cho:Gene Product(s): Difference between revisions

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|-
|-
!align=left {{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
||
||
YdjQ
Cho
|-
|-
!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
endonuclease of nucleotide excision repair<ref name='LIB:Riley_2006'/>, YdjQ<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Cho<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B1741<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''endonuclease of nucleotide excision repair<ref name='LIB:Riley_2006'/>, YdjQ<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Cho<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B1741<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , dinM, ECK1739, JW1730, sosD, ydjQ, b1741''
|-
|-
!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=3.1.25.- 3.1.25.-]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.- 3.1.25.-]<ref name='LIB:Riley_2006'/>


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I46aa7b3cf0ab3"  class=" tableEdit GO_table_product dataTable"   
|- {{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
|-  
|-  
|
|


|
|
GO:0006974
GO:0005737
|
cytoplasm
|
 
|
 
|
 
|
C
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
|
Missing: evidence, reference
|-
|
 
|
GO:0004518
|
nuclease activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR000305
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0004518
|
|
response to DNA damage stimulus
nuclease activity
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0227
SP_KW:KW-0267
|
|
P
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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intracellular
intracellular
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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C
C
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0004518
GO:0006281
|
|
nuclease activity
DNA repair
|
|
GO_REF:0000002<br />GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR000305<br />SP_KW:KW-0267
InterPro:IPR000305
|
|
F
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0009432
GO:0006281
|
|
SOS response
DNA repair
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0742
SP_KW:KW-0228
|
|
P
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0016787
GO:0006281
|
|
hydrolase activity
DNA repair
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0378
SP_KW:KW-0234
|
|
F
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0005515
GO:0006974
|
|
protein binding
response to DNA damage stimulus
|
|
PMID:15690043
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IPI: Inferred from Physical Interaction
IEA: Inferred from Electronic Annotation
|
|
UniProtKB:P0A6F5
SP_KW:KW-0227
|
|
F
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
|
GO:0005737
GO:0009432
|
|
cytoplasm
SOS response
|
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0742
|
|
C
P
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|
 
|
|
GO:0006950
GO:0016787
|
|
response to stress
hydrolase activity
|
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0378
|
|
P
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|


|
|
GO:0006281
GO:0006974
|
|
DNA repair
response to DNA damage stimulus
|
|
GO_REF:0000002<br />GO_REF:0000004<br />GO_REF:0000004<br />GO_REF:0000004
PMID:10760155
|
|
IEA: Inferred from Electronic Annotation
IEP: Inferred from Expression Pattern
|
|
InterPro:IPR000305<br />SP_KW:KW-0228<br />SP_KW:KW-0234<br />SP_KW:KW-0742
 
|
|
P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
 
|
|
complete  
complete  


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Experiment(s):EBI-1140667<br />  
Experiment(s):EBI-1140667<br />  
|-
|
Protein
|
groL
|


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PMID:19402753
|
MALDI(Z-score):17.053160
|-
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Protein
|
groS
|
 
|
PMID:19402753
|
MALDI(Z-score):28.255864
 
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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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CFRSALKRCA GACCGKESHE EHALRLRQSL ERLRVVCWPW QGAVALKEQH PEMTQYHIIQ
CFRSALKRCA GACCGKESHE EHALRLRQSL ERLRVVCWPW QGAVALKEQH PEMTQYHIIQ
NWLWLGAVNS LEEATTLIRT PAGFDHDGYK ILCKPLLSGN YEITELDPAN DQRAS</pre>  
NWLWLGAVNS LEEATTLIRT PAGFDHDGYK ILCKPLLSGN YEITELDPAN DQRAS</pre>  
|-
!align=left {{table heading style}} |Length
||
295
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
33.74 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
33.739 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
9.0 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
40910 - 42035 (calc based on 9 Y, 5 W, and 9 C residues)  
40,910 - 42,035 (calc based on 9 Y, 5 W, and 9 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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<!--
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|- {{table heading style}}
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
34..109
|
[http://pfam.janelia.org/family/PF01541 PF01541  GIY-YIG catalytic domain]
|


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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>cho
<beststructure>
562</beststructure>
gene=cho
 
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=cho&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P76213 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=cho&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P76213 PSI-PRED (P76213)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P76213 Genomes TO Protein (P76213)] (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 *****        -->
</td><tr><table><!--Structure_notes--></protect>
===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/16129695 GI:16129695]
|
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_416255.1 GeneID:948996]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6937-MONOMER EcoCyc:G6937-MONOMER]
Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0005807
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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/P76213 UniProtKB/Swiss-Prot:P76213]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:G6937
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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:P76213|UniProt:P76213]]
EcoGene:EG13993
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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=PF01541 PFAM:PF01541]
[http://www.ncbi.nlm.nih.gov/gene?term=948996 GeneID:948996]
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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_416255 RefSeq:NP_416255]
RegulonDB:ECK120003525
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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=P76213 ModBase:P76213]
EchoBASE:EB3749
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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__
</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0006281_!_DNA repair]][[Category:GO:0006950_!_response to stress]][[Category:GO:0009432_!_SOS response]]
[[Category:Proteins]]

Latest revision as of 20:42, 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

Cho

Synonyms

endonuclease of nucleotide excision repair[1], YdjQ[2][1], Cho[2][1], B1741[2][1] , dinM, ECK1739, JW1730, sosD, ydjQ, b1741

Product description

endonuclease of nucleotide excision repair[2][3]

Endonuclease involved in excision repair, cuts 3' of lesion; requires UvrAB[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:0004518

nuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000305

F

Seeded from EcoCyc (v14.0)

complete

GO:0004518

nuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0267

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000305

C

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000305

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0228

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0234

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0227

P

Seeded from EcoCyc (v14.0)

complete

GO:0009432

SOS response

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0742

P

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

PMID:10760155[5]

IEP: Inferred from Expression Pattern

P

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

groL

PMID:15690043[6]

Experiment(s):EBI-883032

Protein

rplQ

PMID:16606699[7]

Experiment(s):EBI-1140667

Protein

dnaK

PMID:16606699[7]

Experiment(s):EBI-1140667

Protein

rpsI

PMID:16606699[7]

Experiment(s):EBI-1140667

Protein

groL

PMID:16606699[7]

Experiment(s):EBI-1140667

Protein

uspG

PMID:16606699[7]

Experiment(s):EBI-1140667

Protein

groL

PMID:19402753[8]

MALDI(Z-score):17.053160

Protein

groS

PMID:19402753[8]

MALDI(Z-score):28.255864

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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 

MVRRLTSPRL EFEAAAIYEY PEHLRSFLND LPTRPGVYLF HGESDTMPLY IGKSVNIRSR
VLSHLRTPDE AAMLRQSRRI SWICTAGEIG ALLLEARLIK EQQPLFNKRL RRNRQLCALQ
LNEKRVDVVY AKEVDFSRAP NLFGLFANRR AALQALQTIA DEQKLCYGLL GLEPLSRGRA
CFRSALKRCA GACCGKESHE EHALRLRQSL ERLRVVCWPW QGAVALKEQH PEMTQYHIIQ
NWLWLGAVNS LEEATTLIRT PAGFDHDGYK ILCKPLLSGN YEITELDPAN DQRAS
Length

295

Mol. Wt

33.739 kDa

pI

9.0 (calculated)

Extinction coefficient

40,910 - 42,035 (calc based on 9 Y, 5 W, and 9 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

34..109

PF01541 GIY-YIG catalytic domain

PMID:19920124[9]

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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=cho 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:16129695

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948996

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005807

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76213

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6937

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13993

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948996

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003525

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3749

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 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. ↑ Fernández De Henestrosa, AR et al. (2000) Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol. Microbiol. 35 1560-72 PubMed
  6. ↑ Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 7.4 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ 8.0 8.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  9. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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