alx:Gene Product(s): Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Fixing Pfam accessions and motif notes fields.
touch table
 
(11 intermediate revisions by 2 users not shown)
Line 44: Line 44:
!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
predicted inner membrane protein, part of terminus<ref name='LIB:Riley_2006'/>, B3088<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Alx<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YgjT<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted inner membrane protein, part of terminus<ref name='LIB:Riley_2006'/>, B3088<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Alx<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YgjT<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK3079, JW5515, ygjT, b3088''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
Line 75: Line 75:
*  
*  
****************************************************************************************** -->{{Product_GO_help}}
****************************************************************************************** -->{{Product_GO_help}}
{|   id="K46aad103e5283"  class=" tableEdit GO_table_product dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46aad103e5283"  class=" tableEdit GO_table_product dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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
|-  
|-  
|
|
Line 206: Line 206:
*  
*  
****************************************************************************************** -->{{Product_interactions_help}}
****************************************************************************************** -->{{Product_interactions_help}}
{|   id="R46aad1047781b"  class=" tableEdit Product_interactions_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46aad1047781b"  class=" tableEdit Product_interactions_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
Line 227: Line 227:
*  
*  
****************************************************************************************** -->{{Product_localization_help}}
****************************************************************************************** -->{{Product_localization_help}}
{|   id="O46aad1053fa41"  class=" tableEdit Product_localization_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46aad1053fa41"  class=" tableEdit Product_localization_table"   
|- {{table heading style}}
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
|-  
|-  
|
|
Line 275: Line 275:
****************************************************************************************** -->{{Product_physical_properties_help}}
****************************************************************************************** -->{{Product_physical_properties_help}}
{|  id="Y46aad106d65cd"  class=" tableEdit Product_phys_prop_table"   
{|  id="Y46aad106d65cd"  class=" tableEdit Product_phys_prop_table"   
|-
!align=left {{table heading style}} |Name
||


|-
|-
Line 301: Line 305:
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
69,900 (calc based on 10 Y, 10 W, and C residues)
69,900 (calc based on 10 Y, 10 W, and 0 C residues)


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 321: Line 325:
*  
*  
****************************************************************************************** -->{{Product_domains_motifs_help}}
****************************************************************************************** -->{{Product_domains_motifs_help}}
{|   id="Q46aad10753559"  class=" tableEdit Product_motif_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46aad10753559"  class=" tableEdit Product_motif_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References
!|Type!!Residues!!Description!!Notes!!References
Line 373: Line 377:
||
||
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/P42601 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=P42601 PSI-PRED (P42601)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P42601 Genomes TO Protein (P42601)] (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)


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 418: Line 420:
*  
*  
****************************************************************************************** -->{{Product_resources_help}}
****************************************************************************************** -->{{Product_resources_help}}
{|   id="A46aad1081fd16"  class=" tableEdit Product_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46aad1081fd16"  class=" tableEdit Product_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference
Line 440: Line 442:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="V46aad1087fb86"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46aad1087fb86"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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/49176311 GI:49176311]
|
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/YP_026201.1 GeneID:947607]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7607-MONOMER EcoCyc:G7607-MONOMER]
ASAP:ABE-0010151
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P42601 UniProtKB/Swiss-Prot:P42601]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:G7607
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG12731
|
''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:P42601|UniProt:P42601]]
[http://www.ncbi.nlm.nih.gov/gene?term=947607 GeneID:947607]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.janelia.org/protein/P42601 Pfam:P42601]
RegulonDB:ECK120004160
|
|
''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=YP_026201 RefSeq:YP_026201]
EchoBASE:EB2589
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 490: Line 527:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="G46a865301bb71"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a865301bb71"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:59, 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

Alx

Synonyms

predicted inner membrane protein, part of terminus[1], B3088[2][1], Alx[2][1], YgjT[2][1] , ECK3079, JW5515, ygjT, b3088

Product description

putative membrane-bound redox modulator that is induced by high pH[2][3]

Function unknown; induced by alkali; putative membrane transport or efflux protein[4]

EC number (for enzymes)


edit table


Notes

Function

[back to top]


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-0997

C

Seeded from EcoCyc (v14.0)

complete

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:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005496

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

edit table

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
edit table


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 9 predicted transmembrane domains

Daley et al. (2005) [5]

membrane

From EcoCyc[3]


edit table


Notes

Structure and Physical Properties

[back to top]


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 

MNTVGTPLLW GGFAVVVAIM LAIDLLLQGR RGAHAMTMKQ AAAWSLVWVT LSLLFNAAFW
WYLVQTEGRA VADPQALAFL TGYLIEKSLA VDNVFVWLML FSYFSVPAAL QRRVLVYGVL
GAIVLRTIMI FTGSWLISQF DWILYIFGAF LLFTGVKMAL AHEDESGIGD KPLVRWLRGH
LRMTDTIDNE HFFVRKNGLL YATPLMLVLI LVELSDVIFA VDSIPAIFAV TTDPFIVLTS
NLFAILGLRA MYFLLAGVAE RFSMLKYGLA VILVFIGIKM LIVDFYHIPI AVSLGVVFGI
LVMTFIINAW VNYRHDKQRG G
Length

321

Mol. Wt

35.909 kDa

pI

9.4 (calculated)

Extinction coefficient

69,900 (calc based on 10 Y, 10 W, and 0 C residues)

edit table


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

80..284

PF03741 Integral membrane protein TerC family

PMID:19920124[6]

edit table

<motif_map/>

tmhmm.php?gene=alx&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=alx taxon=562,83333 </beststructure>

Models

View models at:

edit table

Structure figures

Notes

Gene Product Resources

[back to top]


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

Resource type Source Notes/Reference
edit table


Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:49176311

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947607

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010151

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P42601

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7607

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12731

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947607

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004160

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2589

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]




References

[back to top]


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. ↑ 3.0 3.1 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

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=alx:Gene_Product(s)&oldid=1494904"