ydeH:Gene Product(s): Difference between revisions

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|-
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!align=left {{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
||
||
YdeH product
YdeH  
|-
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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
conserved protein product<ref name='LIB:Riley_2006'/>, B1535 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YdeG product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YdeH product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''conserved protein<ref name='LIB:Riley_2006'/>, B1535<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YdeG<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YdeH<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK1528, JW1528, ydeG, b1535''
|-
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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conserved protein<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
conserved protein<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


Probable diguanylate cyclase, function unknown<ref name='LIB:EcoGene'/>
|-
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!align=left {{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
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*


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===Notes===
===Notes===
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{{BacktoTop}}
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<protect>
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<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.23083.L46aa6e587f28d-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.23083.L46aa6e587f28d-->
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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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!|Partner Type!!Partner!!Notes
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Protein
|
dld<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1140066<br />
|-
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Protein
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groL<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1140066<br />
|-
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Protein
|
ptsI<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1140066<br />


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===Notes===
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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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GDVVLRTLAT YLASWTRDYE TVYRYGGEEF IIIVKAANDE EACRAGVRIC QLVDNHAITH
GDVVLRTLAT YLASWTRDYE TVYRYGGEEF IIIVKAANDE EACRAGVRIC QLVDNHAITH
SEGHINITVT AGVSRAFPEE PLDVVIGRAD RAMYEGKQTG RNRCMFIDEQ NVINRV</pre>  
SEGHINITVT AGVSRAFPEE PLDVVIGRAD RAMYEGKQTG RNRCMFIDEQ NVINRV</pre>  
|-
!align=left {{table heading style}} |Length
||
296
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
33.86 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
33.863 kDa
|-
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!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
5.6 (calculated)
|-
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!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
39880 - 40505 (calc based on 12 Y, 4 W, and 5 C residues)  
39,880 - 40,505 (calc based on 12 Y, 4 W, and 5 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
 
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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-  
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|
|
Domain
Domain
|
|
157 - 289
129..283
|
[http://pfam.janelia.org/family/PF00990 PF00990  GGDEF domain]
|
|
[[interpro:IPR000160|GGDEF]]
 
|
|
[http://www.uniprot.org/uniprot/P31129#section_features UniProt:P31129]
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>ydeH
<beststructure>
562</beststructure>
gene=ydeH
 
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=ydeH&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P31129 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=ydeH&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P31129 PSI-PRED (P31129)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P31129 Genomes TO Protein (P31129)] (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_notes--></protect>
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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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===Notes===
===Notes===
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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/16129494 GI:16129494]
|
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_416052.1 GeneID:946075]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0005123
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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/P31129 UniProtKB/Swiss-Prot:P31129]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11643-MONOMER EcoCyc:EG11643-MONOMER]
Escherichia coli str. K-12 substr. MG1655
|-  
|
|
[[EcoCyc]]
|
EcoCyc:EG11643
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG11643
|
''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:P31129|UniProt:P31129]]
[http://www.ncbi.nlm.nih.gov/gene?term=946075 GeneID:946075]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00990 PFAM:PF00990]
RegulonDB:ECK120001587
|
|
''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_416052 RefSeq:NP_416052]
EchoBASE:EB1596
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Notes===
===Notes===
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===Categories===
===Categories===
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:Pfam:PF00990_!_GGDEF domain]]

Latest revision as of 20:39, 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

YdeH

Synonyms

conserved protein[1], B1535[2][1], YdeG[2][1], YdeH[2][1] , ECK1528, JW1528, ydeG, b1535

Product description

conserved protein[2][3]

Probable diguanylate cyclase, 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
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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

dld

PMID:16606699[5]

Experiment(s):EBI-1140066

Protein

groL

PMID:16606699[5]

Experiment(s):EBI-1140066

Protein

ptsI

PMID:16606699[5]

Experiment(s):EBI-1140066
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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 

MIKKTTEIDA ILLNLNKAID AHYQWLVSMF HSVVARDASK PEITDNHSYG LCQFGRWIDH
LGPLDNDELP YVRLMDSAHQ HMHNCGRELM LAIVENHWQD AHFDAFQEGL LSFTAALTDY
KIYLLTIRSN MDVLTGLPGR RVLDESFDHQ LRNAEPLNLY LMLLDIDRFK LVNDTYGHLI
GDVVLRTLAT YLASWTRDYE TVYRYGGEEF IIIVKAANDE EACRAGVRIC QLVDNHAITH
SEGHINITVT AGVSRAFPEE PLDVVIGRAD RAMYEGKQTG RNRCMFIDEQ NVINRV
Length

296

Mol. Wt

33.863 kDa

pI

5.6 (calculated)

Extinction coefficient

39,880 - 40,505 (calc based on 12 Y, 4 W, and 5 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

129..283

PF00990 GGDEF domain

PMID:19920124[6]

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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=ydeH 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:16129494

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946075

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005123

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P31129

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11643

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11643

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946075

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001587

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1596

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

Categories

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