Abn2 - Revision history

134.76.38.147 at 15:11, 2 April 2014

2014-04-02T15:11:50Z

Jstuelk at 14:37, 20 February 2014

2014-02-20T14:37:26Z

Raphael2215 at 13:41, 20 February 2014

2014-02-20T13:41:42Z

Raphael2215 at 13:40, 20 February 2014

2014-02-20T13:40:23Z

Raphael2215 at 13:39, 20 February 2014

2014-02-20T13:39:01Z

Jstuelk: /* Extended information on the protein */

2014-02-20T13:31:23Z

‎Extended information on the protein

Jstuelk at 13:29, 20 February 2014

2014-02-20T13:29:43Z

134.76.70.252 at 14:14, 13 May 2013

2013-05-13T14:14:39Z

Awiechert at 11:55, 5 December 2012

2012-12-05T11:55:41Z

134.76.70.252 at 17:31, 7 August 2012

2012-08-07T17:31:30Z

← Older revision		Revision as of 15:11, 2 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' endo-1,5-alpha-L-arabinosidase <br/><br/>~~	+	{{#bank: Abn2}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''abn2''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yxiA ''~~
−	\|-
−	~~\|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=BSU39330 abn2]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 52 kDa, 7.371~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1407 bp, 469 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yxiB]]'', ''[[yxzL]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU39330 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU39330 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU39330 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yxiA_context.gif]]~~
−	\|-
−	\|colspan="2" \|'''[http://genome.jouy.inra.fr/seb/images/details/abnB_4039466_4040875_-1.png Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:abn2_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU39330]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[utilization of specific carbon sources]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU39330
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yxiA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11130]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' glycosyl hydrolase 43 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:''' With linear-alpha-1,5-l-arabinan as the preferred substrate, the enzyme exhibited an apparent K(m) of 2.0 mg ml(-1) and V(max) of 0.25 mmol min(-1) mg(-1) at pH 7.0 and 50°C. [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
−
−	* '''[[Domains]]:'''
−	** N-terminal catalytic domain with a characteristic β-propeller fold and a C-terminal domain whose function is unknown {{PubMed\|24549757}}
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:''' Ca<sup>2+</sup> {{PubMed\|24549757}}
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** extracellular (signal peptide) {{PubMed\|18957862,18408032}}
−
−	~~=== Database entries ===~~
−
−	* '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=2X8F 2X8F] {{PubMed\|20883454}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P42293 P42293]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU39330]
−
−	* '''E.C. number:''' 3.2.1.99
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''abn2'' [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
−
−	* '''[[Sigma factor]]:''' [[SigA]], [[SigH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
−
−	* '''Regulation:'''
−	** repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
−	** expression is stimulated by arabinose and pectin and repressed by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[CcpA]]: transcription repression, unknown [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Isabel de Sa-Nogueira]], Lisboa, Portugal [http://www.itqb.unl.pt/research/biology/microbial-genetics homepage]~~
−
−	~~=Your additional remarks=~~
−
−
−	~~=References=~~
−	~~<pubmed>18607095, 24549757,18408032,18957862 12850135 18408032 20883454</pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 23: / Line 23: @@
 |-
 |style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU39330 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU39330 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU39330 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yxiA_context.gif]]

@@ Line 46: / Line 46: @@
 === Basic information ===
-* '''Locus tag:'''
+* '''Locus tag:''' BSU39330
 ===Phenotypes of a mutant ===

@@ Line 28: / Line 28: @@
 |colspan="2" | '''Genetic context''' <br/> [[Image:yxiA_context.gif]]
 |-
-|colspan="2" |'''[http://genome.jouy.inra.fr/seb/images/details/abnB_4039466_4040875_-1.png Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:abn2_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSUBSU39330]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/seb/images/details/abnB_4039466_4040875_-1.png Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:abn2_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU39330]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxiB]]'', ''[[yxzL]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yxiA_nucleotide.txt     Gene sequence      (+200bp)   ]'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU39330 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU39330 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU39330 DNA_with_flanks]
 |-
 |colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yxiA_context.gif]]
 |-
 |}

@@ Line 72: / Line 72: @@
 * '''[[Domains]]:'''
 * '''Modification:'''
-* '''[[Cofactors]]:'''
+* '''[[Cofactors]]:''' Ca<sup>2+</sup> {{PubMed|24549757}}
 * '''Effectors of protein activity:'''

@@ Line 56: / Line 56: @@
 === Additional information===
 =The protein=
@@ Line 74: / Line 71: @@
 * '''Kinetic information:'''	With linear-alpha-1,5-l-arabinan as the preferred substrate, the enzyme exhibited an apparent K(m) of 2.0 mg ml(-1) and V(max) of 0.25 mmol min(-1) mg(-1) at pH 7.0 and 50°C. [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 84: / Line 81: @@
 * '''[[SubtInteract|Interactions]]:'''
-* '''[[Localization]]:''' extracellular (signal peptide) {{PubMed|18957862,18408032}}
+* '''[[Localization]]:'''
 === Database entries ===
@@ Line 104: / Line 102: @@
 * '''[[Sigma factor]]:''' [[SigA]], [[SigH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
-* '''Regulation:''' repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  expression is stimulated by arabinose and pectin and repressed by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+* '''Regulation:'''
-* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  unknown [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+* '''Regulatory mechanism:'''
 * '''Additional information:'''
@@ Line 132: / Line 133: @@
 =References=
+<pubmed>18607095, 24549757,18408032,18957862 12850135 18408032 20883454</pubmed>
 [[Category:Protein-coding genes]]

@@ 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/BSU39330 abn2]
+|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=BSU39330 abn2]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 7.371

@@ Line 20: / Line 20: @@
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxiB]]'', ''[[hutP]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxiB]]'', ''[[yxzL]]''
 |-
 |style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yxiA_nucleotide.txt     Gene sequence      (+200bp)   ]'''