HemAT - Revision history

Jstuelk: /* Biological materials */

2015-07-03T14:49:33Z

‎Biological materials

Jstuelk: /* Extended information on the protein */

2015-07-03T14:49:11Z

‎Extended information on the protein

Atkovacs at 13:27, 2 July 2015

2015-07-02T13:27:53Z

134.76.70.252 at 14:08, 17 April 2014

2014-04-17T14:08:19Z

134.76.70.252 at 09:31, 17 April 2014

2014-04-17T09:31:35Z

134.76.38.147 at 13:21, 2 April 2014

2014-04-02T13:21:03Z

Jstuelk: /* References */

2014-03-19T15:46:45Z

‎References

134.76.70.252 at 15:56, 11 November 2013

2013-11-11T15:56:29Z

134.76.70.252 at 12:55, 16 May 2013

2013-05-16T12:55:04Z

134.76.70.252 at 09:51, 14 May 2013

2013-05-14T09:51:02Z

← Older revision		Revision as of 14:49, 3 July 2015
Line 1:		Line 1:
−	* '''Description:''' soluble chemotaxis receptor, heme-containing O(2) sensor protein <br/><br/>	+	{{#bank: HemAT}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''hemAT''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yhfV ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| haem-based aerotactic transducer~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| movement towards oxygen~~
−	\|-
−	~~\|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=BSU10380 hemAT]~~
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=HemAT ~~HemAT]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 48 kDa, 5.441~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1296 bp, 432 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yhfU]]'', ''[[yhfW]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU10380 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU10380 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU10380 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:hemAT_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=hemAT_1112620_1113918_-1 Expression at a glance]'''   {{PubMed\|22383849~~}~~}<br/>[[Image:hemAT_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU10380]]~~
−	\|-
−	\|}

−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[motility and chemotaxis]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[SigD regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU10380
−
−	~~===Phenotypes of a mutant ===~~
−	* not essential for pellicle biofilm formation, but mutant is outcompeted by the wild-type strain when competed during pellicle formation {{PubMed\|26122431}}
−	* NCIB3610 ''hemAT'' mutant has higher fitness than ''[[hag]]'' mutant during pellicle formation {{PubMed\|26122431}}
−	* NCIB3610 ''hemAT''-''[[hag]]'' double mutant has similar fitness to single ''[[hag]]'' mutant during pellicle formation {{PubMed\|26122431}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU10380&redirect=T BSU10380]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/hemAT.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13066]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−	* HemAT protein has a moderate oxygen affinity {{PubMed\|11821422}}
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** required for full expression of the ''[[phoD]]-[[tatAD]]-[[tatCD]]'' operon {{PubMed\|23180473}}
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):''' heme
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[HemAT]]-[[TatAC]] {{PubMed\|23180473}}
−
−	* '''[[Localization]]:'''
−	** forms clusters at the cell poles {{PubMed\|21515776}}
−	** homogeneous cytoplasmic distribution in chain-forming cells during the logarithmic phase {{PubMed\|23180473}}
−	** polar foci in individual cells at later growth stages {{PubMed\|23180473}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU10380&redirect=T BSU10380]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1OR4 1OR4] (in cyano-liganded form), [http://www.rcsb.org/pdb/explore.do?structureId=1OR6 1OR6] {{PubMed\|12962628}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O07621 O07621]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU10380]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''hemAT'' {{PubMed\|15033535}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=hemAT_1112620_1113918_-1 hemAT] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigD]] {{PubMed\|15033535}}
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** in minimal medium, HemAT is present with 19,000 +/- 3,900 molecules per cell {{PubMed\|21515776}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 1095 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 1803 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 3169 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 966 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 1236 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−	** TB239 (''hemAT''::''neo'' in 168) {{PubMed\|26122431}}
−	** TB241 (''hemAT''::''neo'' in NCIB3610) {{PubMed\|26122431}}
−	** TB244 ''amyE''::Phy-''sfgfp'' (''hemAT''::''neo'' in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed\|26122431}}
−	** TB243 ''amyE''::Phy-''mKATE2'' (''hemAT''::''neo'' in NCIB3610 with constitutive expressed ''mKATE2'') {{PubMed\|26122431}}
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−	* [[Akos T Kovacs]]
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~== Reviews ==~~
−	~~<pubmed> 23928310 </pubmed>~~
−	~~== Original publications ==~~
−	~~<pubmed>26122431, 10676961,16819829,11481493,15033535 21515776 23180473 22564695</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 93: / Line 93: @@
 * '''[[Localization]]:'''
 ** forms clusters at the cell poles {{PubMed|21515776}}
-** homogeneous cytoplsmic distribution in chain-forming cells during the logarithmic phase {{PubMed|23180473}}
+** homogeneous cytoplasmic distribution in chain-forming cells during the logarithmic phase {{PubMed|23180473}}
 ** polar foci in individual cells at later growth stages {{PubMed|23180473}}

@@ Line 51: / Line 51: @@
 ===Phenotypes of a mutant ===
 === Database entries ===
@@ Line 62: / Line 65: @@
 =The protein=
 === Basic information/ Evolution ===
@@ Line 95: / Line 99: @@
 * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU10380&redirect=T BSU10380]
-* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1OR4 1OR4] (in cyano-liganded form),  [http://www.rcsb.org/pdb/explore.do?structureId=1OR6 1OR6]
+* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1OR4 1OR4] (in cyano-liganded form),  [http://www.rcsb.org/pdb/explore.do?structureId=1OR6 1OR6]	{{PubMed|12962628}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/O07621 O07621]
@@ Line 127: / Line 131: @@
 =Biological materials =
 * '''Mutant:'''
 * '''Expression vector:'''
@@ Line 139: / Line 147: @@
 =Labs working on this gene/protein=
 =Your additional remarks=
@@ Line 146: / Line 155: @@
 <pubmed> 23928310 </pubmed>
 == Original publications ==
-<pubmed>10676961,16819829,11481493,15033535 21515776 23180473 22564695</pubmed>
+<pubmed>26122431, 10676961,16819829,11481493,15033535 21515776 23180473 22564695</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 121: / Line 121: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 1095 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 1803 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''

@@ Line 119: / Line 119: @@
 * '''Additional information:'''
 ** in minimal medium, HemAT is present with 19,000 +/- 3,900 molecules per cell {{PubMed|21515776}}
 =Biological materials =

@@ Line 137: / Line 137: @@
 =References=
-'''Additional publications:''' {{PubMed|22564695}}
+== Reviews ==
-<pubmed>10676961,16819829,11481493,15033535 21515776 23180473</pubmed>
+<pubmed> 23928310 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 15: / Line 15: @@
 |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=BSU10380 hemAT]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/HemAT HemAT]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=HemAT HemAT]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.441

@@ Line 28: / Line 28: @@
   <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=hemAT_1112620_1113918_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:hemAT_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=hemAT_1112620_1113918_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:hemAT_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU10380]]
 |-
 |}

@@ Line 23: / Line 23: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhfU]]'', ''[[yhfW]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU10380 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU10380 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU10380 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU10380 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU10380 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU10380 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:hemAT_context.gif]]