treF:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

treF

Gene Synonym(s)

ECK3504, b3519, JW3487[1], JW3487

Product Desc.

Cytoplasmic trehalase[2]

Product Synonyms(s)

cytoplasmic trehalase[1], B3519[3][1], TreF[3][1] , ECK3504, JW3487, b3519

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): treF[3]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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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

treF

Mnemonic

Trehalose

Synonyms

ECK3504, b3519, JW3487[1], JW3487

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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

79.05 minutes 

MG1655: 3667615..3669264
<gbrowseImage> name=NC_000913:3667615..3669264 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3599084..3600733
<gbrowseImage> name=NC_012967:3599084..3600733 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3556109..3557758
<gbrowseImage> name=NC_012759:3556109..3557758 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3970823..3969174
<gbrowseImage> name=NC_007779:3969174..3970823 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3765360..3767009
<gbrowseImage> name=NC_010473:3765360..3767009 source=DH10B preset=GeneLocation </gbrowseImage>

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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

Coding Start (SO:0000323)

MG1655

3667615

Edman degradation

PMID:8892826


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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

ΔtreF (Keio:JW3487)

deletion

deletion

PMID:16738554

Shigen
CGSC10583[4]

treF::Tn5KAN-I-SceI (FB21254)

Insertion at nt 1520 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21254

does not contain pKD46

treF::Tn5KAN-I-SceI (FB21255)

Insertion at nt 1520 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21255

contains pKD46

ΔtreF774::kan

PMID:16738554

CGSC:103204


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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

JW3487

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCTCAATCAGAAAATTCAAAA

Primer 2:CCTGGTTCGCCGTACAAACCAAT

25B12S

Kohara Phage

Genobase

PMID:3038334

9G3

Kohara Phage

Genobase

PMID:3038334

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[4]

est. P1 cotransduction: 1% [5]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[4]

est. P1 cotransduction: % [5]

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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:EG12245

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12245

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002128

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948037

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2156

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011497

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

TreF

Synonyms

cytoplasmic trehalase[1], B3519[3][1], TreF[3][1] , ECK3504, JW3487, b3519

Product description

Cytoplasmic trehalase[2]

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:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008928

F

Seeded from EcoCyc (v14.0)

complete

GO:0004555

alpha,alpha-trehalase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01059

F

Seeded from EcoCyc (v14.0)

complete

GO:0004555

alpha,alpha-trehalase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001661

F

Seeded from EcoCyc (v14.0)

complete

GO:0004555

alpha,alpha-trehalase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018232

F

Seeded from EcoCyc (v14.0)

complete

GO:0004555

alpha,alpha-trehalase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.2.1.28

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01059

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0005991

trehalose metabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01059

P

Seeded from EcoCyc (v14.0)

complete

GO:0005991

trehalose metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001661

P

Seeded from EcoCyc (v14.0)

complete

GO:0005991

trehalose metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018232

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

P

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

GO:0016798

hydrolase activity, acting on glycosyl bonds

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

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 Notes References Evidence

Protein

groL

PMID:16606699

Experiment(s):EBI-1146067

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1146067
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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

cytoplasm

From EcoCyc[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 

MLNQKIQNPN PDELMIEVDL CYELDPYELK LDEMIEAEPE PEMIEGLPAS DALTPADRYL
ELFEHVQSAK IFPDSKTFPD CAPKMDPLDI LIRYRKVRRH RDFDLRKFVE NHFWLPEVYS
SEYVSDPQNS LKEHIDQLWP VLTREPQDHI PWSSLLALPQ SYIVPGGRFS ETYYWDSYFT
MLGLAESGRE DLLKCMADNF AWMIENYGHI PNGNRTYYLS RSQPPVFALM VELFEEDGVR
GARRYLDHLK MEYAFWMDGA ESLIPNQAYR HVVRMPDGSL LNRYWDDRDT PRDESWLEDV
ETAKHSGRPP NEVYRDLRAG AASGWDYSSR WLRDTGRLAS IRTTQFIPID LNAFLFKLES
AIANISALKG EKETEALFRQ KASARRDAVN RYLWDDENGI YRDYDWRREQ LALFSAAAIV
PLYVGMANHE QADRLANAVR SRLLTPGGIL ASEYETGEQW DKPNGWAPLQ WMAIQGFKMY
GDDLLGDEIA RSWLKTVNQF YLEQHKLIEK YHIADGVPRE GGGGEYPLQD GFGWTNGVVR
RLIGLYGEP
Length

549

Mol. Wt

63.698 kDa

pI

4.8 (calculated)

Extinction coefficient

136,710 - 137,085 (calc based on 29 Y, 17 W, and 3 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

70..547

PF01204 Trehalase

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=treF 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:16131391

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948037

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011497

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P62601

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12245

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12245

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948037

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002128

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2156

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

27

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

238

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

10a

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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<protect>

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

Transcription unit(s)

treF

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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_000913:3667595..3667635 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:b3519 (EcoliWiki Page)

NCBI GEO profiles for treF

microarray

GenExpDB:b3519 (EcoliWiki Page)

Summary of data for treF 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 (3666524..3667047) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ11; Well:H9[7]

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Notes

Accessions Related to treF Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12245

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2156

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3519

EcoGene

EcoGene:EG12245

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002128

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011497

Escherichia coli str. K-12 substr. MG1655

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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

  • ENSANGP00000015519 (score: 1.000; bootstrap: 100%)
  • ENSANGP00000008628 (score: 0.989)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000030892 (score: 1.000; bootstrap: 100%)
  • ENSAPMP00000004012 (score: 0.293)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT4G24040 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000021565 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00028108 (score: 1.000; bootstrap: 100%)
  • WBGene00033575 (score: 1.000; bootstrap: 100%)
  • WBGene00041665 (score: 0.204)
  • WBGene00029175 (score: 0.194)
  • WBGene00029498 (score: 0.052)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00006608 (score: 1.000; bootstrap: 100%)
  • WBGene00006607 (score: 1.000; bootstrap: 100%)
  • WBGene00006611 (score: 0.203)
  • WBGene00006609 (score: 0.197)
  • WBGene00006610 (score: 0.076)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000018370 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000004347 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0185541 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0003748 (score: 1.000; bootstrap: 100%)
  • FBgn0034121 (score: 0.296)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000264029 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000003433 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000016736 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:1926230 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000007463 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000018054 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YDR001C (score: 1.000; bootstrap: 100%)
  • YBR001C (score: 0.754)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC6607 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000156728 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00030223001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000046574 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

TREF

From SHIGELLACYC

E. coli O157

TREF

From ECOO157CYC

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Do-It-Yourself Web Tools

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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:48208

Pfam (EcoliWiki Page)

PF01204 Trehalase

EcoCyc

EcoCyc:EG12245

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12245

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002128

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2156

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011497

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 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).
  6. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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