yafC:Gene Product(s): Difference between revisions

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Fixing Pfam accessions and motif notes fields.
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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
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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''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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{| 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"   
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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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{| 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"   
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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Experiment(s):EBI-1135942<br />  
Experiment(s):EBI-1135942<br />  
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Protein
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hns
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PMID:19402753
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LCMS(ID Probability):99.6
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Protein
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fis
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PMID:19402753
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LCMS(ID Probability):99.6
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Protein
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rpmB
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PMID:19402753
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LCMS(ID Probability):99.6
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Protein
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dnaJ
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PMID:19402753
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LCMS(ID Probability):99.6
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Protein
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ulaR
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PMID:19402753
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LCMS(ID Probability):99.6
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Protein
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yfhH
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PMID:19402753
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LCMS(ID Probability):99.6


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


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!align=left {{table heading style}} |Name
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{| 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"   
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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/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)


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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference
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{|   id="F46aa2389a0f3b"  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]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11649-MONOMER EcoCyc:EG11649-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/16128195 GI:16128195]
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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_414744.1 GeneID:947507]
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Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0000694
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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/P30864 UniProtKB/Swiss-Prot:P30864]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:EG11649
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG11649
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
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[[uniprot:P30864|UniProt:P30864]]
[http://www.ncbi.nlm.nih.gov/gene?term=947507 GeneID:947507]
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Escherichia coli str. K-12 substr. MG1655
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[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
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[http://pfam.janelia.org/protein/P30864 Pfam:P30864]
RegulonDB:ECK120001593
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[EchoBASE]]
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_414744 RefSeq:NP_414744]
EchoBASE:EB1602
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0006350_!_transcription]][[Category:GO:0016564_!_transcription repressor activity]][[Category:GO:0016563_!_transcription activator activity]]
[[Category:Pfam:PF03466_!_LysR substrate binding domain]]
[[Category:Pfam:PF00126_!_Bacterial regulatory helix-turn-helix protein, lysR family]]

Latest revision as of 20:22, 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

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 Notes 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 Notes 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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References

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

  1. ↑ 1.0 1.1 1.2 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. ↑ 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. ↑ 5.0 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
  6. ↑ Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ 7.0 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. ↑ 8.0 8.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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