GanB - Revision history

134.76.38.147 at 14:48, 2 April 2014

2014-04-02T14:48:21Z

134.76.70.252 at 14:36, 16 May 2013

2013-05-16T14:36:55Z

134.76.70.252 at 11:18, 14 May 2013

2013-05-14T11:18:46Z

134.76.70.252 at 13:53, 13 May 2013

2013-05-13T13:53:26Z

Jstuelk at 13:57, 16 August 2012

2012-08-16T13:57:06Z

Jstuelk: moved YvfO to GanB: 22893383

2012-08-16T13:31:31Z

moved YvfO to GanB: 22893383

134.76.70.252 at 16:06, 7 August 2012

2012-08-07T16:06:01Z

134.76.70.252 at 09:29, 23 April 2012

2012-04-23T09:29:56Z

134.76.70.252 at 06:50, 17 April 2012

2012-04-17T06:50:00Z

Lflorez at 23:31, 8 December 2010

2010-12-08T23:31:12Z

← Older revision		Revision as of 14:48, 2 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' endo-1,4-beta-galactosidase <br/><br/>~~	+	{{#bank: GanB}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ganB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' yvfO''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| endo-1,4-beta-galactosidase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| galactan utilization~~
−	\|-
−	\|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=BSU34120 ganB]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 47 kDa, 8.243~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1287 bp, 429 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[rsbP]]'', ''[[ganA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34120 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34120 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34120 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yvfO_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=ganB_3501651_3502940_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yvfO_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34120]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<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]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[LacR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU34120
−
−	~~===Phenotypes of a mutant ===~~
−	* a ''[[cycB]]-[[ganP]]-[[ganQ]]-[[ganA]]-[[ganB]]'' mutant is impaired in the utilization of galactan {{PubMed\|22893383}}
−
−	~~=== Database entries ===~~
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yvfKLM-lacA-yvfO.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12440]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' Endohydrolysis of (1->4)-beta-D-galactosidic linkages in galactan, generation of galactotriose {{PubMed\|22893383}}
−
−	* '''Protein family:''' glycosyl hydrolase 53 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]]:'''
−	** likely to be extrecellular {{PubMed\|22893383}}
−
−	~~=== Database entries ===~~
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2J74 2J74] (B. licheniformis)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O07013 O07013]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34120]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/3.2.1.89 3.2.1.89]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[cycB]]-[[ganP]]-[[ganQ]]-[[ganA]]-[[ganB]]'' {{PubMed\|9287030}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ganB_3501651_3502940_-1 ganB] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−	** [[LacR]]: transcription repression {{PubMed\|9287030}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>17056685 9287030 22893383 </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=ganB_3501651_3502940_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yvfO_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ganB_3501651_3502940_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yvfO_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34120]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbP]]'', ''[[ganA]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34120 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34120 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34120 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34120 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34120 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34120 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yvfO_context.gif]]

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || galactan utilization
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU34120 ganB]
+|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=BSU34120 ganB]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 8.243
@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbP]]'', ''[[ganA]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15417&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34120 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34120 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34120 Advanced_DNA]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yvfO_context.gif]]

@@ Line 1: / Line 1: @@
-* '''Description:''' arabinogalactan endo-1,4-beta-galactosidase <br/><br/>
+* '''Description:''' endo-1,4-beta-galactosidase <br/><br/>
 {| align="right" border="1" cellpadding="2"
 |-
 |style="background:#ABCDEF;" align="center"|'''Gene name'''
-|''yvfO''
+|''ganB''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' yvfO''
 |-
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || arabinogalactan endo-1,4-beta-galactosidase
+|style="background:#ABCDEF;" align="center"| '''Product''' || endo-1,4-beta-galactosidase
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || galactan utilization
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU34120 yvfO]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU34120 ganB]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 8.243
@@ Line 20: / Line 20: @@
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1287 bp, 429 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbP]]'', ''[[lacA]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbP]]'', ''[[ganA]]''
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15417&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
@@ Line 32: / Line 32: @@
 __TOC__
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 54: / Line 51: @@
 ===Phenotypes of a mutant ===
 === Database entries ===
@@ Line 62: / Line 60: @@
 === Additional information===
@@ Line 70: / Line 66: @@
 === Basic information/ Evolution ===
-* '''Catalyzed reaction/ biological activity:''' Endohydrolysis of (1->4)-beta-D-galactosidic linkages in arabinogalactans (according to Swiss-Prot)
+* '''Catalyzed reaction/ biological activity:''' Endohydrolysis of (1->4)-beta-D-galactosidic linkages in galactan, generation of galactotriose {{PubMed|22893383}}
 * '''Protein family:''' glycosyl hydrolase 53 family (according to Swiss-Prot)
@@ Line 88: / Line 84: @@
 * '''Effectors of protein activity:'''
-* '''Interactions:'''
+* '''[[SubtInteract|Interactions]]:'''
-* '''Localization:'''
+* '''[[Localization]]:'''
 === Database entries ===
@@ Line 105: / Line 102: @@
 =Expression and regulation=
-* '''Operon:''' ''[[cycB]]-[[yvfL]]-[[yvfM]]-[[lacA]]-[[yvfO]]'' {{PubMed|9287030}}
+* '''Operon:'''  ''[[cycB]]-[[ganP]]-[[ganQ]]-[[ganA]]-[[ganB]]'' {{PubMed|9287030}}
-* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ganB_3501651_3502940_-1 yvfO] {{PubMed|22383849}}
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ganB_3501651_3502940_-1 ganB] {{PubMed|22383849}}
 * '''Sigma factor:'''
@@ Line 137: / Line 134: @@
 =References=
-<pubmed>17056685 9287030  </pubmed>
+<pubmed>17056685 9287030 22893383 </pubmed>
 [[Category:Protein-coding genes]]

← Older revision	Revision as of 13:31, 16 August 2012
(No difference)

@@ Line 97: / Line 97: @@
 * '''Operon:''' ''[[cycB]]-[[yvfL]]-[[yvfM]]-[[lacA]]-[[yvfO]]'' {{PubMed|9287030}}
-* '''[[Sigma factor]]:'''
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ganB_3501651_3502940_-1 yvfO] {{PubMed|22383849}}
 * '''Regulation:'''

@@ Line 30: / Line 30: @@
 <br/><br/>
 =The gene=
@@ Line 49: / Line 55: @@
-= Categories containing this gene/protein =
 =The protein=