nlpD:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

nlpD

Gene Synonym(s)

ECK2737, b2742, JW2712[1], JW2712

Product Desc.

NlpD putative outer membrane lipoprotein[2][3]

Lipoprotein, function unknown; may be involved in cell wall formation; may have murein hydrolytic activity[4]

Product Synonyms(s)

predicted outer membrane lipoprotein[1], B2742[2][1], NlpD[2][1] , ECK2737, JW2712, b2742

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): nlpD-rpoS[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]


M23 metalloprotease domain. Binds Congo Red dye, like the homolog Haemophilus somnus LppB outer membrane antigen and possible virulence determinant. nlpD, ygeR, yebA and envC are paralogs. First 25 aa are a type II signal peptide.[4]



Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


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

Standard name

nlpD

Mnemonic

New lipoprotein

Synonyms

ECK2737, b2742, JW2712[1], JW2712

edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<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

61.76 minutes 

MG1655: 2866775..2865636
<gbrowseImage> name=NC_000913:2865636..2866775 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2763614..2762475
<gbrowseImage> name=NC_012967:2762475..2763614 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2751448..2752587
<gbrowseImage> name=NC_012759:2751448..2752587 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2867409..2866270
<gbrowseImage> name=NC_007779:2866270..2867409 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2959317..2958178
<gbrowseImage> name=NC_010473:2958178..2959317 source=DH10B preset=GeneLocation </gbrowseImage>

edit table

</protect>

Notes

Sequence Features

[back to top]


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

Feature Type Strain Genomic Location Evidence Reference Notes
edit table

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

ΔnlpD (Keio:JW2712)

deletion

deletion

PMID:16738554

Shigen
CGSC10134[5]

nlpD::Tn5KAN-I-SceI (FB20920)

Insertion at nt 683 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20920

contains pKD46

ΔnlpD747::kan

PMID:16738554

CGSC:102088

ΔnlpD

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345

ΔnlpD ΔyebA

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345

ΔnlpD ΔygeR

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345

ΔnlpD ΔygeR

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345

ΔnlpD ΔyebA ΔenvC

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345

ΔnlpD ΔygeR ΔenvC

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345

ΔnlpD ΔygeR ΔyebA

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345

ΔnlpD ΔygeR ΔyebA ΔenvC

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345


edit table

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]


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

Resource Resource Type Source Notes/Reference

JW2712

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGCGCGGGAAGCCCAAAATT

Primer 2:CCTCGCTGCGGCAAATAACGCAG

25D2

Kohara Phage

Genobase

PMID:3038334

1B5

Kohara Phage

Genobase

PMID:3038334

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[5]

est. P1 cotransduction: 18% [6]
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10

cysI95::Tn10

Linked marker

CAG12173 = CGSC7425[5]

est. P1 cotransduction: 48% [6]
Synonyms:cysC95::Tn10

edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG12111

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12111

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002015

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947011

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2034

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009004

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name

NlpD

Synonyms

predicted outer membrane lipoprotein[1], B2742[2][1], NlpD[2][1] , ECK2737, JW2712, b2742

Product description

NlpD putative outer membrane lipoprotein[2][3]

Lipoprotein, function unknown; may be involved in cell wall formation; may have murein hydrolytic activity[4]

EC number (for enzymes)


edit table

<protect></protect>

Notes

Function

[back to top]


<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:0000920

cytokinetic cell separation

PMID:19525345

IGI: Inferred from Genetic Interaction

UniProtKB:P0AFS9 UniProtKB:P37690 UniProtKB:Q46798


P

Seeded from EcoCyc (v14.0)

complete

GO:0000920

cytokinetic cell separation

PMID:19525345

IGI: Inferred from Genetic Interaction

UniProtKB:P37690


P

complete

GO:0004222

metalloendopeptidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002886

F

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-0997

C

Seeded from EcoCyc (v14.0)

complete

GO:0000920

cytokinetic cell separation

PMID:19525345

IGI: Inferred from Genetic Interaction

UniProtKB:P0AFS9 UniProtKB:P37690 UniProtKB:Q46798


P

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:0006508

proteolysis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002886

P

Seeded from EcoCyc (v14.0)

complete

GO:0032155

cell division site part

PMID:19525345

IDA: Inferred from Direct Assay

C

enriched at division sites with clear constrictions

complete

GO:0016998

cell wall macromolecule catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002482

P

Seeded from EcoCyc (v14.0)

complete

GO:0016998

cell wall macromolecule catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018392

P

Seeded from EcoCyc (v14.0)

complete

GO:0031225

anchored to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9901

C

Seeded from EcoCyc (v14.0)

complete

GO:0032155

cell division site part

PMID:19525345

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

edit table

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

yfiD

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplK

PMID:19402753

LCMS(ID Probability):99.6

Protein

ompA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmG

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmC

PMID:19402753

LCMS(ID Probability):99.6

Protein

hns

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.6

Protein

acpP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplE

PMID:19402753

LCMS(ID Probability):99.6

Protein

arpA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6

Protein

cspC

PMID:19402753

LCMS(ID Probability):99.6

Protein

nusG

PMID:19402753

LCMS(ID Probability):99.6

Protein

elbB

PMID:19402753

MALDI(Z-score):28.124797

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.6

Protein

yeeX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmD

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplL

PMID:19402753

LCMS(ID Probability):99.6

edit table

</protect>

Notes

Localization

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

Compartment Description Evidence Reference/Source Notes

outer membrane

Outer membrane

PMID:15174130

EchoLocation:nlpD


edit table

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<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 

MSAGSPKFTV RRIAALSLVS LWLAGCSDTS NPPAPVSSVN GNAPANTNSG MLITPPPKMG
TTSTAQQPQI QPVQQPQIQA TQQPQIQPVQ PVAQQPVQME NGRIVYNRQY GNIPKGSYSG
STYTVKKGDT LFYIAWITGN DFRDLAQRNN IQAPYALNVG QTLQVGNASG TPITGGNAIT
QADAAEQGVV IKPAQNSTVA VASQPTITYS ESSGEQSANK MLPNNKPTAT TVTAPVTVPT
ASTTEPTVSS TSTSTPISTW RWPTEGKVIE TFGASEGGNK GIDIAGSKGQ AIIATADGRV
VYAGNALRGY GNLIIIKHND DYLSAYAHND TMLVREQQEV KAGQKIATMG STGTSSTRLH
FEIRYKGKSV NPLRYLPQR
Length

379

Mol. Wt

40.148 kDa

pI

9.9 (calculated)

Extinction coefficient

41,370 - 41,495 (calc based on 13 Y, 4 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.

Type Residues Description Notes References

motif

1-25

UniProt Manual:Signal Peptides

UniProt:P0ADA3

Domain

123..166

PF01476 LysM domain

PMID:19920124

Domain

277..372

PF01551 Peptidase family M23

PMID:19920124

edit table

<motif_map/>

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

Structures

<beststructure> gene=nlpD taxon=562,83333 </beststructure>

Models

View models at:

edit table
</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


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

Resource type Source Notes/Reference
edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16130649

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947011

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009004

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ADA3

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12111

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12111

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947011

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002015

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2034

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

5.04E+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

1349

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

695

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

683

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

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

Transcription unit(s)

nlpD-rpoS

edit table
Figure courtesy of RegulonDB

</protect>

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]


<protect><gbrowseImage> name=NC_000913:2866755..2866795 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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]


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

Allele Name Mutation Phenotype Reference
edit table


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

Type Reference Notes

microarray

GEO Profiles:b2742 (EcoliWiki Page)

NCBI GEO profiles for nlpD

microarray

GenExpDB:b2742 (EcoliWiki Page)

Summary of data for nlpD from multiple microarray studies

edit table


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 (2866699..2866974) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ09; Well:A6[7]

edit table

<protect></protect>

Notes

Accessions Related to nlpD Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG12111

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2034

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2742

EcoGene

EcoGene:EG12111

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002015

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009004

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


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

Organism Homologs (Statistics) Comments

Shigella flexneri

NLPD

From SHIGELLACYC

E. coli O157

NLPD

From ECOO157CYC

edit table


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


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

Database Accession Notes

Pfam (EcoliWiki Page)

PF01551 Peptidase family M23

Pfam (EcoliWiki Page)

PF01476 LysM domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:51261

EcoCyc

EcoCyc:EG12111

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12111

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002015

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2034

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009004

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

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 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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=nlpD:On_One_Page&oldid=221136"