holC:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
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DNA polymerase III, chi subunit<ref name='LIB:Riley_2006'/>, B4259<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HolC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''DNA polymerase III, chi subunit<ref name='LIB:Riley_2006'/>, B4259<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HolC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK4252, JW4216, b4259''
|-
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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{|   id="A46ab294a664b6"  class=" tableEdit GO_table_product dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46ab294a664b6"  class=" tableEdit GO_table_product dataTable"   
|- {{table_heading_style}}
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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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PMID:9722585
PMID:9722585
|
|
IPI: Inferred from Physical Interaction
IPI: Inferred from Physical Interaction
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{|   id="N46ab295764c8d"  class=" tableEdit Product_interactions_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46ab295764c8d"  class=" tableEdit Product_interactions_table dataTable"   
|- {{table heading style}}
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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Protein
Protein
|
|
[[rpsN:Gene_Product(s)|rpsN]]
rpsN
|
|


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Protein
Protein
|
|
[[rpmC:Gene_Product(s)|rpmC]]
rpmC
|
|


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Protein
Protein
|
|
[[rplS:Gene_Product(s)|rplS]]
rplS
|
|


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Protein
Protein
|
|
[[rplB:Gene_Product(s)|rplB]]
rplB
|
|


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Protein
Protein
|
|
[[rpmG:Gene_Product(s)|rpmG]]
rpmG
|
|


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Protein
Protein
|
|
[[pinR:Gene_Product(s)|pinR]]
pinR
|
|


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Protein
Protein
|
|
[[rplD:Gene_Product(s)|rplD]]
rplD
|
|


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Protein
Protein
|
|
[[rpmB:Gene_Product(s)|rpmB]]
rpmB
|
|


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Protein
Protein
|
|
[[topA:Gene_Product(s)|topA]]
topA
|
|


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Protein
Protein
|
|
[[topB:Gene_Product(s)|topB]]
topB
|
|


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Protein
Protein
|
|
[[yoaA:Gene_Product(s)|yoaA]]
yoaA
|
 
|
PMID:19402753
|
MALDI(Z-score):52.626611
|-
|
Protein
|
guaB
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.0
|-
|
Protein
|
holA
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):38.190892
|-
|
Protein
|
ssb
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):38.945294
|-
|
Protein
|
holE
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
dnaQ
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):36.204812
|-
|
Protein
|
dnaX
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):28.856428
|-
|
Protein
|
holB
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):38.273953
|-
|
Protein
|
recQ
|
|


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PMID:19402753
PMID:19402753
|
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MALDI(Z-score):52.626611
MALDI(Z-score):27.692516
|-  
|-  
|
|
Protein
Protein
|
|
Subunits of [[:Category:Complex:DNA polymerase III, holoenzyme|DNA polymerase III, holoenzyme]]
priA
|
 
|
PMID:19402753
|
MALDI(Z-score):25.941626
|-
|
Protein
|
|
could be indirect
holD
|
|


|
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):17.053160
|-  
|-  
|
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Protein
Protein
|
|
[[guaB:Gene_Product(s)|guaB]]
rplL
|
|


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PMID:19402753
PMID:19402753
|
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LCMS(ID Probability):99.0
LCMS(ID Probability):99.6
|-
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Protein
|
Subunits of [[:Category:Complex:DNA polymerase III, holoenzyme|DNA polymerase III, holoenzyme]]
|
could be indirect
|
 
|


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!|Compartment!!Description!!Evidence!!Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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{|   id="E46ab295b102fd"  class=" tableEdit Product_motif_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46ab295b102fd"  class=" tableEdit Product_motif_table dataTable"   
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!|Type!!Residues!!Description!!Notes!!References
!|Type!!Residues!!Description!!Notes!!References
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View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P28905 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P28905 PSI-PRED (P28905)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P28905 Genomes TO Protein (P28905)] (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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!|Resource type!!Source!!Notes/Reference
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{|   id="E46ab295c52a99"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46ab295c52a99"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|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]])
|
[http://www.ncbi.nlm.nih.gov/protein/16132081 GI:16132081]
|
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_418680.1 GeneID:948787]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0013948
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P28905 UniProtKB/Swiss-Prot:P28905]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG11413
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11413-MONOMER EcoCyc:EG11413-MONOMER]
EcoGene:EG11413
|
|
''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]])
|
|
[http://www.uniprot.org/uniprot/P28905 UniProt:P28905]
[http://www.ncbi.nlm.nih.gov/gene?term=948787 GeneID:948787]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.janelia.org/protein/P28905 Pfam:P28905]
RegulonDB:ECK120001379
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[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_418680 RefSeq:NP_418680]
EchoBASE:EB1385
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 21:14, 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

HolC

Synonyms

DNA polymerase III, chi subunit[1], B4259[2][1], HolC[2][1] , ECK4252, JW4216, b4259

Product description

DNA polymerase III, χ subunit[2][3];

Component of DNA polymerase III, preinitiation complex[3]; DNA polymerase III, holoenzyme[3]

DNA polymerase III, chi subunit[4]

EC number (for enzymes)
edit table


Notes

Function

[back to top]


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:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007459

F

Seeded from EcoCyc (v14.0)

complete

GO:0003887

DNA-directed DNA polymerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007459

F

Seeded from EcoCyc (v14.0)

complete

GO:0003887

DNA-directed DNA polymerase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.7.7

F

Seeded from EcoCyc (v14.0)

complete

GO:0003887

DNA-directed DNA polymerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0239

F

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007459

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0235

P

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

GO:0016779

nucleotidyltransferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0548

F

Seeded from EcoCyc (v14.0)

complete

GO:0043847

DNA polymerase III, DnaX complex, chi/psi subcomplex

PMID:12888503[5]

IPI: Inferred from Physical Interaction

UniProtKB:P0AGE0


C

complete

GO:0032298

positive regulation of DNA-dependent DNA replication initiation

PMID:9989506[6]

IDA: Inferred from Direct Assay

P

complete

GO:0003887

DNA-directed DNA polymerase activity

PMID:9722585[7]

IPI: Inferred from Physical Interaction

UniProtKB:P18022


F

complete

GO:0043847

DNA polymerase III, DnaX complex, chi/psi subcomplex

PMID:9722585[7]

IPI: Inferred from Physical Interaction

UniProtKB:P0AGE0


C

complete

edit table

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

Subunits of DNA polymerase III, preinitiation complex

could be indirect

Protein

ssb

PMID:15690043[8]

Experiment(s):EBI-880166, EBI-885330

Protein

yoaA

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

clpA

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

dnaK

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

dnaX

PMID:15690043[8]

Experiment(s):EBI-880166, EBI-885330

Protein

glnD

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

holA

PMID:15690043[8]

Experiment(s):EBI-880166, EBI-885330

Protein

holB

PMID:15690043[8]

Experiment(s):EBI-880166, EBI-885330

Protein

intE

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

lon

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

priA

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

recQ

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

rplB

PMID:15690043[8]

Experiment(s):EBI-880166, EBI-885330

Protein

rplC

PMID:15690043[8]

Experiment(s):EBI-880166, EBI-885330

Protein

rplD

PMID:15690043[8]

Experiment(s):EBI-880166, EBI-885330

Protein

rpsB

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

rpsJ

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

sbcB

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

secA

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

topA

PMID:15690043[8]

Experiment(s):EBI-880166, EBI-885330

Protein

topB

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

uvrA

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

yhiR

PMID:15690043[8]

Experiment(s):EBI-880166

Protein

pinR

PMID:15690043[8]

Experiment(s):EBI-885330

Protein

holE

PMID:15690043[8]

Experiment(s):EBI-885330

Protein

rplL

PMID:15690043[8]

Experiment(s):EBI-885330

Protein

rplS

PMID:15690043[8]

Experiment(s):EBI-885330

Protein

rplV

PMID:15690043[8]

Experiment(s):EBI-885330

Protein

rpmB

PMID:15690043[8]

Experiment(s):EBI-885330

Protein

rpmC

PMID:15690043[8]

Experiment(s):EBI-885330

Protein

rpmG

PMID:15690043[8]

Experiment(s):EBI-885330

Protein

rpsE

PMID:15690043[8]

Experiment(s):EBI-885330

Protein

rpsN

PMID:15690043[8]

Experiment(s):EBI-885330

Protein

ubiB

PMID:16606699[9]

Experiment(s):EBI-1147770

Protein

ygjN

PMID:16606699[9]

Experiment(s):EBI-1147770

Protein

rpsN

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

rpmC

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

rplB

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):37.515585

Protein

rpmG

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

pinR

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753[10]

LCMS(ID Probability):99.0 MALDI(Z-score):19.138029

Protein

rpmB

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

topA

PMID:19402753[10]

LCMS(ID Probability):99.4 MALDI(Z-score):26.853643

Protein

topB

PMID:19402753[10]

LCMS(ID Probability):92.5 MALDI(Z-score):29.045604

Protein

yoaA

PMID:19402753[10]

MALDI(Z-score):52.626611

Protein

guaB

PMID:19402753[10]

LCMS(ID Probability):99.0

Protein

holA

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):38.190892

Protein

ssb

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):38.945294

Protein

holE

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

dnaQ

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):36.204812

Protein

dnaX

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):28.856428

Protein

holB

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):38.273953

Protein

recQ

PMID:19402753[10]

MALDI(Z-score):27.692516

Protein

priA

PMID:19402753[10]

MALDI(Z-score):25.941626

Protein

holD

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):17.053160

Protein

rplL

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

Subunits of DNA polymerase III, holoenzyme

could be indirect


edit table


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

[back to top]


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 

MKNATFYLLD NDTTVDGLSA VEQLVCEIAA ERWRSGKRVL IACEDEKQAY RLDEALWARP
AESFVPHNLA GEGPRGGAPV EIAWPQKRSS SRRDILISLR TSFADFATAF TEVVDFVPYE
DSLKQLARER YKAYRVAGFN LNTATWK
Length

147

Mol. Wt

16.632 kDa

pI

6.1 (calculated)

Extinction coefficient

29,450 - 29,700 (calc based on 5 Y, 4 W, and 2 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

1..143

PF04364 DNA polymerase III chi subunit, HolC

PMID:19920124[11]

edit table

<motif_map/>

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

Structures

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

Models

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Structure figures

Notes

Gene Product Resources

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Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16132081

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948787

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013948

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P28905

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11413

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11413

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948787

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001379

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1385

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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  1. ↑ 1.0 1.1 1.2 1.3 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. ↑ 3.0 3.1 3.2 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. ↑ Witte, G et al. (2003) DNA polymerase III chi subunit ties single-stranded DNA binding protein to the bacterial replication machinery. Nucleic Acids Res. 31 4434-40 PubMed
  6. ↑ Yuzhakov, A et al. (1999) Trading places on DNA--a three-point switch underlies primer handoff from primase to the replicative DNA polymerase. Cell 96 153-63 PubMed
  7. ↑ 7.0 7.1 Glover, BP & McHenry, CS (1998) The chi psi subunits of DNA polymerase III holoenzyme bind to single-stranded DNA-binding protein (SSB) and facilitate replication of an SSB-coated template. J. Biol. Chem. 273 23476-84 PubMed
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 8.13 8.14 8.15 8.16 8.17 8.18 8.19 8.20 8.21 8.22 8.23 8.24 8.25 8.26 8.27 8.28 8.29 8.30 8.31 8.32 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  9. ↑ 9.0 9.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  10. ↑ 10.00 10.01 10.02 10.03 10.04 10.05 10.06 10.07 10.08 10.09 10.10 10.11 10.12 10.13 10.14 10.15 10.16 10.17 10.18 10.19 10.20 10.21 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  11. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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