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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	gtrB
Gene Synonym(s)	ECK2345, b2351, JW2347, yfdH^[1], JW2347, yfdH
Product Desc.	CPS-53 (KpLE1) prophage; bactoprenyl glucosyl transferase^[2]^[3]
Product Synonyms(s)	CPS-53 (KpLE1) prophage; bactoprenol glucosyl transferase^[1], B2351^[2]^[1], GtrB^[2]^[1] , ECK2345, JW2347, yfdH, b2351
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yfdG^[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	gtrB
Mnemonic
Synonyms	ECK2345, b2351, JW2347, yfdH^[1], JW2347, yfdH
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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	53.16 minutes	MG1655: 2466236..2467156 <gbrowseImage> name=NC_000913:2466236..2467156 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 2352041..2352961 <gbrowseImage> name=NC_012759:2352041..2352961 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2473660..2474580 <gbrowseImage> name=NC_007779:2473660..2474580 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2558001..2558921 <gbrowseImage> name=NC_010473:2558001..2558921 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
ΔyfdH (Keio:JW2347)	deletion	deletion			PMID:16738554	Shigen CGSC9879^[4]
ΔyfdH::kan	deletion		Biolog:respiration	unable to respire N-Acetyl-D-glucosamine	PMID:16095938
ΔyfdH758::kan					PMID:16738554	CGSC:104708
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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
JW2347	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAGATATCTCTTGTAGTTCC Primer 2:CCTTTTTTGACTCTCTTGATGAT
6F7	Kohara Phage	Genobase	PMID:3038334
3A11	Kohara Phage	Genobase	PMID:3038334
zfb-223::Tn10	Linked marker	CAG18484 = CGSC7406^[4]	est. P1 cotransduction: 1% ^[5] Synonyms:zej-223::Tn10
zfd-1::Tn10	Linked marker	CAG18467 = CGSC7408^[4]	est. P1 cotransduction: 39% ^[5] Synonyms:zfb-1::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:G7220	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3884	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2351
EcoGene	EcoGene:EG14132	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007763	Escherichia coli str. K-12 substr. MG1655
EcoCyc (EcoliWiki Page)	ECOCYC:G7220	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:949098	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003795	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	GtrB
Synonyms	CPS-53 (KpLE1) prophage; bactoprenol glucosyl transferase^[1], B2351^[2]^[1], GtrB^[2]^[1] , ECK2345, JW2347, yfdH, b2351
Product description	CPS-53 (KpLE1) prophage; bactoprenyl glucosyl transferase^[2]^[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:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016757	transferase activity, transferring glycosyl groups	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0328	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	rpsA	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsH	PMID:19402753	LCMS(ID Probability):99.6
Protein	fusA	PMID:19402753	LCMS(ID Probability):99.4
Protein	rpsM	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpmB	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsF	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsT	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsJ	PMID:19402753	LCMS(ID Probability):99.6
Protein	atpC	PMID:19402753	LCMS(ID Probability):99.4
Protein	rpsC	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplS	PMID:19402753	LCMS(ID Probability):99.6
Protein	rfaD	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplX	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplB	PMID:19402753	LCMS(ID Probability):99.6
Protein	yjgA	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplD	PMID:19402753	LCMS(ID Probability):99.6
Protein	rne	PMID:19402753	LCMS(ID Probability):99.6
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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
plasma membrane	C-terminus localized in the cytoplasm with 2 predicted transmembrane domains	Daley et al. (2005) ^[6]
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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 MKISLVVPVF NEEEAIPIFY KTVREFEELK SYEVEIVFIN DGSKDATESI INALAVSDPL VVPLSFTRNF GKEPALFAGL DHATGDAIIP IDVDLQDPIE VIPHLIEKWQ AGADMVLAKR SDRSTDGRLK RKTAEWFYKL HNKISNPKIE ENVGDFRLMS RDVVENIKLM PERNLFMKGI LSWVGGKTDI VEYVRAERIA GDTKFNGWKL WNLALEGITS FSTFPLRIWT YIGLVVASVA FIYGAWMILD TIIFGNAVRG YPSLLVSILF LGGIQMIGIG VLGEYIGRTY IETKKRPKYI IKRVKK
Length	306
Mol. Wt	34.636 kDa
pI	8.4 (calculated)
Extinction coefficient	53,400 (calc based on 10 Y, 7 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	Notes	References
Domain	4..168	PF00535 Glycosyl transferase family 2		PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=yfdH 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:16130283	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:949098	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007763	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77293	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7220	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14132	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:949098	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003795	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3884	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	Reference(s)
Protein	E. coli K-12 MC4100	2.29E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	1260	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	639	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	1036	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	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)
yfdG
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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_000913:2466216..2466256 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:b2351 (EcoliWiki Page)	NCBI GEO profiles for yfdH
microarray	GenExpDB:b2351 (EcoliWiki Page)	Summary of data for yfdH 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 gtrB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7220	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3884	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2351
EcoGene	EcoGene:EG14132	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003795	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007763	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
Anopheles gambiae	ENSANGP00000014803 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000001461 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G20575 (score: 1.000; bootstrap: 73%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000010153 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00034254 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00022044 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000017029 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000006730 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040801-115 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040801-123 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0231708 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0032799 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA10126-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000032816 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000001585 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000003701 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000020440 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1330239 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000023437 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000016150 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YPR183W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC31G56c (score: 1.000; bootstrap: 69%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000152489 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000026906 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	GTRBI	From SHIGELLACYC
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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)	PF00535 Glycosyl transferase family 2
Superfamily (EcoliWiki Page)	SUPERFAMILY:53448
Panther (EcoliWiki Page)	PTHR10859:SF37
EcoCyc	EcoCyc:G7220	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14132	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003795	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3884	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007763	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).
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

gtrB: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 gtrB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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