amiD:Gene Product(s): Difference between revisions

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Refreshing information from GenBank record NC_000913
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{|   id="H46aa480a80641"  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="H46aa480a80641"  class=" tableEdit GO_table_product dataTable"   
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!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46aa480af2b9f"  class=" tableEdit Product_interactions_table dataTable"   
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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
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{|   id="E46aa480d1e0c5"  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="E46aa480d1e0c5"  class=" tableEdit Product_motif_table dataTable"   
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!|Type!!Residues!!Description!!Notes!!References
!|Type!!Residues!!Description!!Notes!!References
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View models at:
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/P75820 Protein Model Portal]
* [http://www.proteinmodelportal.org/query/uniprot/P75820 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P75820 PSI-PRED (P75820)]
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P75820 Genomes TO Protein (P75820)] (GTOP)


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!|Resource type!!Source!!Notes/Reference
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{|   id="T46aa480e0f293"  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="T46aa480e0f293"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[ASAP]]
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ASAP:ABE-0002947
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
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[http://www.uniprot.org/uniprot/P75820 UniProtKB/Swiss-Prot:P75820]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:G6452
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG13687
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/gene?term=945494 GeneID:945494]
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Escherichia coli str. K-12 substr. MG1655
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[[RegulonDB]]
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RegulonDB:ECK120003052
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB3451
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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Latest revision as of 20:31, 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

AmiD

Synonyms

predicted amidase and lipoprotein[1], YbjR[2][1], B0867[2][1] , ECK0858, JW0851, ybjR, b0867

Product description

predicted amidase and lipoprotein[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:0008745

N-acetylmuramoyl-L-alanine amidase activity

PMID:17526703[4]

IDA: Inferred from Direct Assay

F

complete

GO:0019867

outer membrane

PMID:17526703[4]

IDA: Inferred from Direct Assay

C

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:0008270

zinc ion binding

PMID:17526703[4]

IDA: Inferred from Direct Assay

F

complete

GO:0007047

cellular cell wall organization

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0961

P

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc (v14.0)

complete

GO:0008745

N-acetylmuramoyl-L-alanine amidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002502

F

Seeded from EcoCyc (v14.0)

complete

GO:0008745

N-acetylmuramoyl-L-alanine amidase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.5.1.28

F

Seeded from EcoCyc (v14.0)

complete

GO:0009253

peptidoglycan catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002502

P

Seeded from EcoCyc (v14.0)

complete

GO:0009279

cell outer membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0998

C

Seeded from EcoCyc (v14.0)

complete

GO:0031225

anchored to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9901

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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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 

MRRFFWLVAA ALLLAGCAGE KGIVEKEGYQ LDTRRQAQAA YPRIKVLVIH YTADDFDSSL
ATLTDKQVSS HYLVPAVPPR YNGKPRIWQL VPEQELAWHA GISAWRGATR LNDTSIGIEL
ENRGWQKSAG VKYFAPFEPA QIQALIPLAK DIIARYHIKP ENVVAHADIA PQRKDDPGPL
FPWQQLAQQG IGAWPDAQRV NFYLAGRAPH TPVDTASLLE LLARYGYDVK PDMTPREQRR
VIMAFQMHFR PTLYNGEADA ETQAIAEALL EKYGQD
Length

276

Mol. Wt

31.072 kDa

pI

7.8 (calculated)

Extinction coefficient

56,380 - 56,505 (calc based on 12 Y, 7 W, and 1 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

35..180

PF01510 N-acetylmuramoyl-L-alanine amidase

PMID:19920124[5]

edit table
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=amiD 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:16128835

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945494

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002947

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P75820

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6452

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13687

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945494

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003052

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3451

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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 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. ↑ 4.0 4.1 4.2 Uehara, T & Park, JT (2007) An anhydro-N-acetylmuramyl-L-alanine amidase with broad specificity tethered to the outer membrane of Escherichia coli. J. Bacteriol. 189 5634-41 PubMed
  5. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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