ppdD: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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predicted major pilin subunit<ref name='LIB:Riley_2006'/>, B0108<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PpdD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted major pilin subunit<ref name='LIB:Riley_2006'/>, B0108<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PpdD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0107, JW0104, b0108''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-  
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GO:0042995
GO:0009289
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cell projection
pilus
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GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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SP_KW:KW-0966
SP_KW:KW-0281
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C
C
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Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  
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GO:0009289
GO:0009289
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fimbrium
pilus
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GO_REF:0000002<br />GO_REF:0000004
GO_REF:0000023
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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InterPro:IPR001082<br />SP_KW:KW-0281
SP_SL:SL-0113
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C
C
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Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
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GO:0007155
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cell adhesion
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GO_REF:0000002
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IEA: Inferred from Electronic Annotation
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InterPro:IPR001082
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P
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Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
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complete  
complete  


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence


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!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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!align=left {{table heading style}} |Name
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GGLDTCDGGS NGIPSPTTTR YVSAMSVAKG VVSLTGQESL NGLSVVMTPG WDNANGVTGW
GGLDTCDGGS NGIPSPTTTR YVSAMSVAKG VVSLTGQESL NGLSVVMTPG WDNANGVTGW
TRNCNIQSDS ALQQACEDVF RFDDAN</pre>  
TRNCNIQSDS ALQQACEDVF RFDDAN</pre>  
|-
!align=left {{table heading style}} |Length
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146
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
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15.62 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
15.621 kDa
|-
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!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
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4.4 (calculated)
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!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
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16960 - 17460 (calc based on 4 Y, 2 W, and 4 C residues)  
16,960 - 17,460 (calc based on 4 Y, 2 W, and 4 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
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|- {{table heading style}}
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
5..24
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[http://pfam.janelia.org/family/PF07963 PF07963  Prokaryotic N-terminal methylation motif]
|
 
|
PMID:19920124


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<td>
<!-- motifs column 2-->
<motif_map/>
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<table><tr valign='top'><td>
<span id="Structure"></span><big>'''Structure'''</big>
<span id='Structure'></span><big>'''Structure'''</big><br />
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!align=left {{table heading style}} |Structures
!align=left {{table heading style}} |Structures
||
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<beststructure>ppdD
<beststructure>
562</beststructure>
gene=ppdD
 
taxon=562,83333
</beststructure>
|-
|-
!align=left {{table heading style}} |Models
!align=left {{table heading style}} |Models
||
||
View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=ppdD&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P36647 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=ppdD&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P36647 PSI-PRED (P36647)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P36647 Genomes TO Protein (P36647)] (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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<!--Structure_notes--></protect>
</td><td></protect>
==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference


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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12107-MONOMER EcoCyc:EG12107-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/16128101 GI:16128101]
|
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Escherichia coli str. K-12 substr. MG1655
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/NP_414650.1 GeneID:945817]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0000372
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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]])
|
[http://www.uniprot.org/uniprot/P36647 UniProtKB/Swiss-Prot:P36647]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[[EcoCyc]]
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EcoCyc:EG12107
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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]])
[[EcoGene]]
|
|
[[uniprot:P36647|UniProt:P36647]]
EcoGene:EG12107
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://pfam.sanger.ac.uk/family?acc=PF07963 PFAM:PF07963]
[http://www.ncbi.nlm.nih.gov/gene?term=945817 GeneID:945817]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_414650 RefSeq:NP_414650]
RegulonDB:ECK120002012
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://salilab.org/modbase/searchbyid?databaseID=P36647 ModBase:P36647]
EchoBASE:EB2031
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0009289_!_fimbrium]]

Latest revision as of 20:21, 17 February 2015

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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

PpdD

Synonyms

predicted major pilin subunit[1], B0108[2][1], PpdD[2][1] , ECK0107, JW0104, b0108

Product description

prepilin peptidase dependent protein[2][3]

Type IV pilin; function unknown; first 6 residues may be cleaved by prepilin peptidase to leave an N-terminal methylphenylalanine[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:0009289

pilus

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0281

C

Seeded from EcoCyc (v14.0)

complete

GO:0009289

pilus

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0113

C

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
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Notes

Localization

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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 

MDKQRGFTLI ELMVVIGIIA ILSAIGIPAY QNYLRKAALT DMLQTFVPYR TAVELCALEH
GGLDTCDGGS NGIPSPTTTR YVSAMSVAKG VVSLTGQESL NGLSVVMTPG WDNANGVTGW
TRNCNIQSDS ALQQACEDVF RFDDAN
Length

146

Mol. Wt

15.621 kDa

pI

4.4 (calculated)

Extinction coefficient

16,960 - 17,460 (calc based on 4 Y, 2 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.

Type Residues Description Notes References

Domain

5..24

PF07963 Prokaryotic N-terminal methylation motif

PMID:19920124[5]

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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=ppdD taxon=562,83333 </beststructure>

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 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:16128101

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945817

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000372

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P36647

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12107

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12107

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945817

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002012

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2031

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 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. ↑ 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. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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