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Standard Name	yaaW
Gene Synonym(s)	ECK0011, b0011, JW0010, htpY^[1], htgA, htpY
Product Desc.	conserved protein^[2]^[3] Function unknown^[4]
Product Synonyms(s)	conserved protein^[1], B0011^[2]^[1], HtpY^[2]^[1], YaaW^[2]^[1] , ECK0011, htgA, htpY, JW0010, b0011
Function from GO	<GO_nr />
Knock-Out Phenotype	transcription unit(s): yaaW^[2]
Regulation/Expression
Regulation/Activity
Quick Links
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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], htgA, htpY
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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	0.23 minutes	MG1655: 11356..10643	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 10643..11356	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 11356..10643	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 11356..10643	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: Type	Phenotype: Description	Reference	Availability	Comments
yaaW(del) (Keio:JW0010)	deletion	deletion			PMID:16738554	Shigen
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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
JW0010	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATGTTAATTACCTGAATGA Primer 2:CCGACCTGAGTGGCGCTAACCAT
9E4	Kohara Phage	Genobase	PMID:3038334
9E4	Kohara Phage	Genobase	PMID:3038334
6H3	Kohara Phage	Genobase	PMID:3038334
6H3	Kohara Phage	Genobase	PMID:3038334
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.

Database	Accession	Notes
EcoCyc	EcoCyc:G6082	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4086	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0011
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C0016
EcoGene	EcoGene:EG14340	Escherichia coli str. K-12 substr. MG1655
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:Z0011
ASAP	ASAP:ABE-0000037	Escherichia coli str. K-12 substr. MG1655
EcoCyc (EcoliWiki Page)	ECOCYC:G6082	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944771	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002702	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	YaaW
Synonyms	conserved protein^[1], B0011^[2]^[1], HtpY^[2]^[1], YaaW^[2]^[1] , ECK0011, htgA, htpY, JW0010, b0011
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
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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 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	237
Mol. Wt	26.665 kDa
pI	9.7 (calculated)
Extinction coefficient	15,470 - 15,720 (calc based on 3 Y, 2 W, and 2 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	58..228	PF03981 Ubiquinol-cytochrome C chaperone	Pfam:P75617
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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=yaaW 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
EcoCyc	EcoCyc:G6082	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProt:P75617
PFAM (EcoliWiki Page)	PFAM:PF03667
RefSeq (EcoliWiki Page)	RefSeq:NP_414552
NCBI (Protein) (EcoliWiki Page)	GI:16128005	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944771	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000037	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P75617	Escherichia coli str. K-12 substr. MG1655
EcoCyc (EcoliWiki Page)	ECOCYC:G6082	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14340	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944771	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002702	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4086	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 MG1655	30	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	5^a	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	2^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
yaaW
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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_000913:11336..11376 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: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 Name	Resource Type	Description	Source	Notes
	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.

Database	Accession	Notes
EcoCyc	EcoCyc:G6082	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4086	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0011
EcoGene	EcoGene:EG14340	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002702	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000037	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	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.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF03981 Ubiquinol-cytochrome C chaperone
EcoCyc	EcoCyc:G6082	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14340	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002702	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4086	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000037	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 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

yaaW: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 yaaW Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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