YcdA - Revision history

Jstuelk: /* Database entries */

2014-11-27T15:45:29Z

‎Database entries

134.76.70.252 at 09:56, 17 April 2014

2014-04-17T09:56:15Z

134.76.38.147 at 12:55, 2 April 2014

2014-04-02T12:55:27Z

Jstuelk at 19:20, 18 June 2013

2013-06-18T19:20:08Z

134.76.70.252 at 12:29, 16 May 2013

2013-05-16T12:29:03Z

134.76.70.252 at 09:24, 14 May 2013

2013-05-14T09:24:46Z

134.76.70.252 at 12:04, 13 May 2013

2013-05-13T12:04:50Z

134.76.70.252 at 09:28, 8 August 2012

2012-08-08T09:28:40Z

134.76.70.252 at 08:34, 8 August 2012

2012-08-08T08:34:49Z

Jstuelk: Reverted edits by 134.76.70.252 (talk) to last revision by Jstuelk

2012-08-07T10:52:35Z

Reverted edits by 134.76.70.252 (talk) to last revision by Jstuelk

← Older revision		Revision as of 15:45, 27 November 2014
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−	* '''Description:~~''' lipoprotein, required for swarming motility<br/><br/>~~	+	{{#bank: YcdA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ycdA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| lipoprotein~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| swarming motility~~
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02780 ycdA]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 39 kDa, 4.706~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1062 bp, 354 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yccK]]'', ''[[ycdB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02780 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02780 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02780 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ycdA_context.gif]]~~
−	~~<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>~~
−	\|-
−	\|colspan="2" \|'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ycdA_299438_300502_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ycdA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02780]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}},~~
−	~~{{SubtiWiki category\|[[motility and chemotaxis]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[Abh regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[AbrB regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[DegU regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU02780
−
−	~~===Phenotypes of a mutant ===~~
−	* reduced swarming motility {{PubMed\|22496484}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU02780&redirect=T BSU02780]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ycdA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12757]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** lipoprotein {{PubMed\|22496484}}
−	** membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU02780&redirect=T BSU02780]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34538 O34538]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU02780]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''ycdA'' {{PubMed\|22496484}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ycdA_299438_300502_-1 ycdA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−	** [[Abh]] and [[AbrB]]: synergistic transcription repression {{PubMed\|20817675}}
−	** [[DegU]]-P: transcription activation {{PubMed\|22496484}}
−	** [[SwrA]]: modulation of [[DegU]]-P activity at the ''ycdA'' promoter {{PubMed\|22496484}}
−
−	* '''Additional information:'''
−	** The mRNA has a long 5' leader region. This may indicate RNA-based regulation {{PubMed\|20525796}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 173 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 2289 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>18763711,20817675 20525796 22496484</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 122: / Line 122: @@
 * '''Additional information:'''
 ** The mRNA has a long 5' leader region. This may indicate RNA-based regulation {{PubMed|20525796}}
 =Biological materials =

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ycdA.html]
@@ Line 92: / Line 93: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 35: / Line 35: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 113: / Line 109: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ycdA_299438_300502_-1 ycdA] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 144: / Line 140: @@
 =References=
-'''Additional publications:''' {{PubMed|20817675}}
+<pubmed>18763711,20817675 20525796 22496484</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 27: / Line 27: @@
   <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 |-
-|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ycdA_299438_300502_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ycdA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ycdA_299438_300502_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ycdA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02780]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yccK]]'', ''[[ycdB]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02780 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02780 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02780 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02780 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02780 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02780 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ycdA_context.gif]]

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || swarming motility
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU02780 ycdA]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02780 ycdA]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 4.706
@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yccK]]'', ''[[ycdB]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12072&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02780 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02780 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02780 Advanced_DNA]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ycdA_context.gif]]