EcoliWiki - User contributions [en]

HOGENOM

2014-05-08T17:41:28Z

Shabnam: Table edited by Shabnam via TableEdit

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{| {{Prettytable}} width='30%' align="right" id="X536bc0a9bb902" class=" tableEdit Database_table"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://pbil.univ-lyon1.fr/databases/hogenom/home.php?contents=homologous HOGENOM]
|-
!align=left {{table heading style}} |What:
||
Database of Complete Genome Homologous Genes Families
|-
!align=left {{table heading style}} |Who:
||
Guy Perriere et. al. (France)
|-
!align=left {{table heading style}} |Updates:
||

|-
!align=left {{table heading style}} |Upcoming events:
||

|-
!align=left {{table heading style}} |Web Services:
||

|- class="tableEdit_footer"
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==About {{PAGENAME}}==
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[[Category:Databases]]

HOGENOM

2014-05-08T17:37:28Z

Shabnam: /* External Links */

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{| {{Prettytable}} width='30%' align="right" id="X536bc0a9bb902" class=" tableEdit Database_table"

|-
!align=left {{table heading style}} |Link/URL:
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!align=left {{table heading style}} |What:
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HOGENOM

2014-05-08T17:36:41Z

Shabnam: /* External Links */

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{| {{Prettytable}} width='30%' align="right" id="X536bc0a9bb902" class=" tableEdit Database_table"

|-
!align=left {{table heading style}} |Link/URL:
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!align=left {{table heading style}} |What:
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==External Links==
[{{{1|http://pbil.univ-lyon1.fr/databases/hogenom/home.php?contents=homologous}}} {{HOGENOM}}] URL:{{{1|http://pbil.univ-lyon1.fr/databases/hogenom/home.php?contents=homologous}}}

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[[Category:Databases]]

HOGENOM

2014-05-08T17:34:20Z

Shabnam: New Template:Database Page

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[[Category:Databases]]

PhenomicDB

2013-11-12T17:31:46Z

Shabnam: Table edited by Shabnam via TableEdit

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{| {{Prettytable}} width='30%' align="right" id="E5282657994923" class=" tableEdit Database_table"

|-
!align=left {{table heading style}} |Link/URL:
||
http://www.phenomicdb.de/
|-
!align=left {{table heading style}} |What:
||
a multi-species genotype/phenotype database
|-
!align=left {{table heading style}} |Who:
||
Department of Bioinformatics, University of Applied Science Giessen, Giessen, Germany
|-
!align=left {{table heading style}} |Updates:
||

|-
!align=left {{table heading style}} |Upcoming events:
||

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||

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PhenomicDB

2013-11-12T17:29:29Z

Shabnam:

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{| {{Prettytable}} width='30%' align="right" id="E5282657994923" class=" tableEdit Database_table"

|-
!align=left {{table heading style}} |Link/URL:
|-
!align=left {{table heading style}} |What:
|-
!align=left {{table heading style}} |Who:
|-
!align=left {{table heading style}} |Updates:
|-
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|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183383.E5282657994923&page=183383&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table]
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==About {{PAGENAME}}==
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PhenomicDB

2013-11-12T17:26:11Z

Shabnam: New Template:Database Page

User:Rwgriffin

2013-06-17T23:32:13Z

Shabnam: Fill User: Page!

Click "edit table" in the last row to add information to the table. Click [[Help:Adding_your_information|here]] to find out how to add more information to your user page.



{| id="X51bf9c7d9c911" class=" tableEdit User_info_table"

|-
!align=left |Name (Last, First)
||
Griffin,Richard, Griffin,Richard
|-
!align=left |Organization
||
Prairie View A &amp M University
|-
!align=left |Position
||

|-
!align=left |Address
||

|-
!align=left |Contact Info
||

|-
!align=left |Website(s)
||

|-
!align=left |Interests
||

|-
!align=left |Genes
||

|-
!align=left |Lab members
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183245.X51bf9c7d9c911&page=183245&pagename={{FULLPAGENAMEE}}&type=1&template=User_info_table edit table] ||
|}


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

User:Rwgriffin

2013-06-17T23:32:13Z

Shabnam: New User: Page!

PMID:21718539

2013-04-08T20:36:15Z

Shabnam: Fill PMID: Page!

{{RightTOC}}


{| id="L51632a3f5ce2a" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Angiuoli, SV, Dunning Hotopp, JC, Salzberg, SL and Tettelin, H''' (2011) Improving pan-genome annotation using whole genome multiple alignment. ''BMC Bioinformatics'' '''12''':272
|-
!align=left |Abstract
||
Rapid annotation and comparisons of genomes from multiple isolates (pan-genomes) is becoming commonplace due to advances in sequencing technology. Genome annotations can contain inconsistencies and errors that hinder comparative analysis even within a single species. Tools are needed to compare and improve annotation quality across sets of closely related genomes.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21718539 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142524 PMC3142524]
Online version:[http://dx.doi.org/10.1186/1471-2105-12-272 10.1186/1471-2105-12-272]
|-
!align=left |Keywords
||
Bacteria/genetics; Chromosome Mapping; Genome, Bacterial; Molecular Sequence Annotation; Sequence Alignment/methods

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182991.L51632a3f5ce2a&page=182991&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Y51632a3fa3992" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182991.Y51632a3fa3992&page=182991&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

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

PMID:21718539

2013-04-08T20:36:15Z

Shabnam: New PMID: Page!

Phage lambda nu3:Gene Product(s)

2012-08-20T18:01:58Z

Shabnam: Table edited by Shabnam via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|Phage lambda nu3}}{{Tab|Gene|Phage lambda nu3}}{{Tab On|Gene Product(s)|Phage lambda nu3}}{{Tab|Expression|Phage lambda nu3}}{{Tab|Evolution|Phage lambda nu3}}{{Tab|On One Page|Phage lambda nu3}}{{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}}
{| class=" tableEdit Product_nomenclature_table"

|-
!align=left {{table heading style}} |Standard name
||
nu3
|-
!align=left {{table heading style}} |Synonyms
||
nu3, lambdap06
|-
!align=left {{table heading style}} |Product description
||
capsid assembly protein (core protein <ref name='LIB:Lambda_II'/>)
|-
!align=left {{table heading style}} |EC number (for enzymes)
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79..B46b169606ab87&page=103683&pagename={{FULLPAGENAMEE}}&type=1&template=Product_nomenclature_table edit table] ||
|}

{{Product_nomenclature_help}}
<protect></protect>
===Notes===

==Function==
{{BacktoTop}}
<protect>
<big>'''Gene Ontology'''</big>

{{Product_GO_help}}
{| class=" tableEdit GO_table_product dataTable"
|- {{table_heading_style}}
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-
|

|

|
<input type="hidden" name="field[2]" />
|
PMID:1090075
|
IMP: Inferred from Mutant Phenotype
|

|
<input type="hidden" name="field[6]" />
|

|
Missing: GO ID

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79..P46a415cdb6e69&page=103683&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_product edit table] || || || || || || || ||
|}

{{Product_GO_help}}

<big>'''Interactions '''</big>
<protect>
{{Product_interactions_help}}
{| id="W4a848f824baa2" class=" tableEdit Product_interactions_table dataTable"
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.103683.W4a848f824baa2&page=103683&pagename={{FULLPAGENAMEE}}&type=0&template=Product_interactions_table edit table] || || || ||
|}
</protect>


===Notes===

==Localization==

{{Product_localization_help}}
{| class=" tableEdit Product_localization_table"
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79..O46a415ce233ac&page=&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table] || || || ||
|}

{{Product_localization_help}}
<protect></protect>

===Notes===

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

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

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

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

<pre>MDATRQMFAQ KVSAYTGLSV QVVLDTEAAV YSGQEAIDAG LADELVNSTD AITVMRDALD
ARKSRLSGGR MTKETQSTTV SATASQADVT DVVPATEGEN ASAAQPDVNA QITAAVAAEN
SRIMGILNCE EAHGREEQAR VLAETPGMTV KTARRILAAA PQSAQARSDT ALDRLMQGAP
APLAAGNPAS DAVNDLLNTP V</pre>
|-
!align=left {{table heading style}} |Length
||
201
|-
!align=left {{table heading style}} |Mol. Wt
||
20.811 kDa
|-
!align=left {{table heading style}} |pI
||
4.4 (calculated)
|-
!align=left {{table heading style}} |Extinction coefficient
||
2,980 - 3,105 (calc based on 2 Y, W, and 1 C residues)

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79..W46a415ce536a5&page=&pagename={{FULLPAGENAMEE}}&type=1&template=Product_phys_prop_table edit table] ||
|}

{{Product_physical_properties_help}}

<big>'''Domains/Motifs/Modification Sites'''</big><table>
<tr align="left" valign="top">
<td>
{{Product_domains_motifs_help}}
{| class=" tableEdit Product_motif_table dataTable"
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79..E46a415ce83fa5&page=&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table] || || || ||
|}

{{Product_domains_motifs_help}}</td>
<td>


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

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

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

|-
!align=left {{table heading style}} |Structures
||
<beststructure>
gene=Phage_lambda_nu3
taxon=10710
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79..X46a415ceb47f4&page=&pagename={{FULLPAGENAMEE}}&type=1&template=Product_structure_table edit table] ||
|}

{{Product_structure_help}}
</td><td></protect>
==== Structure figures ====

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

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

{{Product_resources_help}}
{| class=" tableEdit Product_resource_table"
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79..Y46a415cee4d12&page=&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table] || ||
|}

{{Product_resources_help}}
<protect></protect>
===Notes===

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

{{Gene_accessions_help}}
{| class=" tableEdit Gene_accessions_table"
|- {{table_heading_style}}
!|Database!!Accession!!Notes

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79..Z46a415cf21486&page=&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|}

{{Product_accessions_help}}
<protect></protect>
===Notes===

==Links==
{{BacktoTop}}


{| class=" tableEdit Links_table"
|- {{table_heading_style}}
!|Name!!URL!!Comments

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79..P46b16967cb1f4&page=&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|}

{{Links_help}}

<noinclude>
==References==
{{BacktoTop}}
{{RefHelp}}
<references />
__NOTOC__
===Categories===
{{BacktoTop}}

PMID:6220514

2012-08-20T16:50:25Z

Shabnam: Fill PMID: Page!

{{RightTOC}}


{| id="Z50326ad067d25" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Tsui, LC and Hendrix, RW''' (1983) Role of gene T in phage lambda tail assembly.''Virology'' '''125''':265-73
|-
!align=left |Abstract
||
We have studied the phenotype of a heat-sensitive mutation that defines lambda tail gene T. Induction and growth at the nonpermissive temperature of a lambda Tts40 prophage results in production of morphologically normal but biologically inactive tails, which can be activated in vitro by lysates supplying the products of genes T, U, and Z. Thus, gene T acts between genes V and U in the tail assembly pathway or immediately after the completion of tail shaft polymerization. lambda Tts40 lysates also contain a substantial number of morphologically normal phage particles which are deficient in cleavage of the minor tail protein gpH. This result is consistent with the fact that gpH cleavage normally occurs later in the assembly pathway than the time found for gene T action. Purified lambda Tts40 virions that were produced at the permissive temperature are normal with respect to gpH cleavage. However, they are more sensitive to heat inactivation than are wild-type virions, suggesting that the T gene product is in the virion. At the permissive temperature, the mutant protein made by lambda Tts40 is active in vivo even if it has been synthesized at the nonpermissive temperature.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6220514 PubMed]

|-
!align=left |Keywords
||
Bacteriophage lambda; Genes, Viral; Genetic Complementation Test; Hot Temperature; Mutation; Viral Proteins; Viral Tail Proteins

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182654.Z50326ad067d25&page=182654&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="H50326ad0db83d" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182654.H50326ad0db83d&page=182654&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

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

PMID:6220514

2012-08-20T16:50:22Z

Shabnam: New PMID: Page!

ampC:Gene

2012-05-17T19:51:41Z

Shabnam: Table edited by Shabnam via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|ampC}}{{Tab On|Gene|ampC}}{{Tab|Gene Product(s)|ampC}}{{Tab|Expression|ampC}}{{Tab|Evolution|ampC}}{{Tab|On One Page|ampC}}{{TabsBottom}}
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References |References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude><protect>
==Nomenclature==
{{BacktoTop}}

{{Gene_nomenclature_help}}
{| id="J46aa086c39a3a" class=" tableEdit Gene_nomenclature_table"

|-
!align=left {{table_heading_style}} |Standard name
||
''ampC''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Ampicillin
|-
!align=left {{table_heading_style}} |Synonyms
||
''ECK4146, b4150, JW4111, ampA''<ref name='LIB:Riley_2006'/>, ampA''

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18865.J46aa086c39a3a&page=18865&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table] ||
|}


</protect>
===Notes===

==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>

{{Gene_location_help}}
{| id="G46aa086cbd26a" class=" tableEdit Gene_location_table"
|- {{table_heading_style}}
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|
MG1655
|
94.31 minutes, 94.31 minutes 
|
MG1655: 4376967..4375834 <gbrowseImage>
name=NC_000913:4375834..4376967
source=MG1655
preset=GeneLocation
</gbrowseImage>

|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10040 EcoCyc]
{{GBrowseLink|MG1655|NC_000913|4374834|4377967|GBrowse(MG1655)}}

|
{{GBrowseFastaLink|MG1655|NC_000913|4375834|4376967|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10040 EcoCyc Sequence Dump]
|-
|
[[REL606]]
|

|
NC_012967: 4357655..4356522 <gbrowseImage>
name=NC_012967:4356522..4357655
source=REL606
preset=GeneLocation
</gbrowseImage>

|
{{GBrowseLink|REL606|NC_012967|4356522|4357655|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4356522|4357655|FASTA Dump}}
|-
|
[[BW2952]]
|

|
NC_012759: 4314569..4315702 <gbrowseImage>
name=NC_012759:4314569..4315702
source=BW2952
preset=GeneLocation
</gbrowseImage>

|
{{GBrowseLink|BW2952|NC_012759|4314569|4315702|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|4314569|4315702|FASTA Dump}}
|-
|
W3110
|
 
|
W3110: 4383624..4382491 <gbrowseImage>
name=AC_000091:4382491..4383624
source=W3110
preset=GeneLocation
</gbrowseImage>

|
{{GBrowseLink|W3110|AC_000091|4381491|4384624|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|AC_000091|4382491|4383624|FASTA Dump}}
|-
|
[[DH10B]]
|

|
DH10B: 4477329..4476196 <gbrowseImage>
name=NC_010473:4476196..4477329
source=DH10B
preset=GeneLocation
</gbrowseImage>

|
{{GBrowseLink|DH10B|NC_010473|4473930|4479595|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|4473930|4479595|FASTA Dump}}

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18865.G46aa086cbd26a&page=18865&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table] || || || ||
|}


</protect>
===Notes===

==Sequence Features==
{{BacktoTop}}

{{Gene_sequence_features_help}}
{| id="F46aa086d850da" class=" tableEdit Gene_sequence_features_table"
|- {{table_heading_style}}
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
4375837
|
Edman degradation
|
PMID:6795623 
|

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18865.F46aa086d850da&page=18865&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table] || || || || ||
|}


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

==Alleles and Phenotypes==
{{BacktoTop}}

{{Gene_alleles_help}}
{| {{Prettytable}} id="U46aa086dd060f" class=" tableEdit Gene_allele_table dataTable"
|- {{table_heading_style}}
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
ampCS80D,E,G
|

|
S80D,E,G
|

|
Loss of activity
|

|

|
seeded from [http://www.uniprot.org/uniprot/P00811 UniProt:P00811]
|-
|
ampCK83Q,T
|

|
K83Q,T
|

|
Lowers activity more than 1000- fold and increases protein stability
|

|

|
seeded from [http://www.uniprot.org/uniprot/P00811 UniProt:P00811]
|-
|
ampCK331A
|

|
K331A
|

|
Lowers activity more than 1000- fold
|

|

|
seeded from [http://www.uniprot.org/uniprot/P00811 UniProt:P00811]
|-
|
ampCN168D,H
|

|
N168D,H
|

|
Lowers activity more than 1000- fold
|

|

|
seeded from [http://www.uniprot.org/uniprot/P00811 UniProt:P00811]
|-
|
ampCY166E
|

|
Y166E
|

|
Lowers activity more than 1000- fold
|

|

|
seeded from [http://www.uniprot.org/uniprot/P00811 UniProt:P00811]
|-
|
ΔampC (Keio:JW4111)
|
deletion
|
deletion
|

|

|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen] [http://cgsc2.biology.yale.edu/Strain.php?ID=109241 CGSC10960]<ref name='LIB:cgsc'/>
|

|-
|
''ampC12''
|

|

|

|

|

|
[[cgscmutation:10039|CGSC:10039]]
|

|-
|
''ampC11''
|

|

|

|

|

|
[[cgscmutation:11804|CGSC:11804]]
|

|-
|
''ampC3''
|

|

|

|

|

|
[[cgscmutation:11809|CGSC:11809]]
|

|-
|
''ampC777(del)::kan''
|

|

|

|

|
PMID:16738554
|
[[cgscmutation:99998|CGSC:99998]]
|

|-
|
ampC
|

|

|
Resistant to
|
ampicillin resistance
|
PMID:4945191
|

|

|-
|
ampC
|
Gene duplication in the ampC gene region
|

|
Resistant to
|
Ampicillin-hyperresistant mutants of Ecoli K12 with multiple gene duplications in the ampC gene region overproduced at least six proteins during anaerobic growth. All but two of the proteins were also overproduced during aerobic growth.
|
PMID:391567
|

|

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18865.U46aa086dd060f&page=18865&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table] || || || || || || ||
|}


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

==Genetic Interactions==
{{BacktoTop}}
<protect>
{{Genetic_interaction_help}}
{| id="V4e04b7496eaa3" class=" tableEdit Genetic_interaction_table dataTable"
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.18865.V4e04b7496eaa3&page=18865&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table] || || || || || ||
|}
</protect>


===Notes===

==Genetic Resources==
{{BacktoTop}}

{{Gene_resources_help}}
{| id="J46aa086e98292" class=" tableEdit Gene_resource_table"
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
|-
|
JW4111
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691

Status:Clone OK

Primer 1:GCCTTCAAAACGACGCTCTGCGC

Primer 2:CCtTGTAGAGCGTTAAGAATCTG
|-
|
[[:Category:Kohara_Phage:1D4|1D4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=650 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:3H6|3H6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=651 Genobase]
|
PMID:3038334
|-
|
[[cadB:Gene|cadB2231::Tn10]]
|
Linked marker
|
CAG18488 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40596 CGSC7479]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 50% <ref name='LIB:Nichols_linked_Tn'/> 
Synonyms:zjd-2231::Tn10
|-
|
[[cycA:Gene|cycA30::Tn10]]
|
Linked marker
|
CAG12073 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40604 CGSC7482]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 10% <ref name='LIB:Nichols_linked_Tn'/>

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18865.J46aa086e98292&page=18865&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table] || || ||
|}


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

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

{{Gene_accessions_help}}
{| id="F46aa086f466cf" class=" tableEdit Gene_accessions_table"
|- {{table_heading_style}}
!|Database!!Accession!!Notes
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10040 ECOCYC:EG10040]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
[http://ecogene.org/geneinfo.php?eg_id=EG10040 EcoGene:EG10040]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=948669 GeneID:948669]
|
Escherichia coli str. K-12 substr. MG1655

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18865.F46aa086f466cf&page=18865&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|}


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

==Links==
{{BacktoTop}}


{| id="E46a7215a0b06e" class=" tableEdit Links_table"
|- {{table_heading_style}}
!|Name!!URL!!Comments

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18865.E46a7215a0b06e&page=18865&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|}


<noinclude><protect>
==References==
{{BacktoTop}}
{{RefHelp}}
<references />
__NOTOC__
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:amp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

ampC:Gene

2012-05-17T19:47:49Z

Shabnam: Table edited by Shabnam via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|ampC}}{{Tab On|Gene|ampC}}{{Tab|Gene Product(s)|ampC}}{{Tab|Expression|ampC}}{{Tab|Evolution|ampC}}{{Tab|On One Page|ampC}}{{TabsBottom}}
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References |References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude><protect>
==Nomenclature==
{{BacktoTop}}

{{Gene_nomenclature_help}}
{| id="J46aa086c39a3a" class=" tableEdit Gene_nomenclature_table"

|-
!align=left {{table_heading_style}} |Standard name
||
''ampC''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Ampicillin
|-
!align=left {{table_heading_style}} |Synonyms
||
''ECK4146, b4150, JW4111, ampA''<ref name='LIB:Riley_2006'/>, ampA''

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18865.J46aa086c39a3a&page=18865&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table] ||
|}


</protect>
===Notes===

==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>

{{Gene_location_help}}
{| id="G46aa086cbd26a" class=" tableEdit Gene_location_table"
|- {{table_heading_style}}
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|
MG1655
|
94.31 minutes, 94.31 minutes 
|
MG1655: 4376967..4375834 <gbrowseImage>
name=NC_000913:4375834..4376967
source=MG1655
preset=GeneLocation
</gbrowseImage>

|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10040 EcoCyc]
{{GBrowseLink|MG1655|NC_000913|4374834|4377967|GBrowse(MG1655)}}

|
{{GBrowseFastaLink|MG1655|NC_000913|4375834|4376967|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10040 EcoCyc Sequence Dump]
|-
|
[[REL606]]
|

|
NC_012967: 4357655..4356522 <gbrowseImage>
name=NC_012967:4356522..4357655
source=REL606
preset=GeneLocation
</gbrowseImage>

|
{{GBrowseLink|REL606|NC_012967|4356522|4357655|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4356522|4357655|FASTA Dump}}
|-
|
[[BW2952]]
|

|
NC_012759: 4314569..4315702 <gbrowseImage>
name=NC_012759:4314569..4315702
source=BW2952
preset=GeneLocation
</gbrowseImage>

|
{{GBrowseLink|BW2952|NC_012759|4314569|4315702|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|4314569|4315702|FASTA Dump}}
|-
|
W3110
|
 
|
W3110: 4383624..4382491 <gbrowseImage>
name=AC_000091:4382491..4383624
source=W3110
preset=GeneLocation
</gbrowseImage>

|
{{GBrowseLink|W3110|AC_000091|4381491|4384624|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|AC_000091|4382491|4383624|FASTA Dump}}
|-
|
[[DH10B]]
|

|
DH10B: 4477329..4476196 <gbrowseImage>
name=NC_010473:4476196..4477329
source=DH10B
preset=GeneLocation
</gbrowseImage>

|
{{GBrowseLink|DH10B|NC_010473|4473930|4479595|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|4473930|4479595|FASTA Dump}}

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18865.G46aa086cbd26a&page=18865&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table] || || || ||
|}


</protect>
===Notes===

==Sequence Features==
{{BacktoTop}}

{{Gene_sequence_features_help}}
{| id="F46aa086d850da" class=" tableEdit Gene_sequence_features_table"
|- {{table_heading_style}}
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
4375837
|
Edman degradation
|
PMID:6795623 
|

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18865.F46aa086d850da&page=18865&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table] || || || || ||
|}


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

==Alleles and Phenotypes==
{{BacktoTop}}

{{Gene_alleles_help}}
{| {{Prettytable}} id="U46aa086dd060f" class=" tableEdit Gene_allele_table dataTable"
|- {{table_heading_style}}
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
ampCS80D,E,G
|

|
S80D,E,G
|

|
Loss of activity
|

|

|
seeded from [http://www.uniprot.org/uniprot/P00811 UniProt:P00811]
|-
|
ampCK83Q,T
|

|
K83Q,T
|

|
Lowers activity more than 1000- fold and increases protein stability
|

|

|
seeded from [http://www.uniprot.org/uniprot/P00811 UniProt:P00811]
|-
|
ampCK331A
|

|
K331A
|

|
Lowers activity more than 1000- fold
|

|

|
seeded from [http://www.uniprot.org/uniprot/P00811 UniProt:P00811]
|-
|
ampCN168D,H
|

|
N168D,H
|

|
Lowers activity more than 1000- fold
|

|

|
seeded from [http://www.uniprot.org/uniprot/P00811 UniProt:P00811]
|-
|
ampCY166E
|

|
Y166E
|

|
Lowers activity more than 1000- fold
|

|

|
seeded from [http://www.uniprot.org/uniprot/P00811 UniProt:P00811]
|-
|
ΔampC (Keio:JW4111)
|
deletion
|
deletion
|

|

|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen] [http://cgsc2.biology.yale.edu/Strain.php?ID=109241 CGSC10960]<ref name='LIB:cgsc'/>
|

|-
|
''ampC12''
|

|

|

|

|

|
[[cgscmutation:10039|CGSC:10039]]
|

|-
|
''ampC11''
|

|

|

|

|

|
[[cgscmutation:11804|CGSC:11804]]
|

|-
|
''ampC3''
|

|

|

|

|

|
[[cgscmutation:11809|CGSC:11809]]
|

|-
|
''ampC777(del)::kan''
|

|

|

|

|
PMID:16738554
|
[[cgscmutation:99998|CGSC:99998]]
|

|-
|
ampC
|

|

|
Resistant to
|
ampicillin resistance
|
PMID:4945191
|

|

|-
|
ampC
|
Gene Duplication
|

|
Resistant to
|
Ampicillin-hyperresistant mutants of Ecoli K12 with multiple gene duplications in the ampC gene region overproduced at least six proteins during anaerobic growth. All but two of the proteins were also overproduced during aerobic growth.
|
PMID:391567
|

|

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18865.U46aa086dd060f&page=18865&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table] || || || || || || ||
|}


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

==Genetic Interactions==
{{BacktoTop}}
<protect>
{{Genetic_interaction_help}}
{| id="V4e04b7496eaa3" class=" tableEdit Genetic_interaction_table dataTable"
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.18865.V4e04b7496eaa3&page=18865&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table] || || || || || ||
|}
</protect>


===Notes===

==Genetic Resources==
{{BacktoTop}}

{{Gene_resources_help}}
{| id="J46aa086e98292" class=" tableEdit Gene_resource_table"
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
|-
|
JW4111
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691

Status:Clone OK

Primer 1:GCCTTCAAAACGACGCTCTGCGC

Primer 2:CCtTGTAGAGCGTTAAGAATCTG
|-
|
[[:Category:Kohara_Phage:1D4|1D4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=650 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:3H6|3H6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=651 Genobase]
|
PMID:3038334
|-
|
[[cadB:Gene|cadB2231::Tn10]]
|
Linked marker
|
CAG18488 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40596 CGSC7479]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 50% <ref name='LIB:Nichols_linked_Tn'/> 
Synonyms:zjd-2231::Tn10
|-
|
[[cycA:Gene|cycA30::Tn10]]
|
Linked marker
|
CAG12073 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40604 CGSC7482]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 10% <ref name='LIB:Nichols_linked_Tn'/>

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===Notes===

==Accessions in Other Databases==
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{{Gene_accessions_help}}
{| id="F46aa086f466cf" class=" tableEdit Gene_accessions_table"
|- {{table_heading_style}}
!|Database!!Accession!!Notes
|-
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10040 ECOCYC:EG10040]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
[http://ecogene.org/geneinfo.php?eg_id=EG10040 EcoGene:EG10040]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/gene?term=948669 GeneID:948669]
|
Escherichia coli str. K-12 substr. MG1655

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===Notes===

==Links==
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{| id="E46a7215a0b06e" class=" tableEdit Links_table"
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!|Name!!URL!!Comments

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<noinclude><protect>
==References==
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{{RefHelp}}
<references />
__NOTOC__
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:amp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]