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Gene |

Product(s) |

Expression|

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Standard Name	ytfN
Gene Synonym(s)	ECK4217, b4221, JW4180, ytfO^[1], ytfO
Product Desc.	conserved protein^[2]^[3] Function unknown^[4]
Product Synonyms(s)	conserved protein^[1], B4221^[2]^[1], YtfO^[2]^[1], YtfN^[2]^[1] , ECK4217, JW4180, ytfO, b4221
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ytfM^[2]
Regulation/Activity
Quick Links
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Notes

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May have signal peptide (weak prediction), or an uncleaved signal anchor (predicted single N-terminal TM region). Putative ytfMNP operon.^[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	ytfN
Mnemonic	Systematic nomenclature
Synonyms	ECK4217, b4221, JW4180, ytfO^[1], ytfO
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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	95.74 minutes	MG1655: 4442135..4445914 <gbrowseImage> name=NC_000913:4442135..4445914 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4427869..4431648 <gbrowseImage> name=NC_012967:4427869..4431648 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4380870..4384649 <gbrowseImage> name=NC_012759:4380870..4384649 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4448792..4452571 <gbrowseImage> name=NC_007779:4448792..4452571 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4542497..4546276 <gbrowseImage> name=NC_010473:4542497..4546276 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	Comments
ΔytfN (Keio:JW4180)	deletion	deletion	PMID:16738554	Shigen CGSC11010^[5]
zjf-920::Tn10	Insertion at 4,442,823 bp in MG1655 (NC_000913)		adapted from Nichols et al.^[6]	CAG12019 = CGSC7484^[5]	Synonyms: zjh-901::Tn10, zjg-920::Tn10
ΔytfN770::kan			PMID:16738554	CGSC:106086
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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
JW4180	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGTTTATGGAAAAAAATCAG Primer 2:CCAAACTCGAACTGATAGAGCAA
5B5	Kohara Phage	Genobase	PMID:3038334
E1H3	Kohara Phage	Genobase	PMID:3038334
cycA30::Tn10	Linked marker	CAG12073 = CGSC7482^[5]	est. P1 cotransduction: 57% ^[6]
mdoB202::Tn10	Linked marker	CAG18430 = CGSC7488^[5]	est. P1 cotransduction: % ^[6] Synonyms:zjj-202::Tn10, zji-202::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
NCBI (EcoliWiki Page)	GeneID:948742	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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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Product(s)

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Nomenclature

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

Standard name	YtfN
Synonyms	conserved protein^[1], B4221^[2]^[1], YtfO^[2]^[1], YtfN^[2]^[1] , ECK4217, JW4180, ytfO, b4221
Product description	conserved protein^[2]^[3] Function unknown^[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
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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
Protein	yoaB		PMID:19402753	LCMS(ID Probability):99.6
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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 MSLWKKISLG VVIVILLLLG SVAFLVGTTS GLHLVFKAAD RWVPGLDIGK VTGGWRDLTL SDVRYEQPGV AVKAGNLHLA VGLECLWNSS VCINDLALKD IQVNIDSKKM PPSEQVEEEE DSGPLDLSTP YPITLTRVAL DNVNIKIDDT TVSVMDFTSG LNWQEKTLTL KPTSLKGLLI ALPKVAEVAQ EEVVEPKIEN PQPDEKPLGE TLKDLFSRPV LPEMTDVHLP LNLNIEEFKG EQLRVTGDTD ITVSTMLLKV SSIDGNTKLD ALDIDSSQGI VNASGTAQLS DNWPVDITLN STLNVEPLKG EKVKLKMGGA LREQLEIGVN LSGPVDMDLR AQTRLAEAGL PLNVEVNSKQ LYWPFTGEKQ YQADDLKLKL TGKMTDYTLS MRTAVKGQEI PPATITLDAK GNEQQVNLDK LTVAALEGKT ELKALLDWQQ AISWRGELTL NGINTAKEFP DWPSKLNGLI KTRGSLYGGT WQMDVPELKL TGNVKQNKVN VDGTLKGNSY MQWMIPGLHL ELGPNSAEVK GELGVKDLNL DATINAPGLD NALPGLGGTA KGLVKVRGTV EAPQLLADIT ARGLRWQELS VAQVRVEGDI KSTDQIAGKL DVRVEQISQP DVNINLVTLN AKGSEKQHEL QLRIQGEPVS GQLNLAGSFD RKEERWKGTL SNTRFQTPVG PWSLTRDIAL DYRNKEQKIS IGPHCWLNPN AELCVPQTID AGAEGRAVVN LNRFDLAMLK PFMPETTQAS GIFTGKADVA WDTTKEGLPQ GSITLSGRNV QVTQTVNDAA LPVAFQTLNL TAELRNNRAE LGWTIRLTNN GQFDGQVQVT DPQGRRNLGG NVNIRNFNLA MINPIFTRGE KAAGMVSANL RLGGDVQSPQ LFGQLQVTGV DIDGNFMPFD MQPSQLAVNF NGMRSTLAGT VRTQQGEIYL NGDADWSQIE NWRARVTAKG SKVRITVPPM VRMDVSPDVV FEATPNLFTL DGRVDVPWAR IVVHDLPESA VGVSSDVVML NDNLQPEEPK TASIPINSNL IVHVGNNVRI DAFGLKARLT GDLNVVQDKQ GLGLNGQINI PEGRFHAYGQ DLIVRKGELL FSGPPDQPYL NIEAIRNPDA TEDDVIAGVR VTGLADEPKA EIFSDPAMSQ QAALSYLLRG QGLESDQSDS AAMTSMLIGL GVAQSGQIVG KIGETFGVSN LALDTQGVGD SSQVVVSGYV LPGLQVKYGV GIFDSIATLT LRYRLMPKLY LEAVSGVDQA LDLLYQFEF
Length	1,259
Mol. Wt	136.781 kDa
pI	4.8 (calculated)
Extinction coefficient	140,830 - 141,330 (calc based on 17 Y, 21 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	915..1259	PF04357 Family of unknown function (DUF490)		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=ytfN 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:16132043	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948742	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P39321	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948742	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	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)
Protein	E. coli K-12 MC4100	1.04E+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	Ecoli K-12	0.617+/-0.048	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.032283673	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	127	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	54	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	68	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)
ytfM
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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_000913:4442115..4442155 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:b4221 (EcoliWiki Page)	NCBI GEO profiles for ytfN
microarray	GenExpDB:b4221 (EcoliWiki Page)	Summary of data for ytfN 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 ytfN 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:b4221
RegulonDB	RegulonDB:	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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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000026075 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YTFN	From SHIGELLACYC
E. coli O157	YTFN	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)	PF04357 Family of unknown function (DUF490)
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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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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 ^1.8 ^1.9 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 ^2.7 ^2.8 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 ^5.3 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 ^6.2 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).

ytfN: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 ytfN Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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