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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	quuD
Gene Synonym(s)	ECK0543, b0551, JW0539, ybcQ^[1], JW0539, ybcQ
Product Desc.	hypothetical protein^[2]; Antitermination protein Q-like protein^[3]
Product Synonyms(s)	DLP12 prophage; predicted antitermination protein^[1], B0551^[2]^[1], YbcQ^[2]^[1] , ECK0543, JW0539, ybcQ, b0551
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): quuD^[2]
Regulation/Activity
Quick Links
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Notes

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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	quuD
Mnemonic	Q protein nomenclature Q protein nomenclature Q protein nomenclature Q protein nomenclature
Synonyms	ECK0543, b0551, JW0539, ybcQ^[1], JW0539, ybcQ
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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	12.35 minutes	MG1655: 573179..573562 <gbrowseImage> name=NC_000913:573179..573562 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 545846..546229 <gbrowseImage> name=NC_012967:545846..546229 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 475939..476322 <gbrowseImage> name=NC_012759:475939..476322 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 573179..573562 <gbrowseImage> name=NC_007779:573179..573562 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 512511..512894 <gbrowseImage> name=NC_010473:512511..512894 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)	Phenotype: Type	Phenotype: Description	Reference	Availability
ΔybcQ (Keio:JW0539)	deletion	deletion			PMID:16738554	Shigen CGSC8671^[4]
ΔybcQ::kan	deletion		Biolog:respiration	unable to respire a-Ketobutyrate	PMID:16095938
ΔybcQ::kan	deletion		Biolog:respiration	unable to respire a-Ketoglutarate	PMID:16095938
ΔybcQ760::kan					PMID:16738554	CGSC:103694
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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
JW0539	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCGTGATATTCAGATGGTTCT Primer 2:CCATTAGAGTTATTAACAACGAT
23E10	Kohara Phage	Genobase	PMID:3038334
purK79::Tn10	Linked marker	CAG12171 = CGSC7342^[4]	est. P1 cotransduction: 46% ^[5] Synonyms:purE79::Tn10
dsbG601::Tn10	Linked marker	CAG12149 = CGSC7346^[4]	est. P1 cotransduction: 3% ^[5] Synonyms:zbd-601::Tn10, zbe-601::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:G6307	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3397	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0551
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C1559
EcoGene	EcoGene:EG13633	Escherichia coli str. K-12 substr. MG1655
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:Z1786
ASAP	ASAP:ABE-0001883	Escherichia coli str. K-12 substr. MG1655
EcoCyc (EcoliWiki Page)	ECOCYC:G6307	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945177	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002915	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	QuuD
Synonyms	DLP12 prophage; predicted antitermination protein^[1], B0551^[2]^[1], YbcQ^[2]^[1] , ECK0543, JW0539, ybcQ, b0551
Product description	hypothetical protein^[2]; Antitermination protein Q-like protein^[3]
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
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010534	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0030401	transcription antiterminator activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010534	F	Seeded from EcoCyc (v14.0)	complete
	GO:0031564	transcription antitermination	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0889	P	Seeded from EcoCyc (v14.0)	complete
	GO:0045449	regulation of transcription	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010534	P	Seeded from EcoCyc (v14.0)	complete
	GO:0045449	regulation of transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0805	P	Seeded from EcoCyc (v14.0)	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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<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 MRDIQMVLER WGAWAANNHE DVTWSSIAAG FKGLITSKVK SRPQCCDDDA MIICGCMARL KKNNSDLHDL LVDYYVVGMT FMSLAGKHCC SDGYIGKRLQ KAEGIIEGML MALDIRLEMD IVVNNSN
Length	127
Mol. Wt	14.176 kDa
pI	6.3 (calculated)
Extinction coefficient	20,970 - 21,720 (calc based on 3 Y, 3 W, and 6 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..126	PF06530 Phage antitermination protein Q		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=ybcQ 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:16128534	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945177	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001883	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:Q47274	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6307	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13633	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945177	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002915	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3397	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	6^a	molecules/cell/generation	Medium: MOPS Complete 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	6^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	6^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)
ybcQ
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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_000913:573159..573199 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:b0551 (EcoliWiki Page)	NCBI GEO profiles for ybcQ
microarray	GenExpDB:b0551 (EcoliWiki Page)	Summary of data for ybcQ 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 quuD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6307	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3397	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0551
EcoGene	EcoGene:EG13633	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002915	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001883	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	YBCQ	From SHIGELLACYC
E. coli O157	Z1786	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)	PF06530 Phage antitermination protein Q
EcoCyc	EcoCyc:G6307	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13633	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002915	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3397	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001883	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 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).

quuD: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 quuD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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