trmD:Gene Product(s): Difference between revisions

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!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''
|-
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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}}
|- {{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:0009019
GO:0003723
|
|
tRNA (guanine-N1-)-methyltransferase activity
RNA binding
|
|
GO_REF:0000003<br />GO_REF:0000020
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
EC:2.1.1.31<br />HAMAP:MF_00605
InterPro:IPR002649
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0005737
GO:0009451
|
|
cytoplasm
RNA modification
|
|
GO_REF:0000004
 
|
|
IEA: Inferred from Electronic Annotation
 
|
|
SP_KW:KW-0963
 
|
|
C
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
|
|
complete
Missing: evidence, reference
|-  
|-  
|
|


|
|
GO:0003723
GO:0005737
|
|
RNA binding
cytoplasm
|
|
GO_REF:0000002
GOA:hamap<br />GO_REF:0000020
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR002649
HAMAP:MF_00605
|
|
F
C
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0006400
GO:0005737
|
|
tRNA modification
cytoplasm
|
|
GO_REF:0000020
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
HAMAP:MF_00605
SP_KW:KW-0963
|
|
P
C
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0008033
GO:0005737
|
|
tRNA processing
cytoplasm
|
|
GO_REF:0000002<br />GO_REF:0000004
GO_REF:0000023
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR002649<br />SP_KW:KW-0819
SP_SL:SL-0086
|
|
P
C
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0008168
GO:0009019
|
|
methyltransferase activity
tRNA (guanine-N1-)-methyltransferase activity
|
|
GO_REF:0000004
GOA:hamap<br />GO_REF:0000020
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0489
HAMAP:MF_00605
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0008175
GO:0009019
|
|
tRNA methyltransferase activity
tRNA (guanine-N1-)-methyltransferase 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 <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0016740
GO:0009019
|
|
transferase activity
tRNA (guanine-N1-)-methyltransferase activity
|
|
GO_REF:0000004
GOA:spec<br />GO_REF:0000003
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0808
EC:2.1.1.31
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25510.E46aab2df2b20e&page=25510&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table]</span> || || || || || || || ||
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<!--box uid=421aa90e079fa326b6494f812ad13e79.25510.E46aab2df2b20e-->
<span id="Interactions"></span><big>'''Interactions'''</big>
<!--box uid=421aa90e079fa326b6494f812ad13e79.25510.U46aab2e80e16a-->
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{| 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}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
|-  
|-  
|
Protein
|
Subunits of [[:Category:Complex:tRNA (guanine-1-)-methyltransferase|tRNA (guanine-1-)-methyltransferase]]
|
could be indirect
|
|


|
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GO:0030488
|-
|
|
tRNA methylation
Protein
|
|
PMID:342495
dnaX
|
|
IMP: Inferred from Mutant Phenotype
 
|
PMID:19402753
|
MALDI(Z-score):28.759733
|-
|
Protein
|
holA
|
|


|
|
P
PMID:19402753
|
MALDI(Z-score):32.609818
|-
|
Protein
|
dnaE
|
 
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
PMID:19402753
|
|
complete
MALDI(Z-score):18.854791
|-  
|-  
|
|
Protein
|
holD
|
 
|
PMID:19402753
|
|
GO:0009451
MALDI(Z-score):21.182048
|-
|
|
RNA modification
Protein
|
|
holC
|
|
 
|
|
PMID:19402753
|
|
P
MALDI(Z-score):27.442857
|-
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
Protein
|
dnaQ
|
|
required fields missing 


|- class="tableEdit_footer"
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PMID:19402753
|}
|
<!--box uid=421aa90e079fa326b6494f812ad13e79.25510.E46aab2df2b20e-->
MALDI(Z-score):29.343986
 
<span id="Interactions"></span><big>'''Interactions'''</big>
<!--box uid=421aa90e079fa326b6494f812ad13e79.25510.U46aab2e80e16a-->
<!--
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{|  id="U46aab2e80e16a"  class=" tableEdit Product_interactions_table dataTable" 
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
|-  
|-  
|
|
Protein
Protein
|
|
Subunits of [[:Category:Complex:tRNA (guanine-1-)-methyltransferase|tRNA (guanine-1-)-methyltransferase]]
holB
|
|
could be indirect
 
|
|
 
PMID:19402753
|
|
MALDI(Z-score):38.943183


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{|   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}}
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!|Compartment!!Description!!Evidence!!Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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!align=left {{table heading style}} |Name
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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"   
|- {{table heading style}}
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!|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


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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)


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{| 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"   
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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"   
|- {{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]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11023-MONOMER EcoCyc:EG11023-MONOMER]
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]]
|
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]]


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!|Name!!URL!!Comments
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{{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

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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

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