ghrA:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
2-ketoacid reductase<ref name='LIB:Riley_2006'/>, B1033<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, GhrA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YcdW<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''2-ketoacid reductase<ref name='LIB:Riley_2006'/>, B1033<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, GhrA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YcdW<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK1019, JW5146, ycdW, b1033''
|-
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.79 1.1.1.79]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.79 1.1.1.79]<ref name='LIB:Riley_2006'/>


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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
|-  
|-  
|
|


|
|
GO:0016491
GO:0005488
|
|
oxidoreductase activity
binding
|
|
GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0560
InterPro:IPR016040
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0016616
GO:0005737
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|
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
cytoplasm
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|
GO_REF:0000002
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR006140
SP_KW:KW-0963
|
|
F
C
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0048037
GO:0005737
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|
cofactor binding
cytoplasm
|
|
GO_REF:0000002
GO_REF:0000023
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR006140
SP_SL:SL-0086
|
|
F
C
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
|
GO:0005737
GO:0005886
|
|
cytoplasm
plasma membrane
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|
GOA:hamap<br />GO_REF:0000020
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|
IEA: Inferred from Electronic Annotation
|
|
HAMAP:MF_01666
|
|
C  
C
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|


|
|
GO:0003824
GO:0008152
|
|
catalytic activity
metabolic process
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR016040
InterPro:IPR016040
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
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|
GO:0016618
|
hydroxypyruvate reductase activity
|
EcoCyc_REF:BiochemJ354-707
|
IDA: Inferred from Direct Assay
|
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0005488
GO:0016618
|
|
binding
hydroxypyruvate reductase activity
|
|
GO_REF:0000002
GOA:hamap<br />GO_REF:0000020
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR016040
HAMAP:MF_01666
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0005886
GO:0016618
|
|
plasma membrane
hydroxypyruvate reductase activity
|
|
GO_REF:0000020
GOA:spec<br />GO_REF:0000003
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
HAMAP:MF_01666
EC:1.1.1.81
|
|
C
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0008152
GO:0030267
|
|
metabolic process
glyoxylate reductase (NADP) activity
|
|
GO_REF:0000002
EcoCyc_REF:BiochemJ354-707
|
|
IEA: Inferred from Electronic Annotation
IDA: Inferred from Direct Assay
|
|
InterPro:IPR016040
 
|
|
P
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0016618
GO:0030267
|
|
hydroxypyruvate reductase activity
glyoxylate reductase (NADP) activity
|
|
GO_REF:0000020<br />GO_REF:0000003
GOA:hamap<br />GO_REF:0000020
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
HAMAP:MF_01666<br />EC:1.1.1.81
HAMAP:MF_01666
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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glyoxylate reductase (NADP) activity
glyoxylate reductase (NADP) activity
|
|
GO_REF:0000020<br />GO_REF:0000003
GOA:spec<br />GO_REF:0000003
|
IEA: Inferred from Electronic Annotation
|
EC:1.1.1.79
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0033554
|
cellular response to stress
|
PMID:19767843
|
IEP: Inferred from Expression Pattern
|
 
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0048037
|
cofactor binding
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
HAMAP:MF_01666<br />EC:1.1.1.79
InterPro:IPR006140
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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oxidation reduction
oxidation reduction
|
|
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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P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
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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GVHVVEDDLL AALDSGKVKG AMLDVFNREP LPPESPLWQH PRVTITPHVA AITRPAEAVE
GVHVVEDDLL AALDSGKVKG AMLDVFNREP LPPESPLWQH PRVTITPHVA AITRPAEAVE
YISRTIAQLE KGERVCGQVD RARGY</pre>  
YISRTIAQLE KGERVCGQVD RARGY</pre>  
|-
!align=left {{table heading style}} |Length
||
325
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
35.34 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
36.837 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
7.3 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
66920 - 67295 (calc based on 8 Y, 10 W, and 3 C residues)  
66,920 - 67,295 (calc based on 8 Y, 10 W, and 3 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
|
104..277
|
[http://pfam.janelia.org/family/PF02826 PF02826  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain]
|


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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>ghrA
<beststructure>
562</beststructure>
gene=ghrA
 
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=ghrA&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P75913 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=ghrA&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P75913 PSI-PRED (P75913)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P75913 Genomes TO Protein (P75913)] (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 ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
<protect><!--          ***** PLEASE DO NOT EDIT BELOW THIS LINE *****        -->
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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
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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=G6539-MONOMER EcoCyc:G6539-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/90111205 GI:90111205]
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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_415551.2 GeneID:946431]
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Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0003503
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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/P75913 UniProtKB/Swiss-Prot:P75913]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:G6539
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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]]
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[[uniprot:P75913|UniProt:P75913]]
EcoGene:EG13869
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
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[http://pfam.sanger.ac.uk/family?acc=PF02826 PFAM:PF02826]
[http://www.ncbi.nlm.nih.gov/gene?term=946431 GeneID:946431]
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Escherichia coli str. K-12 substr. MG1655
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[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_415551 RefSeq:NP_415551]
RegulonDB:ECK120003135
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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=P75913 ModBase:P75913]
EchoBASE:EB3628
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
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===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:GO:0005737_!_cytoplasm]]
[[Category:Proteins]]

Latest revision as of 20:33, 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

YcdW

Synonyms

2-ketoacid reductase[1], B1033[2][1], GhrA[2][1], YcdW[2][1] , ECK1019, JW5146, ycdW, b1033

Product description

G6539[2][3]

Glyoxylate/hydroxypyruvate reductase; activity higher on glyoxylate than hydroxypyruvate[4]

EC number (for enzymes)
edit table


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:0005488

binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

F

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:0005886

plasma membrane

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01666

C

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

P

Seeded from EcoCyc (v14.0)

complete

GO:0016618

hydroxypyruvate reductase activity

EcoCyc_REF:BiochemJ354-707

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016618

hydroxypyruvate reductase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01666

F

Seeded from EcoCyc (v14.0)

complete

GO:0016618

hydroxypyruvate reductase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.1.1.81

F

Seeded from EcoCyc (v14.0)

complete

GO:0030267

glyoxylate reductase (NADP) activity

EcoCyc_REF:BiochemJ354-707

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0030267

glyoxylate reductase (NADP) activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01666

F

Seeded from EcoCyc (v14.0)

complete

GO:0030267

glyoxylate reductase (NADP) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.1.1.79

F

Seeded from EcoCyc (v14.0)

complete

GO:0033554

cellular response to stress

PMID:19767843[5]

IEP: Inferred from Expression Pattern

P

Seeded from EcoCyc (v14.0)

complete

GO:0048037

cofactor binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006140

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

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
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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
edit table


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 

MRINFAQRFS GVSMDIIFYH PTFDTQWWIE ALRKAIPQAR VRAWKSGDND SADYALVWHP
PVEMLAGRDL KAVFALGAGV DSILSKLQAH PEMLNPSVPL FRLEDTGMGE QMQEYAVSQV
LHWFRRFDDY RIQQNSSHWQ PLPEYHREDF TIGILGAGVL GSKVAQSLQT WRFPLRCWSR
TRKSWPGVQS FAGREELSAF LSQCRVLINL LPNTPETVGI INQQLLEKLP DGAYLLNLAR
GVHVVEDDLL AALDSGKVKG AMLDVFNREP LPPESPLWQH PRVTITPHVA AITRPAEAVE
YISRTIAQLE KGERVCGQVD RARGY
Length

325

Mol. Wt

36.837 kDa

pI

7.3 (calculated)

Extinction coefficient

66,920 - 67,295 (calc based on 8 Y, 10 W, and 3 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

Domain

104..277

PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain

PMID:19920124[6]

edit table

<motif_map/>

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

Structures

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

Models

View models at:

edit table

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:90111205

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946431

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003503

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P75913

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6539

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13869

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946431

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003135

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3628

Escherichia coli str. K-12 substr. MG1655

edit table


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 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. ↑ Moen, B et al. (2009) Global responses of Escherichia coli to adverse conditions determined by microarrays and FT-IR spectroscopy. Can. J. Microbiol. 55 714-28 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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