EcoliHub logo

Try the new EcoliHub and let us know what you'd like to see.

nlpA:On One Page

From EcoliWiki

Jump to: navigation, search
Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

[back to top]



See Help:Quickview for help with entering information in the Quickview table.

Standard Name

nlpA

Gene Synonym(s)

ECK3651, b3661, JW3635[1]

Product Desc.

lipoprotein-28[2][3]

Lipoprotein-28, inner membrane protein, function unknown[4]

Product Synonyms(s)

cytoplasmic membrane lipoprotein-28[1], B3661[2][1], NlpA[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): nlpA[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(nlpA)    Textpresso(nlpA)

edit table

See Help:Quickview for help with entering information in the Quickview table.

Notes

[back to top]


Pathogenicity island eip (EAEC strain 042) has inserted in the adjacent yicS-nepI intergenic region. First 23 aa are a type II signal peptide. Mutants have reduced OM vesiculation (McBroom, 2006).[4]



Gene

[back to top]


Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

nlpA

Mnemonic

New lipoprotein

Synonyms

ECK3651, b3661, JW3635[1]

edit table

Notes

Location(s) and DNA Sequence

[back to top]


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

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

82.7 minutes 

MG1655: 3838016..3837198
gbrowse_img.php?coord=3837198..3838016&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3799925..3799107
gbrowse_img.php?coord=3799107..3799925&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3800422..3801240
gbrowse_img.php?coord=3800422..3801240&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3935600..3934782
gbrowse_img.php?coord=3934782..3935600&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 3725531..3726349
gbrowse_img.php?coord=3725531..3726349&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

edit table

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature typeLocationDescription
edit table

Notes

Alleles and Phenotypes

[back to top]


See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

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

ΔnlpA (Keio:JW3635)

deletion

deletion

PMID:16738554

Shigen

nlpA::kan

Other

nonessential

PMID:2841301

nlpA3085::Tn10

PMID:9829956 PMID:2540407

CGSC:59412


edit table

Notes

Genetic Resources

[back to top]


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

ResourceResource TypeSourceNotes/Reference

JW3635

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAACTGACAACACATCATCT

Primer 2:CCCCAGCCAGGCACCGCGCCACC

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[5]

est. P1 cotransduction: 72% [6]

zid-501::Tn10

Linked marker

CAG18499 = CGSC7458[5]

est. P1 cotransduction: 22% [6]

edit table

Notes

Accessions in Other Databases

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10657

EchoBASE (EcoliWiki Page)

EchoBASE:EB0651

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3661

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4583

EcoGene (EcoliWiki Page)

EcoGene:EG10657

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:NLPA

CGSC (EcoliWiki Page)

CGSC:35704

ASAP (EcoliWikiPage)

ASAP:ABE-0011964


edit table

Notes

Links

[back to top]



Product(s)

[back to top]



Nomenclature

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

Standard name

NlpA

Synonyms

cytoplasmic membrane lipoprotein-28[1], B3661[2][1], NlpA[2][1]

Product description

lipoprotein-28[2][3]

Lipoprotein-28, inner membrane protein, function unknown[4]

EC number (for enzymes)


edit table

Notes

Function

[back to top]


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:0016020

membrane

GO_REF:0000004
GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0397
SP_KW:KW-0472

C

Seeded from EcoCyc 12.5 [7]

complete

GO:0005886

plasma membrane

GO_REF:0000004
GO_REF:0000004
GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997
SP_KW:KW-1003
SP_SL:SL-0037

C

Seeded from EcoCyc [8]

complete

edit table

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner TypePartnerNotesReferencesEvidence

Protein

nadE

PMID:16606699

Experiment(s):EBI-1146441

Protein

ymfG

PMID:16606699

Experiment(s):EBI-1146441

Protein

rplS

PMID:16606699

Experiment(s):EBI-1146441

Protein

rplV

PMID:16606699

Experiment(s):EBI-1146441

Protein

ycgL

PMID:16606699

Experiment(s):EBI-1146441

Protein

rpsD

PMID:16606699

Experiment(s):EBI-1146441

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1146441

edit table

Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes

plasma membrane


edit table

Notes

Structure and Physical Properties

[back to top]


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

Sequence

at EcoCyc 

MKLTTHHLRT GAALLLAGIL LAGCDQSSSD AKHIKVGVIN GAEQDVAEVA KKVAKEKYGL
DVELVGFSGS LLPNDATNHG ELDANVFQHR PFLEQDNQAH GYKLVAVGNT FVFPMAGYSK
KIKTVAQIKE GATVAIPNDP TNLGRALLLL QKEKLITLKE GKGLLPTALD ITDNPRHLQI
MELEGAQLPR VLDDPKVDVA IISTTYIQQT GLSPVHDSVF IEDKNSPYVN ILVAREDNKN
AENVKEFLQS YQSPEVAKAA ETIFNGGAVP GW
Length

272

Mol. Wt

29.423 kDa

pI

5.7 (calculated)

Extinction coefficient

14,440 - 14,565 (calc based on 6 Y, 1 W, and 1 C residues)

edit table


Domains/Motifs/Modification Sites

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

TypeResiduesDescriptionNotesReferences

motif

1-23

UniProt Manual:Signal Peptides

UniProt:P04846


edit table


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

Structures
Models

View models at:

edit table

Structure figures

Notes

Gene Product Resources

[back to top]


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

Resource typeSourceNotes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10657-MONOMER

UniProt (EcoliWiki Page)

UniProt:P04846

PFAM (EcoliWiki Page)

PFAM:PF03180

RefSeq (EcoliWiki Page)

RefSeq:NP_418117


edit table

Notes

Links

[back to top]




Expression

[back to top]



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

[back to top]


See Help:Cellular levels

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

Notes

Transcription and Transcriptional Regulation

[back to top]


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

Transcription unit(s)

nlpA

edit table
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

[back to top]


gbrowse_img.php?coord=3837996..3838036&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

[back to top]


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

Allele NameMutationPhenotypeReference
edit table


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

TypeReferenceNotes

microarray

GEO Profiles:b3661 (EcoliWiki Page)

NCBI GEO profiles for nlpA

microarray

GenExpDB:b3661 (EcoliWiki Page)

Summary of data for nlpA from multiple microarray studies

edit table


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource NameResource TypeDescriptionSourceNotes

GFP Fusion

Intergenic region (3837533..3838251) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ09; Well:B4[9]

edit table

Notes

Accessions Related to nlpA Expression

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10657

EchoBASE (EcoliWiki Page)

EchoBASE:EB0651

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3661

EcoGene (EcoliWiki Page)

EcoGene:EG10657


edit table

Notes

Links

[back to top]



Evolution

[back to top]



Homologs in Other Organisms

[back to top]



Do-It-Yourself Web Tools

Notes

Families

[back to top]


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

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF03180


edit table

Notes

Links

[back to top]



References

[back to top]


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 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 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 4.2 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 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).
  7. ↑ EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  8. ↑ EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  9. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

Categories

[back to top]


Retrieved from "http://ecoliwiki.net/colipedia/index.php/nlpA:On_One_Page"
Personal tools