EcoliWiki - User contributions [en]

nlpD:Gene Product(s)

2016-03-15T19:28:48Z

Saleksander: Table edited by Saleksander via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|nlpD}}{{Tab|Gene|nlpD}}{{Tab On|Gene Product(s)|nlpD}}{{Tab|Expression|nlpD}}{{Tab|Evolution|nlpD}}{{Tab|On One Page|nlpD}}{{TabsBottom}}
{|
|-
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Function |Function]]
|{{Sub}}[[#Interactions |Interactions]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References| References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude>
==Nomenclature==

{{Product_nomenclature_help}}
{| id="M46aabb603e6a2" class=" tableEdit Product_nomenclature_table"

|-
!align=left {{table heading style}} |Standard name
||
NlpD
|-
!align=left {{table heading style}} |Synonyms
||
''predicted outer membrane lipoprotein<ref name='LIB:Riley_2006'/>, B2742<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, NlpD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2737, JW2712, b2742''
|-
!align=left {{table heading style}} |Product description
||
NlpD putative outer membrane lipoprotein<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>

Lipoprotein, function unknown; may be involved in cell wall formation; may have murein hydrolytic activity<ref name='LIB:EcoGene'/>
|-
!align=left {{table heading style}} |EC number (for enzymes)
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25811.M46aabb603e6a2&page=25811&pagename={{FULLPAGENAMEE}}&type=1&template=Product_nomenclature_table edit table] ||
|}


<protect></protect>
===Notes===

==Function==
{{BacktoTop}}
<protect>
<big>'''Gene Ontology'''</big> 
{{Product_GO_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="H46aabb614b6bb" class=" tableEdit GO_table_product dataTable"
|- {{table_heading_style}}
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-
|

|
GO:0000920
|
cytokinetic cell separation
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:P0AFS9
UniProtKB:P37690
UniProtKB:Q46798

|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0001896
|
autolysis
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:P0AFS9
UniProtKB:P37690
UniProtKB:Q46798

|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0000920
|
cytokinetic cell separation
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:P37690

|
P
|

|
complete
|-
|

|
GO:0004222
|
metalloendopeptidase activity
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR002886
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0005886
|
plasma membrane
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0997
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0000920
|
cytokinetic cell separation
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:P0AFS9
UniProtKB:P37690
UniProtKB:Q46798

|
P
|

|
complete
|-
|

|
GO:0005886
|
plasma membrane
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-1003
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0001896
|
autolysis
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:Q46798
UniProtKB:P0AFS9
UniProtKB:P37690

|
P
|
ampicillin- induced autolysis
|
complete
|-
|

|
GO:0006508
|
proteolysis
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR002886
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0032155
|
cell division site part
|
PMID:19525345
|
IDA: Inferred from Direct Assay
|

|
C
|
enriched at division sites with clear constrictions
|
complete
|-
|

|
GO:0016998
|
cell wall macromolecule catabolic process
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR002482
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0016998
|
cell wall macromolecule catabolic process
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR018392
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0031225
|
anchored to membrane
|
GO_REF:0000023
|
IEA: Inferred from Electronic Annotation
|
SP_SL:SL-9901
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0032155
|
cell division site part
|
PMID:19525345
|
IDA: Inferred from Direct Assay
|

|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25811.H46aabb614b6bb&page=25811&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table] || || || || || || || ||
|}


<big>'''Interactions'''</big>

{{Product_interactions_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="H46aabb61d07c2" class=" tableEdit Product_interactions_table dataTable"
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
|-
|
Protein
|
yfiD
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rplK
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
ompA
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rpmG
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rpmC
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
hns
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rpsP
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
acpP
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rpsT
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
hupA
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rpsN
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rplE
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
arpA
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rpsJ
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rpmB
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rplD
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
cspC
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
nusG
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
elbB
|

|
PMID:19402753
|
MALDI(Z-score):28.124797
|-
|
Protein
|
rplW
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
yeeX
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rpmD
|

|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rplL
|

|
PMID:19402753
|
LCMS(ID Probability):99.6

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25811.H46aabb61d07c2&page=25811&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table] || || || ||
|}


</protect>
===Notes===

==Localization==

{{Product_localization_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Q46aabb62971e2" class=" tableEdit Product_localization_table"
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
|-
|
outer membrane
|

|

|

|

|-
|
Outer membrane
|
|PMID:15174130
|
[http://www.york.ac.uk/res/thomas/Echolocation.cfm?EB_SubLocID=EB2034 EchoLocation:nlpD]
|

|

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25811.Q46aabb62971e2&page=25811&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table] || || || ||
|}


<protect></protect>

===Notes===

==Structure and Physical Properties==
{{BacktoTop}}
<protect>
<big>'''Physical Properties'''</big>

{{Product_physical_properties_help}}
{| id="G46aabb6435a41" class=" tableEdit Product_phys_prop_table"

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

|-
!align=left {{table heading style}} |Sequence
||
[http://biocyc.org/ECOLI/sequence-aa?object=EG12111-MONOMER at EcoCyc]
<pre>MSAGSPKFTV RRIAALSLVS LWLAGCSDTS NPPAPVSSVN GNAPANTNSG MLITPPPKMG
TTSTAQQPQI QPVQQPQIQA TQQPQIQPVQ PVAQQPVQME NGRIVYNRQY GNIPKGSYSG
STYTVKKGDT LFYIAWITGN DFRDLAQRNN IQAPYALNVG QTLQVGNASG TPITGGNAIT
QADAAEQGVV IKPAQNSTVA VASQPTITYS ESSGEQSANK MLPNNKPTAT TVTAPVTVPT
ASTTEPTVSS TSTSTPISTW RWPTEGKVIE TFGASEGGNK GIDIAGSKGQ AIIATADGRV
VYAGNALRGY GNLIIIKHND DYLSAYAHND TMLVREQQEV KAGQKIATMG STGTSSTRLH
FEIRYKGKSV NPLRYLPQR</pre>
|-
!align=left {{table heading style}} |Length
||
379
|-
!align=left {{table heading style}} |Mol. Wt
||
40.148 kDa
|-
!align=left {{table heading style}} |pI
||
9.9 (calculated)
|-
!align=left {{table heading style}} |Extinction coefficient
||
41,370 - 41,495 (calc based on 13 Y, 4 W, and 1 C residues)

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25811.G46aabb6435a41&page=25811&pagename={{FULLPAGENAMEE}}&type=1&template=Product_phys_prop_table edit table] ||
|}


<big>'''Domains/Motifs/Modification Sites'''</big><table>
<tr align="left" valign="top">
<td>
{{Product_domains_motifs_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Q46aabb64a5258" class=" tableEdit Product_motif_table dataTable"
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References
|-
|
motif
|
1-25
|
[[uniprotmanual:signal|UniProt Manual:Signal Peptides]]
|
[http://www.uniprot.org/uniprot/P0ADA3#section_features UniProt:P0ADA3]
|

|-
|
Domain
|
123..166
|
[http://pfam.janelia.org/family/PF01476 PF01476 LysM domain]
|

|
PMID:19920124
|-
|
Domain
|
277..372
|
[http://pfam.janelia.org/family/PF01551 PF01551 Peptidase family M23]
|

|
PMID:19920124

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25811.Q46aabb64a5258&page=25811&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table] || || || ||
|}
</td>
<td>


<motif_map/>
</td>
</tr>
</table>

<table><tr valign='top'><td>
<big>'''Structure'''</big> 

{{Product_structure_help}}
{| id="B46a8524cbbc1b" class=" tableEdit Product_structure_table"

|-
!align=left {{table heading style}} |Structures
||
<beststructure>
gene=nlpD
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/P0ADA3 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0ADA3 PSI-PRED (P0ADA3)]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0ADA3 Genomes TO Protein (P0ADA3)] (GTOP)

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25811.B46a8524cbbc1b&page=25811&pagename={{FULLPAGENAMEE}}&type=1&template=Product_structure_table edit table] ||
|}


</td><td></protect>
==== Structure figures ====

<protect>
</td><tr><table></protect>
===Notes===

==Gene Product Resources==
{{BacktoTop}}

{{Product_resources_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="A46aabb656f3a2" class=" tableEdit Product_resource_table"
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25811.A46aabb656f3a2&page=25811&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table] || ||
|}


<protect></protect>
===Notes===

==Accessions in Other Databases==
{{BacktoTop}}

{{Gene_accessions_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="N46aabb65cde2d" class=" tableEdit Gene_accessions_table"
|- {{table_heading_style}}
!|Database!!Accession!!Notes
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16130649 GI:16130649]
|
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_417222.1 GeneID:947011]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0009004
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P0ADA3 UniProtKB/Swiss-Prot:P0ADA3]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG12111
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG12111
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=947011 GeneID:947011]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120002015
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EchoBASE]]
|
EchoBASE:EB2034
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25811.N46aabb65cde2d&page=25811&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|}


<protect></protect>
===Notes===

==Links==
{{BacktoTop}}


{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="T46a8525034b43" class=" tableEdit Links_table"
|- {{table_heading_style}}
!|Name!!URL!!Comments

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25811.T46a8525034b43&page=25811&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|}


<noinclude>
==References==
{{BacktoTop}}
{{RefHelp}}
<references />
__NOTOC__
===Categories===
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Location:outer membrane]]
[[Category:Pfam:PF01476_!_LysM domain]]
[[Category:Pfam:PF01551_!_Peptidase family M23]]

ygeR:Gene Product(s)

2016-03-15T19:26:55Z

Saleksander: Table edited by Saleksander via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|ygeR}}{{Tab|Gene|ygeR}}{{Tab On|Gene Product(s)|ygeR}}{{Tab|Expression|ygeR}}{{Tab|Evolution|ygeR}}{{Tab|On One Page|ygeR}}{{TabsBottom}}
{|
|-
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Function |Function]]
|{{Sub}}[[#Interactions |Interactions]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References| References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude>
==Nomenclature==

{{Product_nomenclature_help}}
{| id="Z46aac36fb7bea" class=" tableEdit Product_nomenclature_table"

|-
!align=left {{table heading style}} |Standard name
||
YgeR
|-
!align=left {{table heading style}} |Synonyms
||
''Tetratricopeptide repeat transcriptional regulator<ref name='LIB:Riley_2006'/>, B2865<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YgeR<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2861, JW2833, b2865''
|-
!align=left {{table heading style}} |Product description
||
putative lipoprotein<ref name='LIB:EcoCyc10.6'/>; putative lipoprotein; predicted DNA-binding transcriptional regulator<ref name='LIB:EcoCyc11.1'/>

Novel lipoprotein, function unknown, metalloprotease homolog; M23 family<ref name='LIB:EcoGene'/>
|-
!align=left {{table heading style}} |EC number (for enzymes)
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.26088.Z46aac36fb7bea&page=26088&pagename={{FULLPAGENAMEE}}&type=1&template=Product_nomenclature_table edit table] ||
|}


<protect></protect>
===Notes===

==Function==
{{BacktoTop}}
<protect>
<big>'''Gene Ontology'''</big> 
{{Product_GO_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="U46aac370c4f5a" class=" tableEdit GO_table_product dataTable"
|- {{table_heading_style}}
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-
|

|
GO:0000920
|
cytokinetic cell separation
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:P0ADA3
UniProtKB:P37690
UniProtKB:Q46798

|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0001896
|
autolysis
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:P0ADA3
UniProtKB:P37690
UniProtKB:Q46798

|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0004222
|
metalloendopeptidase activity
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR002886
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0005886
|
plasma membrane
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-1003
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0006508
|
proteolysis
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR002886
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0000920
|
cytokinetic cell separation
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:P37690

|
P
|

|
complete
|-
|

|
GO:0016020
|
membrane
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0472
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0016998
|
cell wall macromolecule catabolic process
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR002482
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0000920
|
cytokinetic cell separation
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:P0ADA3
UniProtKB:P37690
UniProtKB:Q46798

|
P
|

|
complete
|-
|

|
GO:0016998
|
cell wall macromolecule catabolic process
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR018392
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0001896
|
autolysis
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:P0ADA3
UniProtKB:P37690
UniProtKB:Q46798

|
P
|
ampicillin- induced autolysis
|
complete
|-
|

|
GO:0031225
|
anchored to membrane
|
GO_REF:0000023
|
IEA: Inferred from Electronic Annotation
|
SP_SL:SL-9901
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.26088.U46aac370c4f5a&page=26088&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table] || || || || || || || ||
|}


<big>'''Interactions'''</big>

{{Product_interactions_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O46aac3755a909" class=" tableEdit Product_interactions_table dataTable"
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
|-
|
Protein
|
rplL
|

|
PMID:19402753
|
LCMS(ID Probability):99.6

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.26088.O46aac3755a909&page=26088&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table] || || || ||
|}


</protect>
===Notes===

==Localization==

{{Product_localization_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="X46a8596e392e7" class=" tableEdit Product_localization_table"
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
|-
|
Outer membrane
|
|PMID:15174130
|
[http://www.york.ac.uk/res/thomas/Echolocation.cfm?EB_SubLocID=EB2860 EchoLocation:ygeR]
|

|

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.26088.X46a8596e392e7&page=26088&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table] || || || ||
|}


<protect></protect>

===Notes===

==Structure and Physical Properties==
{{BacktoTop}}
<protect>
<big>'''Physical Properties'''</big>

{{Product_physical_properties_help}}
{| id="Q46aac37746258" class=" tableEdit Product_phys_prop_table"

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

|-
!align=left {{table heading style}} |Sequence
||
[http://biocyc.org/ECOLI/sequence-aa?object=G7484-MONOMER at EcoCyc]
<pre>MFFKRGKILS AGRLNKKSLG IVMLLSVGLL LAGCSGSKSS DTGTYSGSVY TVKRGDTLYR
ISRTTGTSVK ELARLNGISP PYTIEVGQKL KLGGAKSSSI TRKSTAKSTT KTASVTPSSA
VPKSSWPPVG QRCWLWPTTG KVIMPYSTAD GGNKGIDISA PRGTPIYAAG AGKVVYVGNQ
LRGYGNLIMI KHSEDYITAY AHNDTMLVNN GQSVKAGQKI ATMGSTDAAS VRLHFQIRYR
ATAIDPLRYL PPQGSKPKC</pre>
|-
!align=left {{table heading style}} |Length
||
259
|-
!align=left {{table heading style}} |Mol. Wt
||
27.555 kDa
|-
!align=left {{table heading style}} |pI
||
10.6 (calculated)
|-
!align=left {{table heading style}} |Extinction coefficient
||
34,380 - 34,755 (calc based on 12 Y, 3 W, and 3 C residues)

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.26088.Q46aac37746258&page=26088&pagename={{FULLPAGENAMEE}}&type=1&template=Product_phys_prop_table edit table] ||
|}


<big>'''Domains/Motifs/Modification Sites'''</big><table>
<tr align="left" valign="top">
<td>
{{Product_domains_motifs_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="G46aac377b6336" class=" tableEdit Product_motif_table dataTable"
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References
|-
|
motif
|
1-25
|
[[uniprotmanual:signal|UniProt Manual:Signal Peptides]]
|
[http://www.uniprot.org/uniprot/Q46798#section_features UniProt:Q46798]
|

|-
|
Domain
|
42..85
|
[http://pfam.janelia.org/family/PF01476 PF01476 LysM domain]
|

|
PMID:19920124
|-
|
Domain
|
143..238
|
[http://pfam.janelia.org/family/PF01551 PF01551 Peptidase family M23]
|

|
PMID:19920124

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.26088.G46aac377b6336&page=26088&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table] || || || ||
|}
</td>
<td>


<motif_map/>
</td>
</tr>
</table>

<table><tr valign='top'><td>
<big>'''Structure'''</big> 

{{Product_structure_help}}
{| id="B46a8596fcc1fe" class=" tableEdit Product_structure_table"

|-
!align=left {{table heading style}} |Structures
||
<beststructure>
gene=ygeR
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/Q46798 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=Q46798 PSI-PRED (Q46798)]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=Q46798 Genomes TO Protein (Q46798)] (GTOP)

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.26088.B46a8596fcc1fe&page=26088&pagename={{FULLPAGENAMEE}}&type=1&template=Product_structure_table edit table] ||
|}


</td><td></protect>
==== Structure figures ====

<protect>
</td><tr><table></protect>
===Notes===

==Gene Product Resources==
{{BacktoTop}}

{{Product_resources_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="F46aac37880d79" class=" tableEdit Product_resource_table"
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.26088.F46aac37880d79&page=26088&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table] || ||
|}


<protect></protect>
===Notes===

==Accessions in Other Databases==
{{BacktoTop}}

{{Gene_accessions_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="W46aac378dfd8f" class=" tableEdit Gene_accessions_table"
|- {{table_heading_style}}
!|Database!!Accession!!Notes
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/90111503 GI:90111503]
|
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_417341.4 GeneID:947352]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0009407
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/Q46798 UniProtKB/Swiss-Prot:Q46798]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:G7484
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG13048
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=947352 GeneID:947352]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120004047
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EchoBASE]]
|
EchoBASE:EB2860
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.26088.W46aac378dfd8f&page=26088&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|}


<protect></protect>
===Notes===

==Links==
{{BacktoTop}}


{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="X46a859735179b" class=" tableEdit Links_table"
|- {{table_heading_style}}
!|Name!!URL!!Comments

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.26088.X46a859735179b&page=26088&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|}


<noinclude>
==References==
{{BacktoTop}}
{{RefHelp}}
<references />
__NOTOC__
===Categories===
{{BacktoTop}}
[[Category:Proteins]]

yebA:Gene Product(s)

2016-03-15T19:24:59Z

Saleksander: Table edited by Saleksander via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|yebA}}{{Tab|Gene|yebA}}{{Tab On|Gene Product(s)|yebA}}{{Tab|Expression|yebA}}{{Tab|Evolution|yebA}}{{Tab|On One Page|yebA}}{{TabsBottom}}
{|
|-
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Function |Function]]
|{{Sub}}[[#Interactions |Interactions]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References| References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude>
==Nomenclature==

{{Product_nomenclature_help}}
{| id="T46aa821e3160b" class=" tableEdit Product_nomenclature_table"

|-
!align=left {{table heading style}} |Standard name
||
YebA
|-
!align=left {{table heading style}} |Synonyms
||
''predicted peptidase<ref name='LIB:Riley_2006'/>, YebA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B1856<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK1857, JW5304, b1856''
|-
!align=left {{table heading style}} |Product description
||
conserved protein<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>

Putative metalloprotease, function unknown; M37 family<ref name='LIB:EcoGene'/>
|-
!align=left {{table heading style}} |EC number (for enzymes)
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23816.T46aa821e3160b&page=23816&pagename={{FULLPAGENAMEE}}&type=1&template=Product_nomenclature_table edit table] ||
|}


<protect></protect>
===Notes===

==Function==
{{BacktoTop}}
<protect>
<big>'''Gene Ontology'''</big> 
{{Product_GO_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="E46aa821f391bb" class=" tableEdit GO_table_product dataTable"
|- {{table_heading_style}}
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-
|

|
GO:0000920
|
cytokinetic cell separation
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:P0ADA3
UniProtKB:P37690
UniProtKB:Q46798

|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0001896
|
autolysis
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:Q46798
UniProtKB:P0ADA3
UniProtKB:P37690

|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0004222
|
metalloendopeptidase activity
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR002886
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0005886
|
plasma membrane
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-1003
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0006508
|
proteolysis
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR002886
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0007047
|
cellular cell wall organization
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0961
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0008233
|
peptidase activity
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0645
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0008237
|
metallopeptidase activity
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0482
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0008270
|
zinc ion binding
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0862
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0016020
|
membrane
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0472
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0016021
|
integral to membrane
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0812
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0016021
|
integral to membrane
|
GO_REF:0000023
|
IEA: Inferred from Electronic Annotation
|
SP_SL:SL-9904
|
C
|
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:0016998
|
cell wall macromolecule catabolic process
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR002482
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0016998
|
cell wall macromolecule catabolic process
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR018392
|
P
|
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:0000920
|
cytokinetic cell separation
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:P37690

|
P
|

|
complete
|-
|

|
GO:0000920
|
cytokinetic cell separation
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:P0ADA3
UniProtKB:P37690
UniProtKB:Q46798

|
P
|

|
complete
|-
|

|
GO:0001896
|
autolysis
|
PMID:19525345
|
IGI: Inferred from Genetic Interaction
|
UniProtKB:P0ADA3
UniProtKB:P37690
UniProtKB:Q46798

|
P
|
ampicillin- induced autolysis
|
complete

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23816.E46aa821f391bb&page=23816&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table] || || || || || || || ||
|}


<big>'''Interactions'''</big>

{{Product_interactions_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="G46aa821fbac83" class=" tableEdit Product_interactions_table dataTable"
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23816.G46aa821fbac83&page=23816&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table] || || || ||
|}


</protect>
===Notes===

==Localization==

{{Product_localization_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="E46a812ec4fcf6" class=" tableEdit Product_localization_table"
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23816.E46a812ec4fcf6&page=23816&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table] || || || ||
|}


<protect></protect>

===Notes===

==Structure and Physical Properties==
{{BacktoTop}}
<protect>
<big>'''Physical Properties'''</big>

{{Product_physical_properties_help}}
{| id="F46aa82219d18a" class=" tableEdit Product_phys_prop_table"

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

|-
!align=left {{table heading style}} |Sequence
||
[http://biocyc.org/ECOLI/sequence-aa?object=EG10013-MONOMER at EcoCyc]
<pre>MLGSLTVLTL AVAVWRPYVY HRDATPIVKT IELEQNEIRS LLPEASEPID QAAQEDEAIP
QDELDDKIAG EAGVHEYVVS TGDTLSSILN QYGIDMGDIT QLAAADKELR NLKIGQQLSW
TLTADGELQR LTWEVSRRET RTYDRTAANG FKMTSEMQQG EWVNNLLKGT VGGSFVASAR
NAGLTSAEVS AVIKAMQWQM DFRKLKKGDE FAVLMSREML DGKREQSQLL GVRLRSEGKD
YYAIRAEDGK FYDRNGTGLA KGFLRFPTAK QFRISSNFNP RRTNPVTGRV APHRGVDFAM
PQGTPVLSVG DGEVVVAKRS GAAGYYVAIR HGRSYTTRYM HLRKILVKPG QKVKRGDRIA
LSGNTGRSTG PHLHYEVWIN QQAVNPLTAK LPRTEGLTGS DRREFLAQAK EIVPQLRFD</pre>
|-
!align=left {{table heading style}} |Length
||
419
|-
!align=left {{table heading style}} |Mol. Wt
||
46.657 kDa
|-
!align=left {{table heading style}} |pI
||
9.7 (calculated)
|-
!align=left {{table heading style}} |Extinction coefficient
||
52,370 (calc based on 13 Y, 6 W, and 0 C residues)

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23816.F46aa82219d18a&page=23816&pagename={{FULLPAGENAMEE}}&type=1&template=Product_phys_prop_table edit table] ||
|}


<big>'''Domains/Motifs/Modification Sites'''</big><table>
<tr align="left" valign="top">
<td>
{{Product_domains_motifs_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Q46aa822214bea" class=" tableEdit Product_motif_table dataTable"
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
312..407
|
[http://pfam.janelia.org/family/PF01551 PF01551 Peptidase family M23]
|

|
PMID:19920124
|-
|
Domain
|
94..176
|
[http://pfam.janelia.org/family/PF04225 PF04225 Opacity-associated protein A LysM-like domain]
|

|
PMID:19920124
|-
|
Domain
|
10..40
|
[http://pfam.janelia.org/family/PF08525 PF08525 Opacity-associated protein A N-terminal motif]
|

|
PMID:19920124

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23816.Q46aa822214bea&page=23816&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table] || || || ||
|}
</td>
<td>


<motif_map/>
</td>
</tr>
</table>

<table><tr valign='top'><td>
<big>'''Structure'''</big> 

{{Product_structure_help}}
{| id="N46a812ee37f4a" class=" tableEdit Product_structure_table"

|-
!align=left {{table heading style}} |Structures
||
<beststructure>
gene=yebA
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/P0AFS9 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0AFS9 PSI-PRED (P0AFS9)]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0AFS9 Genomes TO Protein (P0AFS9)] (GTOP)

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23816.N46a812ee37f4a&page=23816&pagename={{FULLPAGENAMEE}}&type=1&template=Product_structure_table edit table] ||
|}


</td><td></protect>
==== Structure figures ====

<protect>
</td><tr><table></protect>
===Notes===

==Gene Product Resources==
{{BacktoTop}}

{{Product_resources_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="N46aa8222ccdb8" class=" tableEdit Product_resource_table"
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23816.N46aa8222ccdb8&page=23816&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table] || ||
|}


<protect></protect>
===Notes===

==Accessions in Other Databases==
{{BacktoTop}}

{{Gene_accessions_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="J46aa82233451a" class=" tableEdit Gene_accessions_table"
|- {{table_heading_style}}
!|Database!!Accession!!Notes
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/90111345 GI:90111345]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0006189
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P0AFS9 UniProtKB/Swiss-Prot:P0AFS9]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG10013
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG10013
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=946376 GeneID:946376]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120000011
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/NP_416370.2 GeneID:946376]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EchoBASE]]
|
EchoBASE:EB0013
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23816.J46aa82233451a&page=23816&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|}


<protect></protect>
===Notes===

==Links==
{{BacktoTop}}


{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="B46a812f2d5753" class=" tableEdit Links_table"
|- {{table_heading_style}}
!|Name!!URL!!Comments

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23816.B46a812f2d5753&page=23816&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|}


<noinclude>
==References==
{{BacktoTop}}
{{RefHelp}}
<references />
__NOTOC__
===Categories===
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Pfam:PF01551_!_Peptidase family M23]]
[[Category:Pfam:PF04225_!_Opacity-associated protein A LysM-like domain]]
[[Category:Pfam:PF08525_!_Opacity-associated protein A N-terminal motif]]

envC:Gene Product(s)

2016-03-15T19:11:33Z

Saleksander: Table edited by Saleksander via TableEdit

pdxK:Gene Product(s)

2015-10-21T00:52:30Z

Saleksander: Table edited by Saleksander via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|pdxK}}{{Tab|Gene|pdxK}}{{Tab On|Gene Product(s)|pdxK}}{{Tab|Expression|pdxK}}{{Tab|Evolution|pdxK}}{{Tab|On One Page|pdxK}}{{TabsBottom}}
{|
|-
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Function |Function]]
|{{Sub}}[[#Interactions |Interactions]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References| References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude>
==Nomenclature==

{{Product_nomenclature_help}}
{| id="E46aaa6b3b4982" class=" tableEdit Product_nomenclature_table"

|-
!align=left {{table heading style}} |Standard name
||
PdxK
|-
!align=left {{table heading style}} |Synonyms
||
''pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase<ref name='LIB:Riley_2006'/>, B2418<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PdxL<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, ThiJ<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YfeI<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PdxK<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2413, JW2411, pdxL, thiJ, yfeI, b2418''
|-
!align=left {{table heading style}} |Product description
||
PdxK<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>;

Component of [[:Category:Complex:PDXK-CPLX|PDXK-CPLX]]<ref name='LIB:EcoCyc10.6'/>

B6-vitamer kinase; pyridoxine (PN)/pyridoxal (PL)/pyridoxamine (PM) kinase<ref name='LIB:EcoGene'/>
|-
!align=left {{table heading style}} |EC number (for enzymes)
||
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35]<ref name='LIB:Riley_2006'/>

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25070.E46aaa6b3b4982&page=25070&pagename={{FULLPAGENAMEE}}&type=1&template=Product_nomenclature_table edit table] ||
|}


<protect></protect>
===Notes===

==Function==
{{BacktoTop}}
<protect>
<big>'''Gene Ontology'''</big> 
{{Product_GO_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="C46aaa6b53632f" class=" tableEdit GO_table_product dataTable"
|- {{table_heading_style}}
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-
|

|
GO:0005737
|
cytoplasm
|

|

|

|
C
|
Seeded from Riley et al 2006 <ref name='LIB:Riley_2006'/>.
|
Missing: evidence, reference
|-
|

|
GO:0008478
|
pyridoxal kinase activity
|
PMID:4917899
PMID:8764513
|
IMP: Inferred from Mutant Phenotype
|

|
F
|

|
complete
|-
|

|
GO:0000166
|
nucleotide binding
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0547
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0000287
|
magnesium ion binding
|
GOA:hamap GO_REF:0000020
|
IEA: Inferred from Electronic Annotation
|
HAMAP:MF_01638
|
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:0004340
|
glucokinase activity
|
GOA:hamap GO_REF:0000020
|
IEA: Inferred from Electronic Annotation
|
HAMAP:MF_01638
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0005524
|
ATP binding
|
GOA:hamap GO_REF:0000020
|
IEA: Inferred from Electronic Annotation
|
HAMAP:MF_01638
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0005524
|
ATP binding
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0067
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0006096
|
glycolysis
|
GOA:hamap GO_REF:0000020
|
IEA: Inferred from Electronic Annotation
|
HAMAP:MF_01638
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0008270
|
zinc ion binding
|
GOA:hamap GO_REF:0000020
|
IEA: Inferred from Electronic Annotation
|
HAMAP:MF_01638
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0008478
|
pyridoxal kinase activity
|
PMID:16740960
|
IDA: Inferred from Direct Assay
|

|
F
|

|
complete
|-
|

|
GO:0008270
|
zinc ion binding
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0862
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0008478
|
pyridoxal kinase activity
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR004625
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0008478
|
pyridoxal kinase activity
|
GOA:spec GO_REF:0000003
|
IEA: Inferred from Electronic Annotation
|
EC:2.7.1.35
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0008478
|
pyridoxal kinase activity
|
PMID:4917899
|
IMP: Inferred from Mutant Phenotype
|

|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0008478
|
pyridoxal kinase activity
|
PMID:8764513
|
IMP: Inferred from Mutant Phenotype
|

|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0008615
|
pyridoxine biosynthetic process
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR004625
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25070.C46aaa6b53632f&page=25070&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table] || || || || || || || ||
|}


<big>'''Interactions'''</big>

{{Product_interactions_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="I46aaa6bd3a0ab" class=" tableEdit Product_interactions_table dataTable"
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
|-
|
Protein
|
Subunits of [[:Category:Complex:PDXK-CPLX|PDXK-CPLX]]
|
could be indirect
|

|

|-
|
Protein
|
dnaK 
|

|
PMID:16606699
|
Experiment(s):EBI-1142759 
|-
|
Protein
|
rplQ 
|

|
PMID:16606699
|
Experiment(s):EBI-1142759 

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25070.I46aaa6bd3a0ab&page=25070&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table] || || || ||
|}


</protect>
===Notes===

==Localization==

{{Product_localization_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="K46a83f4e3a9be" class=" tableEdit Product_localization_table"
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25070.K46a83f4e3a9be&page=25070&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table] || || || ||
|}


<protect></protect>

===Notes===

==Structure and Physical Properties==
{{BacktoTop}}
<protect>
<big>'''Physical Properties'''</big>

{{Product_physical_properties_help}}
{| id="X46aaa6bf90133" class=" tableEdit Product_phys_prop_table"

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

|-
!align=left {{table heading style}} |Sequence
||
[http://biocyc.org/ECOLI/sequence-aa?object=PDXK-MONOMER at EcoCyc]
<pre>MSSLLLFNDK SRALQADIVA VQSQVVYGSV GNSIAVPAIK QNGLNVFAVP TVLLSNTPHY
DTFYGGAIPD EWFSGYLRAL QERDALRQLR AVTTGYMGTA SQIKILAEWL TALRKDHPDL
LIMVDPVIGD IDSGIYVKPD LPEAYRQYLL PLAQGITPNI FELEILTGKN CRDLDSAIAA
AKSLLSDTLK WVVVTSASGN EENQEMQVVV VTADSVNVIS HSRVKTDLKG TGDLFCAQLI
SGLLKGKALT DAVHRAGLRV LEVMRYTQQH ESDELILPPL AEA</pre>
|-
!align=left {{table heading style}} |Length
||
283
|-
!align=left {{table heading style}} |Mol. Wt
||
30.847 kDa
|-
!align=left {{table heading style}} |pI
||
5.1 (calculated)
|-
!align=left {{table heading style}} |Extinction coefficient
||
29,910 - 30,160 (calc based on 9 Y, 3 W, and 2 C residues)

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25070.X46aaa6bf90133&page=25070&pagename={{FULLPAGENAMEE}}&type=1&template=Product_phys_prop_table edit table] ||
|}


<big>'''Domains/Motifs/Modification Sites'''</big><table>
<tr align="left" valign="top">
<td>
{{Product_domains_motifs_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Y46aaa6c00a345" class=" tableEdit Product_motif_table dataTable"
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
47..275
|
[http://pfam.janelia.org/family/PF08543 PF08543 Phosphomethylpyrimidine kinase]
|

|
PMID:19920124

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25070.Y46aaa6c00a345&page=25070&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table] || || || ||
|}
</td>
<td>


<motif_map/>
</td>
</tr>
</table>

<table><tr valign='top'><td>
<big>'''Structure'''</big> 

{{Product_structure_help}}
{| id="C46a83f4fef4a5" class=" tableEdit Product_structure_table"

|-
!align=left {{table heading style}} |Structures
||
<beststructure>
gene=pdxK
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/P40191 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P40191 PSI-PRED (P40191)]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P40191 Genomes TO Protein (P40191)] (GTOP)

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25070.C46a83f4fef4a5&page=25070&pagename={{FULLPAGENAMEE}}&type=1&template=Product_structure_table edit table] ||
|}


</td><td></protect>
==== Structure figures ====

<protect>
</td><tr><table></protect>
===Notes===

==Gene Product Resources==
{{BacktoTop}}

{{Product_resources_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="R46aaa6c0c60da" class=" tableEdit Product_resource_table"
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25070.R46aaa6c0c60da&page=25070&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table] || ||
|}


<protect></protect>
===Notes===

==Accessions in Other Databases==
{{BacktoTop}}

{{Gene_accessions_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="P46aaa6c12f781" class=" tableEdit Gene_accessions_table"
|- {{table_heading_style}}
!|Database!!Accession!!Notes
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16130344 GI:16130344]
|
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_416913.1 GeneID:946881]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0007973
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P40191 UniProtKB/Swiss-Prot:P40191]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:G7259
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG12642
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=946881 GeneID:946881]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120003833
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EchoBASE]]
|
EchoBASE:EB2519
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25070.P46aaa6c12f781&page=25070&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|}


<protect></protect>
===Notes===

==Links==
{{BacktoTop}}


{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="S46a83f52bf56e" class=" tableEdit Links_table"
|- {{table_heading_style}}
!|Name!!URL!!Comments

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25070.S46a83f52bf56e&page=25070&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|}


<noinclude>
==References==
{{BacktoTop}}
{{RefHelp}}
<references />
__NOTOC__
===Categories===
{{BacktoTop}}
[[Category:Proteins]]
[[Category:RefGenome_Annotated_Gene]]

paaK:Gene Product(s)

2015-07-02T21:55:40Z

Saleksander: Table edited by Saleksander via TableEdit

2015-03-16T19:11:12Z

Saleksander:

[[Category:Help|Preferences]]
Registered users can customize EcoliWiki by changing their preferences.
==User profile==
You can edit your real name, and this section provides a link to allow the user to change their password or email. Other email options, such as the choice to receive emails when specific changes are made to wiki pages
==Appearance==
You can customize the appearance of the wiki by choosing a different skin. Monobook is the default skin. If you know of a mediawiki skin that you would like us to make available, please contact us and we'll see what we can do.
This tab also allows for image size to be specified, as well as some advanced appearance options.
==Date and time==
Change your time zone and date formatting options.
==Editing==
Alter the default editing window size, how editing is initiated, preview options and external editor capabilities. Please note, not all of these options have been extensively tested in our wiki, so please let us know if you experience any difficulties when using these settings.
==Recent changes==
This tab changes the default number of days and edits shown in the [Special:RecentChanges Recent Changes] section, as well as how the changes can be displayed. You can also opt to hide minor or patrolled edits.
==Watchlist==
Vary the number of days and the changes that are displayed in the [Special:Watchlist Watchlist]. Also, you can choose to hide certain edits or automatically add pages you modify to your [Special:Watchlist Watchlist].
==Search==
Define the number of hits displayed. Importantly, you can also change which namespaces are searched by default.
==Misc.==
Options involving diffs.

EcoliWiki:Membership

2015-03-16T18:35:27Z

Saleksander:

Help:Accounts

2015-03-16T18:09:45Z

Saleksander: /* Can I customize EcoliWiki? */

[[Category:Help|Accounts]]
==How can I get an account in EcoliWiki?==
If you would like an account to be created for you at EcoliWiki.org, simply send an email with the user name you want to use to {{Email}} and the EcoliWiki Staff will get you set-up. You'll receive an email with a temporary password that you can use to log in. Once you log in, you will be prompted to create a new password.

==Can I invite new users to join EcoliWiki?==
Yes, simply click the '''[[EcoliWiki:Membership|Accounts]]''' link in the sidebar on the left. Next, under the '''Create a Registered User''' section, click '''Create an account'''. You'll need to know the user name the person wants to use. Once you have that, type in the username and the email address of the person you wish to invite and click '''by email'''. An email will be sent to the person and they will be able to complete registration.

==What do I do if I forget my username?==
Click [http://ecoliwiki.net/colipedia/index.php?title=Special%3AListUsers&username=&group=&limit=500 here] to bring up a list of registered user names. Hopefully, you can identify your username and the crisis will be averted. If you cannot, email the EcoliWiki staff at {{Email}} and someone will reply with your username.

==What do I do if I forget my password?==
If you forget your password, type in your username and click the '''email password ''' button. A temporary password will be emailed to the email account on file. Once you log in, you will be prompted to enter a new password.

==How do I change my username?==
Contact the EcoliWiki Staff at {{Email}} for changing your username.

==How do I change my password?==
To change your password, click the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the user profile tab, you will have to enter your old password, then type the new one. You will have to retype the new one to verify spelling, then click the Save button.

==Can I customize EcoliWiki?==
Yes. You may customize the style in which you display the information by clicking the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the '''Appearance''' tab, you may click the display ('''skin''') that best suits you. You may preview these styles by clicking the '''preview''' button to the right of the style name. Once you have made your selection, click the '''Save''' button to apply the new setting.

==What is the '''Watchlist''' link and how do I add topics to my watchlist?==
If you have a particular page or topic of specific interest to you, you can add it to the watchlist and you can opt to receive an email notification when that page is modified (you select the email option under the user profile tab). To add pages to your watchlist, go to the [[Special:Preferences|my preferences link]] in the upper right hand corner of your browser. Under the '''watchlist''' tab, select the boxes of the pages you want to watch. Click the '''Save''' button to apply the new setting.

==What is the '''Contributions''' link?==
Ecoliwiki keeps track of all the contributions you make to the wiki. Once you've logged in, you can click on this link and see a history of the contributions you've made.

Help:Accounts

2015-03-16T18:07:33Z

Saleksander: /* What is the my watchlist link and how do I add topics to my watchlist? */

[[Category:Help|Accounts]]
==How can I get an account in EcoliWiki?==
If you would like an account to be created for you at EcoliWiki.org, simply send an email with the user name you want to use to {{Email}} and the EcoliWiki Staff will get you set-up. You'll receive an email with a temporary password that you can use to log in. Once you log in, you will be prompted to create a new password.

==Can I invite new users to join EcoliWiki?==
Yes, simply click the '''[[EcoliWiki:Membership|Accounts]]''' link in the sidebar on the left. Next, under the '''Create a Registered User''' section, click '''Create an account'''. You'll need to know the user name the person wants to use. Once you have that, type in the username and the email address of the person you wish to invite and click '''by email'''. An email will be sent to the person and they will be able to complete registration.

==What do I do if I forget my username?==
Click [http://ecoliwiki.net/colipedia/index.php?title=Special%3AListUsers&username=&group=&limit=500 here] to bring up a list of registered user names. Hopefully, you can identify your username and the crisis will be averted. If you cannot, email the EcoliWiki staff at {{Email}} and someone will reply with your username.

==What do I do if I forget my password?==
If you forget your password, type in your username and click the '''email password ''' button. A temporary password will be emailed to the email account on file. Once you log in, you will be prompted to enter a new password.

==How do I change my username?==
Contact the EcoliWiki Staff at {{Email}} for changing your username.

==How do I change my password?==
To change your password, click the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the user profile tab, you will have to enter your old password, then type the new one. You will have to retype the new one to verify spelling, then click the Save button.

==Can I customize EcoliWiki?==
Yes. You may customize the style in which you display the information by clicking the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the '''skins''' tab, you may click the display that best suits you. You may preview these styles by clicking the '''preview''' button to the right of the style name. once you have made your selection, click the '''Save''' button to apply the new setting.

==What is the '''Watchlist''' link and how do I add topics to my watchlist?==
If you have a particular page or topic of specific interest to you, you can add it to the watchlist and you can opt to receive an email notification when that page is modified (you select the email option under the user profile tab). To add pages to your watchlist, go to the [[Special:Preferences|my preferences link]] in the upper right hand corner of your browser. Under the '''watchlist''' tab, select the boxes of the pages you want to watch. Click the '''Save''' button to apply the new setting.

==What is the '''Contributions''' link?==
Ecoliwiki keeps track of all the contributions you make to the wiki. Once you've logged in, you can click on this link and see a history of the contributions you've made.

Help:Accounts

2015-03-16T18:07:23Z

Saleksander: /* What is the my contributions link? */

[[Category:Help|Accounts]]
==How can I get an account in EcoliWiki?==
If you would like an account to be created for you at EcoliWiki.org, simply send an email with the user name you want to use to {{Email}} and the EcoliWiki Staff will get you set-up. You'll receive an email with a temporary password that you can use to log in. Once you log in, you will be prompted to create a new password.

==Can I invite new users to join EcoliWiki?==
Yes, simply click the '''[[EcoliWiki:Membership|Accounts]]''' link in the sidebar on the left. Next, under the '''Create a Registered User''' section, click '''Create an account'''. You'll need to know the user name the person wants to use. Once you have that, type in the username and the email address of the person you wish to invite and click '''by email'''. An email will be sent to the person and they will be able to complete registration.

==What do I do if I forget my username?==
Click [http://ecoliwiki.net/colipedia/index.php?title=Special%3AListUsers&username=&group=&limit=500 here] to bring up a list of registered user names. Hopefully, you can identify your username and the crisis will be averted. If you cannot, email the EcoliWiki staff at {{Email}} and someone will reply with your username.

==What do I do if I forget my password?==
If you forget your password, type in your username and click the '''email password ''' button. A temporary password will be emailed to the email account on file. Once you log in, you will be prompted to enter a new password.

==How do I change my username?==
Contact the EcoliWiki Staff at {{Email}} for changing your username.

==How do I change my password?==
To change your password, click the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the user profile tab, you will have to enter your old password, then type the new one. You will have to retype the new one to verify spelling, then click the Save button.

==Can I customize EcoliWiki?==
Yes. You may customize the style in which you display the information by clicking the [[Special:Preferences|my preferences link]] in the upper right hand corner of the browser window. Under the '''skins''' tab, you may click the display that best suits you. You may preview these styles by clicking the '''preview''' button to the right of the style name. once you have made your selection, click the '''Save''' button to apply the new setting.

==What is the '''my watchlist''' link and how do I add topics to my watchlist?==
If you have a particular page or topic of specific interest to you, you can add it to the watchlist and you can opt to receive an email notification when that page is modified (you select the email option under the user profile tab). To add pages to your watchlist, go to the [[Special:Preferences|my preferences link]] in the upper right hand corner of your browser. Under the '''watchlist''' tab, select the boxes of the pages you want to watch. Click the '''Save''' button to apply the new setting.

==What is the '''Contributions''' link?==
Ecoliwiki keeps track of all the contributions you make to the wiki. Once you've logged in, you can click on this link and see a history of the contributions you've made.

MediaWiki:Sitenotice

2015-02-11T21:16:34Z

Saleksander: Blanked the page

2013-06-13T21:01:25Z

Saleksander:

{{Note| This page is currently under construction, and much of the information is currently just a placeholder- it may not apply to PRD1 at all.}}

Bacteriophage PRD1 is a member of the ''Tectiviridae'' family<ref name='LIB:Bacteriophages'/> and is closely related to the other lipid-containing phages PR3, PR4, PR5, and L17<ref name='PMID:7320707'/>. It is a plasmid-dependent phage that has been shown to infect a variety of gram-negative hosts, including Escherichia coli, with the requirement that hosts contain incompatibility group plasmids P, W, or N<ref name='PMID:4211861'/>. Notably, PRD1 has 110 bp inverted terminal repeats<ref name='PMID:2251117'/> and a covalently bound terminal protein on the 5' ends<ref name='PMID:6620455'/> of the 14,927bp genome.

The full sequence is available from NCBI as [http://www.ncbi.nlm.nih.gov/nuccore/159192286 NCBI Reference Sequence: NC_001421.2]

== Morphology ==
Phage PRD1, like the other ''Tectiviridae'', has an inflexible icosahedral protein structure surrounding a lipid membrane<ref name='LIB:Bacteriophages'/>. The linear dsDNA is contained inside this lipid-protein vesicle<ref name='PMID:1853567'/>. The phage has a molecular mass of about 66x106 Da; by weight it is 15% DNA, 15% lipid, and the remaining weight is due to protein content<ref name='PMID:7793328'/>. The phage capsid is about 65.5 nm, measured as the diameter between two parallel edges, with a maximum diameter of 69.8nm when measured between vertices<ref name='LIB:Bacteriophages'/>.

The rigid coat is comprised mainly of the 43.1 kDa<ref name=PMID:2196741'/> protein P3, which forms 240 trimeric units with 6-fold symmetry<ref name='PMID:8557027'/> arranged in β-sheets<ref name='PMID:2383568'/>. A single face of the icosahedron contains 12 copies of the trimeric P3 in a pseudo T=25 lattice<ref name='LIB:Bacteriophages'/>. The capsid also contains the 34.3 kDa <ref name=PMID:2196741'/>P5 as the minor coat protein<ref name='PMID:8557027'/>, and pentamers of the 13.7kDa P31 forms the vertices<ref name='PMID:10448038'/>. The major and minor proteins contribute to a spike structure at the vertices<ref name='PMID:10448038'/><ref name='PMID:10956048'/>

One study has shown the viral capsid can possess a membranous tail 140 Å in diameter that does not seem to be necessary for infection. <ref name='PMID:10448038'/>

Protein P2 is required for adsorption to the host <ref name='PMID:10542170'/>

The membrane contains host lipids<ref name='LIB:Bacteriophages'/> as well as P20, P22<ref name='PMID:11741849'/>

== Genome Organization ==
[http://www.ncbi.nlm.nih.gov/nuccore/159192286 159192286 on NCBI]

<gbrowseImage>
name=NC_001421:1..14927
source=bacteriophage_PRD1
width=800
type=Genes
</gbrowseImage>

PRD1 has a linear, 14927 bp genome of DNA. There are

There are 11 genes encoded on the genome; two are overlapping in-frame genes. Five of the encoded proteins make up the viron, three are needed for synthesis and the rest are for assembly. <ref name='PMID:9224870'/> The genes are generally referred to by Roman numerals I-XI as listed on the [[:Category:Gene_List:Phage_f1| Phage f1]] page. Genes are in the order [[Phage_f1_II:Gene| II]] [[Phage_f1_X:Gene| (X)]], [[Phage_f1_V:Gene| V]], [[Phage_f1_VII:Gene| VII]], [[Phage_f1_IX:Gene| IX]], [[Phage_f1_VIII:Gene| VIII]], [[Phage_f1_III:Gene| III]], [[Phage_f1_VI:Gene| VI]], [[Phage_f1_I:Gene| I]] [[Phage_f1_XI:Gene| (XI)]], [[Phage_f1_IV:Gene| IV]], intergenic region (IG or IGR). <ref name='LIB:Bacteriophages'/> The IGR contains the packing signal (PS) as well as sequences that dictate termination, nicking for replication, and the binding of [[Phage_f1_II:Gene_Product(s)| protein II]] and IHF. <ref name='LIB:Bacteriophages'/>

== Life cycle ==

==== Adsorption and Injection ====

==== DNA replication ====

PMID:8331725

==== Packaging ====

==== Lysis ====

== See also ==
* [[:Category:Gene_List:Phage_f1| Phage f1 Gene List]]
* [[Phage_M13| Phage M13]]
* [http://www.ncbi.nlm.nih.gov/nuccore/J02448 J02448 on NCBI]
* [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=10863&lvl=3&lin=f&keep=1&srchmode=1&unlock Phage f1 taxonomy on NCBI]
* [http://www.ictvdb.org/ICTVdB/00.035.htm International Committee on Taxonomy of Viruses]

== References ==
{{RefHelp}}
<references/>

[[Category:Inovirus]]

Phage PRD1

2013-06-13T19:01:37Z

Saleksander:

Phage PRD1

2013-06-13T18:02:55Z

Saleksander:

{{Note| This page is currently under construction, and much of the information is currently just a placeholder- it may not apply to PRD1 at all.}}

Bacteriophage PRD1 is a member of the ''Tectiviridae'' family<ref name='LIB:Bacteriophages'/> and is closely related to the other lipid-containing phages PR3, PR4, PR5, and L17<ref name='PMID:7320707'/>. It is a plasmid-dependent phage that has been shown to infect a variety of gram-negative hosts, including Escherichia coli, with the requirement that hosts contain incompatibility group plasmids P, W, or N<ref name='PMID:4211861'/>. Notably, PRD1 has 110 bp inverted terminal repeats<ref name='PMID:2251117'/> and a covalently bound terminal protein on the 5' ends<ref name='PMID:6620455'/> of the 14,927bp genome.

The full sequence is available from NCBI as [http://www.ncbi.nlm.nih.gov/nuccore/159192286 NCBI Reference Sequence: NC_001421.2]

== Morphology ==
Phage PRD1, like the other ''Tectiviridae'', has an inflexible icosahedral protein structure surrounding a lipid membrane<ref name='LIB:Bacteriophages'/>. Inside the lipid-protein vesicle is the linear strand of DNA.<ref name='PMID:1853567'/> The phage has a molecular mass of about 66x106 Da; by weight it is 15% DNA, 15% lipid, and the remaining weight is due to protein content<ref name='PMID:11591347'/>. The phage capsid is about 65.5 nm, measured as the diameter between two parallel edges, with a maximum diameter of 69.8nm when measured between vertices<ref name='LIB:Bacteriophages'/>.

The rigid coat is comprised mainly of 240 copies of the 43.1 kDa<ref name=PMID:2196741'/> protein P3, which exist as trimers with 6-fold symmetry<ref name='PMID:8557027'/> arranged in β-sheets<ref name='PMID:2383568'/>. A single face of the icosahedron contains 12 copies of the trimeric P3 in a pseudo T=25 lattice<ref name='LIB:Bacteriophages'/>. The 34.3 kDa <ref name=PMID:2196741'/>P5 forms the vertices of the capsid<ref name='PMID:8557027'/>.

The thousands of identical major coat proteins that make up the sheath are slightly curved, enlongated proteins about 70 Å by 10 Å and are arranged in an α-helix. [5] [6] These sheath proteins slightly overlap and are oriented just slightly off of perpendicular (20°) to the length of the filament; they are interdigitated and slope radially (with a 5-fold rotation axis and 2-fold helical axis) to form a fishscale-like coating for the DNA core. [1] [5]

The ends of the filament are sealed with protein caps. The end that is extruded first appears blunt and contains 3-5 copies of each pVII and pIX, while about 5 copies each of pIII and pVI seal off the terminally extruded end and give it a bead-like appearance.[1] [2]

The λ phage has an icosahedral head (with T=7) about 50-60 nm in diameter, and a flexible, long noncontractile tail about 150nm in length.[8][7][9][10] The head is formed from the proteins E, D, B, W, FII, B*, X1, and X2. [11] The head is the capsid, and contains a single double-stranded DNA molecule about 48 kb in length; by weight the genome is about 32x106 Da and comprises about half of the phage's weight.[8] The tail consists of a 135nm hollow tube finished with a 15nm conical cap.[8] The inside diameter of the tail is about 3nm, with an outside diameter of 9-18nm due to knob-like structures that make the tail appear rough.[8] The wt λ does not have tail fibers, although these may be present on certain strains.[7]

== Genome Organization ==
[http://www.ncbi.nlm.nih.gov/nuccore/159192286 159192286 on NCBI]

<gbrowseImage>
name=NC_001421:1..14927
source=bacteriophage_PRD1
width=800
type=Genes
</gbrowseImage>

PRD1 has a linear, 14927 bp genome of DNA. There are

There are 11 genes encoded on the genome; two are overlapping in-frame genes. Five of the encoded proteins make up the viron, three are needed for synthesis and the rest are for assembly. <ref name='PMID:9224870'/> The genes are generally referred to by Roman numerals I-XI as listed on the [[:Category:Gene_List:Phage_f1| Phage f1]] page. Genes are in the order [[Phage_f1_II:Gene| II]] [[Phage_f1_X:Gene| (X)]], [[Phage_f1_V:Gene| V]], [[Phage_f1_VII:Gene| VII]], [[Phage_f1_IX:Gene| IX]], [[Phage_f1_VIII:Gene| VIII]], [[Phage_f1_III:Gene| III]], [[Phage_f1_VI:Gene| VI]], [[Phage_f1_I:Gene| I]] [[Phage_f1_XI:Gene| (XI)]], [[Phage_f1_IV:Gene| IV]], intergenic region (IG or IGR). <ref name='LIB:Bacteriophages'/> The IGR contains the packing signal (PS) as well as sequences that dictate termination, nicking for replication, and the binding of [[Phage_f1_II:Gene_Product(s)| protein II]] and IHF. <ref name='LIB:Bacteriophages'/>

== Life cycle ==

==== Adsorption and Injection ====

==== DNA replication ====

PMID:8331725

==== Packaging ====

==== Lysis ====

== See also ==
* [[:Category:Gene_List:Phage_f1| Phage f1 Gene List]]
* [[Phage_M13| Phage M13]]
* [http://www.ncbi.nlm.nih.gov/nuccore/J02448 J02448 on NCBI]
* [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=10863&lvl=3&lin=f&keep=1&srchmode=1&unlock Phage f1 taxonomy on NCBI]
* [http://www.ictvdb.org/ICTVdB/00.035.htm International Committee on Taxonomy of Viruses]

== References ==
{{RefHelp}}
<references/>

[[Category:Inovirus]]

Phage PRD1

2013-06-12T21:04:17Z

Saleksander:

{{Note| This page is currently under construction, and much of the information is currently just a placeholder- it may not apply to PRD1 at all.}}

Bacteriophage PRD1 is a member of the ''Tectiviridae'' family<ref name='LIB:Bacteriophages'/> and is closely related to the other lipid-containing phages PR3, PR4, PR5, and L17.<ref name='PMID:7320707'/> It is a plasmid-dependent phage that has been shown to infect a variety of gram-negative hosts, including Escherichia coli, with the requirement that hosts contain incompatibility group plasmids P, W, or N.<ref name='PMID:4211861'/> Notably, PRD1 has 110 bp inverted terminal repeats<ref name='PMID:2251117'/> and a covalently bound terminal protein on the 5' ends<ref name='PMID:6620455'/> of the 14,927bp genome.

The full sequence is available from NCBI as [http://www.ncbi.nlm.nih.gov/nuccore/159192286 NCBI Reference Sequence: NC_001421.2]

== Morphology ==
Phage PRD1, like the other ''Tectiviridae'', has an inflexible icosahedral protein structure surrounding a lipid membrane.<ref name='LIB:Bacteriophages'/> Inside the lipid-protein vesicle is the linear strand of DNA.<ref name='PMID:1853567'/> The phage has a molecular mass of about 66x106 Da; by weight it is 15% DNA, 15% lipid, and the remaining weight is due to protein content.<ref name='PMID:11591347'/> The whole phage is about 65.5 nm, measured as the diameter between two parallel edges, with a maximum diameter of 69.8nm when measured between vertices<ref name='LIB:Bacteriophages'/>.

The rigid coat is comprised mainly of 240 copies of the trimeric, 43.1 kDa<ref name='PMID:2383568'/> protein P3<ref name='PMID:8557027'/>, with the 34.3 kDa<ref name='PMID:2383568'/> P5 at the vertices<ref name='PMID:8557027'/>. A single face of the icosahedron contains 12 copies of the trimeric P3 in a T=25 lattice<ref name='LIB:Bacteriophages'/>.

The thousands of identical major coat proteins that make up the sheath are slightly curved, enlongated proteins about 70 Å by 10 Å and are arranged in an α-helix. [5] [6] These sheath proteins slightly overlap and are oriented just slightly off of perpendicular (20°) to the length of the filament; they are interdigitated and slope radially (with a 5-fold rotation axis and 2-fold helical axis) to form a fishscale-like coating for the DNA core. [1] [5]

The ends of the filament are sealed with protein caps. The end that is extruded first appears blunt and contains 3-5 copies of each pVII and pIX, while about 5 copies each of pIII and pVI seal off the terminally extruded end and give it a bead-like appearance.[1] [2]

The λ phage has an icosahedral head (with T=7) about 50-60 nm in diameter, and a flexible, long noncontractile tail about 150nm in length.[8][7][9][10] The head is formed from the proteins E, D, B, W, FII, B*, X1, and X2. [11] The head is the capsid, and contains a single double-stranded DNA molecule about 48 kb in length; by weight the genome is about 32x106 Da and comprises about half of the phage's weight.[8] The tail consists of a 135nm hollow tube finished with a 15nm conical cap.[8] The inside diameter of the tail is about 3nm, with an outside diameter of 9-18nm due to knob-like structures that make the tail appear rough.[8] The wt λ does not have tail fibers, although these may be present on certain strains.[7]

== Genome Organization ==
[http://www.ncbi.nlm.nih.gov/nuccore/159192286 159192286 on NCBI]

<gbrowseImage>
name=NC_001421:1..14927
source=bacteriophage_PRD1
width=800
type=Genes
</gbrowseImage>

PRD1 has a linear, 14927 bp genome of DNA. There are

There are 11 genes encoded on the genome; two are overlapping in-frame genes. Five of the encoded proteins make up the viron, three are needed for synthesis and the rest are for assembly. <ref name='PMID:9224870'/> The genes are generally referred to by Roman numerals I-XI as listed on the [[:Category:Gene_List:Phage_f1| Phage f1]] page. Genes are in the order [[Phage_f1_II:Gene| II]] [[Phage_f1_X:Gene| (X)]], [[Phage_f1_V:Gene| V]], [[Phage_f1_VII:Gene| VII]], [[Phage_f1_IX:Gene| IX]], [[Phage_f1_VIII:Gene| VIII]], [[Phage_f1_III:Gene| III]], [[Phage_f1_VI:Gene| VI]], [[Phage_f1_I:Gene| I]] [[Phage_f1_XI:Gene| (XI)]], [[Phage_f1_IV:Gene| IV]], intergenic region (IG or IGR). <ref name='LIB:Bacteriophages'/> The IGR contains the packing signal (PS) as well as sequences that dictate termination, nicking for replication, and the binding of [[Phage_f1_II:Gene_Product(s)| protein II]] and IHF. <ref name='LIB:Bacteriophages'/>

== Life cycle ==

==== Adsorption and Injection ====

==== DNA replication ====

PMID:8331725

==== Packaging ====

==== Lysis ====

== See also ==
* [[:Category:Gene_List:Phage_f1| Phage f1 Gene List]]
* [[Phage_M13| Phage M13]]
* [http://www.ncbi.nlm.nih.gov/nuccore/J02448 J02448 on NCBI]
* [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=10863&lvl=3&lin=f&keep=1&srchmode=1&unlock Phage f1 taxonomy on NCBI]
* [http://www.ictvdb.org/ICTVdB/00.035.htm International Committee on Taxonomy of Viruses]

== References ==
{{RefHelp}}
<references/>

[[Category:Inovirus]]