trmD:Gene Product(s): Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
ecocyc_update_annotations.php
touch table
 
(30 intermediate revisions by 2 users not shown)
Line 44: Line 44:
!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
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''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
Line 77: Line 77:
*  
*  
****************************************************************************************** -->{{Product_GO_help}}
****************************************************************************************** -->{{Product_GO_help}}
{|   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}}
|- {{table_heading_style}}
!|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:0009451
GO:0003723
|
|
RNA modification
RNA binding
|
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR002649
|
|
P
F
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|


|
|
GO:0003723
GO:0009451
|
|
RNA binding
RNA modification
|
|
GOA:interpro<br />GO_REF:0000002
 
|
|
IEA: Inferred from Electronic Annotation
 
|
|
InterPro:IPR002649
 
|
|
F
P
|
|
Seeded from [[EcoCyc]] (v14.0)
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
|
|
Missing: evidence, reference
|-  
|-  
|
|
Line 136: Line 136:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 155: Line 155:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 174: Line 174:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 193: Line 193:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 212: Line 212:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 231: Line 231:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 246: Line 246:
*  
*  
****************************************************************************************** -->{{Product_interactions_help}}
****************************************************************************************** -->{{Product_interactions_help}}
{|   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"   
|- {{table heading style}}
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
Line 260: Line 260:
|
|
   
   
|-
|
Protein
|
dnaX
|
|
PMID:19402753
|
MALDI(Z-score):28.759733
|-
|
Protein
|
holA
|
|
PMID:19402753
|
MALDI(Z-score):32.609818
|-
|
Protein
|
dnaE
|
|
PMID:19402753
|
MALDI(Z-score):18.854791
|-
|
Protein
|
holD
|
|
PMID:19402753
|
MALDI(Z-score):21.182048
|-
|
Protein
|
holC
|
|
PMID:19402753
|
MALDI(Z-score):27.442857
|-
|
Protein
|
dnaQ
|
|
PMID:19402753
|
MALDI(Z-score):29.343986
|-
|
Protein
|
holB
|
|
PMID:19402753
|
MALDI(Z-score):38.943183


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 278: Line 355:
*  
*  
****************************************************************************************** -->{{Product_localization_help}}
****************************************************************************************** -->{{Product_localization_help}}
{|   id="M46a84aca424a5"  class=" tableEdit Product_localization_table"   
{| 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"   
|- {{table heading style}}
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 304: Line 381:
****************************************************************************************** -->{{Product_physical_properties_help}}
****************************************************************************************** -->{{Product_physical_properties_help}}
{|  id="V46aab2ea66dfb"  class=" tableEdit Product_phys_prop_table"   
{|  id="V46aab2ea66dfb"  class=" tableEdit Product_phys_prop_table"   
|-
!align=left {{table heading style}} |Name
||


|-
|-
Line 346: Line 427:
*  
*  
****************************************************************************************** -->{{Product_domains_motifs_help}}
****************************************************************************************** -->{{Product_domains_motifs_help}}
{|   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"   
|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
22..221
|
[http://pfam.janelia.org/family/PF01746 PF01746  tRNA (Guanine-1)-methyltransferase]
|
|
PMID:19920124


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 384: Line 476:
||
||
View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P0A873 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0A873 PSI-PRED (P0A873)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0A873 Genomes TO Protein (P0A873)] (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)


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 429: Line 519:
*  
*  
****************************************************************************************** -->{{Product_resources_help}}
****************************************************************************************** -->{{Product_resources_help}}
{|   id="N46aab2eb9f2bf"  class=" tableEdit Product_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46aab2eb9f2bf"  class=" tableEdit Product_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference
Line 451: Line 541:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   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"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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/16130528 GI:16130528]
|
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_417098.1 GeneID:947099]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0008576
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P0A873 UniProtKB/Swiss-Prot:P0A873]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11023-MONOMER EcoCyc:EG11023-MONOMER]
EcoCyc:EG11023
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG11023
|
''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:P0A873|UniProt:P0A873]]
[http://www.ncbi.nlm.nih.gov/gene?term=947099 GeneID:947099]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF01746 PFAM:PF01746]
RegulonDB:ECK120001012
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_417098 RefSeq:NP_417098]
EchoBASE:EB1016
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 501: Line 626:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="P46a84acf53b39"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P46a84acf53b39"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments
Line 522: Line 647:
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0009451_!_RNA modification]][[Category:GO:0030488_!_tRNA methylation]][[Category:Complex:tRNA (guanine-1-)-methyltransferase]]

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)
edit table


Notes

Function

[back to top]


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

edit table

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

edit table


Notes

Localization

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

Compartment Description Evidence Reference/Source Notes
edit table


Notes

Structure and Physical Properties

[back to top]


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)

edit table


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]

edit table

<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:

edit table

Structure figures

Notes

Gene Product Resources

[back to top]


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

Resource type Source Notes/Reference
edit table


Notes

Accessions in Other Databases

[back to top]


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

edit table


Notes

Links

[back to top]




References

[back to top]


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

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=trmD:Gene_Product(s)&oldid=1494471"