage> name=NC_007779:2663019..2663900 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2754150..2755031 <gbrowseImage> name=NC_010473:2754150..2755031 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
ΔyfhR (Keio:JW2518)	deletion	deletion	PMID:16738554	Shigen CGSC10005^[5]
ΔyfhR779::kan			PMID:16738554	CGSC:104790
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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
JW2518	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATAAAGAAGTCGCAAGGAAA Primer 2:CCGTTCTGCGGATTCAACGCGCT
5E10	Kohara Phage	Genobase	PMID:3038334
6F10	Kohara Phage	Genobase	PMID:3038334
purC80::Tn10	Linked marker	CAG18470 = CGSC7413^[5]	est. P1 cotransduction: 2% ^[6]
zfh-208::Tn10	Linked marker	CAG18481 = CGSC7417^[5]	est. P1 cotransduction: 97% ^[6] Synonyms:zff-208::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:G7328	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13453	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003900	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945059	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3226	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008340	Escherichia coli str. K-12 substr. MG1655
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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	YfhR
Synonyms	predicted peptidase^[1], B2534^[2]^[1], YfhR^[2]^[1] , ECK2531, JW2518, b2534
Product description	predicted peptidase^[2]^[3] Function unknown, S9 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:IPR001375	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008236	serine-type peptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001375	F	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	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9904	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	References	Evidence
Protein	prs	PMID:16606699	Experiment(s):EBI-1143181
Protein	caiD	PMID:16606699	Experiment(s):EBI-1143181
Protein	groL	PMID:16606699	Experiment(s):EBI-1143181
Protein	dps	PMID:16606699	Experiment(s):EBI-1143181
Protein	suhB	PMID:16606699	Experiment(s):EBI-1143181
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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 MIKKSQGKVM ALPVNKRVPK ILFILFVVAF CVYLVPRVAI NFFYYPDDKI YGPDPWSAES VEFTAKDGTR LQGWFIPSST GPADNAIATI IHAHGNAGNM SAHWPLVSWL PERNFNVFMF DYRGFGKSKG TPSQAGLLDD TQSAINVVRH RSDVNPQRLV LFGQSIGGAN ILDVIGRGDR EGIRAVILDS TFASYATIAN QMIPGSGYLL DESYSGENYI ASVSPIPLLL IHGKADHVIP WQHSEKLYSL AKEPKRLILI PDGEHIDAFS DRHGDVYREQ MVDFILSALN PQN
Length	293
Mol. Wt	32.516 kDa
pI	7.0 (calculated)
Extinction coefficient	43,890 - 44,015 (calc based on 11 Y, 5 W, and 1 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	103..292	PF00326 Prolyl oligopeptidase family		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=yfhR taxon=562,83333 </beststructure>

Models

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Structure figures

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Notes

Gene Product Resources

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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:226524738	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945059	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008340	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77538	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7328	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13453	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945059	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003900	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3226	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	2^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)
yfhR
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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_000913:2662365..2662405 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:b2534 (EcoliWiki Page)	NCBI GEO profiles for yfhR
microarray	GenExpDB:b2534 (EcoliWiki Page)	Summary of data for yfhR 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 (2662171..2662425) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ17; Well:C2^[7]
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Notes

Accessions Related to yfhR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7328	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3226	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2534
EcoGene	EcoGene:EG13453	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003900	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008340	Escherichia coli str. K-12 substr. MG1655
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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
Anopheles gambiae	ENSANGP00000005169 (score: 1.000; bootstrap: 60%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000025550 (score: 1.000; bootstrap: 79%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G20520 (score: 1.000; bootstrap: 68%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000003149 (score: 1.000; bootstrap: 82%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00030054 (score: 1.000; bootstrap: 65%) WBGene00034526 (score: 0.117) WBGene00039742 (score: 0.110) WBGene00040829 (score: 0.063)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00010561 (score: 1.000; bootstrap: 71%) WBGene00008497 (score: 0.099) WBGene00044003 (score: 0.091) WBGene00008498 (score: 0.069)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000009028 (score: 1.000; bootstrap: 76%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000005286 (score: 1.000; bootstrap: 88%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-051120-54 (score: 1.000; bootstrap: 75%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0188509 (score: 1.000; bootstrap: 83%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0025109 (score: 1.000; bootstrap: 68%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA15028-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000027178 (score: 1.000; bootstrap: 72%)	From Inparanoid:20070104
Homo sapiens	ENSP00000330222 (score: 1.000; bootstrap: 51%) ENSP00000258884 (score: 0.672) ENSP00000250974 (score: 0.643) ENSP00000346816 (score: 0.630) ENSP00000350939 (score: 0.331) ENSP00000333435 (score: 0.240)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000024842 (score: 1.000; bootstrap: 50%) ENSMMUP00000021731 (score: 0.613) ENSMMUP00000016211 (score: 0.490)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000003224 (score: 1.000; bootstrap: 73%) ENSMODP00000005442 (score: 1.000; bootstrap: 70%) ENSMODP00000024206 (score: 0.757)	From Inparanoid:20070104
Mus musculus	MGI:1916154 (score: 1.000; bootstrap: 77%)	From Inparanoid:20070104
Oryza gramene	Q6YSE8 (score: 1.000; bootstrap: 83%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000035925 (score: 1.000; bootstrap: 49%) ENSPTRP00000024264 (score: 0.508) ENSPTRP00000012586 (score: 0.266)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000019563 (score: 1.000; bootstrap: 75%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YNL320W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC32H83 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000159682 (score: 1.000; bootstrap: 75%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00026010001 (score: 1.000; bootstrap: 69%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000005694 (score: 1.000; bootstrap: 77%)	From Inparanoid:20070104
Shigella flexneri	S2753	From SHIGELLACYC
E. coli O157	Z3802	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)	PF00326 Prolyl oligopeptidase family
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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 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

yfhR: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 yfhR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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