cynR:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
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DNA-binding transcriptional dual regulator<ref name='LIB:Riley_2006'/>, B0338<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, CynR<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, cyn operon positive regulator<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''DNA-binding transcriptional dual regulator<ref name='LIB:Riley_2006'/>, B0338<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, CynR<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, cyn operon positive regulator<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0335, JW5894, b0338''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="L46aa294fbbac4"  class=" tableEdit GO_table_product dataTable" 
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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:0006350
|
transcription
|
GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0804
|
P
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|
 
|
GO:0006355
|
regulation of transcription, DNA-dependent
|
GO_REF:0000002<br />GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR000847<br />SP_KW:KW-0805
|
P
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|
 
|
GO:0005737
|
cytoplasm
|
GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0963
|
C
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
|
complete
|-
|
 
|
GO:0003700
|
transcription factor activity
|
GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR000847
|
F
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-  
|-  
|
|
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DNA binding
DNA binding
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003677
|
DNA binding
|
GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0238
|
F
|
Seeded from EcoCyc
|
|
complete  
complete  
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transcription factor activity
transcription factor activity
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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F
F
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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cytoplasm
cytoplasm
|
|
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-0963<br />SP_SL:SL-0086
SP_KW:KW-0963
|
|
C
C
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
NOT
|
GO:0006805
|
xenobiotic metabolic process
|
|


|
|
 
GO:0005737
|
|
 
cytoplasm
|
|
P
GO_REF:0000023
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
IEA: Inferred from Electronic Annotation
|
required field missing
|-
|
|
 
SP_SL:SL-0086
|
|
GO:0016564
C
|
transcription repressor activity
|
PMID:8253686
 
|
IDA: Inferred from Direct Assay
|
 
|
|
F
Seeded from [[EcoCyc]] (v14.0)
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
|
|
complete  
complete  
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|
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GO:0016563
GO:0006350
|
|
transcription activator activity
transcription
|
|
PMID:1592818
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IMP: Inferred from Mutant Phenotype
IEA: Inferred from Electronic Annotation
|
|
 
SP_KW:KW-0804
|
|
F
P
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0016563
GO:0006355
|
|
transcription activator activity
regulation of transcription, DNA-dependent
|
|
PMID:8253686
GOA:interpro
GO_REF:0000002
|
|
IDA: Inferred from Direct Assay
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR000847


|
F
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
|
complete
|-
|


|
GO:0006350
|
transcription
|
GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0804
|
|
P
P
|
|
Seeded from EcoCyc
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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DNA
DNA
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PMID:8253686
PMID:8253686
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Self
Self
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PMID:1592818
PMID:1592818
PMID:14973045
PMID:14973045
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!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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!align=left {{table heading style}} |Name
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!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
32.96 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
32.961 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
6.66<ref name='LIB:EcoCyc10.6'/>
6.8 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
19940 - 20315 (calc based on 6 Y, 2 W, and 3 C residues)  
19,940 - 20,315 (calc based on 6 Y, 2 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
|-  
|-  
|
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Domain
Domain
|
|
1 - 58
86..291
|
|
[[interpro:IPR000847|HTH lysR-type]]
[http://pfam.janelia.org/family/PF03466 PF03466  LysR substrate binding domain]
|
|
[http://www.uniprot.org/uniprot/P27111#section_features UniProt:P27111]


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PMID:19920124
|-
|
Domain
|
3..62
|
[http://pfam.janelia.org/family/PF00126 PF00126  Bacterial regulatory helix-turn-helix protein, lysR family]
|
 
|
PMID:19920124
 
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</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>cynR
<beststructure>
562</beststructure>
gene=cynR
 
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=cynR&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P27111 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=cynR&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P27111 PSI-PRED (P27111)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P27111 Genomes TO Protein (P27111)] (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 ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===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=PD00291 EcoCyc:PD00291]
[http://www.ncbi.nlm.nih.gov/protein/157783149 GI:157783149]
|
|
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_414872.3 GeneID:945001]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0001165
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P27111 UniProtKB/Swiss-Prot:P27111]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG11421
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG11421
|
''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:P27111|UniProt:P27111]]
[http://www.ncbi.nlm.nih.gov/gene?term=945001 GeneID:945001]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[RegulonDB]]
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_414872 RefSeq:NP_414872]
RegulonDB:ECK120001385
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
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[http://salilab.org/modbase/searchbyid?databaseID=P27111 ModBase:P27111]
EchoBASE:EB1391
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
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<references/>
<references />
__NOTOC__
__NOTOC__
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===Categories===
===Categories===
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0006350_!_transcription]][[Category:GO:0006805_!_xenobiotic metabolic process]][[Category:GO:0016564_!_transcription repressor activity]][[Category:GO:0005737_!_cytoplasm]][[Category:GO:0016563_!_transcription activator activity]]

Latest revision as of 20:24, 17 February 2015

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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

CynR

Synonyms

DNA-binding transcriptional dual regulator[1], B0338[2][1], CynR[2][1], cyn operon positive regulator[2][1] , ECK0335, JW5894, b0338

Product description

CynR transcriptional dual regulator[2][3]

Transcriptional activator of cyn operon[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:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000847

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000847


P

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

DNA

PMID:8253686[5]

Protein

Self

PMID:1592818[6]

PMID:14973045[7]


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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 

MLSRHINYFL AVAEHGSFTR AASALHVSQP ALSQQIRQLE ESLGVPLFDR SGRTIRLTDA
GEVWRQYASR ALQELGAGKR AIHDVADLTR GSLRIAVTPT FTSYFIGPLM ADFYARYPSI
TLQLQEMSQE KIEDMLCRDE LDVGIAFAPV HSPELEAIPL LTESLALVVA QHHPLAVHEQ
VALSRLHDEK LVLLSAEFAT REQIDHYCEK AGLHPQVVIE ANSISAVLEL IRRTSLSTLL
PAAIATQHDG LKAISLAPPL LERTAVLLRR KNSWQTAAAK AFLHMALDKC AVVGGNESR
Length

299

Mol. Wt

32.961 kDa

pI

6.8 (calculated)

Extinction coefficient

19,940 - 20,315 (calc based on 6 Y, 2 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

86..291

PF03466 LysR substrate binding domain

PMID:19920124[8]

Domain

3..62

PF00126 Bacterial regulatory helix-turn-helix protein, lysR family

PMID:19920124[8]

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<motif_map/>

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

Structures

<beststructure> gene=cynR 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:157783149

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945001

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001165

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P27111

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11421

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11421

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945001

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001385

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1391

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. ↑ Lamblin, AF & Fuchs, JA (1993) Expression and purification of the cynR regulatory gene product: CynR is a DNA-binding protein. J. Bacteriol. 175 7990-9 PubMed
  6. ↑ Sung, YC & Fuchs, JA (1992) The Escherichia coli K-12 cyn operon is positively regulated by a member of the lysR family. J. Bacteriol. 174 3645-50 PubMed
  7. ↑ Mariño-Ramírez, L et al. (2004) Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome by use of lambda repressor fusions. J. Bacteriol. 186 1311-9 PubMed
  8. ↑ 8.0 8.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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