exbD:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
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membrane spanning protein in TonB-ExbB-ExbD complex<ref name='LIB:Riley_2006'/>, B3005<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, ExbD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''membrane spanning protein in TonB-ExbB-ExbD complex<ref name='LIB:Riley_2006'/>, B3005<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, ExbD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2998, JW2973, b3005''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P46aacbdb0c784"  class=" tableEdit GO_table_product dataTable"   
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!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Protein
Protein
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[[groS:Gene_Product(s)|groS]]
groS
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Protein
Protein
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[[ihfA:Gene_Product(s)|ihfA]]
ihfA
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Protein
Protein
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[[cspC:Gene_Product(s)|cspC]]
cspC
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Protein
Protein
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[[dps:Gene_Product(s)|dps]]
dps
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Protein
Protein
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[[rplJ:Gene_Product(s)|rplJ]]
rplJ
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Protein
Protein
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[[acpP:Gene_Product(s)|acpP]]
acpP
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Protein
Protein
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[[ompA:Gene_Product(s)|ompA]]
ompA
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Protein
Protein
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[[fimA:Gene_Product(s)|fimA]]
fimA
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Protein
Protein
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[[arpA:Gene_Product(s)|arpA]]
arpA
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Protein
Protein
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[[adk:Gene_Product(s)|adk]]
adk
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Protein
Protein
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[[efp:Gene_Product(s)|efp]]
efp
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Protein
Protein
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[[osmY:Gene_Product(s)|osmY]]
osmY
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PMID:19402753
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LCMS(ID Probability):99.6
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Protein
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rplL
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Protein
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[[rplL:Gene_Product(s)|rplL]]
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PMID:19402753
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LCMS(ID Probability):99.6


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!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
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4,470 (calc based on 3 Y, W, and C residues)
4,470 (calc based on 3 Y, 0 W, and 0 C residues)


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!|Type!!Residues!!Description!!Notes!!References
!|Type!!Residues!!Description!!Notes!!References
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View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P0ABV2 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0ABV2 PSI-PRED (P0ABV2)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0ABV2 Genomes TO Protein (P0ABV2)] (GTOP)
* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46aacbeb6345e"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10272-MONOMER EcoCyc:EG10272-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/16130903 GI:16130903]
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Escherichia coli str. K-12 substr. MG1655
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[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/protein/NP_417478.1 GeneID:946345]
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Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0009866
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
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[http://www.uniprot.org/uniprot/P0ABV2 UniProtKB/Swiss-Prot:P0ABV2]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:EG10272
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG10272
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
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[http://www.uniprot.org/uniprot/P0ABV2 UniProt:P0ABV2]
[http://www.ncbi.nlm.nih.gov/gene?term=946345 GeneID:946345]
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Escherichia coli str. K-12 substr. MG1655
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[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
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[http://pfam.janelia.org/protein/P0ABV2 Pfam:P0ABV2]
RegulonDB:ECK120000266
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[EchoBASE]]
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_417478 RefSeq:NP_417478]
EchoBASE:EB0268
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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Latest revision as of 20:58, 17 February 2015

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

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

ExbD

Synonyms

membrane spanning protein in TonB-ExbB-ExbD complex[1], B3005[2][1], ExbD[2][1] , ECK2998, JW2973, b3005

Product description

ExbD uptake of enterochelin; tonB-dependent uptake of B colicins[2][3];

Component of TonB energy transducing system[3]; Outer Membrane Ferric Citrate Transport System[3]; Outer Membrane Ferrichrome Transport System[3]; Outer Membrane Ferric Enterobactin Transport System[3]; vitamin B12 outer membrane transport complex[3]; ferric dicitrate uptake system[3]; ferrichrome uptake system[3]; Ferric Enterobactin Transport System[3]; vitamin B12 transport system[3]

Uptake of enterochelin; resistance or sensitivity to colicins; similarity with TolR[4]

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.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0005215

transporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003400

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: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:0006810

transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003400

P

Seeded from EcoCyc (v14.0)

complete

GO:0006810

transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0813

P

Seeded from EcoCyc (v14.0)

complete

GO:0015031

protein transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0653

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003400

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9906

C

Seeded from EcoCyc (v14.0)

complete

GO:0043213

bacteriocin transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0080

P

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

Subunits of TonB energy transducing system

could be indirect

Protein

groS

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

ihfA

PMID:19402753[5]

LCMS(ID Probability):99.4

Protein

cspC

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

dps

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

rplJ

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

acpP

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

ompA

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

fimA

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

arpA

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

adk

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

efp

PMID:19402753[5]

LCMS(ID Probability):99.0

Protein

osmY

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

rplL

PMID:19402753[5]

LCMS(ID Probability):99.6

Protein

Subunits of Outer Membrane Ferric Citrate Transport System

could be indirect

Protein

Subunits of Outer Membrane Ferrichrome Transport System

could be indirect

Protein

Subunits of Outer Membrane Ferric Enterobactin Transport System

could be indirect

Protein

Subunits of vitamin B12 outer membrane transport complex

could be indirect

Protein

Subunits of ferric dicitrate uptake system

could be indirect

Protein

Subunits of ferrichrome uptake system

could be indirect

Protein

Subunits of Ferric Enterobactin Transport System

could be indirect

Protein

Subunits of vitamin B12 transport system

could be indirect


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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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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 

MAMHLNENLD DNGEMHDINV TPFIDVMLVL LIIFMVAAPL ATVDVKVNLP ASTSTPQPRP
EKPVYLSVKA DNSMFIGNDP VTDETMITAL NALTEGKKDT TIFFRADKTV DYETLMKVMD
TLHQAGYLKI GLVGEETAKA K
Length

141

Mol. Wt

15.526 kDa

pI

4.6 (calculated)

Extinction coefficient

4,470 (calc based on 3 Y, 0 W, and 0 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

11..137

PF02472 Biopolymer transport protein ExbD/TolR

PMID:19920124[6]

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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=exbD taxon=562,83333 </beststructure>

Models

View models at:

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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 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:16130903

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946345

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009866

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ABV2

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10272

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10272

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946345

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000266

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0268

Escherichia coli str. K-12 substr. MG1655

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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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.00 3.01 3.02 3.03 3.04 3.05 3.06 3.07 3.08 3.09 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.00 5.01 5.02 5.03 5.04 5.05 5.06 5.07 5.08 5.09 5.10 5.11 5.12 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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