pflD:Gene Product(s): Difference between revisions

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Adding "length" to the physical properties table.
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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
predicted formate acetyltransferase 2 (pyruvate formate lyase II)<ref name='LIB:Riley_2006'/>, B3951<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YijL<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PflD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, pyruvate formate-lyase 2<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted formate acetyltransferase 2 (pyruvate formate lyase II)<ref name='LIB:Riley_2006'/>, B3951<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YijL<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PflD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, pyruvate formate-lyase 2<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK3942, JW3923, yijL, b3951''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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|- {{table_heading_style}}
|- {{table_heading_style}}
!|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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catalytic activity
catalytic activity
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
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|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
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complete  
complete  
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cytoplasm
cytoplasm
|
|
GO_REF:0000002<br />GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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|
InterPro:IPR004184<br />SP_KW:KW-0963
InterPro:IPR004184
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C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005737
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cytoplasm
|
GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0963
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C
|
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
|
 
|
GO:0005737
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cytoplasm
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GO_REF:0000023
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IEA: Inferred from Electronic Annotation
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SP_SL:SL-0086
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|
C
C
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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glucose metabolic process
glucose metabolic process
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|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
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|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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metabolic process
metabolic process
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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acyltransferase activity
acyltransferase activity
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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formate C-acetyltransferase activity
formate C-acetyltransferase activity
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|
GO_REF:0000002<br />GO_REF:0000003
GOA:interpro<br />GO_REF:0000002
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|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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|
InterPro:IPR004184<br />EC:2.3.1.54
InterPro:IPR004184
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|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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|
complete  
complete  
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|
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GO:0016740
GO:0008861
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|
transferase activity
formate C-acetyltransferase activity
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GO_REF:0000004
GOA:spec<br />GO_REF:0000003
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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SP_KW:KW-0808
EC:2.3.1.54
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|
F
F
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|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  
|-  
|-  
|
|
 
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GO:0009061
GO:0016740
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anaerobic respiration
transferase activity
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GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
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SP_KW:KW-0808
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P
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
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required fields missing 
complete


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Experiment(s):EBI-1147132<br />  
Experiment(s):EBI-1147132<br />  


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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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!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
85.96 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
85.961 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
5.8 (calculated)
|-
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!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
73230 - 74480 (calc based on 27 Y, 6 W, and 10 C residues)  
73,230 - 74,480 (calc based on 27 Y, 6 W, and 10 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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46ab104462cf0"  class=" tableEdit Product_motif_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
643..747
|
[http://pfam.janelia.org/family/PF01228 PF01228  Glycine radical]
|
 
|
PMID:19920124
|-  
|-  
|
|
Domain
Domain
|
|
645 - 765
1..626
|
[http://pfam.janelia.org/family/PF02901 PF02901  Pyruvate formate lyase]
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|
Glycine radical
 
|
|
[http://www.uniprot.org/uniprot/P32674#section_features UniProt:P32674]
PMID:19920124


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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
</tr>
</table>


 
<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
||
||
<beststructure>pflD
<beststructure>
562</beststructure>
gene=pflD
 
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=pflD&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P32674 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=pflD&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P32674 PSI-PRED (P32674)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P32674 Genomes TO Protein (P32674)] (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
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16131789 GI:16131789]
|
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_418386.1 GeneID:948454]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11910-MONOMER EcoCyc:EG11910-MONOMER]
Escherichia coli str. K-12 substr. MG1655
|-  
|
|
[[ASAP]]
|
ASAP:ABE-0012934
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P32674 UniProtKB/Swiss-Prot:P32674]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[[EcoCyc]]
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EcoCyc:EG11910
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
|
|
[[uniprot:P32674|UniProt:P32674]]
EcoGene:EG11910
|
|
''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=PF02901 PFAM:PF02901]
[http://www.ncbi.nlm.nih.gov/gene?term=948454 GeneID:948454]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[RegulonDB]]
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_418386 RefSeq:NP_418386]
RegulonDB:ECK120001838
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
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[http://salilab.org/modbase/searchbyid?databaseID=P32674 ModBase:P32674]
EchoBASE:EB1854
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
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__NOTOC__
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===Categories===
===Categories===
{{BacktoTop}}
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0009061_!_anaerobic respiration]]

Latest revision as of 21:10, 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

PflD

Synonyms

predicted formate acetyltransferase 2 (pyruvate formate lyase II)[1], B3951[2][1], YijL[2][1], PflD[2][1], pyruvate formate-lyase 2[2][1] , ECK3942, JW3923, yijL, b3951

Product description

formate acetyltransferase 2[2][3]

Putative pyruvate formate lyase II[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:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001150

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004184

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0006006

glucose metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004184

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001150

P

Seeded from EcoCyc (v14.0)

complete

GO:0008415

acyltransferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0012

F

Seeded from EcoCyc (v14.0)

complete

GO:0008861

formate C-acetyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004184

F

Seeded from EcoCyc (v14.0)

complete

GO:0008861

formate C-acetyltransferase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.3.1.54

F

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

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

sdhA

PMID:16606699[5]

Experiment(s):EBI-1147132

Protein

ppc

PMID:16606699[5]

Experiment(s):EBI-1147132
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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 

MTNRISRLKT ALFANTREIS LERALLYTAS HRQTEGEPVI LRRAKATAYI LEHVEISIRD
EELIAGNRTV KPRAGIMSPE MDPYWLLKEL DQFPTRPQDR FAISEEDKRI YREELFPYWE
KRSMKDFING QMTDEVKAAT NTQIFSINQT DKGQGHIIID YPRLLNHGLG ELVAQMQQHC
QQQPENHFYQ AALLLLEASQ KHILRYAELA ETMAANCTDA QRREELLTIA EISRHNAQHK
PQTFWQACQL FWYMNIILQY ESNASSLSLG RFDQYMLPFY QTSLTQGEDA AFLKELLESL
WVKCNDIVLL RSTSSARYFA GFPTGYTALL GGLTENGRSA VNVLSFLCLD AYQSVQLPQP
NLGVRTNALI DTPFLMKTAE TIRFGTGIPQ IFNDEVVVPA FLNRGVSLED ARDYSVVGCV
ELSIPGRTYG LHDIAMFNLL KVMEICLHEN EGNAALTYEG LLEQIRAKIS HYITLMVEGS
NICDIGHRDW APVPLLSSFI SDCLEKGRDI TDGGARYNFS GVQGIGIANL SDSLHALKGM
VFEQQRLSFD ELLSVLKANF ATPEGEKVRA RLINRFEKYG NDIDEVDNIS AELLRHYCKE
VEKYQNPRGG YFTPGSYTVS AHVPLGSVVG ATPDGRFAGE QLADGGLSPM LGQDAQGPTA
VLKSVSKLDN TLLSNGTLLN VKFTPATLEG EAGLRKLADF LRAFTQLKLQ HIQFNVVNAD
TLREAQQRPQ DYAGLVVRVA GYSAFFVELS KEIQDDIIRR TAHQL
Length

765

Mol. Wt

85.961 kDa

pI

5.8 (calculated)

Extinction coefficient

73,230 - 74,480 (calc based on 27 Y, 6 W, and 10 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

643..747

PF01228 Glycine radical

PMID:19920124[6]

Domain

1..626

PF02901 Pyruvate formate lyase

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=pflD 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:16131789

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948454

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012934

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P32674

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11910

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11910

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948454

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001838

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1854

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 1.3 1.4 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 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. ↑ 5.0 5.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  6. ↑ 6.0 6.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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