ylaB:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
conserved inner membrane protein<ref name='LIB:Riley_2006'/>, B0457<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YlaB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''conserved inner membrane protein<ref name='LIB:Riley_2006'/>, B0457<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YlaB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0451, JW5062, b0457''
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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:0016021
GO:0005886
|
plasma membrane
|
GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
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SP_KW:KW-1003
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C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0016020
|
|
integral to membrane
membrane
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0812
SP_KW:KW-0472
|
|
C
C
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
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GO:0005886
GO:0016021
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|
plasma membrane
integral to membrane
|
|
GO_REF:0000004<br />GO_REF:0000023
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-1003<br />SP_SL:SL-0039
SP_KW:KW-0812
|
|
C
C
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
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complete  
complete  
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|
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GO:0016020
GO:0016021
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membrane
integral to membrane
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GO_REF:0000004
GO_REF:0000023
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0472
SP_SL:SL-9909
|
|
C
C
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence


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!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
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Daley et al. (2005) <ref name=PMID:15919996/>
Daley et al. (2005) <ref name=PMID:15919996/>
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!align=left {{table heading style}} |Name
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IYLDDFGTGY SSLSYLQDLD VDILKIDKSF VDALEYKNVT PHIIEMAKTL KLKMVAEGIE
IYLDDFGTGY SSLSYLQDLD VDILKIDKSF VDALEYKNVT PHIIEMAKTL KLKMVAEGIE
TSKQEEWLRQ HGVHYGQGWL YSKALPKEDF LRWAEQHL</pre>  
TSKQEEWLRQ HGVHYGQGWL YSKALPKEDF LRWAEQHL</pre>  
|-
!align=left {{table heading style}} |Length
||
518
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
58.72 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
58.933 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
6.1 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
99810 - 100185 (calc based on 19 Y, 13 W, and 3 C residues)  
99,810 - 100,185 (calc based on 19 Y, 13 W, and 3 C residues)


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|- {{table heading style}}
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-  
|-  
|
|
Domain
Domain
|
|
268 - 516
272..502
|
|
[[interpro:IPR001633|EAL]]
[http://pfam.janelia.org/family/PF00563 PF00563  EAL domain]
|
|
[http://www.uniprot.org/uniprot/P77473#section_features UniProt:P77473]
 
|-
|
Domain
|
7 - 29
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
245 - 267
|
Predicted membrane-spanning helix.
|
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
PMID:19920124


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</td>
</td>
<td>
<td>
<!-- motifs column 2-->
<motif_map/>
{{TMHMM Picture|ylaB}}
{{TMHMM Picture|ylaB}}
</td>
</td>
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</table>
</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>ylaB
<beststructure>
562</beststructure>
gene=ylaB
 
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=ylaB&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P77473 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=ylaB&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P77473 PSI-PRED (P77473)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P77473 Genomes TO Protein (P77473)] (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>
</td><td></protect>
==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
<protect><!--          ***** PLEASE DO NOT EDIT BELOW THIS LINE *****        -->
</td><tr><table><!--Structure_notes--></protect>
===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://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6252-MONOMER EcoCyc:G6252-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/90111138 GI:90111138]
|
|
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_414990.2 GeneID:948951]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0001584
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P77473 UniProtKB/Swiss-Prot:P77473]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:G6252
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG14237
|
''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:P77473|UniProt:P77473]]
[http://www.ncbi.nlm.nih.gov/gene?term=948951 GeneID:948951]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00563 PFAM:PF00563]
RegulonDB:ECK120002862
|
|
''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_414990 RefSeq:NP_414990]
EchoBASE:EB3988
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
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===Categories===
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:Pfam:PF00563_!_EAL domain]]

Latest revision as of 20:25, 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

YlaB

Synonyms

conserved inner membrane protein[1], B0457[2][1], YlaB[2][1] , ECK0451, JW5062, b0457

Product description

conserved protein[2]; conserved inner membrane protein[3]

Putative cyclic-di-GMP phosphodiesterase, 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:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9909

C

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
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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

plasma membrane

C-terminus localized in the cytoplasm with 2 predicted transmembrane domains

Daley et al. (2005) [5]


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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 

MLVRTRHLVG LISGVLILSV LLPVGLSIWL AHQQVETSFI EELDTYSSRV AIRANKVATQ
GKDALQELER WQGAACSEAH LMEMRRVSYS YRYIQEVAYI DNNVPQCSSL EHESPPDTFP
EPGKISKDGY RVWLTSHNDL GIIRYMVAMG TAHYVVMIDP ASFIDVIPYS SWQIDAAIIG
NAHNVVITSS DEIAQGIITR LQKTPGEHIE NNGIIYDILP LPEMNISIIT WASTKMLQKG
WHRQVFIWLP LGLVIGLLAA MFVLRILRRI QSPHHRLQDA IENRDICVHY QPIVSLANGK
IVGAEALARW PQTDGSWLSP DSFIPLAQQT GLSEPLTLLI IRSVFEDMGD WLRQHPQQHI
SINLESPVLT SEKIPQLLRD MINHYQVNPR QIALELTERE FADPKTSAPI ISRYREAGHE
IYLDDFGTGY SSLSYLQDLD VDILKIDKSF VDALEYKNVT PHIIEMAKTL KLKMVAEGIE
TSKQEEWLRQ HGVHYGQGWL YSKALPKEDF LRWAEQHL
Length

518

Mol. Wt

58.933 kDa

pI

6.1 (calculated)

Extinction coefficient

99,810 - 100,185 (calc based on 19 Y, 13 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

272..502

PF00563 EAL domain

PMID:19920124[6]

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<motif_map/>

tmhmm.php?gene=ylaB&show=pic&.jpg
Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=ylaB 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:90111138

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948951

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001584

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P77473

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6252

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14237

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948951

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002862

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3988

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. ↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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