holD:Gene Product(s): Difference between revisions

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)	2.7.7.7^[1]
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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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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^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)
↑ ^2.0 ^2.1 ^2.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^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
↑ ^6.0 ^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
↑ ^7.00 ^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
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

holD:Gene Product(s): Difference between revisions

Latest revision as of 21:15, 17 February 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

Navigation menu

@@ Line 40: / Line 40: @@
 !align=left {{table heading style}} |Standard name
 ||
-HolD product
+HolD
 |-
 !align=left {{table heading style}} |Synonyms
 ||
-DNA polymerase III, psi subunit product<ref name='LIB:Riley_2006'/>, B4372 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HolD product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>
+''DNA polymerase III, psi subunit <ref name='LIB:Riley_2006'/>, B4372 <ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HolD <ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK4363, JW4334, b4372''
 |-
 !align=left {{table heading style}} |Product description
 ||
-DNA polymerase III, &psi; subunit<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>;
+DNA polymerase III, ψ subunit<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>;
 Component of [[:Category:Complex:DNA polymerase III, preinitiation complex|DNA polymerase III, preinitiation complex]]<ref name='LIB:EcoCyc11.1'/>; [[:Category:Complex:DNA polymerase III, holoenzyme|DNA polymerase III, holoenzyme]]<ref name='LIB:EcoCyc11.1'/>
@@ Line 77: / Line 77: @@
 *
 ****************************************************************************************** -->{{Product_GO_help}}
-{|   id="O46ab302205651"  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="O46ab302205651"  class=" tableEdit GO_table_product dataTable"
 |- {{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
 |-
 |
@@ Line 303: / Line 303: @@
 *
 ****************************************************************************************** -->{{Product_interactions_help}}
-{|   id="U46ab302f2eb27"  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="U46ab302f2eb27"  class=" tableEdit Product_interactions_table dataTable"
 |- {{table heading style}}
 !|Partner Type!!Partner!!Notes!!References!!Evidence
@@ Line 504: / Line 504: @@
 |
 Experiment(s):EBI-885289<br />
+|-
+|
+Protein
+|
+rplU
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+ugpB
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.0
+|-
+|
+Protein
+|
+secA
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):18.742787
+|-
+|
+Protein
+|
+topB
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):26.973960
+|-
+|
+Protein
+|
+holA
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):38.580856
+|-
+|
+Protein
+|
+recQ
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):26.090050
+|-
+|
+Protein
+|
+ssb
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6 MALDI(Z-score):17.053160
+|-
+|
+Protein
+|
+dnaX
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6 MALDI(Z-score):28.766064
+|-
+|
+Protein
+|
+holE
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6 MALDI(Z-score):18.001668
+|-
+|
+Protein
+|
+rplL
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
 |-
 |
@@ Line 533: / Line 643: @@
 *
 ****************************************************************************************** -->{{Product_localization_help}}
-{|   id="K46ab303110f03"  class=" tableEdit Product_localization_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46ab303110f03"  class=" tableEdit Product_localization_table"
 |- {{table heading style}}
-!|Compartment!!Description!!Evidence!!Source!!Notes
+!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
 |- class="tableEdit_footer"
@@ Line 559: / Line 669: @@
 ****************************************************************************************** -->{{Product_physical_properties_help}}
 {|   id="J46ab303247f6e"  class=" tableEdit Product_phys_prop_table"
+|-
+!align=left {{table heading style}} |Name
+||
 |-
@@ Line 599: / Line 713: @@
 *
 ****************************************************************************************** -->{{Product_domains_motifs_help}}
-{|   id="S46ab3032c02a1"  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="S46ab3032c02a1"  class=" tableEdit Product_motif_table dataTable"
 |- {{table heading style}}
 !|Type!!Residues!!Description!!Notes!!References
@@ Line 648: / Line 762: @@
 ||
 View models at:
-* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
+* [http://www.proteinmodelportal.org/query/uniprot/P28632 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=P28632 PSI-PRED (P28632)]
-* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
+* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P28632 Genomes TO Protein (P28632)] (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)
 |- class="tableEdit_footer"
@@ Line 693: / Line 805: @@
 *
 ****************************************************************************************** -->{{Product_resources_help}}
-{|   id="R46ab30342bcee"  class=" tableEdit Product_resource_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46ab30342bcee"  class=" tableEdit Product_resource_table"
 |- {{table_heading_style}}
 !|Resource type!!Source!!Notes/Reference
@@ Line 715: / Line 827: @@
 *
 ****************************************************************************************** -->{{Gene_accessions_help}}
-{|   id="X46ab30349350e"  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="X46ab30349350e"  class=" tableEdit Gene_accessions_table"
 |- {{table_heading_style}}
 !|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/16132190 GI:16132190]
+|
+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_418789.1 GeneID:948890]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[ASAP]]
+|
+ASAP:ABE-0014340
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+|
+[http://www.uniprot.org/uniprot/P28632 UniProtKB/Swiss-Prot:P28632]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
 |
-[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11414-MONOMER EcoCyc:EG11414-MONOMER]
+[[EcoCyc]]
 |
+EcoCyc:EG11414
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[[EcoGene]]
+|
+EcoGene:EG11414
+|
+''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]])
 |
-[[uniprot:P28632|UniProt:P28632]]
+[http://www.ncbi.nlm.nih.gov/gene?term=948890 GeneID:948890]
 |
+Escherichia coli str. K-12 substr. MG1655
 |-
 |
-[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
+[[RegulonDB]]
 |
-[http://pfam.janelia.org/protein/P28632 Pfam:P28632]
+RegulonDB:ECK120001380
 |
+''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_418789 RefSeq:NP_418789]
+EchoBASE:EB1386
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |- class="tableEdit_footer"
@@ Line 765: / Line 912: @@
 *
 ****************************************************************************************** -->
-{|   id="W46ab303928b0e"  class=" tableEdit Links_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46ab303928b0e"  class=" tableEdit Links_table"
 |- {{table_heading_style}}
 !|Name!!URL!!Comments
@@ Line 786: / Line 933: @@
 {{BacktoTop}}
 [[Category:Proteins]]
-[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0006261_!_DNA-dependent DNA replication]][[Category:Complex:DNA polymerase III, preinitiation complex]][[Category:Complex:DNA polymerase III, holoenzyme]][[Category:Products with structures in PDB]]
-[[Category:Pfam:PF03603_!_DNA polymerase III psi subunit]]

holD:Gene Product(s): Difference between revisions

Latest revision as of 21:15, 17 February 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

Navigation menu

Search