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Gene |

Product(s) |

Expression|

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Standard Name	stfQ
Gene Synonym(s)	stfQ, ECK1540, b1547, JW1540, ydfN^[1]^[2]^[3], JW1540, ydfN
Product Desc.	Qin prophage; predicted side tail fibre assembly protein^[3]^[2] Function unknown, Qin prophage^[4]
Product Synonyms(s)	Qin prophage; predicted side tail fibre assembly protein^[1], B1547^[3]^[1], StfQ^[3]^[1], StfQ^[3]^[1] , ECK1540, JW1540, ydfN, b1547
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): tfaQ^[3], nohA^[3]
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	stfQ
Mnemonic
Synonyms	stfQ, ECK1540, b1547, JW1540, ydfN^[1]^[2]^[3], JW1540, ydfN
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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	35.19 minutes	MG1655: 1633871..1632909 <gbrowseImage> name=NC_000913:1632909..1633871 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 1524968..1525930 <gbrowseImage> name=NC_012759:1524968..1525930 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1637561..1636599 <gbrowseImage> name=NC_007779:1636599..1637561 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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
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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

22D11

Kohara Phage

Genobase

PMID:3038334

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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:G6821	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3587	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1547
EcoGene	EcoGene:EG13826	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005168	Escherichia coli str. K-12 substr. MG1655
EcoCyc (EcoliWiki Page)	ECOCYC:G6821	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946098	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003410	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	StfQ
Synonyms	Qin prophage; predicted side tail fibre assembly protein^[1], B1547^[3]^[1], StfQ^[3]^[1], StfQ^[3]^[1] , ECK1540, JW1540, ydfN, b1547
Product description	Qin prophage; predicted side tail fibre assembly protein^[3]^[2] Function unknown, Qin prophage^[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
	GO:0005198	structural molecule activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005003	F	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	References	Evidence
Protein	acnA	PMID:16606699	Experiment(s):EBI-1140113
Protein	sdhA	PMID:16606699	Experiment(s):EBI-1140113
Protein	lacZ	PMID:16606699	Experiment(s):EBI-1140113
Protein	secB	PMID:16606699	Experiment(s):EBI-1140113
Protein	yhbU	PMID:16606699	Experiment(s):EBI-1140113
Protein	yhiR	PMID:16606699	Experiment(s):EBI-1140113
Protein	rplB	PMID:16606699	Experiment(s):EBI-1140113
Protein	mtlD	PMID:16606699	Experiment(s):EBI-1140113
Protein	prs	PMID:16606699	Experiment(s):EBI-1140113
Protein	hrpB	PMID:16606699	Experiment(s):EBI-1140113
Protein	yebT	PMID:16606699	Experiment(s):EBI-1140113
Protein	ldcA	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):39.354556
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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 MNITALTDNT QGAAGLELYE VYNNGYPTAY GNIIHLKGMT AVGEGELLIG WSGTSGAHAP AFIRSRRDTT DANWSPWAQL YTSAHPPAEF YPVGAPIPWP SDTVPSGYAL MQGQTFDKSA YPKLAVAYPS GVIPDMRGWT IKGKPASGRA VLSQEQDGIK SHTHSASASS TDLGTETTSS FDYGTKSTNN TGAHTHSISG TANSAGAHQH KSSGAFGGTN TSIFPNGYTA ISNLSAGIMS TTSGSGQTRN AGKTSSDGAH THSLSGTAAS AGAHAHTVGI GAHTHSVAIG SHGHTITVNA AGNAENTVKN IAFNYIVRLA
Length	320
Mol. Wt	32.901 kDa
pI	7.6 (calculated)
Extinction coefficient	45,380 (calc based on 12 Y, 5 W, and 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	References
Domain	157..170	PF03335 Phage tail fibre repeat	PMID:19920124
Domain	189..202	PF03335 Phage tail fibre repeat	PMID:19920124
Domain	203..216	PF03335 Phage tail fibre repeat	PMID:19920124
Domain	255..268	PF03335 Phage tail fibre repeat	PMID:19920124
Domain	269..281	PF03335 Phage tail fibre repeat	PMID:19920124
Domain	278..291	PF03335 Phage tail fibre repeat	PMID:19920124
Domain	287..300	PF03335 Phage tail fibre repeat	PMID:19920124
Domain	94..141	PF07484 Phage Tail Collar Domain	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=ydfN 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:16129506	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946098	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005168	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77515	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6821	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13826	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946098	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003410	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3587	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	0^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	0^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	0^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)
tfaQ
nohA
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File:.jpg

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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_000913:1633851..1633891 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:b1547 (EcoliWiki Page)	NCBI GEO profiles for ydfN
microarray	GenExpDB:b1547 (EcoliWiki Page)	Summary of data for ydfN 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 stfQ Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6821	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3587	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1547
EcoGene	EcoGene:EG13826	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003410	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005168	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
Bos taurus	ENSBTAP00000038746 (score: 1.000; bootstrap: 51%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00027418 (score: 1.000; bootstrap: 100%) WBGene00027434 (score: 0.138) WBGene00027431 (score: 0.127) WBGene00027401 (score: 0.082)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00019540 (score: 1.000; bootstrap: 76%) WBGene00008707 (score: 0.087) WBGene00022649 (score: 0.086)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000000690 (score: 1.000; bootstrap: 68%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000016155 (score: 1.000; bootstrap: 67%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0189911 (score: 1.000; bootstrap: 93%) DDB0185120 (score: 0.186) DDB0203095 (score: 0.073) DDB0168484 (score: 0.062)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000031553 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000322544 (score: 1.000; bootstrap: 78%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000003259 (score: 1.000; bootstrap: 52%)	From Inparanoid:20070104
Oryza gramene	Q6KA29 (score: 1.000; bootstrap: 67%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YDR534C (score: 1.000; bootstrap: 95%) YOR383C (score: 0.107)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBPJ46642 (score: 1.000; bootstrap: 61%)	From Inparanoid:20070104
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Notes

Families

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

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:88874
Pfam (EcoliWiki Page)	PF03335 Phage tail fibre repeat
Pfam (EcoliWiki Page)	PF03335 Phage tail fibre repeat
Pfam (EcoliWiki Page)	PF03335 Phage tail fibre repeat
Pfam (EcoliWiki Page)	PF03335 Phage tail fibre repeat
Pfam (EcoliWiki Page)	PF03335 Phage tail fibre repeat
Pfam (EcoliWiki Page)	PF03335 Phage tail fibre repeat
Pfam (EcoliWiki Page)	PF03335 Phage tail fibre repeat
Pfam (EcoliWiki Page)	PF07484 Phage Tail Collar Domain
EcoCyc	EcoCyc:G6821	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13826	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003410	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3587	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005168	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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 ^3.11 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.

stfQ: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 stfQ Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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