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lptD:On One Page

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Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

lptD

Gene Synonym(s)

ECK0055, b0054, JW0053, ostA, yabG, imp[1]

Product Desc.

exported protein required for envelope biosynthesis and integrity[2][3]

Product Synonyms(s)

exported protein required for envelope biosynthesis and integrity[1], B0054[2][1], YabG[2][1], OstA[2][1], Imp[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): lptD-surA-pdxA[2], lptD[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(imp)    Textpresso(imp)

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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

lptD

Mnemonic

LPS transport

Synonyms

ECK0055, b0054, JW0053, ostA, yabG, imp[1]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

1.18 minutes 

MG1655: 57109..54755
gbrowse_img.php?coord=54755..57109&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 58950..61304
gbrowse_img.php?coord=58950..61304&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 57109..54755
gbrowse_img.php?coord=54755..57109&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 57109..54755
gbrowse_img.php?coord=54755..57109&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

imp4213


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW0053

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAAAAACGTATCCCCACTCT

Primer 2:CCCAAAGTGTTTTGATACGGCAG

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[4]

est. P1 cotransduction: 44% [5]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[4]

est. P1 cotransduction: 33% [5]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

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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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11569

EchoBASE (EcoliWiki Page)

EchoBASE:EB1529

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0054

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0067

EcoGene (EcoliWiki Page)

EcoGene:EG11569

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:G7E-6

CGSC (EcoliWiki Page)

CGSC:36754

ASAP (EcoliWikiPage)

ASAP:ABE-0000183


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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

LptD

Synonyms

exported protein required for envelope biosynthesis and integrity[1], B0054[2][1], YabG[2][1], OstA[2][1], Imp[2][1]

Product description

exported protein required for envelope biosynthesis and integrity[2][3]

EC number (for enzymes)


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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0006979

response to oxidative stress

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0009279

cell outer membrane

C

Seeded from EcoCyc 11.1[3].

required fields missing

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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 TypePartnerNotesReferencesEvidence
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

CompartmentDescriptionEvidenceSourceNotes

outer membrane

Outer Membrane

PMID:9298646

EchoLocation:imp


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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MKKRIPTLLA TMIATALYSQ QGLAADLASQ CMLGVPSYDR PLVQGDTNDL PVTINADHAK
GDYPDDAVFT GSVDIMQGNS RLQADEVQLH QKEAPGQPEP VRTVDALGNV HYDDNQVILK
GPKGWANLNT KDTNVWEGDY QMVGRQGRGK ADLMKQRGEN RYTILDNGSF TSCLPGSDTW
SVVGSEIIHD REEQVAEIWN ARFKVGPVPI FYSPYLQLPV GDKRRSGFLI PNAKYTTTNY
FEFYLPYYWN IAPNMDATIT PHYMHRRGNI MWENEFRYLS QAGAGLMELD YLPSDKVYED
EHPNDDSSRR WLFYWNHSGV MDQVWRFNVD YTKVSDPSYF NDFDNKYGSS TDGYATQKFS
VGYAVQNFNA TVSTKQFQVF SEQNTSSYSA EPQLDVNYYQ NDVGPFDTRI YGQAVHFVNT
RDDMPEATRV HLEPTINLPL SNNWGSINTE AKLLATHYQQ TNLDWYNSRN TTKLDESVNR
VMPQFKVDGK MVFERDMEML APGYTQTLEP RAQYLYVPYR DQSDIYNYDS SLLQSDYSGL
FRDRTYGGLD RIASANQVTT GVTSRIYDDA AVERFNISVG QIYYFTESRT GDDNITWEND
DKTGSLVWAG DTYWRISERW GLRGGIQYDT RLDNVATSNS SIEYRRDEDR LVQLNYRYAS
PEYIQATLPK YYSTAEQYKN GISQVGAVAS WPIADRWSIV GAYYYDTNAN KQADSMLGVQ
YSSCCYAIRV GYERKLNGWD NDKQHAVYDN AIGFNIELRG LSSNYGLGTQ EMLRSNILPY QNTL
Length

784

Mol. Wt

89.672 kDa

pI

5.0 (calculated)

Extinction coefficient

185,420 - 185,920 (calc based on 58 Y, 18 W, and 4 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.

TypeResiduesDescriptionNotes

motif

1-24

UniProt Manual:Signal Peptides

UniProt:P31554

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

Structures
Models

View models at:

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Structure figures

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 typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11569-MONOMER

UniProt (EcoliWiki Page)

UniProt:P31554

PFAM (EcoliWiki Page)

PFAM:PF04453

RefSeq (EcoliWiki Page)

RefSeq:NP_414596


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Notes

Links

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NameURLComments
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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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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)

lptD-surA-pdxA

imp

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Figure courtesy of RegulonDB

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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gbrowse_img.php?coord=57089..57129&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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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Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

microarray

GEO Profiles:b0054 (EcoliWiki Page)

NCBI GEO profiles for imp

microarray

GenExpDB:b0054 (EcoliWiki Page)

Summary of data for imp 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 NameResource TypeDescriptionSourceNotes

GFP Fusion

Intergenic region (57013..57395) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ11; Well:D6[6]

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Notes

Accessions Related to lptD Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11569

EchoBASE (EcoliWiki Page)

EchoBASE:EB1529

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0054

EcoGene (EcoliWiki Page)

EcoGene:EG11569


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Notes

Links

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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.

OrganismHomologs (Statistics)Comments

Shigella flexneri

G7V-674

From SHIGELLACYC

E. coli O157

G7E-6

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.

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF04453


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Notes

Links

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NameURLComments
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References

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

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 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. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

Categories

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