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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	rffE
Gene Synonym(s)	ECK3778, b3786, JW5600, nfrC, wecB, mnaA, yifF^[1], yifF
Product Desc.	UDP-GlcNAc-2-epimerase; needed for ECA (enterobacterial common antigen) synthesis^[2]
Product Synonyms(s)	UDP-N-acetyl glucosamine-2-epimerase^[1], B3786^[3]^[1], YifF^[3]^[1], RffE^[3]^[1], NfrC^[3]^[1], WecB^[3]^[1] , ECK3778, JW5600, nfrC, wecB, yifF, b3786
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rfe^[3]
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

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	rffE
Mnemonic	Rough
Synonyms	ECK3778, b3786, JW5600, nfrC, wecB, mnaA, yifF^[1], yifF
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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	85.53 minutes, 85.53 minutes	MG1655: 3968156..3969286 <gbrowseImage> name=NC_000913:3968156..3969286 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3931933..3933063 <gbrowseImage> name=NC_012967:3931933..3933063 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3857825..3858955 <gbrowseImage> name=NC_012759:3857825..3858955 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3666548..3665418 <gbrowseImage> name=NC_007779:3665418..3666548 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4067076..4068206 <gbrowseImage> name=NC_010473:4067076..4068206 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
ΔrffE (Keio:JW5600)	deletion	deletion			PMID:16738554	Shigen
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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
JW5600	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAGTACTGACTGTATTTGG Primer 2:CCTAGTGATATCCGATTATTTTT
7B1	Kohara Phage	Genobase	PMID:3038334
ilvD500::Tn10	Linked marker	CAG18431 = CGSC7462^[4]	est. P1 cotransduction: 59% ^[5] Synonyms:ilv500::Tn10
metEo-3079::Tn10	Linked marker	CAG18491 = CGSC7464^[4]	est. P1 cotransduction: 18% ^[5] Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.
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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:EG11451	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11451	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001414	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944789	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1420	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012372	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	RffE
Synonyms	UDP-N-acetyl glucosamine-2-epimerase^[1], B3786^[3]^[1], YifF^[3]^[1], RffE^[3]^[1], NfrC^[3]^[1], WecB^[3]^[1] , ECK3778, JW5600, nfrC, wecB, yifF, b3786
Product description	UDP-GlcNAc-2-epimerase; needed for ECA (enterobacterial common antigen) synthesis^[2]
EC number (for enzymes)	5.1.3.14^[1]
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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:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006047	UDP-N-acetylglucosamine metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003331	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008761	UDP-N-acetylglucosamine 2-epimerase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003331	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008761	UDP-N-acetylglucosamine 2-epimerase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:5.1.3.14	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009103	lipopolysaccharide biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003331	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009597	detection of virus	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0580	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016853	isomerase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0413	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046718	entry of virus into host cell	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0580	P	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
cytoplasm
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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 MKVLTVFGTR PEAIKMAPLV HALAKDPFFE AKVCVTAQHR EMLDQVLKLF SIVPDYDLNI MQPGQGLTEI TCRILEGLKP ILAEFKPDVV LVHGDTTTTL ATSLAAFYQR IPVGHVEAGL RTGDLYSPWP EEANRTLTGH LAMYHFSPTE TSRQNLLREN VADSRIFITG NTVIDALLWV RDQVMSSDKL RSELAANYPF IDPDKKMILV TGHRRESFGR GFEEICHALA DIATTHQDIQ IVYPVHLNPN VREPVNRILG HVKNVILIDP QEYLPFVWLM NHAWLILTDS GGIQEEAPSL GKPVLVMRDT TERPEAVTAG TVRLVGTDKQ RIVEEVTRLL KDENEYQAMS RAHNPYGDGQ ACSRILEALK NNRISL
Length	376
Mol. Wt	42.244 kDa
pI	6.3 (calculated)
Extinction coefficient	35,410 - 35,910 (calc based on 9 Y, 4 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	Notes	References
Domain	21..370	PF02350 UDP-N-acetylglucosamine 2-epimerase		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=rffE 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:49176409	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944789	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012372	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P27828	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11451	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11451	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944789	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001414	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1420	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	Reference(s)
Protein	E. coli K-12 MC4100	2.98E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	1326	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	200	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	690	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	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)
rfe
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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_000913:3968136..3968176 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:b3786 (EcoliWiki Page)	NCBI GEO profiles for rffE
microarray	GenExpDB:b3786 (EcoliWiki Page)	Summary of data for rffE 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 rffE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11451	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1420	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3786
EcoGene	EcoGene:EG11451	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001414	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012372	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	WECB	From SHIGELLACYC
E. coli O157	WECB	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)	PF02350 UDP-N-acetylglucosamine 2-epimerase
Panther (EcoliWiki Page)	PTHR18964:SF2
Superfamily (EcoliWiki Page)	SUPERFAMILY:53756
EcoCyc	EcoCyc:EG11451	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11451	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001414	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1420	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012372	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 ^1.12 ^1.13 ^1.14 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).

rffE: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 rffE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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