lhr: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

lhr

Gene Synonym(s)

ECK1649, b1653, JW1645, rhlF[1], rhlF

Product Desc.

member of ATP-dependent helicase superfamily II[2][3]

Putative ATP-dependent helicase[4]

Product Synonyms(s)

predicted ATP-dependent helicase[1], B1653[2][1], RhlF[2][1], Lhr[2][1] , ECK1649, JW1645, rhlF, b1653

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): lhr[2], rnt-lhr[2]

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

lhr

Mnemonic

Long helicase related protein

Synonyms

ECK1649, b1653, JW1645, rhlF[1], rhlF

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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

37.22 minutes, 37.22 minutes 

MG1655: 1727111..1731727
<gbrowseImage> name=NC_000913:1727111..1731727 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1706281..1710897
<gbrowseImage> name=NC_012967:1706281..1710897 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1619170..1623786
<gbrowseImage> name=NC_012759:1619170..1623786 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1730801..1735417
<gbrowseImage> name=NC_007779:1730801..1735417 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1817682..1822298
<gbrowseImage> name=NC_010473:1817682..1822298 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
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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

Δlhr (Keio:JW1645)

deletion

deletion

PMID:16738554

Shigen
CGSC9400[5]

lhr::Tn5KAN-2 (FB20406)

Insertion at nt 2019 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20406

contains pKD46

Δlhr::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

Δlhr-731::kan

PMID:16738554

CGSC:101658


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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

JW1645

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCAGATAATCCAGACCCTTC

Primer 2:CCTCCCCAATCCAGCCCTTGTGG

6F11

Kohara Phage

Genobase

PMID:3038334

4H6

Kohara Phage

Genobase

PMID:3038334

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[5]

est. P1 cotransduction: % [6]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[5]

est. P1 cotransduction: 10% [6]
Synonyms:zdh-925::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:EG11548

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11548

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001502

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946156

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1510

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005525

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

Lhr

Synonyms

predicted ATP-dependent helicase[1], B1653[2][1], RhlF[2][1], Lhr[2][1] , ECK1649, JW1645, rhlF, b1653

Product description

member of ATP-dependent helicase superfamily II[2][3]

Putative ATP-dependent helicase[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:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0347

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013701

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0008026

ATP-dependent helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

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:0016818

hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013701

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

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

gadB

PMID:19402753

MALDI(Z-score):20.856819

Protein

rplE

PMID:19402753

MALDI(Z-score):23.350094

Protein

adhE

PMID:19402753

MALDI(Z-score):26.433007

Protein

gapA

PMID:19402753

MALDI(Z-score):29.454886

Protein

rfaD

PMID:19402753

MALDI(Z-score):18.830342

Protein

eno

PMID:19402753

MALDI(Z-score):32.995052

Protein

yfiD

PMID:19402753

MALDI(Z-score):23.668016

Protein

ahpC

PMID:19402753

MALDI(Z-score):29.069352

Protein

rpsD

PMID:19402753

MALDI(Z-score):28.076805

Protein

glpK

PMID:19402753

MALDI(Z-score):19.651066

Protein

pta

PMID:19402753

MALDI(Z-score):25.021562

Protein

pgk

PMID:19402753

MALDI(Z-score):35.413594

Protein

pflB

PMID:19402753

MALDI(Z-score):23.831553

Protein

wrbA

PMID:19402753

MALDI(Z-score):20.856868

Protein

tsf

PMID:19402753

MALDI(Z-score):27.459882

Protein

carB

PMID:19402753

MALDI(Z-score):18.907029

Protein

ompA

PMID:19402753

MALDI(Z-score):29.316825

Protein

pstS

PMID:19402753

MALDI(Z-score):25.927379

Protein

rpsA

PMID:19402753

MALDI(Z-score):21.444198

Protein

rpoA

PMID:19402753

MALDI(Z-score):33.286609

Protein

dps

PMID:19402753

MALDI(Z-score):36.995187

Protein

tig

PMID:19402753

MALDI(Z-score):32.975547

Protein

cdd

PMID:19402753

MALDI(Z-score):28.079038

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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 

MADNPDPSSL LPDVFSPATR DWFLRAFKQP TAVQPQTWHV AARSEHALVI APTGSGKTLA
AFLYALDRLF REGGEDTREA HKRKTSRILY ISPIKALGTD VQRNLQIPLK GIADERRRRG
ETEVNLRVGI RTGDTPAQER SKLTRNPPDI LITTPESLYL MLTSRARETL RGVETVIIDE
VHAVAGSKRG AHLALSLERL DALLHTSAQR IGLSATVRSA SDVAAFLGGD RPVTVVNPPA
MRHPQIRIVV PVANMDDVSS VASGTGEDSH AGREGSIWPY IETGILDEVL RHRSTIVFTN
SRGLAEKLTA RLNELYAARL QRSPSIAVDA AHFESTSGAT SNRVQSSDVF IARSHHGSVS
KEQRAITEQA LKSGELRCVV ATSSLELGID MGAVDLVIQV ATPLSVASGL QRIGRAGHQV
GGVSKGLFFP RTRRDLVDSA VIVECMFAGR LENLTPPHNP LDVLAQQTVA AAAMDALQVD
EWYSRVRRAA PWKDLPRRVF DATLDMLSGR YPSGDFSAFR PKLVWNRETG ILTARPGAQL
LAVTSGGTIP DRGMYSVLLP EGEEKAGSRR VGELDEEMVY ESRVNDIITL GATSWRIQQI
TRDQVIVTPA PGRSARLPFW RGEGNGRPAE LGEMIGDFLH LLADGAFFSG TIPPWLAEEN
TIANIQGLIE EQRNATGIVP GSRHLVLERC RDEIGDWRII LHSPYGRRVH EPWAVAIAGR
IHALWGADAS VVASDDGIVA RIPDTDGKLP DAAIFLFEPE KLLQIVREAV GSSALFAARF
RECAARALLM PGRTPGHRTP LWQQRLRASQ LLEIAQGYPD FPVILETLRE CLQDVYDLPA
LERLMRRLNG GEIQISDVTT TTPSPFATSL LFGYVAEFMY QSDAPLAERR ASVLSLDSEL
LRNLLGQVDP GELLDPQVIR QVEEELQRLA PGRRAKGEEG LFDLLRELGP MTVEDLAQRH
TGSSEEVASY LENLLAVKRI FPAMISGQER LACMDDAARL RDALGVRLPE SLPEIYLHRV
SYPLRDLFLR YLRAHALVTA EQLAHEFSLG IAIVEEQLQQ LREQGLVMNL QQDIWVSDEV
FRRLRLRSLQ AAREATRPVA ATTYARLLLE RQGVLPATDG SPALFASTSP GVYEGVDGVM
RVIEQLAGVG LPASLWESQI LPARVRDYSS EMLDELLATG AVIWSGQKKL GEDDGLVALH
LQEYAAESFT PAEADQANRS ALQQAIVAVL ADGGAWFAQQ ISQRIRDKIG ESVDLSALQE
ALWALVWQGV ITSDIWAPLR ALTRSSSNAR TSTRRSHRAR RGRPVYAQPV SPRVSYNTPN
LAGRWSLLQV EPLNDTERML ALAENMLDRY GIISRQAVIA ENIPGGFPSM QTLCRSMEDS
GRIMRGRFVE GLGGAQFAER LTIDRLRDLA TQATQTRHYT PVALSANDPA NVWGNLLPWP
AHPATLVPTR RAGALVVVSG GKLLLYLAQG GKKMLVWQEK EELLAPEVFH ALTTALRREP
RLRFTLTEVN DLPVRQTPMF TLLREAGFSS SPQGLDWG
Length

1,538

Mol. Wt

169.383 kDa

pI

6.7 (calculated)

Extinction coefficient

177,730 - 178,605 (calc based on 27 Y, 25 W, and 7 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

31..224

PF00270 DEAD/DEAH box helicase

PMID:19920124

Domain

347..419

PF00271 Helicase conserved C-terminal domain

PMID:19920124

Domain

678..868

PF08494 DEAD/H associated

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=lhr 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:16129611

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946156

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005525

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P30015

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11548

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11548

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946156

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001502

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1510

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Ecoli K-12

4.216+/-0.15

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.011048527

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

5

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

16

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

0a

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)

lhr

rnt-lhr

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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_000913:1727091..1727131 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:b1653 (EcoliWiki Page)

NCBI GEO profiles for lhr

microarray

GenExpDB:b1653 (EcoliWiki Page)

Summary of data for lhr 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 lhr Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11548

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1510

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1653

EcoGene

EcoGene:EG11548

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001502

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005525

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Apis mellifera

  • ENSAPMP00000013487 (score: 1.000; bootstrap: 100%)
  • ENSAPMP00000031644 (score: 0.452)
  • ENSAPMP00000013488 (score: 0.226)

From Inparanoid:20070104

E. coli O157

LHR

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

Pfam (EcoliWiki Page)

PF00271 Helicase conserved C-terminal domain

Pfam (EcoliWiki Page)

PF00270 DEAD/DEAH box helicase

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Panther (EcoliWiki Page)

PTHR11752:SF38

Pfam (EcoliWiki Page)

PF08494 DEAD/H associated

EcoCyc

EcoCyc:EG11548

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11548

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001502

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1510

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005525

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 1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).

Categories

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