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Expression|

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Standard Name	stfR
Gene Synonym(s)	ECK1367, b1372, JW1366, ynaB^[1], ynaB
Product Desc.	putative membrane protein^[2]^[3] Side-tail fiber protein, Rac prophage^[4]
Product Synonyms(s)	Rac prophage; predicted tail fiber protein^[1], B1372^[2]^[1], YnaB^[2]^[1], StfR^[2]^[1] , ECK1367, JW1366, ynaB, b1372
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): lomR_1^[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	stfR
Mnemonic	Side-tail fiber
Synonyms	ECK1367, b1372, JW1366, ynaB^[1], ynaB
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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	30.76 minutes	MG1655: 1427073..1430435 <gbrowseImage> name=NC_000913:1427073..1430435 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 1319132..1322494 <gbrowseImage> name=NC_012759:1319132..1322494 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1430763..1434125 <gbrowseImage> name=NC_007779:1430763..1434125 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1516469..1519831 <gbrowseImage> name=NC_010473:1516469..1519831 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
ΔstfR (Keio:JW1366)	deletion	deletion	PMID:16738554	Shigen CGSC9210^[5]
ΔstfR735::kan			PMID:16738554	CGSC:103044
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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
JW1366	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCAGTAAAGATTTCAGGTGT Primer 2:CCTGCAAGCCTCACAATATAGTT
2C3	Kohara Phage	Genobase	PMID:3038334
4E7	Kohara Phage	Genobase	PMID:3038334
recT3061::Tn10	Linked marker	CAG12081 = CGSC7375^[5]	est. P1 cotransduction: 55% ^[6] Synonyms:zcj-3061::Tn10, zda-3061::Tn10
zhj-3076::Tn10	Linked marker	CAG18640 = CGSC7453^[5]	est. P1 cotransduction: 80% ^[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:G6695	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13370	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003290	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945207	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3152	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004595	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	StfR
Synonyms	Rac prophage; predicted tail fiber protein^[1], B1372^[2]^[1], YnaB^[2]^[1], StfR^[2]^[1] , ECK1367, JW1366, ynaB, b1372
Product description	putative membrane protein^[2]^[3] Side-tail fiber protein, Rac 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	rplB	PMID:16606699	Experiment(s):EBI-1139684
Protein	yegQ	PMID:16606699	Experiment(s):EBI-1139684
Protein	polA	PMID:16606699	Experiment(s):EBI-1139684
Protein	arpA	PMID:16606699	Experiment(s):EBI-1139684
Protein	pgaC	PMID:16606699	Experiment(s):EBI-1139684
Protein	metL	PMID:16606699	Experiment(s):EBI-1139684
Protein	aceE	PMID:16606699	Experiment(s):EBI-1139684
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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 MNMAVKISGV LKDGTGKPVQ NCTIQLKAKR NSTTVVVNTL ASENPDEAGR YSMDVEYGQY SVILLVEGFP PSHAGTITVY EDSQPGTLND FLGAMTEDDA RPEALRRFEL MVEEVARNAS AVAQNTAAAK KSASDASTSA REAATHAADA ADSARAASTS AGQAASSAQS ASSSAGTAST KATEASKSAA AAESSKSAAA TSAGAAKTSE TNASASLQSA ATSASTATTK ASEAATSARD AAASKEAAKS SETNASSSAS SAASSATAAG NSAKAAKTSE TNARSSETAA GQSASAAAGS KTAAASSASA ASTSAGQASA SATAAGKSAE SAASSASTAT TKAGEATEQA SAAARSASAA KTSETNAKAS ETSAESSKTA AASSASSAAS SASSASASKD EATRQASAAK SSATTASTKA TEAAGSATAA AQSKSTAESA ATRAETAAKR AEDIASAVAL EDASTTKKGI VQLSSATNST SETLAATPKA VKSAYDNAEK RLQKDQNGAD IPDKGCFLNN INAVSKTDFA DKRGMRYVRV NAPAGATSGK YYPVVVMRSA GSVSELASRV IITTATRTAG DPMNNCEFNG FVMPGGWTDR GRYAYGMFWQ YQNNERAIHS IMMSNKGDDL RSVFYVDGAA FPVFAFIEDG LSISAPGADL VVNDTTYKFG ATNPATECIA ADVILDFKSG RGFYESHSLI VNDNLSCKKL FATDEIVARG GNQIRMIGGE YGALWRNDGA KTYLLLTNQG DVYGGWNTLR PFAIDNATGE LVIGTKLSAS LNGNALTATK LQTPRRVSGV EFDGSKDITL TAAHVAAFAR RATDTYADAD GGVPWNAESG AYNVTRSGDS YILVNFYTGV GSCRTLQMKA HYRNGGLFYR SSRDGYGFEE DWAEVYTSKN LPPESYPVGA PIPWPSDTVP SGYALMQGQA FDKSAYPKLA AAYPSGVIPD MRGWTIKGKP ASGRAVLSQE QDGIKSHTHS ASASSTDLGT KTTSSFDYGT KSTNNTGAHT HSVSGSTNSA GAHTHSLANV NTASANSGAG SASTRLSVVH NQNYATSSAG AHTHSLSGTA ASAGAHAHTV GIGAHTHSVA IGSHGHTITV NAAGNAENTV KNIAFNYIVR LA
Length	1,122
Mol. Wt	114.025 kDa
pI	7.7 (calculated)
Extinction coefficient	91,680 - 92,430 (calc based on 32 Y, 8 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	References
Domain	970..983	PF03335 Phage tail fibre repeat	PMID:19920124
Domain	1002..1015	PF03335 Phage tail fibre repeat	PMID:19920124
Domain	1016..1029	PF03335 Phage tail fibre repeat	PMID:19920124
Domain	1055..1068	PF03335 Phage tail fibre repeat	PMID:19920124
Domain	1069..1082	PF03335 Phage tail fibre repeat	PMID:19920124
Domain	1078..1089	PF03335 Phage tail fibre repeat	PMID:19920124
Domain	1087..1100	PF03335 Phage tail fibre repeat	PMID:19920124
Domain	907..954	PF07484 Phage Tail Collar Domain	PMID:19920124
Domain	1..134	PF08400 Prophage tail fibre N-terminal	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=stfR 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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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:90111261	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945207	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004595	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76072	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6695	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13370	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945207	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003290	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3152	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	2	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	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)
lomR_1
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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_000913:1427053..1427093 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:b1372 (EcoliWiki Page)	NCBI GEO profiles for stfR
microarray	GenExpDB:b1372 (EcoliWiki Page)	Summary of data for stfR 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 (1426919..1427106) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ17; Well:H8^[7]
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Notes

Accessions Related to stfR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6695	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3152	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1372
EcoGene	EcoGene:EG13370	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003290	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004595	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
Shigella flexneri	S0758	From SHIGELLACYC
E. coli O157	Z1918	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:49464
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
Pfam (EcoliWiki Page)	PF08400 Prophage tail fibre N-terminal
EcoCyc	EcoCyc:G6695	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13370	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003290	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3152	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004595	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 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

stfR: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 stfR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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