trmD: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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tRNA (guanine-1-)-methyltransferase<ref name='LIB:Riley_2006'/>, B2607<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, TrmD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''tRNA (guanine-1-)-methyltransferase<ref name='LIB:Riley_2006'/>, B2607<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, TrmD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2604, JW2588, b2607''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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{|   id="E46aab2df2b20e"  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="E46aab2df2b20e"  class=" tableEdit GO_table_product dataTable"   
|- {{table_heading_style}}
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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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{|   id="U46aab2e80e16a"  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="U46aab2e80e16a"  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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Protein
Protein
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[[dnaX:Gene_Product(s)|dnaX]]
dnaX
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PMID:19402753
PMID:19402753
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MALDI(Z-score):28.759733  
MALDI(Z-score):28.759733  
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Protein
Protein
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[[holA:Gene_Product(s)|holA]]
holA
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PMID:19402753
PMID:19402753
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MALDI(Z-score):32.609818  
MALDI(Z-score):32.609818  
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Protein
Protein
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[[dnaE:Gene_Product(s)|dnaE]]
dnaE
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PMID:19402753
PMID:19402753
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MALDI(Z-score):18.854791  
MALDI(Z-score):18.854791  
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Protein
Protein
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[[holD:Gene_Product(s)|holD]]
holD
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PMID:19402753
PMID:19402753
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MALDI(Z-score):21.182048  
MALDI(Z-score):21.182048  
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Protein
Protein
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[[holC:Gene_Product(s)|holC]]
holC
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PMID:19402753
PMID:19402753
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MALDI(Z-score):27.442857  
MALDI(Z-score):27.442857  
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Protein
Protein
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[[dnaQ:Gene_Product(s)|dnaQ]]
dnaQ
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PMID:19402753
PMID:19402753
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MALDI(Z-score):29.343986  
MALDI(Z-score):29.343986  
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Protein
Protein
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[[holB:Gene_Product(s)|holB]]
holB
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PMID:19402753
PMID:19402753
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MALDI(Z-score):38.943183  
MALDI(Z-score):38.943183  


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46a84aca424a5"  class=" tableEdit Product_localization_table"   
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!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
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{|   id="B46aab2ead63da"  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="B46aab2ead63da"  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/P0A873 Protein Model Portal]
* [http://www.proteinmodelportal.org/query/uniprot/P0A873 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0A873 PSI-PRED (P0A873)]
* [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=P0A873 Genomes TO Protein (P0A873)] (GTOP)


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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference
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{|   id="D46aab2ec09153"  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="D46aab2ec09153"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/protein/16130528 GI:16130528]
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Escherichia coli str. K-12 substr. MG1655
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[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/protein/NP_417098.1 GeneID:947099]
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Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0008576
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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/P0A873 UniProtKB/Swiss-Prot:P0A873]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:EG11023
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG11023
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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=947099 GeneID:947099]
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Escherichia coli str. K-12 substr. MG1655
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[[RegulonDB]]
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RegulonDB:ECK120001012
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB1016
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:53, 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

TrmD

Synonyms

tRNA (guanine-1-)-methyltransferase[1], B2607[2][1], TrmD[2][1] , ECK2604, JW2588, b2607

Product description

TrmD[2][3];

Component of tRNA (guanine-1-)-methyltransferase[3]

tRNA m(1)G37 methyltransferase[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:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002649

F

Seeded from EcoCyc (v14.0)

complete

GO:0009451

RNA modification

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00605

C

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:0009019

tRNA (guanine-N1-)-methyltransferase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00605

F

Seeded from EcoCyc (v14.0)

complete

GO:0009019

tRNA (guanine-N1-)-methyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002649

F

Seeded from EcoCyc (v14.0)

complete

GO:0009019

tRNA (guanine-N1-)-methyltransferase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.1.1.31

F

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

Subunits of tRNA (guanine-1-)-methyltransferase

could be indirect

Protein

dnaX

PMID:19402753[5]

MALDI(Z-score):28.759733

Protein

holA

PMID:19402753[5]

MALDI(Z-score):32.609818

Protein

dnaE

PMID:19402753[5]

MALDI(Z-score):18.854791

Protein

holD

PMID:19402753[5]

MALDI(Z-score):21.182048

Protein

holC

PMID:19402753[5]

MALDI(Z-score):27.442857

Protein

dnaQ

PMID:19402753[5]

MALDI(Z-score):29.343986

Protein

holB

PMID:19402753[5]

MALDI(Z-score):38.943183

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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 

MWIGIISLFP EMFRAITDYG VTGRAVKNGL LSIQSWSPRD FTHDRHRTVD DRPYGGGPGM
LMMVQPLRDA IHAAKAAAGE GAKVIYLSPQ GRKLDQAGVS ELATNQKLIL VCGRYEGIDE
RVIQTEIDEE WSIGDYVLSG GELPAMTLID SVSRFIPGVL GHEASATEDS FAEGLLDCPH
YTRPEVLEGM EVPPVLLSGN HAEIRRWRLK QSLGRTWLRR PELLENLALT EEQARLLAEF
KTEHAQQQHK HDGMA
Length

255

Mol. Wt

28.422 kDa

pI

5.7 (calculated)

Extinction coefficient

36,440 - 36,690 (calc based on 6 Y, 5 W, and 2 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

22..221

PF01746 tRNA (Guanine-1)-methyltransferase

PMID:19920124[6]

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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=trmD 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:16130528

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947099

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008576

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A873

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11023

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11023

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947099

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001012

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1016

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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 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 5.2 5.3 5.4 5.5 5.6 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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