ylaB:Gene Product(s): Difference between revisions

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|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Gene Product Resources|Resources]]
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{|{{Prettytable}}
{|  id="F46aa311d761c5"  class=" tableEdit Product_nomenclature_table" 
 
|-
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!{{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
|
||
YlaB product
YlaB  
|-
|-
!{{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
|
||
conserved inner membrane protein product<ref name='LIB:Riley_2006'/>, B0457 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YlaB product<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''
|-
|-
!{{table heading style}} |Product description
!align=left {{table heading style}} |Product description
|
||
conserved protein<ref name='LIB:EcoCyc10.6'/>; conserved inner membrane protein<ref name='LIB:EcoCyc11.1'/>
conserved protein<ref name='LIB:EcoCyc10.6'/>; conserved inner membrane protein<ref name='LIB:EcoCyc11.1'/>


Putative cyclic-di-GMP phosphodiesterase, function unknown<ref name='LIB:EcoGene'/>
|-
|-
!{{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
|
||
*
 
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===Notes===
===Notes===
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<protect>
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<big>'''Gene Ontology'''</big>
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.20571.Q46aa311e6d807-->
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|- {{table_heading_style}}
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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
|-class='sortbottom'
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|
 
|
GO:0005886
|
plasma membrane
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GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
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SP_KW:KW-1003
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C
|
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
|
 
|
GO:0016020
|
membrane
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GOA:spkw<br />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<br />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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<span id="Interactions"></span><big>'''Interactions'''</big>
<span id="Interactions"></span><big>'''Interactions'''</big>
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!Partner Type!!Partner!!Notes
!|Partner Type!!Partner!!Notes!!References!!Evidence
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<!--Function_notes--></protect>
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===Notes===
===Notes===
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!Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
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plasma membrane
|
C-terminus localized in the cytoplasm with 2 predicted transmembrane domains
|
Daley et al. (2005) <ref name=PMID:15919996/>
|
 
|
 
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!align=left {{table heading style}} |Name
||
 
|-
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!{{table heading style}} |Sequence
!align=left {{table heading style}} |Sequence
|
||
[http://biocyc.org/ECOLI/sequence-aa?object=G6252-MONOMER at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=G6252-MONOMER at EcoCyc]  
<pre>MLVRTRHLVG LISGVLILSV LLPVGLSIWL AHQQVETSFI EELDTYSSRV AIRANKVATQ
<pre>MLVRTRHLVG LISGVLILSV LLPVGLSIWL AHQQVETSFI EELDTYSSRV AIRANKVATQ
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TSKQEEWLRQ HGVHYGQGWL YSKALPKEDF LRWAEQHL</pre>  
TSKQEEWLRQ HGVHYGQGWL YSKALPKEDF LRWAEQHL</pre>  
|-
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!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Length
|
||
58.72 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
518
|-
|-
!{{table heading style}} |pI
!align=left {{table heading style}} |Mol. Wt
|
||
58.933 kDa
|-
|-
!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |pI
|
||
99810 - 100185 (calc based on 19 Y, 13 W, and 3 C residues)  
6.1 (calculated)
|-
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!align=left {{table heading style}} |Extinction coefficient
||
99,810 - 100,185 (calc based on 19 Y, 13 W, and 3 C residues)
 
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<big>'''Domains/Motifs/Modification Sites'''</big>
 
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
<table>
<tr align="left" valign="top">
<td>
 
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|- {{table heading style}}
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!Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-class='sortbottom'
|-
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Domain
|
272..502
|
[http://pfam.janelia.org/family/PF00563 PF00563  EAL domain]
|
 
|
PMID:19920124
 
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<span id="Structure"></span><big>'''Structure'''</big>
</td>
<td>
<!-- motifs column 2-->
<motif_map/>
{{TMHMM Picture|ylaB}}
</td>
</tr>
</table>
 
<table><tr valign='top'><td>
<span id='Structure'></span><big>'''Structure'''</big><br />
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|- {{table heading style}}
 
!Structure Type!!Organism!!Accession!!Residues covered!!Notes
|-
|-class='sortbottom'
!align=left {{table heading style}} |Structures
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20571.A46a7c28becb22&page=20571&pagename={{FULLPAGENAMEE}} edit table] || || || ||
||
<beststructure>
gene=ylaB
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/P77473 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P77473 PSI-PRED (P77473)]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P77473 Genomes TO Protein (P77473)] (GTOP)
 
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<!--Structure_notes--></protect>
</td><td></protect>
==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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!|Resource type!!Source!!Notes/Reference
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===Notes===
===Notes===
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[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]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6252-MONOMER EcoCyc:G6252-MONOMER] 
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]])
|
|
[http://www.expasy.ch/cgi-bin/sprot-search-ac?P77473 UniProt:P77473]
[http://www.ncbi.nlm.nih.gov/gene?term=948951 GeneID:948951]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://www.sanger.ac.uk/Software/Pfam/ 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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===Notes===
===Notes===
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===Categories===
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[[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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