adiC:Gene Product(s): Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Added Pfam categories.
touch table
 
(13 intermediate revisions by 3 users not shown)
Line 44: Line 44:
!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
arginine:agmatin<ref name='LIB:Riley_2006'/>, B4115 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YjdD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YjdE<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, AdiC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''arginine:agmatin<ref name='LIB:Riley_2006'/>, B4115<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YjdD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YjdE<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, AdiC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , aniC, ECK4108, JW4076, yjdD, yjdE, b4115''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
Line 77: Line 77:
*  
*  
****************************************************************************************** -->{{Product_GO_help}}
****************************************************************************************** -->{{Product_GO_help}}
{|   id="X46ab1dac253d1"  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="X46ab1dac253d1"  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 360: Line 360:
*  
*  
****************************************************************************************** -->{{Product_interactions_help}}
****************************************************************************************** -->{{Product_interactions_help}}
{|   id="P46ab1db792b9b"  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="P46ab1db792b9b"  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 392: Line 392:
*  
*  
****************************************************************************************** -->{{Product_localization_help}}
****************************************************************************************** -->{{Product_localization_help}}
{|   id="N46ab1db8df4e3"  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="N46ab1db8df4e3"  class=" tableEdit Product_localization_table"   
|- {{table heading style}}
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
|-  
|-  
|
|
Line 440: Line 440:
****************************************************************************************** -->{{Product_physical_properties_help}}
****************************************************************************************** -->{{Product_physical_properties_help}}
{|  id="H46ab1dbb1dadb"  class=" tableEdit Product_phys_prop_table"   
{|  id="H46ab1dbb1dadb"  class=" tableEdit Product_phys_prop_table"   
|-
!align=left {{table heading style}} |Name
||


|-
|-
Line 488: Line 492:
*  
*  
****************************************************************************************** -->{{Product_domains_motifs_help}}
****************************************************************************************** -->{{Product_domains_motifs_help}}
{|   id="L46ab1dbb95713"  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="L46ab1dbb95713"  class=" tableEdit Product_motif_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References
!|Type!!Residues!!Description!!Notes!!References
Line 499: Line 503:
[http://pfam.janelia.org/family/PF00324 PF00324  Amino acid permease]
[http://pfam.janelia.org/family/PF00324 PF00324  Amino acid permease]
|
|
[http://pfam.janelia.org/protein/P60061 Pfam:P60061]
 
|
|
PMID:19920124


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 540: Line 544:
||
||
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/P60061 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=P60061 PSI-PRED (P60061)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P60061 Genomes TO Protein (P60061)] (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 585: Line 587:
*  
*  
****************************************************************************************** -->{{Product_resources_help}}
****************************************************************************************** -->{{Product_resources_help}}
{|   id="E46ab1dbc6c40d"  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="E46ab1dbc6c40d"  class=" tableEdit Product_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference
Line 607: Line 609:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="R46ab1dbcd1153"  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="R46ab1dbcd1153"  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/16131941 GI:16131941]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=YJDE-MONOMER EcoCyc:YJDE-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
|
[http://www.ncbi.nlm.nih.gov/protein/NP_418539.1 GeneID:948628]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0013473
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P60061 UniProtKB/Swiss-Prot:P60061]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG12462
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG12462
|
''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:P60061|UniProt:P60061]]
[http://www.ncbi.nlm.nih.gov/gene?term=948628 GeneID:948628]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00324 PFAM:PF00324]
RegulonDB:ECK120002306
|
|
''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_418539 RefSeq:NP_418539]
EchoBASE:EB2355
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 657: Line 694:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="N46ab1dbfb5c85"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46ab1dbfb5c85"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments
Line 678: Line 715:
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0015292_!_uniporter activity]][[Category:GO:0051454_!_cellular pH elevation]][[Category:GO:0015300_!_solute:solute antiporter activity]][[Category:Complex:AdiC arginine:agmatine antiporter]][[Category:Location:plasma membrane]]
[[Category:Pfam:PF00324_!_Amino acid permease]]

Latest revision as of 21:12, 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

AdiC

Synonyms

arginine:agmatin[1], B4115[2][1], YjdD[2][1], YjdE[2][1], AdiC[2][1] , aniC, ECK4108, JW4076, yjdD, yjdE, b4115

Product description

AdiC Arginine:Agmatine Antiporter[2]; AdiC[3];

Component of AdiC arginine:agmatine antiporter[3]

Arginine:agmatine antiporter; arginine-dependent acid resistance; acid-inducible membrane 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:0006810

transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004841

P

Seeded from EcoCyc (v14.0)

complete

GO:0006810

transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0813

P

Seeded from EcoCyc (v14.0)

complete

GO:0006865

amino acid transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002293

P

Seeded from EcoCyc (v14.0)

complete

GO:0006865

amino acid transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0029

P

Seeded from EcoCyc (v14.0)

complete

GO:0015171

amino acid transmembrane transporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002293

F

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002293

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004841

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

GO:0055085

transmembrane transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002293

P

Seeded from EcoCyc (v14.0)

complete

GO:0055085

transmembrane transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004841

P

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

Protein

Subunits of AdiC arginine:agmatine antiporter

could be indirect


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 11 predicted transmembrane domains

Daley et al. (2005) [5]

plasma 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 

MSSDADAHKV GLIPVTLMVS GNIMGSGVFL LPANLASTGG IAIYGWLVTI IGALGLSMVY
AKMSFLDPSP GGSYAYARRC FGPFLGYQTN VLYWLACWIG NIAMVVIGVG YLSYFFPILK
DPLVLTITCV VVLWIFVLLN IVGPKMITRV QAVATVLALI PIVGIAVFGW FWFRGETYMA
AWNVSGLGTF GAIQSTLNVT LWSFIGVESA SVAAGVVKNP KRNVPIATIG GVLIAAVCYV
LSTTAIMGMI PNAALRVSAS PFGDAARMAL GDTAGAIVSF CAAAGCLGSL GGWTLLAGQT
AKAAADDGLF PPIFARVNKA GTPVAGLIIV GILMTIFQLS SISPNATKEF GLVSSVSVIF
TLVPYLYTCA ALLLLGHGHF GKARPAYLAV TTIAFLYCIW AVVGSGAKEV MWSFVTLMVI
TAMYALNYNR LHKNPYPLDA PISKD
Length

445

Mol. Wt

46.843 kDa

pI

9.0 (calculated)

Extinction coefficient

85,830 - 86,830 (calc based on 17 Y, 11 W, and 8 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

14..429

PF00324 Amino acid permease

PMID:19920124[6]

edit table

<motif_map/>

tmhmm.php?gene=adiC&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=adiC 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:16131941

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948628

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013473

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P60061

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12462

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12462

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948628

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002306

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2355

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 1.4 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 2.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 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=adiC:Gene_Product(s)&oldid=1495855"