fdhD: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
||
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formate dehydrogenase formation protein<ref name='LIB:Riley_2006'/>, B3895<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, FdhD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''formate dehydrogenase formation protein<ref name='LIB:Riley_2006'/>, B3895<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, FdhD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK3888, JW3866, b3895''
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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:0009326
GO:0005737
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|
formate dehydrogenase complex
cytoplasm
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GO_REF:0000002
GOA:hamap<br />GO_REF:0000020
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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InterPro:IPR003786
HAMAP:MF_00187
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C
C
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  
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GO:0008863
GO:0005737
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formate dehydrogenase activity
cytoplasm
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GO_REF:0000002
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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InterPro:IPR003786
SP_KW:KW-0963
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F
C
|
|
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
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GO_REF:0000004
GO_REF:0000023
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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SP_KW:KW-0963
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)
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complete  
complete  
|-  
|-  
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|
 
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GO:0008863
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formate dehydrogenase activity
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GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
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InterPro:IPR003786
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F
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Seeded from [[EcoCyc]] (v14.0)
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complete
|-
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GO:0009061
 
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anaerobic respiration
GO:0009326
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formate dehydrogenase complex
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GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
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InterPro:IPR003786
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P
C
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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-1146919<br />  
Experiment(s):EBI-1146919<br />  
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Protein
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map
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PMID:19402753
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MALDI(Z-score):38.741739
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Protein
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gatZ
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PMID:19402753
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MALDI(Z-score):23.393145
|-
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Protein
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iscS
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PMID:19402753
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LCMS(ID Probability):99.6 MALDI(Z-score):46.320178
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Protein
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ibpB
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PMID:19402753
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MALDI(Z-score):35.294336
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Protein
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narJ
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PMID:19402753
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LCMS(ID Probability):99.6
|-
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Protein
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rpsN
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PMID:19402753
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LCMS(ID Probability):99.6
|-
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Protein
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dnaJ
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PMID:19402753
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MALDI(Z-score):34.017231
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Protein
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groS
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PMID:19402753
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MALDI(Z-score):28.256905
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Protein
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lysU
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PMID:19402753
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MALDI(Z-score):25.833714
 
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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
||
||
30.56 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
30.558 kDa
|-
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!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
6.4 (calculated)
|-
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!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
22460 - 23335 (calc based on 4 Y, 3 W, and 7 C residues)  
22,460 - 23,335 (calc based on 4 Y, 3 W, and 7 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}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
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38..276
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[http://pfam.janelia.org/family/PF02634 PF02634  FdhD/NarQ family]
|
 
|
PMID:19920124


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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
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</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>fdhD
<beststructure>
562</beststructure>
gene=fdhD
 
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=fdhD&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P32177 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=fdhD&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P32177 PSI-PRED (P32177)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P32177 Genomes TO Protein (P32177)] (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://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11859-MONOMER EcoCyc:EG11859-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/16131735 GI:16131735]
|
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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]])
|
[http://www.ncbi.nlm.nih.gov/protein/NP_418331.1 GeneID:948393]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[[ASAP]]
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ASAP:ABE-0012714
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P32177 UniProtKB/Swiss-Prot:P32177]
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Escherichia coli str. K-12 substr. MG1655
|-
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[[EcoCyc]]
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EcoCyc:EG11859
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[[EcoGene]]
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EcoGene:EG11859
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[[uniprot:P32177|UniProt:P32177]]
[http://www.ncbi.nlm.nih.gov/gene?term=948393 GeneID:948393]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF02634 PFAM:PF02634]
RegulonDB:ECK120001790
|
|
''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]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_418331 RefSeq:NP_418331]
EchoBASE:EB1805
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
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===Categories===
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0009061_!_anaerobic respiration]]

Latest revision as of 21:09, 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

FdhD

Synonyms

formate dehydrogenase formation protein[1], B3895[2][1], FdhD[2][1] , ECK3888, JW3866, b3895

Product description

affects formate dehydrogenase-N[2][3]

Redox enzyme maturation protein (REMP) for FdnG/FdoG; required for formate dehydrogenase activity; probable cytoplasmic protein[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:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00187

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:0008863

formate dehydrogenase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003786

F

Seeded from EcoCyc (v14.0)

complete

GO:0009326

formate dehydrogenase complex

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003786

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

Protein

aceE

PMID:15690043[5]

Experiment(s):EBI-886164

Protein

aceF

PMID:15690043[5]

Experiment(s):EBI-886164

Protein

iscS

PMID:15690043[5]

Experiment(s):EBI-886164, EBI-887896

Protein

lpdA

PMID:15690043[5]

Experiment(s):EBI-886164

Protein

lysU

PMID:15690043[5]

Experiment(s):EBI-886164

Protein

rpsB

PMID:15690043[5]

Experiment(s):EBI-886164

Protein

tatE

PMID:16606699[6]

Experiment(s):EBI-1146919

Protein

gltJ

PMID:16606699[6]

Experiment(s):EBI-1146919

Protein

lolB

PMID:16606699[6]

Experiment(s):EBI-1146919

Protein

groL

PMID:16606699[6]

Experiment(s):EBI-1146919

Protein

cspE

PMID:16606699[6]

Experiment(s):EBI-1146919

Protein

yncC

PMID:16606699[6]

Experiment(s):EBI-1146919

Protein

dapA

PMID:16606699[6]

Experiment(s):EBI-1146919

Protein

atoA

PMID:16606699[6]

Experiment(s):EBI-1146919

Protein

rpmB

PMID:16606699[6]

Experiment(s):EBI-1146919

Protein

ahpC

PMID:16606699[6]

Experiment(s):EBI-1146919

Protein

iscS

PMID:16606699[6]

Experiment(s):EBI-1146919

Protein

ydfX

PMID:16606699[6]

Experiment(s):EBI-1146919

Protein

map

PMID:19402753[7]

MALDI(Z-score):38.741739

Protein

gatZ

PMID:19402753[7]

MALDI(Z-score):23.393145

Protein

iscS

PMID:19402753[7]

LCMS(ID Probability):99.6 MALDI(Z-score):46.320178

Protein

ibpB

PMID:19402753[7]

MALDI(Z-score):35.294336

Protein

narJ

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

dnaJ

PMID:19402753[7]

MALDI(Z-score):34.017231

Protein

groS

PMID:19402753[7]

MALDI(Z-score):28.256905

Protein

lysU

PMID:19402753[7]

MALDI(Z-score):25.833714

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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 

MKKTQRKEIE NVTNITGVRQ IELWRRDDLQ HPRLDEVAEE VPVALVYNGI SHVVMMASPK
DLEYFALGFS LSEGIIESPR DIFGMDVVPS CNGLEVQIEL SSRRFMGLKE RRRALAGRTG
CGVCGVEQLN DIGKPVQPLP FTQTFDLNKL DDALRHLNDF QPVGQLTGCT HAAAWMLPSG
ELVGGHEDVG RHVALDKLLG RRSQEGESWQ QGAVLVSSRA SYEMVQKSAM CGVEILFAVS
AATTLAVEVA ERCNLTLVGF CKPGRATVYT HPQRLSN
Length

277

Mol. Wt

30.558 kDa

pI

6.4 (calculated)

Extinction coefficient

22,460 - 23,335 (calc based on 4 Y, 3 W, and 7 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

38..276

PF02634 FdhD/NarQ family

PMID:19920124[8]

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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=fdhD 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:16131735

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948393

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012714

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P32177

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11859

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11859

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948393

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001790

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1805

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. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  6. ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 6.10 6.11 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 7.8 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  8. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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