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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	rfe
Gene Synonym(s)	ECK3776, b3784, JW3758, wecA^[1], wecA
Product Desc.	UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-P transferase; ECA and O-antigen synthesis, tunicamycin sensitivity^[2]
Product Synonyms(s)	UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase^[1], B3784^[3]^[1], WecA^[3]^[1], Rfe^[3]^[1] , ECK3776, JW3758, wecA, b3784
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rfe^[3]
Regulation/Activity
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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	rfe
Mnemonic	Rough
Synonyms	ECK3776, b3784, JW3758, wecA^[1], wecA
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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	85.48 minutes	MG1655: 3965939..3967042 <gbrowseImage> name=NC_000913:3965939..3967042 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3929716..3930819 <gbrowseImage> name=NC_012967:3929716..3930819 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3855608..3856711 <gbrowseImage> name=NC_012759:3855608..3856711 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3668765..3667662 <gbrowseImage> name=NC_007779:3667662..3668765 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4064859..4065962 <gbrowseImage> name=NC_010473:4064859..4065962 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: Description	Reference	Availability	Comments
Δrfe (Keio:JW3758)	deletion	deletion		PMID:16738554	Shigen CGSC10741^[4]
wecAD276G		D276G	No loss of activity; both in vivo and in vitro			seeded from UniProt:P0AC78
wecAHIHH279GGGG		HIHH279GGGG	Loss of activity. No binding to tunicamycin			seeded from UniProt:P0AC78
wecAD35G		D35G	Decrease in activity; both in vivo and in vitro			seeded from UniProt:P0AC78
wecAD94G		D94G	No loss in activity; both in vivo and in vitro			seeded from UniProt:P0AC78
wecAD156E		D156E	Loss of activity; both in vivo and in vitro; when associated with E-159			seeded from UniProt:P0AC78
wecAD156G		D156G	Loss of activity; both in vivo and in vitro. No binding to tunicamycin; when associated with G-159			seeded from UniProt:P0AC78
wecAD159E		D159E	Loss of activity; both in vivo and in vitro; when associated with E-156			seeded from UniProt:P0AC78
wecAH279S		H279S	Loss of activity. No binding to tunicamycin			seeded from UniProt:P0AC78
wecADD90EE,GG		DD90EE,GG	Loss of activity in vivo. Decrease in activity in vitro. No change in binding to tunicamycin			seeded from UniProt:P0AC78
wecAR265K		R265K	Decrease in activity. Reduces binding to tunicamycin			seeded from UniProt:P0AC78
wecAD159G		D159G	Loss of activity; both in vivo and in vitro. No binding to tunicamycin; when associated with G-156			seeded from UniProt:P0AC78
Δrfe-735::kan				PMID:16738554	CGSC:102676
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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
JW3758	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATTTACTGACAGTGAGTAC Primer 2:CCTTTGGTTAAATTGGGGCTGCC
7B1	Kohara Phage	Genobase	PMID:3038334
2A8	Kohara Phage	Genobase	PMID:3038334
ilvD500::Tn10	Linked marker	CAG18431 = CGSC7462^[4]	est. P1 cotransduction: 64% ^[5] Synonyms:ilv500::Tn10
metEo-3079::Tn10	Linked marker	CAG18491 = CGSC7464^[4]	est. P1 cotransduction: 16% ^[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:EG10840	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10840	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000831	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948789	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0833	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012366	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	Rfe
Synonyms	UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase^[1], B3784^[3]^[1], WecA^[3]^[1], Rfe^[3]^[1] , ECK3776, JW3758, wecA, b3784
Product description	UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-P transferase; ECA and O-antigen synthesis, tunicamycin sensitivity^[2]
EC number (for enzymes)	2.4.1.-^[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:0000287	magnesium ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012750	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	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:0008963	phospho-N-acetylmuramoyl-pentapeptide-transferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000715	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009103	lipopolysaccharide biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012750	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009103	lipopolysaccharide biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0448	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009276	Gram-negative-bacterium-type cell wall	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012750	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:0016021	integral to membrane	PMID:18723618	IDA: Inferred from Direct Assay		C		complete
	GO:0016021	integral to membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000715	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008963	phospho-N-acetylmuramoyl-pentapeptide-transferase activity	PMID:18723618	IDA: Inferred from Direct Assay		F		complete
	GO:0016021	integral to membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012750	C	Seeded from EcoCyc (v14.0)	complete
	GO:0000287	magnesium ion binding	PMID:18723618	IDA: Inferred from Direct Assay		F		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-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016757	transferase activity, transferring glycosyl groups	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0328	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016780	phosphotransferase activity, for other substituted phosphate groups	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012750	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030145	manganese ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012750	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030145	manganese ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0464	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
plasma membrane	C-terminus localized in the cytoplasm with 11 predicted transmembrane domains	Daley et al. (2005) ^[6]
membrane			From EcoCyc^[7]
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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 MNLLTVSTDL ISIFLFTTLF LFFARKVAKK VGLVDKPNFR KRHQGLIPLV GGISVYAGIC FTFGIVDYYI PHASLYLACA GVLVFIGALD DRFDISVKIR ATIQAAVGIV MMVFGKLYLS SLGYIFGSWE MVLGPFGYFL TLFAVWAAIN AFNMVDGIDG LLGGLSCVSF AAIGMILWFD GQTSLAIWCF AMIAAILPYI MLNLGILGRR YKVFMGDAGS TLIGFTVIWI LLETTQGKTH PISPVTALWI IAIPLMDMVA IMYRRLRKGM SPFSPDRQHI HHLIMRAGFT SRQAFVLITL AAALLASIGV LAEYSHFVPE WVMLVLFLLA FFLYGYCIKR AWKVARFIKR VKRRLRRNRG GSPNLTK
Length	367
Mol. Wt	40.959 kDa
pI	10.4 (calculated)
Extinction coefficient	63,370 - 63,995 (calc based on 13 Y, 8 W, and 5 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	73..235	PF00953 Glycosyl transferase family 4		PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=rfe 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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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:16131640	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948789	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012366	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AC78	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10840	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10840	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948789	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000831	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0833	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 MG1655	1448	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	232	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	708	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_000913:3965919..3965959 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b3784 (EcoliWiki Page)	NCBI GEO profiles for rfe
microarray	GenExpDB:b3784 (EcoliWiki Page)	Summary of data for rfe 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 (3965203..3965595) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ05; Well:A11^[8]
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Notes

Accessions Related to rfe Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10840	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0833	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3784
EcoGene	EcoGene:EG10840	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000831	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012366	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	RFE	From SHIGELLACYC
E. coli O157	RFE	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)	PF00953 Glycosyl transferase family 4
Panther (EcoliWiki Page)	PTHR22926:SF2
EcoCyc	EcoCyc:EG10840	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10840	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000831	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0833	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012366	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 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.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 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).
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

rfe: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 rfe Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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