dinF: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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|-
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!{{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
|
||
DinF product
DinF  
|-
|-
!{{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
|
||
DNA-damage-inducible SOS response protein product<ref name='LIB:Riley_2006'/>, DNA-damage-inducible protein F product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, DinF product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B4044 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''DNA-damage-inducible SOS response protein<ref name='LIB:Riley_2006'/>, DNA-damage-inducible protein F<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, DinF<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B4044<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK4036, JW4004, b4044''
|-
|-
!{{table heading style}} |Product description
!align=left {{table heading style}} |Product description
|
||
DinF MATE Transporter<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
DinF MATE Transporter<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


Induced by UV and mitomycin C, function unknown<ref name='LIB:EcoGene'/>
|-
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!{{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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<big>'''Gene Ontology'''</big>
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.28763.F46ab183da7269-->
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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
|-
|-
|
 
|
GO:0005886
|
plasma membrane
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GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
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SP_KW:KW-0997
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C
|
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
|
 
|
GO:0005886
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plasma membrane
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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:0006855
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drug transmembrane transport
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GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
|
InterPro:IPR002528
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0015238
|
drug transmembrane transporter activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR002528
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0015297
|
antiporter activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR002528
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0016020
|
membrane
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR002528
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-  
|
|
 
|
|
GO:0006281
GO:0016020
|
|
DNA repair
membrane
|
|
GOA:spkw<br />SP_KW:GO_REF:0000004
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|
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0472
|
|
P
C
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-
|-  
|
|
 
|
|
GO:0015292
GO:0016021
|
|
uniporter activity
integral to membrane
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|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0812
|
|
F
C
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-
|-  
|
|
 
|
|
GO:0009432
GO:0016021
|
|
SOS response
integral to membrane
|
|
GO_REF:0000023
|
|
IEA: Inferred from Electronic Annotation
|
|
SP_SL:SL-9909
|
|
P
C
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
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<span id="Interactions"></span><big>'''Interactions'''</big>
<span id="Interactions"></span><big>'''Interactions'''</big>
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===Notes===
===Notes===
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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=DINF-MONOMER at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=DINF-MONOMER at EcoCyc]  
<pre>MPPGVAVCFS SLFIRLVCMA FLTSSDKALW HLALPMIFSN ITVPLLGLVD TAVIGHLDSP
<pre>MPPGVAVCFS SLFIRLVCMA FLTSSDKALW HLALPMIFSN ITVPLLGLVD TAVIGHLDSP
Line 204: Line 328:
WLGNHALWLA LTVFLALRGL SLAAIWRRHW RNGTWFAAT</pre>  
WLGNHALWLA LTVFLALRGL SLAAIWRRHW RNGTWFAAT</pre>  
|-
|-
!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Length
|
||
49.65 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
459
|-
|-
!{{table heading style}} |pI
!align=left {{table heading style}} |Mol. Wt
|
||
49.648 kDa
|-
|-
!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |pI
|
||
86400 - 87025 (calc based on 10 Y, 13 W, and 5 C residues)  
10.1 (calculated)
|-
|-
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!align=left {{table heading style}} |Extinction coefficient
||
86,400 - 87,025 (calc based on 10 Y, 13 W, and 5 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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!Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-class='sortbottom'
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Domain
|
35..196
|
[http://pfam.janelia.org/family/PF01554 PF01554  MatE]
|
 
|
PMID:19920124
|-
|
Domain
|
259..421
|
[http://pfam.janelia.org/family/PF01554 PF01554  MatE]
|
 
|
PMID:19920124
 
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<span id="Structure"></span><big>'''Structure'''</big>
</td>
<td>
<!-- motifs column 2-->
<motif_map/>
{{TMHMM Picture|dinF}}
</td>
</tr>
</table>
 
<table><tr valign='top'><td>
<span id='Structure'></span><big>'''Structure'''</big><br />
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!Structure Type!!Organism!!Accession!!Residues covered!!Notes
|-
|-class='sortbottom'
!align=left {{table heading style}} |Structures
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<beststructure>
gene=dinF
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/P28303 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P28303 PSI-PRED (P28303)]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P28303 Genomes TO Protein (P28303)] (GTOP)
 
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<!--Structure_notes--></protect>
</td><td></protect>
==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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===Notes===
===Notes===
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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/162135919 GI:162135919]
|
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_418468.3 GeneID:948554]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0013243
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P28303 UniProtKB/Swiss-Prot:P28303]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG11491
|
''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=DINF-MONOMER EcoCyc:DINF-MONOMER] 
EcoGene:EG11491
|
|
''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]])
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[http://www.expasy.ch/cgi-bin/sprot-search-ac?P28303 UniProt:P28303]
[http://www.ncbi.nlm.nih.gov/gene?term=948554 GeneID:948554]
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Escherichia coli str. K-12 substr. MG1655
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[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
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[http://pfam.sanger.ac.uk/family?acc=PF01554 PFAM:PF01554] 
RegulonDB:ECK120001447
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[EchoBASE]]
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_418468 RefSeq:NP_418468] 
EchoBASE:EB1454
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''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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{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0006281_!_DNA repair]][[Category:GO:0015292_!_uniporter activity]][[Category:GO:0009432_!_SOS response]]

Latest revision as of 21:11, 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

DinF

Synonyms

DNA-damage-inducible SOS response protein[1], DNA-damage-inducible protein F[2][1], DinF[2][1], B4044[2][1] , ECK4036, JW4004, b4044

Product description

DinF MATE Transporter[2][3]

Induced by UV and mitomycin C, 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-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:0006855

drug transmembrane transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002528

P

Seeded from EcoCyc (v14.0)

complete

GO:0015238

drug transmembrane transporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002528

F

Seeded from EcoCyc (v14.0)

complete

GO:0015297

antiporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002528

F

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002528

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
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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 

MPPGVAVCFS SLFIRLVCMA FLTSSDKALW HLALPMIFSN ITVPLLGLVD TAVIGHLDSP
VYLGGVAVGA TATSFLFMLL LFLRMSTTGL TAQAYGAKNP QALARTLVQP LLLALGAGAL
IALLRTPIID LALHIVGGSE AVLEQARRFL EIRWLSAPAS LANLVLLGWL LGVQYARAPV
ILLVVGNILN IVLDVWLVMG LHMNVQGAAL ATVIAEYATL LIGLLMVRKI LKLRGISGEM
LKTAWRGNFR RLLALNRDIM LRSLLLQLCF GAITVLGARL GSDIIAVNAV LMTLLTFTAY
ALDGFAYAVE AHSGQAYGAR DGSQLLDVWR AACRQSGIVA LLFSVVYLLA GEHIIALLTS
LTQIQQLADR YLIWQVILPV VGVWCYLLDG MFIGATRATE MRNSMAVAAA GFALTLLTLP
WLGNHALWLA LTVFLALRGL SLAAIWRRHW RNGTWFAAT
Length

459

Mol. Wt

49.648 kDa

pI

10.1 (calculated)

Extinction coefficient

86,400 - 87,025 (calc based on 10 Y, 13 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

35..196

PF01554 MatE

PMID:19920124[5]

Domain

259..421

PF01554 MatE

PMID:19920124[5]

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<motif_map/>

tmhmm.php?gene=dinF&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=dinF 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:162135919

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948554

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013243

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P28303

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11491

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11491

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948554

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001447

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1454

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 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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