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Standard Name	yiaF
Gene Synonym(s)	ECK3541, b3554, JW5655^[1], JW5655
Product Desc.	conserved protein^[2]^[3] Probable lipoprotein, function unknown; Cys conserved^[4]
Product Synonyms(s)	conserved protein^[1], B3554^[2]^[1], YiaF^[2]^[1] , ECK3541, JW5655, b3554
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yiaF^[2]
Regulation/Activity
Quick Links
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Notes

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YiaF has been identified as a membrane-associated protein by 2D-MS, with a non-uniform membrane distribution, indicating both polar and septal bias. Interpretation of YiaF results in Lai et al. (2004) was complicated by use of a predicted start site at Met(-40). A null mutant has no obvious growth defect (Lai, 2004). Reported MS detection of a fragment from 19R-30E (stated as 50R-69E in Lai, 2004) may indicate the presence of an uncleaved precursor form in minicell membrane preparations. First 25 aa are predicted to be a type II signal peptide. HT_Cmplx47_Mem: MscS+YiaF.^[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	yiaF
Mnemonic	Systematic nomenclature
Synonyms	ECK3541, b3554, JW5655^[1], JW5655
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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	80.1 minutes, 80.1 minutes	MG1655: 3717067..3716357 <gbrowseImage> name=NC_000913:3716357..3717067 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3649502..3648792 <gbrowseImage> name=NC_012967:3648792..3649502 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3604683..3605393 <gbrowseImage> name=NC_012759:3604683..3605393 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3921371..3922081 <gbrowseImage> name=NC_007779:3921371..3922081 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3814644..3813934 <gbrowseImage> name=NC_010473:3813934..3814644 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
ΔyiaF (Keio:JW5655)	deletion	deletion	PMID:16738554	Shigen CGSC11503^[5]
yiaF::Tn5KAN-2 (FB21277)	Insertion at nt 403 in Minus orientation		PMID:15262929	E. coli Genome Project:FB21277	does not contain pKD46
yiaF::Tn5KAN-2 (FB21278)	Insertion at nt 403 in Minus orientation		PMID:15262929	E. coli Genome Project:FB21278	contains pKD46
ΔyiaF738::kan			PMID:16738554	CGSC:105278
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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
JW5655	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCGACAGGAAAGTCCTGCTC Primer 2:CCTTGGGTTGCAGTAACTGCTGT
9F6	Kohara Phage	Genobase	PMID:3038334
zhg-50::Tn10	Linked marker	CAG18450 = CGSC7450^[5]	est. P1 cotransduction: % ^[6] Synonyms:zhf-50::Tn10, zhf-5::Tn10
zic-4901::Tn10	Linked marker	CAG18492 = CGSC7457^[5]	est. P1 cotransduction: % ^[6]
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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:EG12273	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12273	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002154	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948072	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2182	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011606	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	YiaF
Synonyms	conserved protein^[1], B3554^[2]^[1], YiaF^[2]^[1] , ECK3541, JW5655, b3554
Product description	conserved protein^[2]^[3] Probable lipoprotein, function unknown; Cys conserved^[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
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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
plasma membrane			From EcoCyc^[3]
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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 MILPGRLRRK GILQACPGLS LSRQTRVCRC ALFLGERSKK MATGKSCSRW FAPLAALLMV VSLSGCFDKE GDQRKAFIDF LQNTVMRSGE RLPTLTADQK KQFGPFVSDY AILYGYSQQV NQAMDSGLRP VVDSVNAIRV PQDYVTQSGP LREMNGSLGV LAQQLQNAKL QADAAHSALK QSDDLKPVFD QAFTKVVTTP ADALQPLIPA AQTFTQQLVM VGDYIAQQGT QVSFVANGIQ FPTSQQASEY NKLIAPLPAQ HQAFNQAWTT AVTATQ
Length	276
Mol. Wt	30.158 kDa
pI	9.6 (calculated)
Extinction coefficient	19,940 - 20,565 (calc based on 6 Y, 2 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	8..235	PF11254 Protein of unknown function (DUF3053)		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=yiaF 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:90111615	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948072	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011606	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ADK0	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12273	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12273	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948072	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002154	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2182	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	4.53E+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	0.202+/-0.06	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.155633803	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	5946	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	1151	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	2162	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)
yiaF
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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_000913:3717047..3717087 source=MG1655 flip=1 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:b3554 (EcoliWiki Page)	NCBI GEO profiles for yiaF
microarray	GenExpDB:b3554 (EcoliWiki Page)	Summary of data for yiaF 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 (3716697..3717186) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ19; Well:A5^[7]
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Notes

Accessions Related to yiaF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12273	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2182	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3554
EcoGene	EcoGene:EG12273	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002154	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011606	Escherichia coli str. K-12 substr. MG1655
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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	YIAF	From SHIGELLACYC
E. coli O157	YIAF	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)	PF11254 Protein of unknown function (DUF3053)
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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 ^3.2 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 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

yiaF:On One Page

Quickview

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 yiaF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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