SubtiWiki - User contributions [en]

Talk:SubtiPathways

2010-08-19T15:53:13Z

Tkuenzl: /* Proline */

<big>'''Discovered something unusual in the diagrams? Please leave a comment in the corresponding section!'''</big>

__TOC__

== General comments about all diagrams ==
* There seem to be some compatibility problems using Google Chrome. Nonetheless, Mozilla Firefox, Netscape, Microsoft Explorer, Safari, and Opera are working properly.
* write comments here

 

== Carbon metabolism ==

=== Central carbon metabolism ===

* write comments here

=== Utilization of different carbon sources ===

* write comments here

 

== Nitrogen and amino acid metabolism ==

=== Ammonium assimilation and glutamate metabolism (incl. glutamine and arginine) ===

*write comments here

=== Alanine, glycine, serine ===

*write comments here

=== Aspartate, asparagine ===

* write comments here

=== Cysteine, methionine ===

* Repel: Eventuell Einbindung von Extramarkern für die S-Box (bzw. alle riboswitches)???? Es gibt ja dafür extra Seiten im Subtiwiki. Sollte man aber erst mal mit Lope und Arne diskutieren (Jörg)
* Cystin-Aufnahme-Systeme mit aufnehmen: TcyP, TcyABC, TcyJKLMN (Jörg)

=== Histidine ===

*write comments here

=== Isoleucine, valine, leucine ===

* Isoleucin-Abbau: Bcd und YwaA sind zwei unterschiedliche Reaktionen, Bcd geht mit NAD, nicht mit 2-KG (Jörg)

=== Lysine, threonine ===

* write comments here

=== Phenylalanine, tyrosine, tryptophan ===

* write comments here

=== Proline ===

* write comments here

=== Utilization of other nitrogen sources ===

* write comments here

 

== Lipid metabolism ==

=== Fatty acid and phospholipid biosynthesis ===

* The structure of PDGP is wrong (although the name, CDP-diacylglycerol, seems right). Wrong PubChem ID?
* The same applies for phosphatidylglycerol, L-serine, and others.

=== Fatty acid degradation ===

* write comments here

== Nucleotides ==

=== Gene regulation of nucleotides ===

* write comments here

=== Nucleosides catabolism ===

*write comments here

=== Purine metabolism ===

*write comments here

=== Purine catabolism ===

*write comments here

=== Purine salvage pathways ===

* write comments here

=== Pyrimidine metabolism ===

*write comments here

 

== Metabolism of cofactors ==

=== CoA synthesis ===

*write comments here

=== Folate biosynthesis ===

*write comments here

=== Menaquinone ===

*write comments here

=== Riboflavin and FAD synthesis ===

* write comments here

=== Thiamin synthesis ===

* write comments here
 

== Other pathways ==

=== Cellwall ===

*write comments here

=== Stress response ===

* write comments here

=== Phosphorelay ===
* In the interaction between KipI and KipA, that prevents the complex between KinA and KipI, KinA should be released from the complex. This has to be added to the diagram.

=== Sulfate assimilation ===

*write comments here

=== tRNA charging ===

* write comments here

=== Biofilm formation ===

* SlrR bind SinR, according to Losick {{PubMed|20351052}}

Talk:SubtiPathways

2010-08-19T15:53:01Z

Tkuenzl: /* Proline */

<big>'''Discovered something unusual in the diagrams? Please leave a comment in the corresponding section!'''</big>

__TOC__

== General comments about all diagrams ==
* There seem to be some compatibility problems using Google Chrome. Nonetheless, Mozilla Firefox, Netscape, Microsoft Explorer, Safari, and Opera are working properly.
* write comments here

 

== Carbon metabolism ==

=== Central carbon metabolism ===

* write comments here

=== Utilization of different carbon sources ===

* write comments here

 

== Nitrogen and amino acid metabolism ==

=== Ammonium assimilation and glutamate metabolism (incl. glutamine and arginine) ===

*write comments here

=== Alanine, glycine, serine ===

*write comments here

=== Aspartate, asparagine ===

* write comments here

=== Cysteine, methionine ===

* Repel: Eventuell Einbindung von Extramarkern für die S-Box (bzw. alle riboswitches)???? Es gibt ja dafür extra Seiten im Subtiwiki. Sollte man aber erst mal mit Lope und Arne diskutieren (Jörg)
* Cystin-Aufnahme-Systeme mit aufnehmen: TcyP, TcyABC, TcyJKLMN (Jörg)

=== Histidine ===

*write comments here

=== Isoleucine, valine, leucine ===

* Isoleucin-Abbau: Bcd und YwaA sind zwei unterschiedliche Reaktionen, Bcd geht mit NAD, nicht mit 2-KG (Jörg)

=== Lysine, threonine ===

* write comments here

=== Phenylalanine, tyrosine, tryptophan ===

* write comments here

=== Proline ===

* write comments here

 

=== Utilization of other nitrogen sources ===

* write comments here

 

== Lipid metabolism ==

=== Fatty acid and phospholipid biosynthesis ===

* The structure of PDGP is wrong (although the name, CDP-diacylglycerol, seems right). Wrong PubChem ID?
* The same applies for phosphatidylglycerol, L-serine, and others.

=== Fatty acid degradation ===

* write comments here

== Nucleotides ==

=== Gene regulation of nucleotides ===

* write comments here

=== Nucleosides catabolism ===

*write comments here

=== Purine metabolism ===

*write comments here

=== Purine catabolism ===

*write comments here

=== Purine salvage pathways ===

* write comments here

=== Pyrimidine metabolism ===

*write comments here

 

== Metabolism of cofactors ==

=== CoA synthesis ===

*write comments here

=== Folate biosynthesis ===

*write comments here

=== Menaquinone ===

*write comments here

=== Riboflavin and FAD synthesis ===

* write comments here

=== Thiamin synthesis ===

* write comments here
 

== Other pathways ==

=== Cellwall ===

*write comments here

=== Stress response ===

* write comments here

=== Phosphorelay ===
* In the interaction between KipI and KipA, that prevents the complex between KinA and KipI, KinA should be released from the complex. This has to be added to the diagram.

=== Sulfate assimilation ===

*write comments here

=== tRNA charging ===

* write comments here

=== Biofilm formation ===

* SlrR bind SinR, according to Losick {{PubMed|20351052}}

PepT

2010-08-19T14:53:17Z

Tkuenzl: /* Database entries */

* '''Description:''' peptidase T (tripeptidase), zinc-dependent 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pepT''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || peptidase T (tripeptidase)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || peptide degradation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 4.538
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1230 bp, 410 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxjL]]'', ''[[yxjJ]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15918]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pepT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU38920

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pepT.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11842]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Release of the N-terminal residue from a tripeptide (according to Swiss-Prot)

* '''Protein family:''' peptidase M20B family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[YqjE]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?pdbId=3GB0 3GBO] (from ''Bacillus cereus (71% identity''), to be published)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P55179 P55179]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38920]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''pepT'' {{PubMed|10746760}}

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''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>8978088,,10987140, </pubmed>

[[Category:Protein-coding genes]]

PepT

2010-08-19T14:52:45Z

Tkuenzl: /* Database entries */

* '''Description:''' peptidase T (tripeptidase), zinc-dependent 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pepT''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || peptidase T (tripeptidase)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || peptide degradation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 4.538
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1230 bp, 410 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxjL]]'', ''[[yxjJ]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15918]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pepT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU38920

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pepT.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11842]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Release of the N-terminal residue from a tripeptide (according to Swiss-Prot)

* '''Protein family:''' peptidase M20B family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[YqjE]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?pdbId=3GB0 3GBO] (from ''Bacillus cereus (71% identity'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P55179 P55179]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38920]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''pepT'' {{PubMed|10746760}}

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''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>8978088,,10987140, </pubmed>

[[Category:Protein-coding genes]]