rffG:Gene Product(s): Difference between revisions

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<noinclude>{{TabsTop}}
<noinclude>{{TabsTop}}
{{Tab|Quickview|rffG}}{{Tab|Gene|rffG}}{{Tab On|Gene Product(s)|rffG}}{{Tab|Expression|rffG}}{{Tab|Evolution|rffG}}{{Tab|On One Page|rffG}}{{TabsBottom}}
{{Tab|Quickview|rffG}}{{Tab|Gene|rffG}}{{Tab On|Gene Product(s)|rffG}}{{Tab|Expression|rffG}}{{Tab|Evolution|rffG}}{{Tab|On One Page|rffG}}{{TabsBottom}}
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|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Gene Product Resources|Resources]]
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==Nomenclature==
==Nomenclature==
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|-
|-
!{{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
|
||
RffG product
RffG  
|-
|-
!{{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
|
||
dTDP-glucose 4,6-dehydratase<ref name='LIB:Riley_2006'/>, B3788<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Rff<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, NfrC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, RffG<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''dTDP-glucose 4,6-dehydratase<ref name='LIB:Riley_2006'/>, B3788<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Rff<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, NfrC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, RffG<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK3780, JW5598, rff, b3788''
|-
|-
!{{table heading style}} |Product description
!align=left {{table heading style}} |Product description
|
||
dTDP-glucose 4,6-dehydratase 2<ref name='LIB:EcoCyc10.6'/>; dTDP-glucose 4,6-dehydratase 2<ref name='LIB:EcoCyc11.1'/>
dTDP-glucose 4,6-dehydratase 2<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


dTDP-glucose dehydratase; needed for ECA (enterobacterial common antigen) synthesis<ref name='LIB:EcoGene'/>
|-
|-
!{{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
|
||
*[http://www.brenda.uni-koeln.de/php/result_flat.php4?ecno=4.2.1.46 4.2.1.46]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.46 4.2.1.46]<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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==Function==
==Function==
{{BacktoTop}}
<protect>
<protect>
===Gene Ontology===
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.28179.X46ab03c9c1a4a-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46ab03c9c1a4a"  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
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-
|-  
|
|
 
|
|
GO:0005737  
GO:0005737  
|
|
cytoplasm  
cytoplasm
|
|
 
|
|
 
|
|
 
|
|
C  
C
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
|
|
required fields missing 
Missing: evidence, reference
|-
|-
|
 
|
GO:0003824
|
catalytic activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR001509
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003824
|
catalytic activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR016040
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005488
|
binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR016040
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0008152
|
metabolic process
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR016040
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0008460
|
dTDP-glucose 4,6-dehydratase activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR005888
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0008460
|
dTDP-glucose 4,6-dehydratase activity
|
GOA:spec<br />GO_REF:0000003
|
IEA: Inferred from Electronic Annotation
|
EC:4.2.1.46
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0009103
|
lipopolysaccharide biosynthetic process
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0448
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-  
|
|
 
|
|
GO:0009243
GO:0009225
|
|
O antigen biosynthetic process  
nucleotide-sugar metabolic process
|
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR005888
|
|
P  
P
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-
|-  
|
|
 
|
|
GO:0009246
GO:0016829
|
|
enterobacterial common antigen biosynthetic process
lyase activity
|
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0456
|
|
P
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-
|-  
|
|
 
|
|
GO:0009435
GO:0044237
|
|
NAD biosynthetic process  
cellular metabolic process
|
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR001509
|
|
P  
P
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-
|-  
|
|
 
|
|
GO:0042280
GO:0050662
|
|
cell surface antigen activity, host-interacting
coenzyme binding
|
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR001509
|
|
F  
F
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
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===Interactions===
<span id="Interactions"></span><big>'''Interactions'''</big>
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!Partner Type!!Partner!!Notes
!|Partner Type!!Partner!!Notes!!References!!Evidence
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<!--Function_notes--></protect>
<!--Function_notes--></protect>
===Notes===
===Notes===


==Localization==
==Localization==
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!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
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<protect><!--Localization_notes--></protect>
<protect><!--Localization_notes--></protect>
===Notes===
===Notes===


==Structure and Physical Properties==
==Structure and Physical Properties==
{{BacktoTop}}
<protect>
<protect>
===Physical Properties===
<span id="Sequence"></span><big>'''Physical Properties'''</big>
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|-
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!{{table heading style}} |Sequence
!align=left {{table heading style}} |Name
|
||
 
|-
!align=left {{table heading style}} |Sequence
||
[http://biocyc.org/ECOLI/sequence-aa?object=DTDPGLUCDEHYDRAT2-MONOMER at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=DTDPGLUCDEHYDRAT2-MONOMER at EcoCyc]  
<pre>MRKILITGGA GFIGSALVRY IINETSDAVV VVDKLTYAGN LMSLAPVAQS ERFAFEKVDI
<pre>MRKILITGGA GFIGSALVRY IINETSDAVV VVDKLTYAGN LMSLAPVAQS ERFAFEKVDI
Line 191: Line 383:
YAIDASKIAR ELGWLPQETF ESGMRKTVQW YLANESWWKQ VQDGSYQGER LGLKG</pre>  
YAIDASKIAR ELGWLPQETF ESGMRKTVQW YLANESWWKQ VQDGSYQGER LGLKG</pre>  
|-
|-
!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Length
||
355
|-
!align=left {{table heading style}} |Mol. Wt
||
39.754 kDa
|-
!align=left {{table heading style}} |pI
||
5.9 (calculated)
|-
!align=left {{table heading style}} |Extinction coefficient
||
65,320 - 65,945 (calc based on 18 Y, 7 W, and 5 C residues)
 
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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
<td><!--box uid=421aa90e079fa326b6494f812ad13e79.28179.B46ab03ead3e09-->
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!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
|
39.75 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
4..252
|-
|
!{{table heading style}} |pI
[http://pfam.janelia.org/family/PF01370 PF01370  NAD dependent epimerase/dehydratase family]
|
 
|
|
PMID:19920124
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<!-- motifs column 2-->
   
   
<motif_map/>
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<table><tr valign='top'><td>
<span id='Structure'></span><big>'''Structure'''</big><br />
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!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Structures
|
||
65320 - 65945 (calc based on 18 Y, 7 W, and 5 C residues)
<beststructure>
gene=rffG
taxon=562,83333
</beststructure>
|-
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!align=left {{table heading style}} |Models
||
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/P27830 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P27830 PSI-PRED (P27830)]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P27830 Genomes TO Protein (P27830)] (GTOP)
 
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===Domains/Motifs/Modification Sites===
</td><td></protect>
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==== Structure figures ====
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!Type!!Residues!!Description!!Notes
 
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===Structure===
 
 
 
 
 
 
 
 


{{Product_structure_help}}
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</td><tr><table><!--Structure_notes--></protect>
===Notes===
===Notes===




==Gene Product Resources==
==Gene Product Resources==
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!|Resource type!!Source!!Notes/Reference
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<protect><!--Resources_notes--></protect>
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===Notes===
===Notes===


==Accessions in Other Databases==
==Accessions in Other Databases==
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
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[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/49176411 GI:49176411]
|
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/YP_026255.1 GeneID:948300]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0012376
|
''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/P27830 UniProtKB/Swiss-Prot:P27830]
|
Escherichia coli str. K-12 substr. MG1655
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=DTDPGLUCDEHYDRAT2-MONOMER EcoCyc:DTDPGLUCDEHYDRAT2-MONOMER] 
EcoCyc:EG11453
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.expasy.ch/cgi-bin/sprot-search-ac?P27830 UniProt:P27830] 
EcoGene:EG11453
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
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[http://www.sanger.ac.uk/Software/Pfam/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF01370 PFAM:PF01370]
[http://www.ncbi.nlm.nih.gov/gene?term=948300 GeneID:948300]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=YP_026255 RefSeq:YP_026255] 
RegulonDB:ECK120001416
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
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[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://salilab.org/modbase/searchbyid?databaseID=P27830 ModBase:P27830] 
EchoBASE:EB1422
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
{{BacktoTop}}
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<noinclude>
<noinclude>
==References==
==References==
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
[[Category:GO:0005737]][[Category:GO:0009243]][[Category:GO:0009246]][[Category:GO:0009435]][[Category:GO:0042280]]</noinclude>
===Categories===
{{BacktoTop}}
[[Category:Proteins]]

Latest revision as of 21:08, 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

RffG

Synonyms

dTDP-glucose 4,6-dehydratase[1], B3788[2][1], Rff[2][1], NfrC[2][1], RffG[2][1] , ECK3780, JW5598, rff, b3788

Product description

dTDP-glucose 4,6-dehydratase 2[2][3]

dTDP-glucose dehydratase; needed for ECA (enterobacterial common antigen) synthesis[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

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001509

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

F

Seeded from EcoCyc (v14.0)

complete

GO:0005488

binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

F

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:0008460

dTDP-glucose 4,6-dehydratase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005888

F

Seeded from EcoCyc (v14.0)

complete

GO:0008460

dTDP-glucose 4,6-dehydratase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.2.1.46

F

Seeded from EcoCyc (v14.0)

complete

GO:0009103

lipopolysaccharide biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0448

P

Seeded from EcoCyc (v14.0)

complete

GO:0009225

nucleotide-sugar metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005888

P

Seeded from EcoCyc (v14.0)

complete

GO:0016829

lyase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0456

F

Seeded from EcoCyc (v14.0)

complete

GO:0044237

cellular metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001509

P

Seeded from EcoCyc (v14.0)

complete

GO:0050662

coenzyme binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001509

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
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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 

MRKILITGGA GFIGSALVRY IINETSDAVV VVDKLTYAGN LMSLAPVAQS ERFAFEKVDI
CDRAELARVF TEHQPDCVMH LAAESHVDRS IDGPAAFIET NIVGTYTLLE AARAYWNALT
EDKKSAFRFH HISTDEVYGD LHSTDDFFTE TTPYAPSSPY SASKASSDHL VRAWLRTYGL
PTLITNCSNN YGPYHFPEKL IPLMILNALA GKSLPVYGNG QQIRDWLYVE DHARALYCVA
TTGKVGETYN IGGHNERKNL DVVETICELL EELAPNKPHG VAHYRDLITF VADRPGHDLR
YAIDASKIAR ELGWLPQETF ESGMRKTVQW YLANESWWKQ VQDGSYQGER LGLKG
Length

355

Mol. Wt

39.754 kDa

pI

5.9 (calculated)

Extinction coefficient

65,320 - 65,945 (calc based on 18 Y, 7 W, and 5 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

4..252

PF01370 NAD dependent epimerase/dehydratase family

PMID:19920124[5]

edit table

<motif_map/>

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

Structures

<beststructure> gene=rffG 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:49176411

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948300

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012376

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P27830

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11453

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11453

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948300

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001416

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1422

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 1.5 1.6 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. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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