hrpB:Gene: Difference between revisions

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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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*  
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{| id="G46a9a98212287"  class=" tableEdit Gene_nomenclature_table"   
{|   id="G46a9a98212287"  class=" tableEdit Gene_nomenclature_table"   


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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
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''ECK0147, b0148, JW0144, yadO''<ref name='LIB:Riley_2006'/>
''ECK0147, b0148, JW0144, yadO''<ref name='LIB:Riley_2006'/>, yadO''


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*  
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{|   id="F46a9a9828a70d"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46a9a9828a70d"  class=" tableEdit Gene_location_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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3.49 minutes&nbsp;
3.49 minutes&nbsp;
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|
MG1655: 162105..164534<br />{{GBrowseFigureByCoord|162105|164534|ecoli|MG1655}}
MG1655: 162105..164534<br /><gbrowseImage>
name=NC_000913:162105..164534
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12329 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12329 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|161105|165534|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|161105|165534|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|162105|164534|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|162105|164534|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12329 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12329 EcoCyc Sequence Dump]  
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NC_012967: 164956..167385<br />{{GBrowseFigureByCoord|164956|167385|REL606|NC_012967}}
NC_012967: 164956..167385<br /><gbrowseImage>
name=NC_012967:164956..167385
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|REL606|NC_012967|164956|167385|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|164956|167385|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|164956|167385|FASTA Dump}}  
{{GBrowseFastaLink|REL606|NC_012967|164956|167385|FASTA Dump}}  
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[[BW2952]]
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NC_012759: 162104..164533<br /><gbrowseImage>
name=NC_012759:162104..164533
source=BW2952
preset=GeneLocation
</gbrowseImage>
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{{GBrowseLink|BW2952|NC_012759|162104|164533|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|162104|164533|FASTA Dump}}
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&nbsp;
&nbsp;
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W3110: 162105..164534<br />{{GBrowseFigureByCoord|162105|164534|ecoli_W3110|W3110}}
W3110: 162105..164534<br /><gbrowseImage>
name=NC_007779:162105..164534
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|ecoli_W3110|AC_000091|161105|165534|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|161105|165534|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|162105|164534|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|162105|164534|FASTA Dump}}  
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|
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DH10B: 136209..138638<br />{{GBrowseFigureByCoord|136209|138638|ecoli_DH10B|DH10B}}
DH10B: 136209..138638<br /><gbrowseImage>
name=NC_010473:136209..138638
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|ecoli_DH10B|NC_010473|131351|143496|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|131351|143496|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|131351|143496|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|131351|143496|FASTA Dump}}  


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*  
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{|   id="N46a9a98332fb7"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9a98332fb7"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10871.N46a9a98332fb7&page=10871&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
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{| {{Prettytable}} id="P46a9a983737eb"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="P46a9a983737eb"  class=" tableEdit Gene_allele_table dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-  
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&Delta;hrpB (Keio:JW0144)
''hrpB(del)'' (Keio:JW0144)
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deletion
deletion
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PMID:16738554
PMID:16738554
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106695 CGSC8414]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=106695 CGSC8414]<ref name='LIB:cgsc'/>  
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''&#916;hrpB764::kan''
''hrpB(del)''::kan
|
deletion
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[[Biolog]]:respiration
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unable to respire [[Carbon sources|D-Mannose]]
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PMID:16095938
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|-
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''hrpB(del)''::kan
|
deletion
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[[Biolog]]:respiration
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unable to respire [[Carbon sources|Acetate]]
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PMID:16095938
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|-
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''hrpB764(del)''::kan
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.10871.K4e04bd3a5240c-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K4e04bd3a5240c"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.10871.K4e04bd3a5240c&page=10871&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.10871.K4e04bd3a5240c--></protect>
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="E46a9a9841bd7f"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a9a9841bd7f"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCCGAATACTTTTTCGTCCGTCG  
Primer 2:CCCGAATACTTTTTCGTCCGTCG  
|-
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[[:Category:Kohara_Phage:15A7|15A7]]
|
Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=116 Genobase]
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PMID:3038334
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{|   id="U46a9a984a4f06"  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="U46a9a984a4f06"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12329 EcoCyc:EG12329]
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|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2233 EchoBASE:EB2233]
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|-
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0148 EcoliGenExpDB:b0148]
EcoCyc:EG12329
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[EcoGene]]
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[http://BioCyc.org/ECOL199310/new-image?object=C0181 ECOL199310CYC:C0181]
EcoGene:EG12329
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
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[http://ecogene.org/geneinfo.php?eg_id=EG12329 EcoGene:EG12329]
RegulonDB:ECK120002204
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
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[http://BioCyc.org/ECOO157/new-image?object=HRPB ECOO157CYC:HRPB]
[http://www.ncbi.nlm.nih.gov/gene?term=944845 GeneID:944845]
|
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Escherichia coli str. K-12 substr. MG1655
|-  
|-  
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/36926 CGSC:36926]
EchoBASE:EB2233
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000510&formSubmitReturn=1 ASAP:ABE-0000510]
ASAP:ABE-0000510
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:hrp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:hrp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:37, 19 September 2013

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

hrpB

Mnemonic

Helicase-related protein

Synonyms

ECK0147, b0148, JW0144, yadO[1], yadO

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

3.49 minutes 

MG1655: 162105..164534
<gbrowseImage> name=NC_000913:162105..164534 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 164956..167385
<gbrowseImage> name=NC_012967:164956..167385 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 162104..164533
<gbrowseImage> name=NC_012759:162104..164533 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 162105..164534
<gbrowseImage> name=NC_007779:162105..164534 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 136209..138638
<gbrowseImage> name=NC_010473:136209..138638 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

hrpB(del) (Keio:JW0144)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8414[3]

hrpB(del)::kan

deletion

Biolog:respiration

unable to respire D-Mannose

PMID:16095938[4]

hrpB(del)::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]

hrpB764(del)::kan

PMID:16738554[2]

CGSC:101406


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table


Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0144

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTCGTCGTTGCCCGTTGCTGC

Primer 2:CCCGAATACTTTTTCGTCCGTCG

15A7

Kohara Phage

Genobase

PMID:3038334[6]

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[3]

est. P1 cotransduction: 62% [7]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[3]

est. P1 cotransduction: 2% [7]
Synonyms:zae-502::Tn10

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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

EcoCyc

EcoCyc:EG12329

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12329

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002204

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944845

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2233

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000510

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  5. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  6. ↑ Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  7. ↑ 7.0 7.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

Categories

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