AbnA - Revision history

Julian at 12:47, 24 April 2014

2014-04-24T12:47:24Z

Julian at 10:54, 24 April 2014

2014-04-24T10:54:05Z

Julian at 08:25, 22 April 2014

2014-04-22T08:25:22Z

134.76.38.147 at 14:28, 2 April 2014

2014-04-02T14:28:20Z

134.76.70.252 at 14:14, 16 May 2013

2013-05-16T14:14:00Z

134.76.70.252 at 10:57, 14 May 2013

2013-05-14T10:57:50Z

134.76.70.252 at 13:32, 13 May 2013

2013-05-13T13:32:57Z

Jstuelk at 15:24, 21 August 2012

2012-08-21T15:24:20Z

134.76.70.252 at 14:44, 7 August 2012

2012-08-07T14:44:47Z

134.76.70.252 at 10:41, 20 April 2012

2012-04-20T10:41:06Z

← Older revision		Revision as of 12:47, 24 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' endo-1,5-alpha-L-arabinosidase <br/><br/>~~	+	{{#bank: AbnA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''abnA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| endo-1,5-alpha-L-arabinosidase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| arabinan degradation~~
−	\|-
−	\|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=BSU28810 abnA]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 34 kDa, 8.618~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 939 bp, 313 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[araA]]'', ''[[ysdC]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28810 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28810 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28810 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:abnA_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=abnA_2949053_2950024_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:abnA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28810]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−
−	~~<br/><br/><br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[utilization of specific carbon sources]]}},~~
−	~~{{SubtiWiki category\|[[Sporulation#Sporulation_proteins/_other\|sporulation proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[AraR regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[CcpA regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU28810
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU28810&redirect=T BSU28810]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/abnA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11901]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' Endohydrolysis of (1->5)-alpha-arabinofuranosidic linkages in (1->5)-arabinans (according to Swiss-Prot)
−
−	* '''Protein family:''' glycosyl hydrolase 43 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU28810&redirect=T BSU28810]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1UV4 1UV4]
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P94522 P94522]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28810]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/3.2.1.99 3.2.1.99]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[abnA]]'' {{PubMed\|14973026}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=abnA_2949053_2950024_-1 abnA] {{PubMed\|22383849}}
−
−	* '''Sigma factor:''' [[SigA]] {{PubMed\|14973026}}
−
−	* '''Regulation:'''
−	** repressed in the absence of arabinose ([[AraR]]) {{PubMed\|14973026}}
−	** subject to carbon catabolite repression ([[CcpA]]) {{PubMed\|22900538}}
−	* '''Regulatory mechanism:'''
−	** [[AraR]]: transcription repression {{PubMed\|14973026}}
−	** [[CcpA]]: transcription repression {{PubMed\|22900538}}
−
−	* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>15556708,14973026,12884008,22900538,14973026,18957862, </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 42: / Line 42: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[utilization of specific carbon sources]]}},
-{{SubtiWiki category|[[sporulation/ other]]}}
+{{SubtiWiki category|[[Sporulation#Sporulation_proteins/_other|sporulation proteins]]}}
 = This gene is a member of the following [[regulons]] =

@@ Line 41: / Line 41: @@
 = [[Categories]] containing this gene/protein =
-{{SubtiWiki category|[[utilization of specific carbon sources]]}}
+{{SubtiWiki category|[[utilization of specific carbon sources]]}},
 = This gene is a member of the following [[regulons]] =

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/abnA.html]
@@ Line 91: / Line 92: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1UV4 1UV4]

@@ Line 29: / Line 29: @@
   <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=abnA_2949053_2950024_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:abnA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=abnA_2949053_2950024_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:abnA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28810]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[araA]]'', ''[[ysdC]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28810 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28810 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28810 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28810 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28810 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28810 DNA_with_flanks]
 |-
 |-

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU28810 abnA]
+|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=BSU28810 abnA]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 8.618
@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[araA]]'', ''[[ysdC]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14841&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28810 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28810 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28810 Advanced_DNA]
 |-
 |-

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
@@ Line 47: / Line 44: @@
 = This gene is a member of the following [[regulons]] =
-{{SubtiWiki regulon|[[AraR regulon]]}}
+{{SubtiWiki regulon|[[AraR regulon]]}},
 =The gene=
@@ Line 64: / Line 62: @@
 === Additional information===
@@ Line 108: / Line 104: @@
 =Expression and regulation=
-* '''Operon:''' ''[[abnA]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/14973026 PubMed]
+* '''Operon:''' ''[[abnA]]'' {{PubMed|14973026}}
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=abnA_2949053_2950024_-1 abnA] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14973026 PubMed]
+* '''Sigma factor:''' [[SigA]] {{PubMed|14973026}}
 * '''Regulation:'''
-** repressed in the absence of arabinose ([[AraR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14973026 PubMed]
+** repressed in the absence of arabinose ([[AraR]]) {{PubMed|14973026}}
+** subject to carbon catabolite repression ([[CcpA]]) {{PubMed|22900538}}
 * '''Regulatory mechanism:'''
-** [[AraR]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/14973026 PubMed]
+** [[AraR]]:  transcription repression {{PubMed|14973026}}
 * '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
@@ Line 142: / Line 139: @@
 =References=
-<pubmed>15556708,14973026,12884008,,14973026,18957862, </pubmed>
+<pubmed>15556708,14973026,12884008,22900538,14973026,18957862, </pubmed>
 [[Category:Protein-coding genes]]