nemR:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
predicted DNA-binding transcriptional regulator<ref name='LIB:Riley_2006'/>, B1649<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YdhM<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted DNA-binding transcriptional regulator<ref name='LIB:Riley_2006'/>, B1649<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YdhM<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK1645, JW5874, ydhM, b1649''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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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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GO:0006355
GO:0003700
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|
regulation of transcription, DNA-dependent
transcription factor activity
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GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
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InterPro:IPR001647
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P
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|


|
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GO:0003677
GO:0003700
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DNA binding
transcription factor activity
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GO_REF:0000002<br />GO_REF:0000004
PMID:15556475
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IEA: Inferred from Electronic Annotation
ISS: Inferred from Sequence or Structural Similarity
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InterPro:IPR012287<br />SP_KW:KW-0238
Swiss-Prot:P0ACS9
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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transcription factor activity
transcription factor activity
|
|
GO_REF:0000002
PMID:18567656
|
IDA: Inferred from Direct Assay
|
 
|
|
IEA: Inferred from Electronic Annotation
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0016566
|
specific transcriptional repressor activity
|
PMID:15556475
|
ISS: Inferred from Sequence or Structural Similarity
|
Swiss-Prot:P0ACS9
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0016566
|
specific transcriptional repressor activity
|
PMID:18567656
|
IDA: Inferred from Direct Assay
|
|
InterPro:IPR001647
 
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0032582
|
negative regulation of gene-specific transcription
|
PMID:15556475
|
ISS: Inferred from Sequence or Structural Similarity
|
Swiss-Prot:P0ACS9
|
P
|
Seeded from [[EcoCyc]] (v14.0)
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|
complete  
complete  
|-
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|
GO:0032582
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negative regulation of gene-specific transcription
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PMID:18567656
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IDA: Inferred from Direct Assay
|


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P
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Seeded from [[EcoCyc]] (v14.0)
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complete
 
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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Protein
Protein
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[[kdsB:Gene_Product(s)|kdsB]]<br />
kdsB<br />
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|
PMID:15690043
|
Experiment(s):EBI-890408<br />  
|-
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Protein
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kdsB
|
|


|[[PMID:15690043]]<ref name=PMID:15690043/>
|
|
Experiment(s):[http://www.ebi.ac.uk/iintact/search/do/search?searchString=EBI-890408 EBI-890408]<br />
PMID:19402753
|
LCMS(ID Probability):99.4


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


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!align=left {{table heading style}} |Name
||


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DMRSAMDKGA RGVIALLSQA LENGRENHCL TFCGEPLQQA QVLYALWLGA NLQAKISRSF
DMRSAMDKGA RGVIALLSQA LENGRENHCL TFCGEPLQQA QVLYALWLGA NLQAKISRSF
EPLENALAHV KNIIATPAV</pre>  
EPLENALAHV KNIIATPAV</pre>  
|-
!align=left {{table heading style}} |Length
||
199
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
19.07 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
22.275 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
3.5 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
17420 - 18170 (calc based on 8 Y, 1 W, and 6 C residues)  
17,420 - 18,170 (calc based on 8 Y, 1 W, and 6 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
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|- {{table heading style}}
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-  
|-  
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|
Domain
Domain
|
|
7 - 67
13..59
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[http://pfam.janelia.org/family/PF00440 PF00440  Bacterial regulatory proteins, tetR family]
|
|
[[interpro:IPR003012|HTH tetR-type]]
 
|
|
[http://www.uniprot.org/uniprot/P67430#section_features UniProt:P67430]
PMID:19920124


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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
</tr>
</table>


<span id="Structure"></span><big>'''Structure'''</big>
<table><tr valign='top'><td>
<span id='Structure'></span><big>'''Structure'''</big><br />
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|-
!align=left {{table heading style}} |Structures
!align=left {{table heading style}} |Structures
||
||
<beststructure>ydhM
<beststructure>
562</beststructure>
gene=nemR
 
taxon=562,83333
</beststructure>
|-
|-
!align=left {{table heading style}} |Models
!align=left {{table heading style}} |Models
||
||
View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=ydhM&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P67430 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=ydhM&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P67430 PSI-PRED (P67430)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P67430 Genomes TO Protein (P67430)] (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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==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference


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!|Database!!Accession!!Notes
!|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/145698269 GI:145698269]
|
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_416166.3 GeneID:946166]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0005514
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P67430 UniProtKB/Swiss-Prot:P67430]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
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|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6889-MONOMER EcoCyc:G6889-MONOMER]
EcoCyc:G6889
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
|
|
[[uniprot:P67430|UniProt:P67430]]
EcoGene:EG13947
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00440 PFAM:PF00440]
[http://www.ncbi.nlm.nih.gov/gene?term=946166 GeneID:946166]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_416166 RefSeq:NP_416166]
RegulonDB:ECK120003478
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://salilab.org/modbase/searchbyid?databaseID=P67430 ModBase:P67430]
EchoBASE:EB3705
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0006355_!_regulation of transcription, DNA-dependent]]

Latest revision as of 20:41, 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

YdhM

Synonyms

predicted DNA-binding transcriptional regulator[1], B1649[2][1], YdhM[2][1] , ECK1645, JW5874, ydhM, b1649

Product description

hypothetical protein[2]; predicted DNA-binding transcriptional regulator[3]. YdhM binding to the ydhM-nemA promoter is reduced by addition of NEM. Genomic SELEX identifies a binding site for YdhM in the ydhM-nemA promoter region. [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. 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:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001647

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:15556475[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACS9

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:18567656[4]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016566

specific transcriptional repressor activity

PMID:15556475[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACS9

F

Seeded from EcoCyc (v14.0)

complete

GO:0016566

specific transcriptional repressor activity

PMID:18567656[4]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0032582

negative regulation of gene-specific transcription

PMID:15556475[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACS9

P

Seeded from EcoCyc (v14.0)

complete

GO:0032582

negative regulation of gene-specific transcription

PMID:18567656[4]

IDA: Inferred from Direct Assay

P

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

kdsB

PMID:15690043[6]

Experiment(s):EBI-890408

Protein

kdsB

PMID:19402753[7]

LCMS(ID Probability):99.4

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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 

MNKHTEHDTR EHLLATGEQL CLQRGFTGMG LSELLKTAEV PKGSFYHYFR SKEAFGVAML
ERHYAAYHQR LTELLQSGEG NYRDRILAYY QQTLNQFCQH GTISGCLTVK LSAEVCDLSE
DMRSAMDKGA RGVIALLSQA LENGRENHCL TFCGEPLQQA QVLYALWLGA NLQAKISRSF
EPLENALAHV KNIIATPAV
Length

199

Mol. Wt

22.275 kDa

pI

3.5 (calculated)

Extinction coefficient

17,420 - 18,170 (calc based on 8 Y, 1 W, and 6 C residues)

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See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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

13..59

PF00440 Bacterial regulatory proteins, tetR family

PMID:19920124[8]

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

<motif_map/>

Structure
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Structures

<beststructure> gene=nemR 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:145698269

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946166

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005514

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P67430

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6889

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13947

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946166

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003478

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3705

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. ↑ 4.0 4.1 4.2 4.3 Umezawa, Y et al. (2008) The uncharacterized transcription factor YdhM is the regulator of the nemA gene, encoding N-ethylmaleimide reductase. J. Bacteriol. 190 5890-7 PubMed
  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. ↑ Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  7. ↑ 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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