arnD:Gene Product(s): Difference between revisions

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{{Tab|Quickview|yfbH}}{{Tab|Gene|yfbH}}{{Tab On|Gene Product(s)|yfbH}}{{Tab|Expression|yfbH}}{{Tab|Evolution|yfbH}}{{Tab|On One Page|yfbH}}{{TabsBottom}}
{{Tab|Quickview|arnD}}{{Tab|Gene|arnD}}{{Tab On|Gene Product(s)|arnD}}{{Tab|Expression|arnD}}{{Tab|Evolution|arnD}}{{Tab|On One Page|arnD}}{{TabsBottom}}
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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
conserved protein<ref name='LIB:Riley_2006'/>, B2256<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YfbH<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PmrJ<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''conserved protein<ref name='LIB:Riley_2006'/>, B2256<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YfbH<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PmrJ<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2249, JW2250, pbgP4, pmrJ, yfbH, b2256''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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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:0003824
|
catalytic activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011330
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005975
|
carbohydrate metabolic process
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR002509
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005975
|
carbohydrate metabolic process
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011330
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0008610
|
lipid biosynthetic process
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0444
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0009103
|
lipopolysaccharide biosynthetic process
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0448
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0009245
|
lipid A biosynthetic process
|
GOA:hamap<br />GO_REF:0000020
|
IEA: Inferred from Electronic Annotation
|
HAMAP:MF_01870
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0009245
|
lipid A biosynthetic process
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0441
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0016787
|
hydrolase activity
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0378
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0016810
|
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR002509
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0016811
|
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
|
GOA:hamap<br />GO_REF:0000020
|
IEA: Inferred from Electronic Annotation
|
HAMAP:MF_01870
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0016811
|
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
|
GOA:spec<br />GO_REF:0000003
|
IEA: Inferred from Electronic Annotation
|
EC:3.5.1
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0046677
|
response to antibiotic
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0046
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Protein
Protein
|
|
[[groL:Gene_Product(s)|groL]]<br />
groL<br />
|
|


|[[PMID:16606699]]<ref name=PMID:16606699/>
|
|
Experiment(s):[http://www.ebi.ac.uk/iintact/search/do/search?searchString=EBI-1142351 EBI-1142351]<br />  
PMID:16606699
|
Experiment(s):EBI-1142351<br />  


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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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PLLESGNPGT AQIPVTLPTW DEVIGRDVKA EDFNGWLLNR ILRDKGTPVY TIHAEVEGCA
PLLESGNPGT AQIPVTLPTW DEVIGRDVKA EDFNGWLLNR ILRDKGTPVY TIHAEVEGCA
YQHNFVDLLK RAAQEGVTFC PLSELLSETL PLGQVVRGNI AGREGWLGCQ QIAGSR</pre>  
YQHNFVDLLK RAAQEGVTFC PLSELLSETL PLGQVVRGNI AGREGWLGCQ QIAGSR</pre>  
|-
!align=left {{table heading style}} |Length
||
296
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
33.11 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
33.111 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
7.6 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
66460 - 67085 (calc based on 4 Y, 11 W, and 5 C residues)  
66,460 - 67,085 (calc based on 4 Y, 11 W, and 5 C residues)


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{{Product_physical_properties_help}}


<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
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|- {{table heading style}}
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
6..170
|
[http://pfam.janelia.org/family/PF01522 PF01522  Polysaccharide deacetylase]
|
 
|
PMID:19920124


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{{Product_domains_motifs_help}}</td>
<td>
<!-- motifs column 2-->
<motif_map/>
</td>
</tr>
</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>yfbH
<beststructure>
562</beststructure>
gene=arnD
 
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=yfbH&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P76472 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=yfbH&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P76472 PSI-PRED (P76472)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P76472 Genomes TO Protein (P76472)] (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://www.ncbi.nlm.nih.gov/protein/16130191 GI:16130191]
|
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_416759.1 GeneID:945334]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0007462
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7169-MONOMER EcoCyc:G7169-MONOMER]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P76472 UniProtKB/Swiss-Prot:P76472]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:G7169
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
|
|
[[uniprot:P76472|UniProt:P76472]]
EcoGene:EG14092
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://pfam.sanger.ac.uk/family?acc=PF01522 PFAM:PF01522]
[http://www.ncbi.nlm.nih.gov/gene?term=945334 GeneID:945334]
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Escherichia coli str. K-12 substr. MG1655
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[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_416759 RefSeq:NP_416759]
RegulonDB:ECK120003745
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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=P76472 ModBase:P76472]
EchoBASE:EB3845
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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__NOTOC__
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===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:Pfam:PF01522_!_Polysaccharide deacetylase]]

Latest revision as of 20:49, 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

YfbH

Synonyms

conserved protein[1], B2256[2][1], YfbH[2][1], PmrJ[2][1] , ECK2249, JW2250, pbgP4, pmrJ, yfbH, b2256

Product description

conserved protein[2][3]

EC number (for enzymes)
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See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki. 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:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011330

F

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002509

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011330

P

Seeded from EcoCyc (v14.0)

complete

GO:0008610

lipid biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0444

P

Seeded from EcoCyc (v14.0)

complete

GO:0009103

lipopolysaccharide biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0448

P

Seeded from EcoCyc (v14.0)

complete

GO:0009245

lipid A biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01870

P

Seeded from EcoCyc (v14.0)

complete

GO:0009245

lipid A biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0441

P

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

GO:0016810

hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002509

F

Seeded from EcoCyc (v14.0)

complete

GO:0016811

hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01870

F

Seeded from EcoCyc (v14.0)

complete

GO:0016811

hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.5.1

F

Seeded from EcoCyc (v14.0)

complete

GO:0046677

response to antibiotic

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0046

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

Protein

groL

PMID:16606699[4]

Experiment(s):EBI-1142351
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See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

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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See Help:Product_localization for how to add or edit information in this section of EcoliWiki.


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 

MTKVGLRIDV DTFRGTREGV PRLLEILSKH NIQASIFFSV GPDNMGRHLW RLVKPQFLWK
MLRSNAASLY GWDILLAGTA WPGKEIGHAN ADIIREAAKH HEVGLHAWDH HAWQARSGNW
DRQTMIDDIA RGLRTLEEII GQPVTCSAAA GWRADQKVIE AKEAFHLRYN SDCRGAMPFR
PLLESGNPGT AQIPVTLPTW DEVIGRDVKA EDFNGWLLNR ILRDKGTPVY TIHAEVEGCA
YQHNFVDLLK RAAQEGVTFC PLSELLSETL PLGQVVRGNI AGREGWLGCQ QIAGSR
Length

296

Mol. Wt

33.111 kDa

pI

7.6 (calculated)

Extinction coefficient

66,460 - 67,085 (calc based on 4 Y, 11 W, and 5 C residues)

edit table

See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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

6..170

PF01522 Polysaccharide deacetylase

PMID:19920124[5]

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

<motif_map/>

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

Structures

<beststructure> gene=arnD taxon=562,83333 </beststructure>

Models

View models at:

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

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

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:16130191

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945334

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007462

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76472

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7169

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14092

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945334

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003745

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3845

Escherichia coli str. K-12 substr. MG1655

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

Notes

Links

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See Help:Links_table for how to enter or edit information in this section of EcoliWiki.



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. ↑ Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  5. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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