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yaaW:On One Page

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Standard Name

yaaW

Gene Synonym(s)

ECK0011, b0011, JW0010, htpY[1]

Product Desc.

conserved protein[2][3]

Function unknown[4]

Product Synonyms(s)

conserved protein[1], B0011[2][1], HtpY[2][1], YaaW[2][1]

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yaaW[2]

Regulation/Activity


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Notes

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htgA was described as an an ORF on the opposite strand of yaaW, but the relationships among yaaW, htgA and htpY need to be reexamined. yaaW has homologs and looks like a protein-coding gene, whereas the ORF on the opposite strand once labeled htgA does not look like a protein coding gene. It is possible that there is a heat-inducible anti-sense regulatory RNA on the opposite strand of yaaW, but it is unlikely that this putative transcript would encode a functional protein product. A reexaminination shows no heat shock induction or Sigma 32 expression of htgA, consistent with it not being a gene or protein at all (Nonaka, 2006). Mutations in the opposite ORF would also disrupt yaaW and hence the htgA and htpY gene names are used as synonyms for yaaW. The experimental evidence supporting the existence of htgA is likely to be in error and the conclusions of Delaye (2008) regarding evolution of overlapping genes is unlikely to be true; their homology analysis and their analysis of substitutions within htgA are all consistent with htgA being an incorrect annotation; extreme skepticism is warranted when studying supposedly overlapping genes that do not appear to be phage-related in the E. coli chromsome; htgA does not represent the first such case nor does the study of Delaye (2008) appear to be novel; their demonstration that yaaW is likely to be a gene was unnecessary as numerous homologs are readily apparent and profiles (such as COG0443) have defined this gene family for many years.[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

yaaW

Mnemonic
Synonyms

ECK0011, b0011, JW0010, htpY[1]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

0.23 minutes 

MG1655: 11356..10643
gbrowse_img.php?coord=9643..12356&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 11356..10643
gbrowse_img.php?coord=9643..12356&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 11356..10643
gbrowse_img.php?coord=9217..12782&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 10643..11356
gbrowse_img.php?coord=10643..11356&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

ΔyaaW (Keio:JW0010)

deletion

deletion

PMID:16738554

Shigen


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW0010

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAATGTTAATTACCTGAATGA

Primer 2:CCGACCTGAGTGGCGCTAACCAT

thrA34::Tn10

Linked marker

CAG18442 = CGSC7320[5]

est. P1 cotransduction: 69% [6]
Synonyms:thr-34::Tn10

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 45% [6]
Synonyms:car-96::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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G6082

EchoBASE (EcoliWiki Page)

EchoBASE:EB4086

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0011

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0016

EcoGene (EcoliWiki Page)

EcoGene:EG14340

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z0011

ASAP (EcoliWikiPage)

ASAP:ABE-0000037


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Notes

Links

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NameURLComments
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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

YaaW

Synonyms

conserved protein[1], B0011[2][1], HtpY[2][1], YaaW[2][1]

Product description

conserved protein[2][3]

Function unknown[4]

EC number (for enzymes)


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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus
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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 TypePartnerNotesReferencesEvidence
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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

Sequence

at EcoCyc 

MNVNYLNDSD LDFLQHCSEE QLANFARLLT HNEKGKTRLS SVLMRNELFK SMEGHPEQHR
RNWQLIAGEL QHFGGDSIAN KLRGHGKLYR AILLDVSKRL KLKADKEMST FEIEQQLLEQ
FLRNTWKKMD EEHKQEFLHA VDARVNELEE LLPLLMKDKL LAKGVSHLLS SQLTRILRTH
AAMSVLGHGL LRGAGLGGPV GAALNGVKAV SGSAYRVTIP AVLQIACLRR MVSATQV
Length

26.66 kDa (calc) [2]

Mol. Wt
pI

15470 - 15720 (calc based on 3 Y, 2 W, and 2 C residues)

Extinction coefficient


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Domains/Motifs/Modification Sites

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

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

Structures
Models

View models at:

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Structure figures

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 typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G6082-MONOMER

UniProt (EcoliWiki Page)

UniProt:P75617

PFAM (EcoliWiki Page)

PFAM:PF03667

RefSeq (EcoliWiki Page)

RefSeq:NP_414552


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Notes

Links

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NameURLComments
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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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MoleculeOrganism or StrainMolecules per cellGrowth conditionsGrowth rateAssay usedNotesReference(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)

yaaW

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Figure courtesy of RegulonDB

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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gbrowse_img.php?coord=11336..11376&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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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Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

microarray

GEO Profiles:b0011 (EcoliWiki Page)

NCBI GEO profiles for yaaW

microarray

GenExpDB:b0011 (EcoliWiki Page)

Summary of data for yaaW 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 NameResource TypeDescriptionSourceNotes

GFP Fusion

Intergenic region (11279..11401) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ11; Well:H11[7]

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Notes

Accessions Related to yaaW Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G6082

EchoBASE (EcoliWiki Page)

EchoBASE:EB4086

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0011

EcoGene (EcoliWiki Page)

EcoGene:EG14340


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Notes

Links

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NameURLComments
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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.

OrganismHomologs (Statistics)Comments

Shigella flexneri

S0012

From SHIGELLACYC

E. coli O157

Z0011

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.

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF03667


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Notes

Links

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NameURLComments
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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 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. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

Categories

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