holD:Gene Product(s): Difference between revisions

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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWiki Page]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0014340&formSubmitReturn=1 ASAP:ABE-0014340]
ASAP:ABE-0014340
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11414 ECOCYC:EG11414]
EcoCyc:EG11414
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
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[http://ecogene.org/geneinfo.php?eg_id=EG11414 EcoGene:EG11414]
EcoGene:EG11414
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[RegulonDB]]
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RegulonDB:ECK120001380
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB1386
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Revision as of 08:11, 27 May 2013

{{#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

HolD

Synonyms

DNA polymerase III, psi subunit [1], B4372 [2][1], HolD [2][1] , ECK4363, JW4334, b4372

Product description

DNA polymerase III, ψ subunit[2][3];

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

DNA polymerase, psi subunit, clamp loader complex subunit[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:0003887

DNA-directed DNA polymerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004615

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:IPR018382

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:IPR004615

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018382

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:0008408

3'-5' exonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004615

F

Seeded from EcoCyc (v14.0)

complete

GO:0008408

3'-5' exonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018382

F

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

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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

Subunits of DNA polymerase III, preinitiation complex

could be indirect

Protein

ssb

PMID:15690043[5]

Experiment(s):EBI-880133, EBI-885289

Protein

pyrI

PMID:16606699[6]

Experiment(s):EBI-1147919

Protein

ycgL

PMID:16606699[6]

Experiment(s):EBI-1147919

Protein

ynbC

PMID:15690043[5]

Experiment(s):EBI-880133

Protein

dnaX

PMID:15690043[5]

Experiment(s):EBI-880133, EBI-885289

Protein

holA

PMID:15690043[5]

Experiment(s):EBI-880133

Protein

holB

PMID:15690043[5]

Experiment(s):EBI-880133, EBI-885437

Protein

holC

PMID:15690043[5]

Experiment(s):EBI-880133, EBI-880166, EBI-885289, EBI-885330

Protein

recQ

PMID:15690043[5]

Experiment(s):EBI-880133

Protein

rplM

PMID:15690043[5]

Experiment(s):EBI-880133

Protein

rpoC

PMID:15690043[5]

Experiment(s):EBI-880133

Protein

secA

PMID:15690043[5]

Experiment(s):EBI-880133

Protein

topB

PMID:15690043[5]

Experiment(s):EBI-880133

Protein

rplC

PMID:15690043[5]

Experiment(s):EBI-880133

Protein

rplL

PMID:15690043[5]

Experiment(s):EBI-885289

Protein

rplU

PMID:15690043[5]

Experiment(s):EBI-885289

Protein

rpmB

PMID:15690043[5]

Experiment(s):EBI-885289

Protein

rplU

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

ugpB

PMID:19402753[7]

LCMS(ID Probability):99.0

Protein

secA

PMID:19402753[7] 

MALDI(Z-score):18.742787

Protein

topB

PMID:19402753[7] 

MALDI(Z-score):26.973960

Protein

holA

PMID:19402753[7] 

MALDI(Z-score):38.580856

Protein

recQ

PMID:19402753[7] 

MALDI(Z-score):26.090050

Protein

ssb

PMID:19402753[7]

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

Protein

dnaX

PMID:19402753[7]

LCMS(ID Probability):99.6 MALDI(Z-score):28.766064

Protein

holE

PMID:19402753[7]

LCMS(ID Probability):99.6 MALDI(Z-score):18.001668

Protein

rplL

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

Subunits of DNA polymerase III, holoenzyme

could be indirect


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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 

MTSRRDWQLQ QLGITQWSLR RPGALQGEIA IAIPAHVRLV MVANDLPALT DPLVSDVLRA
LTVSPDQVLQ LTPEKIAMLP QGSHCNSWRL GTDEPLSLEG AQVASPALTD LRANPTARAA
LWQQICTYEH DFFPRND
Length

137

Mol. Wt

15.174 kDa

pI

5.7 (calculated)

Extinction coefficient

23,490 - 23,740 (calc based on 1 Y, 4 W, and 2 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

1..128

PF03603 DNA polymerase III psi subunit

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=holD 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:16132190

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948890

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014340

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P28632

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11414

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11414

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948890

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001380

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1386

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 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. ↑ 5.00 5.01 5.02 5.03 5.04 5.05 5.06 5.07 5.08 5.09 5.10 5.11 5.12 5.13 5.14 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  6. ↑ 6.0 6.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 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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