yafC:Gene Product(s): Difference between revisions

Standard name	YafC
Synonyms	predicted DNA-binding transcriptional regulator^[1], B0208^[2]^[1], YafC^[2]^[1] , ECK0208, JW0198, b0208
Product description	predicted DNA-binding transcriptional regulator LYSR-type^[2]^[3] Putative LysR-family transcriptional regulator, function unknown^[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:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000847	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	PMID:15556475^[5]	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P03030	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000847	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:15556475^[5]	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P03030	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016564	transcription repressor activity	PMID:15556475^[5]	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P03030	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	References	Evidence
Protein	ppk	PMID:16606699^[6]	Experiment(s):EBI-1135942
Protein	hns	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	fis	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rpmB	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	dnaJ	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	ulaR	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	yfhH	PMID:19402753^[7]	LCMS(ID Probability):99.6
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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 MKATSEELAI FVSVVESGSF SRAAEQLGQA NSAVSRAVKK LEMKLGVSLL NRTTRQLSLT EEGERYFRRV QSILQEMAAA ESEIMETRNT PRGLLRIDAA TPVVLHFLMP LIKPFRERYP EVTLSLVSSE TIINLIERKV DVAIRAGTLT DSSLRARPLF NSYRKIIASP DYISRYGKPE TIDDLKQHIC LGFTEPASLN TWPIARSDGQ LHEVKYGLSS NSGETLKQLC LSGNGIACLS DYMIDKEIAR GELVELMADK VLPVEMPFSA VYYSDRAVST RIRAFIDFLS EHVKTAPGGA VREA
Length	304
Mol. Wt	33.776 kDa
pI	7.7 (calculated)
Extinction coefficient	18,910 - 19,285 (calc based on 9 Y, 1 W, and 3 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	References
Domain	88..294	PF03466 LysR substrate binding domain	PMID:19920124^[8]
Domain	5..64	PF00126 Bacterial regulatory helix-turn-helix protein, lysR family	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=yafC 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:16128195	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947507	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000694	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P30864	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11649	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11649	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947507	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001593	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1602	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 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
↑ 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.
↑ ^5.0 ^5.1 ^5.2 Pérez-Rueda, E et al. (2004) Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput Biol Chem 28 341-50 PubMed
↑ Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ ^7.0 ^7.1 ^7.2 ^7.3 ^7.4 ^7.5 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
↑ ^8.0 ^8.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

yafC:Gene Product(s): Difference between revisions

Latest revision as of 20:22, 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 35: / Line 35: @@
 *
 ****************************************************************************************** -->{{Product_nomenclature_help}}
-{|  id="A46aa237d9ebb3"  class=" tableEdit Product_nomenclature_table"
+{|   id="A46aa237d9ebb3"  class=" tableEdit Product_nomenclature_table"
 |-
@@ Line 44: / Line 44: @@
 !align=left {{table heading style}} |Synonyms
 ||
-predicted DNA-binding transcriptional regulator<ref name='LIB:Riley_2006'/>, B0208<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YafC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>
+''predicted DNA-binding transcriptional regulator<ref name='LIB:Riley_2006'/>, B0208<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YafC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0208, JW0198, b0208''
 |-
 !align=left {{table heading style}} |Product description
@@ Line 75: / Line 75: @@
 *
 ****************************************************************************************** -->{{Product_GO_help}}
-{|   id="R46aa237e9345b"  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="R46aa237e9345b"  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
 |-
 |
 |
-GO:0006355
+GO:0003677
 |
-regulation of transcription, DNA-dependent
+DNA binding
 |
-GO_REF:0000002<br />GO_REF:0000004
+GOA:spkw<br />SP_KW:GO_REF:0000004
 |
 IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR000847<br />SP_KW:KW-0805
+SP_KW:KW-0238
 |
-P
+F
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 101: / Line 101: @@
 |
-GO:0006350
+GO:0003700
 |
-transcription<input name="field[2]" type="hidden" value="transcription" />
+transcription factor activity
 |
-GO_REF:0000004
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-SP_KW:KW-0804
+InterPro:IPR000847
 |
-P
+F
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 120: / Line 120: @@
 |
-GO:0003700
+GO:0006350
 |
-transcription factor activity
+transcription
 |
-GO_REF:0000002
+GOA:spkw<br />SP_KW:GO_REF:0000004
 |
 IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR000847
+SP_KW:KW-0804
 |
-F
+P
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 139: / Line 139: @@
 |
-GO:0003677
+GO:0006350
 |
-DNA binding
+transcription
 |
-GO_REF:0000004
+PMID:15556475
 |
-IEA: Inferred from Electronic Annotation
+ISS: Inferred from Sequence or Structural Similarity
 |
-SP_KW:KW-0238
+Swiss-Prot:P03030
 |
-F
+P
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 158: / Line 158: @@
 |
-GO:0005515
+GO:0006355
 |
-protein binding
+regulation of transcription, DNA-dependent
 |
-PMID:16606699
+GOA:interpro<br />GO_REF:0000002
 |
-IPI: Inferred from Physical Interaction
+IEA: Inferred from Electronic Annotation
 |
-UniProtKB:P0A7B1
+InterPro:IPR000847
 |
-F
+P
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
 |-
 |
 |
-GO:0016564
+GO:0016563
 |
-transcription repressor activity
+transcription activator activity
 |
+PMID:15556475
 |
+ISS: Inferred from Sequence or Structural Similarity
 |
+Swiss-Prot:P03030
 |
 F
 |
-Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
+Seeded from [[EcoCyc]] (v14.0)
 |
-required fields missing
+complete
 |-
 |
 |
-GO:0016563
+GO:0016564
 |
-transcription activator activity
+transcription repressor activity
 |
+PMID:15556475
 |
+ISS: Inferred from Sequence or Structural Similarity
 |
+Swiss-Prot:P03030
 |
 F
 |
-Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
+Seeded from [[EcoCyc]] (v14.0)
 |
-required fields missing
+complete
 |- class="tableEdit_footer"
@@ Line 225: / Line 225: @@
 *
 ****************************************************************************************** -->{{Product_interactions_help}}
-{|   id="D46aa23869dd78"  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="D46aa23869dd78"  class=" tableEdit Product_interactions_table dataTable"
 |- {{table heading style}}
 !|Partner Type!!Partner!!Notes!!References!!Evidence
@@ Line 239: / Line 239: @@
 |
 Experiment(s):EBI-1135942<br />
+|-
+|
+Protein
+|
+hns
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+fis
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+rpmB
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+dnaJ
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+ulaR
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+yfhH
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
 |- class="tableEdit_footer"
@@ Line 257: / Line 323: @@
 *
 ****************************************************************************************** -->{{Product_localization_help}}
-{|   id="G46a7b4baa7754"  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="G46a7b4baa7754"  class=" tableEdit Product_localization_table"
 |- {{table heading style}}
-!|Compartment!!Description!!Evidence!!Source!!Notes
+!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
 |- class="tableEdit_footer"
@@ Line 282: / Line 348: @@
 *
 ****************************************************************************************** -->{{Product_physical_properties_help}}
-{|  id="K46aa23885e1b4"  class=" tableEdit Product_phys_prop_table"
+{|   id="K46aa23885e1b4"  class=" tableEdit Product_phys_prop_table"
+|-
+!align=left {{table heading style}} |Name
+||
 |-
@@ Line 325: / Line 395: @@
 *
 ****************************************************************************************** -->{{Product_domains_motifs_help}}
-{|   id="V46aa2388b8602"  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="V46aa2388b8602"  class=" tableEdit Product_motif_table dataTable"
 |- {{table heading style}}
 !|Type!!Residues!!Description!!Notes!!References
+|-
+|
+Domain
+|
+..294
+|
+[http://pfam.janelia.org/family/PF03466 PF03466  LysR substrate binding domain]
+|
+|
+PMID:19920124
+|-
+|
+Domain
+|
+..64
+|
+[http://pfam.janelia.org/family/PF00126 PF00126  Bacterial regulatory helix-turn-helix protein, lysR family]
+|
+|
+PMID:19920124
 |- class="tableEdit_footer"
@@ Line 350: / Line 442: @@
 *
 ****************************************************************************************** -->{{Product_structure_help}}
-{|  id="F46a7b4bc47c9d"  class=" tableEdit Product_structure_table"
+{|   id="F46a7b4bc47c9d"  class=" tableEdit Product_structure_table"
 |-
@@ Line 363: / Line 455: @@
 ||
 View models at:
-* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
+* [http://www.proteinmodelportal.org/query/uniprot/P30864 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=P30864 PSI-PRED (P30864)]
-* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
+* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P30864 Genomes TO Protein (P30864)] (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 408: / Line 498: @@
 *
 ****************************************************************************************** -->{{Product_resources_help}}
-{|   id="K46aa23895784f"  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="K46aa23895784f"  class=" tableEdit Product_resource_table"
 |- {{table_heading_style}}
 !|Resource type!!Source!!Notes/Reference
@@ Line 430: / Line 520: @@
 *
 ****************************************************************************************** -->{{Gene_accessions_help}}
-{|   id="F46aa2389a0f3b"  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="F46aa2389a0f3b"  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/16128195 GI:16128195]
+|
+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_414744.1 GeneID:947507]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[ASAP]]
 |
-[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11649-MONOMER EcoCyc:EG11649-MONOMER]
+ASAP:ABE-0000694
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+|
+[http://www.uniprot.org/uniprot/P30864 UniProtKB/Swiss-Prot:P30864]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[EcoCyc]]
+|
+EcoCyc:EG11649
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[[EcoGene]]
+|
+EcoGene:EG11649
+|
+''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:P30864|UniProt:P30864]]
+[http://www.ncbi.nlm.nih.gov/gene?term=947507 GeneID:947507]
 |
+Escherichia coli str. K-12 substr. MG1655
 |-
 |
-[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
+[[RegulonDB]]
 |
-[http://pfam.sanger.ac.uk/family?acc=PF00126 PFAM:PF00126]
+RegulonDB:ECK120001593
 |
+''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_414744 RefSeq:NP_414744]
+EchoBASE:EB1602
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |- class="tableEdit_footer"
@@ Line 480: / Line 605: @@
 *
 ****************************************************************************************** -->
-{|   id="Q46a7b4bfca36e"  class=" tableEdit Links_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a7b4bfca36e"  class=" tableEdit Links_table"
 |- {{table_heading_style}}
 !|Name!!URL!!Comments
@@ Line 501: / Line 626: @@
 {{BacktoTop}}
 [[Category:Proteins]]
-[[Category:GO:0006350_!_transcription]][[Category:GO:0016564_!_transcription repressor activity]][[Category:GO:0016563_!_transcription activator activity]]

yafC:Gene Product(s): Difference between revisions

Latest revision as of 20:22, 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