Difference between revisions of "SubtiPathways"

From SubtiWiki
Jump to: navigation, search
(→‎Publications describing SubtiWiki and SubtiPathways)
 
(67 intermediate revisions by 7 users not shown)
Line 1: Line 1:
−
[[File:Pathway_start_page_small.png|right|link=http://subtipathways.uni-goettingen.de/]]
+
[[File:Pathway_start_page_small.png|right|link=http://subtiwiki.uni-goettingen.de/subtipathways/start.php]]
 
[[File:Legende.jpg|250px|thumb|right|'''legend for ''Subti''Pathways <br/>graphical notation: click to enlarge''']]
 
[[File:Legende.jpg|250px|thumb|right|'''legend for ''Subti''Pathways <br/>graphical notation: click to enlarge''']]
  
 
<big>'''''Subti''Pathways''' is a model of '''''B. subtilis''''' metabolism and regulation in '''SBML/SBGN''' (Systems Biology Markup Language/ Graphical Notation). There is a color code for key metabolites (see the legend on the right side).<br/><br/>It can be used like Google Maps (scroll and zoom to the pathways). The markers of proteins and compounds listed on the right side in each pathway are containing links to the corresponding ''Subti''Wiki and PubChem pages, respectively. There is a short description for each protein in the bubbles, too.</big>
 
<big>'''''Subti''Pathways''' is a model of '''''B. subtilis''''' metabolism and regulation in '''SBML/SBGN''' (Systems Biology Markup Language/ Graphical Notation). There is a color code for key metabolites (see the legend on the right side).<br/><br/>It can be used like Google Maps (scroll and zoom to the pathways). The markers of proteins and compounds listed on the right side in each pathway are containing links to the corresponding ''Subti''Wiki and PubChem pages, respectively. There is a short description for each protein in the bubbles, too.</big>
  
 +
<big>'''Contact:'''</big> [http://wwwuser.gwdg.de/~genmibio/stuelke.html General Microbiology, University of Göttingen], [mailto:jstuelk@gwdg.de send mail]
 +
 +
<br/>
 +
<big>'''Now online: A description of ''Subti''Wiki, ''Subti''Pathways, and ''Subt''Interact in the 2012 Database issue of Nucleic Acids Research'''</big>
 +
<pubmed> 22096228 </pubmed>
 
__NOTOC__
 
__NOTOC__
  
 
<br/>
 
<br/>
  
−
== A collection of important papers on ''B. subtilis'' [[metabolism]] an be found here [[metabolism|here]] ==
+
== A collection of important papers on ''B. subtilis'' [[metabolism]] can be found [[metabolism|here]] ==
 
<br/>
 
<br/>
 
== Carbon metabolism ==
 
== Carbon metabolism ==
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central carbon metabolism] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=7FvYw Central carbon metabolism] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Utilization of different carbon sources] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=ps3UM Utilization of different carbon sources] ===
  
 
<br/>
 
<br/>
 +
 
== Nitrogen and amino acid metabolism ==
 
== Nitrogen and amino acid metabolism ==
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium assimilation and glutamate metabolism (incl. glutamine and arginine)] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=Cog2y Ammonium assimilation and glutamate metabolism (incl. glutamine and arginine)] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/ala_gly_ser.html Alanine, glycine, serine] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=mONyM Alanine, glycine, serine] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/aspartate_asparagine.html Aspartate, asparagine] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=81K4b Aspartate, asparagine] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Cysteine, methionine] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=1Jfrj Cysteine, methionine] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/histidine.html Histidine] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=DNohR Histidine] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/ile_val_leu.html Isoleucine, valine, leucine] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=V2MSg Isoleucine, valine, leucine] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=lysi Lysine, threonine] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=qSUN0 Phenylalanine, tyrosine, tryptophan] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=bM03y Proline] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=JKtpr Utilization of other nitrogen sources] ===
 +
 
 +
<br/>
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/lys_threo.html Lysine, threonine] ===
+
== Lipid metabolism ==
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/phenyl_tyr_tryp.html Phenylalanine, tyrosine, tryptophan] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=fatt Fatty acid metabolism] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/proline.html Proline] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=cnliR Fatty acid and phospholipid biosynthesis] ===
  
 
<br/>
 
<br/>
 +
 
== Nucleotides ==
 
== Nucleotides ==
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Gene regulation of nucleotide metabolism] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=nucl Nucleoside catabolism] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/nucleosides_catabolism.html Nucleoside catabolism] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=etxDX Purine biosynthesis] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/purine_biosynthesis.html Purine biosynthesis] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=bxwTq Purine catabolism] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/purines_catabolism.html Purine catabolism] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=puri Purine salvage pathways] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/purines_salvage_pathways.html Purine salvage pathways] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=pyri Pyrimidine metabolism] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/pyrimidines_metabolism.html Pyrimidine metabolism] ===
+
<br/>
  
−
<br/>
 
 
== Metabolism of cofactors ==
 
== Metabolism of cofactors ==
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/CoA_synthesis.html CoA synthesis] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=cUo5h CoA synthesis] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=faSwm Folate biosynthesis] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=2GTKN Menaquinone] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=4Ww0E Riboflavin and FAD synthesis] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=wTyck Thiamin synthesis] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=8iQpH Biotin synthesis] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=op4I3 Heme biosynthesis] ===
 +
 
 +
===[http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=wAgIW Molybdopterin synthesis] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=3vSpz NAD synthesis] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=Zjt4G Lipoate synthesis] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=moarx Pyridoxalphospahte synthesis] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=AwkEg S-adenosylmethionine synthesis] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/folate_biosynthesis.html Folate biosynthesis] ===
 
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/menaquinone.html Menaquinone] ===
 
  
 
<br/>
 
<br/>
 +
 
== Other pathways ==
 
== Other pathways ==
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/cellwall.html Cell wall] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=LlfNo Peptidoglycan synthesis] [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=RqnXf Peptidoglycan catabolism] [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=aARFz Teichonic acid] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=RDamU ppGpp] [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=Tvl8u cdAMP] [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=E6M7Y cdGMP] ===
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=stre Stress responses] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress responses] ===
+
=== [http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay] ===
  
 
=== [http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Sulfate assimilation] ===
 
=== [http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Sulfate assimilation] ===
  
−
=== [http://subtiwiki.uni-goettingen.de/pathways/tRNA_charging.html tRNA charging] ===
+
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=trna tRNA charging] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=BPSRv Biofilm formation] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=95Yqn Protein secretion] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=V1JFH Acquisition of iron ] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=LNqKW Metal ion homeostasis] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=pM5k3 Trace metal homeostasis] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=4FfA6 Amino acids transporter] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=KheJp Bactoprenol synthesis] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=SO2Za Methylglyoxal pathway] ===
 +
 
 +
=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=YDHgj Respiration] ===
 +
 
 +
== Publications describing ''Subti''Wiki and ''Subti''Pathways ==
 +
<pubmed>19959575 22096228    24178028</pubmed>

Latest revision as of 08:15, 13 May 2014

Pathway start page small.png
legend for SubtiPathways
graphical notation: click to enlarge

SubtiPathways is a model of B. subtilis metabolism and regulation in SBML/SBGN (Systems Biology Markup Language/ Graphical Notation). There is a color code for key metabolites (see the legend on the right side).

It can be used like Google Maps (scroll and zoom to the pathways). The markers of proteins and compounds listed on the right side in each pathway are containing links to the corresponding SubtiWiki and PubChem pages, respectively. There is a short description for each protein in the bubbles, too.

Contact: General Microbiology, University of Göttingen, send mail


Now online: A description of SubtiWiki, SubtiPathways, and SubtInteract in the 2012 Database issue of Nucleic Acids Research



A collection of important papers on B. subtilis metabolism can be found here


Carbon metabolism

Central carbon metabolism

Utilization of different carbon sources


Nitrogen and amino acid metabolism

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

Alanine, glycine, serine

Aspartate, asparagine

Cysteine, methionine

Histidine

Isoleucine, valine, leucine

Lysine, threonine

Phenylalanine, tyrosine, tryptophan

Proline

Utilization of other nitrogen sources


Lipid metabolism

Fatty acid metabolism

Fatty acid and phospholipid biosynthesis


Nucleotides

Nucleoside catabolism

Purine biosynthesis

Purine catabolism

Purine salvage pathways

Pyrimidine metabolism


Metabolism of cofactors

CoA synthesis

Folate biosynthesis

Menaquinone

Riboflavin and FAD synthesis

Thiamin synthesis

Biotin synthesis

Heme biosynthesis

Molybdopterin synthesis

NAD synthesis

Lipoate synthesis

Pyridoxalphospahte synthesis

S-adenosylmethionine synthesis


Other pathways

Peptidoglycan synthesis Peptidoglycan catabolism Teichonic acid

ppGpp cdAMP cdGMP

Stress responses

Phosphorelay

Sulfate assimilation

tRNA charging

Biofilm formation

Protein secretion

Acquisition of iron

Metal ion homeostasis

Trace metal homeostasis

Amino acids transporter

Bactoprenol synthesis

Methylglyoxal pathway

Respiration

Publications describing SubtiWiki and SubtiPathways

Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=SubtiPathways&oldid=205426"