TkmA - Revision history

Jstuelk: /* Phenotypes of a mutant */

2015-08-19T17:16:13Z

‎Phenotypes of a mutant

Jstuelk at 17:14, 19 August 2015

2015-08-19T17:14:32Z

Jstuelk at 17:04, 19 August 2015

2015-08-19T17:04:15Z

Jstuelk at 16:54, 19 August 2015

2015-08-19T16:54:14Z

134.76.38.147 at 14:59, 2 April 2014

2014-04-02T14:59:49Z

Jstuelk: /* Biological materials */

2014-02-06T12:55:21Z

‎Biological materials

Jstuelk: /* References */

2014-02-06T12:00:47Z

‎References

JGerwig: /* Biological materials */

2014-01-31T11:38:19Z

‎Biological materials

Jstuelk at 10:25, 31 January 2014

2014-01-31T10:25:10Z

JGerwig: /* Biological materials */

2014-01-28T08:41:33Z

‎Biological materials

← Older revision		Revision as of 17:16, 19 August 2015
Line 1:		Line 1:
−	* '''Description:~~''' transmembrane modulator of [[PtkA]] activity, activates [[PtkA]] autophosphorylation and substrate phosphorylation <br/><br/>~~	+	{{#bank: TkmA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''tkmA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ywqC ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| modulator of [[PtkA]] activity~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of protein tyrosine phosphorylation~~
−	\|-
−	\|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=BSU36260 tkmA]
−	\|-
−	\|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=TkmA TkmA]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 26 kDa, 4.61~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 744 bp, 248 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ptkA]]'', ''[[ywzD]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36260 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36260 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36260 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ywqC_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=ywqC_3732525_3733271_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:tkmA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36260]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[biofilm formation]]}},~~
−	~~{{SubtiWiki category\|[[protein modification]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[AbrB regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[DegU regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[Spo0A regulon]]}}~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU36260
−
−	~~===Phenotypes of a mutant ===~~
−	* the mutant exhibits a defect in [[biofilm formation]], pronounced on LBGM medium, weak of MSgg medium {{PubMed\|26283769,20815827}}, this can be compensated for by overexpression of ''[[epsA]]'' {{PubMed\|26283769}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU36260&redirect=T BSU36260]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywqCD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12507]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' transmembrane activation of [[PtkA]] protein tyrosine kinase activity
−
−	* '''Protein family:''' cpsC/capA family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' [[EpsA]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[PtkA]]-[[TkmA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
−	** [[FatR]]-[[TkmA]] {{PubMed\|23939619}}
−
−	* '''[[Localization]]:''' cell membrane (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU36260&redirect=T BSU36260]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P96715 P96715]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36260]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[tkmA]]-[[ptkA]]-[[ptpZ]]-[[ugd]]'' {{PubMed\|20815827,12970183}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywqC_3732525_3733271_-1 tkmA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|20815827}}
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−	** [[AbrB]]: transcription repression {{PubMed\|20817675}}
−	** [[Spo0A]]: transcription activation {{PubMed\|26283769}}
−	** [[DegU]]-P: transcription activation {{PubMed\|26283769}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** GP1566 (spc) {{PubMed\|24493247}}, available in [[ Jörg Stülke]]'s lab
−	** GP1567 ''[[epsA]]''::aphA3 ''[[tkmA]]''::spc {{PubMed\|24493247}}, available in [[ Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[ Jörg Stülke]]'s lab
−
−	* '''FLAG-tag construct:''' GP1620 ''tkmA''-FLAG 3x spc (based on [[pGP1331]]) available in [[ Jörg Stülke]]'s lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>12970183, 20815827 20817675 23939619 24493247 26283769</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 57: / Line 57: @@
 ===Phenotypes of a mutant ===
-* the mutant exhibits a defect in [[biofilm formation]], pronounced on LBGM medium, weak of MSgg medium {{PubMed|26283769,20815827}}
+* the mutant exhibits a defect in [[biofilm formation]], pronounced on LBGM medium, weak of MSgg medium {{PubMed|26283769,20815827}}, this can be compensated for by overexpression of ''[[epsA]]'' {{PubMed|26283769}}
 === Database entries ===
@@ Line 76: / Line 76: @@
 * '''Protein family:''' cpsC/capA family (according to Swiss-Prot)
-* '''Paralogous protein(s):''' [[EpsA]], [[TkmA]] can partially replace [[EpsA]] {{PubMed|26283769}}
+* '''Paralogous protein(s):''' [[EpsA]]
 === Extended information on the protein ===

@@ Line 45: / Line 45: @@
 = This gene is a member of the following [[regulons]] =
-{{SubtiWiki regulon|[[AbrB regulon]]}}
+{{SubtiWiki regulon|[[AbrB regulon]]}},
 =The gene=
@@ Line 116: / Line 119: @@
 * '''Regulatory mechanism:'''
 ** [[AbrB]]: transcription repression {{PubMed|20817675}}
 * '''Additional information:'''

@@ Line 54: / Line 54: @@
 ===Phenotypes of a mutant ===
-the mutant exhibits a defect in [[biofilm formation]] {{PubMed|20815827}}
+* the mutant exhibits a defect in [[biofilm formation]], pronounced on LBGM medium, weak of MSgg medium {{PubMed|26283769,20815827}}
 === Database entries ===
 * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU36260&redirect=T BSU36260]
@@ Line 72: / Line 73: @@
 * '''Protein family:''' cpsC/capA family (according to Swiss-Prot)
-* '''Paralogous protein(s):''' [[EpsA]]
+* '''Paralogous protein(s):''' [[EpsA]], [[TkmA]] can partially replace [[EpsA]] {{PubMed|26283769}}
 === Extended information on the protein ===
@@ Line 143: / Line 144: @@
 =References=
-<pubmed>12970183, 20815827 20817675 23939619 24493247 </pubmed>
+<pubmed>12970183, 20815827 20817675 23939619 24493247 26283769</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 56: / Line 56: @@
 the mutant exhibits a defect in [[biofilm formation]] {{PubMed|20815827}}
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywqCD.html]
@@ Line 92: / Line 93: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 121: / Line 121: @@
 * '''Mutant:'''
-** GP1566 (spc), available in [[ Jörg Stülke]]'s lab
+** GP1566 (spc) {{PubMed|24493247}}, available in [[ Jörg Stülke]]'s lab
-** GP1567 ''[[epsA]]''::aphA3 ''[[tkmA]]''::spc, available in [[ Jörg Stülke]]'s lab
+** GP1567 ''[[epsA]]''::aphA3 ''[[tkmA]]''::spc {{PubMed|24493247}}, available in [[ Jörg Stülke]]'s lab
 * '''Expression vector:'''

@@ Line 132: / Line 132: @@
 * '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[ Jörg Stülke]]'s lab
-* '''FLAG-tag construct:''' GP1620 ''tkmA''-FLAG (spc), available in [[ Jörg Stülke]]'s lab
+* '''FLAG-tag construct:''' GP1620 ''tkmA''-FLAG 3x spc (based on [[pGP1331]]) available in [[ Jörg Stülke]]'s lab
 * '''Antibody:'''

@@ Line 62: / Line 62: @@
 === Additional information===
 =The protein=
@@ Line 80: / Line 77: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 124: / Line 121: @@
 * '''Mutant:'''
-** GP1566 (spc), available in [[Stülke]] lab;
+** GP1566 (spc), available in [[ Jörg Stülke]]'s lab
-** GP1567 epsA::aphA3 tkmA::spc, available in [[Stülke]] lab
+** GP1567 ''[[epsA]]''::aphA3 ''[[tkmA]]''::spc, available in [[ Jörg Stülke]]'s lab
 * '''Expression vector:'''
@@ Line 133: / Line 130: @@
 * '''GFP fusion:'''
-* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[ Jörg Stülke]]'s lab
-* '''FLAG-tag construct:''' GP1620 tkmA-FLAG (spc)
+* '''FLAG-tag construct:''' GP1620 ''tkmA''-FLAG (spc), available in [[ Jörg Stülke]]'s lab
 * '''Antibody:'''

← Older revision		Revision as of 08:41, 28 January 2014
Line 134:		Line 134:

	* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab		* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
		+
		+	* '''FLAG-tag construct:''' GP1620 tkmA-FLAG (spc)

	* '''Antibody:'''		* '''Antibody:'''