rnhA:Gene Product(s): Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
No edit summary
touch table
 
(13 intermediate revisions by the same user not shown)
Line 75: Line 75:
*  
*  
****************************************************************************************** -->{{Product_GO_help}}
****************************************************************************************** -->{{Product_GO_help}}
{|   id="N46aa23df910e0"  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="N46aa23df910e0"  class=" tableEdit GO_table_product dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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
Line 453: Line 453:
*  
*  
****************************************************************************************** -->{{Product_interactions_help}}
****************************************************************************************** -->{{Product_interactions_help}}
{|   id="X46aa23f3d4c96"  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="X46aa23f3d4c96"  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 686: Line 686:
PMID:19402753
PMID:19402753
|
|
MALDI(Z-score):22.098379  
MALDI(Z-score):22.098379  
|-  
|-  
|
|
Line 719: Line 719:
PMID:19402753
PMID:19402753
|
|
MALDI(Z-score):27.813338  
MALDI(Z-score):27.813338  
|-  
|-  
|
|
Line 730: Line 730:
PMID:19402753
PMID:19402753
|
|
MALDI(Z-score):28.480234  
MALDI(Z-score):28.480234  
|-  
|-  
|
|
Line 752: Line 752:
PMID:19402753
PMID:19402753
|
|
MALDI(Z-score):20.695516  
MALDI(Z-score):20.695516  
|-  
|-  
|
|
Protein
Protein
|
|
[[yhbY:Gene_Product(s)|yhbY]]
yhbY
|
|


Line 768: Line 768:
Protein
Protein
|
|
[[rpmB:Gene_Product(s)|rpmB]]
rpmB
|
|


Line 779: Line 779:
Protein
Protein
|
|
[[atpA:Gene_Product(s)|atpA]]
atpA
|
|


Line 785: Line 785:
PMID:19402753
PMID:19402753
|
|
MALDI(Z-score):23.243464  
MALDI(Z-score):23.243464  
|-  
|-  
|
|
Protein
Protein
|
|
[[topB:Gene_Product(s)|topB]]
topB
|
|


Line 801: Line 801:
Protein
Protein
|
|
[[topA:Gene_Product(s)|topA]]
topA
|
|


Line 812: Line 812:
Protein
Protein
|
|
[[atpG:Gene_Product(s)|atpG]]
atpG
|
|


Line 818: Line 818:
PMID:19402753
PMID:19402753
|
|
MALDI(Z-score):39.018288  
MALDI(Z-score):39.018288  
|-  
|-  
|
|
Protein
Protein
|
|
[[priA:Gene_Product(s)|priA]]
priA
|
|


Line 829: Line 829:
PMID:19402753
PMID:19402753
|
|
MALDI(Z-score):17.400508  
MALDI(Z-score):17.400508  
|-  
|-  
|
|
Protein
Protein
|
|
[[ssb:Gene_Product(s)|ssb]]
ssb
|
|


Line 845: Line 845:
Protein
Protein
|
|
[[recQ:Gene_Product(s)|recQ]]
recQ
|
|


Line 851: Line 851:
PMID:19402753
PMID:19402753
|
|
MALDI(Z-score):27.556410  
MALDI(Z-score):27.556410  
|-  
|-  
|
|
Protein
Protein
|
|
[[sbcB:Gene_Product(s)|sbcB]]
sbcB
|
|


Line 862: Line 862:
PMID:19402753
PMID:19402753
|
|
MALDI(Z-score):18.452946  
MALDI(Z-score):18.452946  


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 881: Line 881:
*  
*  
****************************************************************************************** -->{{Product_localization_help}}
****************************************************************************************** -->{{Product_localization_help}}
{|   id="Z46a7b52a55da0"  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="Z46a7b52a55da0"  class=" tableEdit Product_localization_table"   
|- {{table heading style}}
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
Line 951: Line 951:
*  
*  
****************************************************************************************** -->{{Product_domains_motifs_help}}
****************************************************************************************** -->{{Product_domains_motifs_help}}
{|   id="D46aa23f5ea789"  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="D46aa23f5ea789"  class=" tableEdit Product_motif_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References
!|Type!!Residues!!Description!!Notes!!References
Line 1,001: Line 1,001:
View models at:
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/P0A7Y4 Protein Model Portal]
* [http://www.proteinmodelportal.org/query/uniprot/P0A7Y4 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0A7Y4 PSI-PRED (P0A7Y4)]
* [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=P0A7Y4 Genomes TO Protein (P0A7Y4)] (GTOP)


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 1,043: Line 1,043:
*  
*  
****************************************************************************************** -->{{Product_resources_help}}
****************************************************************************************** -->{{Product_resources_help}}
{|   id="O46aa241390cac"  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="O46aa241390cac"  class=" tableEdit Product_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference
Line 1,065: Line 1,065:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="L46aa2413da520"  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="L46aa2413da520"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
Line 1,084: Line 1,084:
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWiki Page]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000717&formSubmitReturn=1 ASAP:ABE-0000717]
ASAP:ABE-0000717
|
|
Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
Line 1,098: Line 1,098:
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10860 ECOCYC:EG10860]
EcoCyc:EG10860
|
|
Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10860 EcoGene:EG10860]
EcoGene:EG10860
|
|
Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
Line 1,117: Line 1,117:
|
|
Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120000851
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EchoBASE]]
|
EchoBASE:EB0853
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 1,136: Line 1,150:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="P46a7b5566097e"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P46a7b5566097e"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:22, 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

RnhA

Synonyms

ribonuclease HI, degrades RNA of DNA-RNA hybrids[1], B0214[2][1], Sin[2][1], Cer[2][1], Rnh[2][1], SdrA[2][1], HerA[2][1], DasF[2][1], RnhA[2][1] , cer, dasF, ECK0214, herA, JW0204, rnh, sdrA, sin, b0214

Product description

RNase HI, degrades RNA of DNA-RNA hybrids, participates in DNA replication[2][3]

RNase HI; participates in DNA replication[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:0000287

magnesium ion binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00042

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002156

F

Seeded from EcoCyc (v14.0)

complete

GO:0006508

proteolysis

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012337

F

Seeded from EcoCyc (v14.0)

complete

GO:0004518

nuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0540

F

Seeded from EcoCyc (v14.0)

complete

GO:0004519

endonuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0255

F

Seeded from EcoCyc (v14.0)

complete

GO:0004523

ribonuclease H activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00042

F

Seeded from EcoCyc (v14.0)

complete

GO:0004523

ribonuclease H activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002156

F

Seeded from EcoCyc (v14.0)

complete

GO:0004523

ribonuclease H activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.1.26.4

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00042

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:0006401

RNA catabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00042

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:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0004523

ribonuclease H activity

PMID:4572736[5]

IDA: Inferred from Direct Assay

F

complete

GO:0003676

nucleic acid binding

PMID:4572736[5]

IDA: Inferred from Direct Assay

F

complete

GO:0004519

endonuclease activity

PMID:4572736[5]

IDA: Inferred from Direct Assay

F

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

ssb

PMID:15690043[6]

Experiment(s):EBI-881230, EBI-888507

Protein

aceE

PMID:15690043[6]

Experiment(s):EBI-881230

Protein

aceF

PMID:15690043[6]

Experiment(s):EBI-881230, EBI-888507

Protein

lpdA

PMID:15690043[6]

Experiment(s):EBI-881230

Protein

malP

PMID:15690043[6]

Experiment(s):EBI-881230

Protein

priA

PMID:15690043[6]

Experiment(s):EBI-881230

Protein

recQ

PMID:15690043[6]

Experiment(s):EBI-881230

Protein

rplB

PMID:15690043[6]

Experiment(s):EBI-881230

Protein

rpsC

PMID:15690043[6]

Experiment(s):EBI-881230

Protein

sbcB

PMID:15690043[6]

Experiment(s):EBI-881230

Protein

topA

PMID:15690043[6]

Experiment(s):EBI-881230, EBI-888507

Protein

topB

PMID:15690043[6]

Experiment(s):EBI-881230

Protein

hupA

PMID:15690043[6]

Experiment(s):EBI-888507

Protein

rpmB

PMID:15690043[6]

Experiment(s):EBI-888507

Protein

rpsE

PMID:15690043[6]

Experiment(s):EBI-888507

Protein

rpsI

PMID:15690043[6]

Experiment(s):EBI-888507

Protein

rpsN

PMID:15690043[6]

Experiment(s):EBI-888507

Protein

rpsT

PMID:15690043[6]

Experiment(s):EBI-888507

Protein

yhbY

PMID:15690043[6]

Experiment(s):EBI-888507

Protein

rpsI

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpsC

PMID:19402753[7]

MALDI(Z-score):22.098379

Protein

rpsT

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

atpD

PMID:19402753[7]

MALDI(Z-score):27.813338

Protein

rplB

PMID:19402753[7]

MALDI(Z-score):28.480234

Protein

hupA

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

malP

PMID:19402753[7]

MALDI(Z-score):20.695516

Protein

yhbY

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

atpA

PMID:19402753[7]

MALDI(Z-score):23.243464

Protein

topB

PMID:19402753[7]

LCMS(ID Probability):98.0 MALDI(Z-score):26.888562

Protein

topA

PMID:19402753[7]

LCMS(ID Probability):99.6 MALDI(Z-score):29.004003

Protein

atpG

PMID:19402753[7]

MALDI(Z-score):39.018288

Protein

priA

PMID:19402753[7]

MALDI(Z-score):17.400508

Protein

ssb

PMID:19402753[7]

LCMS(ID Probability):99.6 MALDI(Z-score):6.393986

Protein

recQ

PMID:19402753[7]

MALDI(Z-score):27.556410

Protein

sbcB

PMID:19402753[7]

MALDI(Z-score):18.452946

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 

MLKQVEIFTD GSCLGNPGPG GYGAILRYRG REKTFSAGYT RTTNNRMELM AAIVALEALK
EHCEVILSTD SQYVRQGITQ WIHNWKKRGW KTADKKPVKN VDLWQRLDAA LGQHQIKWEW
VKGHAGHPEN ERCDELARAA AMNPTLEDTG YQVEV
Length

155

Mol. Wt

17.596 kDa

pI

8.4 (calculated)

Extinction coefficient

40,450 - 40,825 (calc based on 5 Y, 6 W, and 3 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

2..142

PF00075 RNase H

PMID:19920124[8]

edit table

<motif_map/>

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

Structures

<beststructure> gene=rnhA 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:16128201

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946955

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000717

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A7Y4

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10860

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10860

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946955

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000851

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0853

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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 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 2.4 2.5 2.6 2.7 2.8 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. ↑ 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 Miller, HI et al. (1973) Ribonuclease H (hybrid) in Escherichia coli. Identification and characterization. J. Biol. Chem. 248 2621-4 PubMed
  6. ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 6.10 6.11 6.12 6.13 6.14 6.15 6.16 6.17 6.18 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  7. ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 7.12 7.13 7.14 7.15 7.16 7.17 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  8. ↑ 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=rnhA:Gene_Product(s)&oldid=1492253"