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Gene |

Product(s) |

Expression|

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Standard Name	efeU
Gene Synonym(s)	Note that this is a pseudogene in K-12 strains, ECK1007, JW1002, JW5141, ycdN, b4490
Product Desc.	Note that this is a pseudogene in K-12 strains. hypothetical protein of the OFeT transport family^[1]^[2]
Product Synonyms(s)	YcdN^[1], B1016^[1], YcdN_1^[1], EfeU_1^[1] , ECK1007, JW1002, JW5141, ycdN, b4490
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ycdN^[1]
Regulation/Activity
Quick Links
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Notes

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This is a pseudogene in K12 strains.

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	efeU
Mnemonic
Synonyms	Note that this is a pseudogene in K-12 strains, ECK1007, JW1002, JW5141, ycdN, b4490
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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	23.29 minutes	MG1655: 1080579..1080689 <gbrowseImage> name=NC_000913:1080579..1080689 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 1081778..1081888 <gbrowseImage> name=NC_007779:1081778..1081888 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
MG1655	23.29 minutes	MG1655: 1080677..1081408 <gbrowseImage> name=NC_000913:1080677..1081408 source=ecoli preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse (MG1655)	FASTA Dump
W3110		W3110: 1081876..1082607 <gbrowseImage> name=NC_007779:1081876..1082607 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse (W3110)	FASTA Dump
MG1655		MG1655: 1080570..1081408 <gbrowseImage> name=NC_000913:1080570..1081408 source=ecoli preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse (MG1655)	FASTA Dump
W3110		W3110: 1081778..1082607 <gbrowseImage> name=NC_007779:1081778..1082607 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse (W3110)	FASTA Dump
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Notes

efeU_1: >gnl|ECOLI|G6525 efeU_1 1081356..1081466 Escherichia coli K-12 substr. MG1655

atgTTTGTTC CGTTTCTCAT TATGTTGCGC GAAGGACTTG AAGCCGCGCT GATTGTCAGT TTGATTGCCA GCTATCTTAA GCGTACCCAG CGAGGCCGAT GGATTGTGtg a

efeU_2: >gnl|ECOLI|G0-10495 efeU_2 1081454..1082185 Escherichia coli K-12 substr. MG1655

atgGATTGTG TGATGTGGAT TGGCGTGTTG CTTGCCGCTG CGTTGTGCCT GGGCTTGGGT ATCTTCATTA ACGAAACCAC CGGCGAATTT CCGCAAAAAG AACAGGAACT GTTTGAAGGT ATCGTGGCGG TGATCGCCGT GGTGATCCTT ACCTGGATGG TTTTCTGGAT GCGCAAAGTG TCGCGCAACG TCAAAGTGCA ACTGGAACAG GCAGTCGATA GCGCATTGCA GCGTGGAAAT CATCATGGCT GGGCGCTGGT GATGATGGTC TTTTTTGCCG TTGCAAGGGA AGGGCTGGAG TCGGTCTTTT TCCTGCTGGC GGCATTTCAA CAAGATGTCG GGATCTGGCC GCCGCTGGGT GCAATGCTCG GTCTTGCTAC TGCCGTGGTG CTAGGCTTCC TGCTCTACTG GGGCGGTATT CGCCTCAATC TTGGTGCATT TTTTAAATGG ACCAGCCTGT TTATTCTCTT CGTCGCCGCA GGGCTGGCAG CTGGTGCCAT TCGCGCATTT CATGAAGCCG GATTGTGGAA CCACTTTCAG GAAATCGCCT TCGATATGAG TGCGGTGCTC TCAACTCACT CGCTGTTTGG CACGCTGATG GAAGGGATTT TTGGCTATCA GGAAGCGCCG AGCGTCAGCG AAGTCGCCGT CTGGTTTATT TATCTCATCC CGGCGCTGGT GGCATTTGCT CTGCCACCAC GCGCAGGGGC GACAGCGTCT CGCTCCGCGt aa

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
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
7B5	Kohara Phage	Genobase	PMID:3038334
1E12	Kohara Phage	Genobase	PMID:3038334
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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
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1016
ASAP (EcoliWikiPage)	ASAP:ABE-0003443
NCBI (EcoliWiki Page)	GeneID:948956	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120016545	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	EfeU
Synonyms	YcdN^[1], B1016^[1], YcdN_1^[1], EfeU_1^[1] , ECK1007, JW1002, JW5141, ycdN, b4490
Product description	Note that this is a pseudogene in K-12 strains. hypothetical protein of the OFeT transport family^[1]^[2]
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

Contributes to

GO:0005381

iron ion transmembrane transporter activity

PMID:16987175

ISS: Inferred from Sequence or Structural Similarity

UniProtKB:P40088

F

complete

GO:0033212

iron assimilation

PMID:16987175

ISS: Inferred from Sequence or Structural Similarity

UniProtKB:P40088

P

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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A mutation in E. coli K-12 disrupts the efeU coding sequence into two polypeptides. The predicted amino acid sequences are:

EfeU_1:

MFVPFLIMLREGLEAALIVSLIASYLKRTQRGRWIV

EfeU_2:

MDCVMWIGVLLAAALCLGLGIFINETTGEFPQKEQELFEGIVAVIAVVILTWMVFWMRKV SRNVKVQLEQAVDSALQRGNHHGWALVMMVFFAVAREGLESVFFLLAAFQQDVGIWPPLG AMLGLATAVVLGFLLYWGGIRLNLGAFFKWTSLFILFVAAGLAAGAIRAFHEAGLWNHFQ EIAFDMSAVLSTHSLFGTLMEGIFGYQEAPSVSEVAVWFIYLIPALVAFALPPRAGATASRSA

<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name	E. coli B strain REL606 YcdN GenBank record# ACT38701.1
Sequence	MGGMFVPFLIMLREGLEAALIVSLIASYLKRTQRGRWIGVMWIGVLLAAALCLGLGIFINETTGEFPQKE QELFEGIVAVIAVVILTWMVFWMRKVSRNVKVQLEQAVDSALQRGNHHGWALVMMVFFAVAREGLESVFF LLAAFQQDVGIWPPLGAMLGLATAVVLGFLLYWGGIRLNLGAFFKWTSLFILFVAAGLAAGAIRAFHEAG LWNHFQEIAFDMSAVLSTHSLFGTLMEGIFGYQEAPSVSEVAVWFIYLIPALVAFALPPRAGATASRSA
Length	279
Mol. Wt	30.589 kDa
pI	7.0 (calculated)
Extinction coefficient	60,960 - 61,085 (calc based on 4 Y, 10 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	1..276	PF03239 Iron permease FTR1 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=efeU_2 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)	GeneID:948956	Escherichia coli str. K-12 substr. MG1655
ASAP (EcoliWiki Page)	ASAP:ABE-0003443	Escherichia coli str. K-12 substr. MG1655
ASAP (EcoliWiki Page)	ASAP:ABE-0285091	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P75901	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948956	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120016545	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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)
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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)
ycdN
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Figure courtesy of RegulonDB

</protect>

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_000913:1080559..1080599 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:b1016 (EcoliWiki Page)	NCBI GEO profiles for efeU_2
microarray	GenExpDB:b1016 (EcoliWiki Page)	Summary of data for efeU_2 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 (1079968..1080600) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ13; Well:C12^[3]
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Notes

Accessions Related to efeU Expression

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

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1016
RegulonDB	RegulonDB:ECK120016545	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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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
Panther (EcoliWiki Page)	PTHR11819:SF51
Pfam (EcoliWiki Page)	PF03239 Iron permease FTR1 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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^2.0 ^2.1 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

efeU: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 efeU Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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