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Microme data

Microme data. Compounds Reactions Pathways Genes / Genomes Polypeptides / Proteins Metabolic networks. Compounds / Reactions. ChEBI : 28’306 molecular structures Rhea : release 23 (June 2011) 4’108 approved master reactions, 3’183 are linked to complete EC numbers.

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Microme data

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  1. Microme data • Compounds • Reactions • Pathways • Genes / Genomes • Polypeptides / Proteins • Metabolic networks

  2. Compounds / Reactions ChEBI : 28’306 molecular structures Rhea : release 23 (June 2011) 4’108 approved master reactions, 3’183 are linked to complete EC numbers. 267 transport reaction 3’667 chemical entities (small molecules) Rhea cross-references: EcoCyc 1’050 MetaCyc 3’312 KEGG 3’276

  3. Compounds / Reactions issues Done: Rhea – UniProt xrefs available (rel 23) (Still) under development Bulk submission tools (ChEBI, Rhea) Reactions with macromolecules Polymerization reactions

  4. Genes / Proteins Genes / Genomes : EnsemblBacteria Polypeptides : UniProt Proteins : There is no reference resources for protein complexes Protein complexes (EcoCyc / MetaCyc) Gene associations (public metabolic networks)

  5. Microme species http://www.ebi.ac.uk/seqdb/confluence/display/Microme/Accession+list

  6. Pathways In its first release, Microme will focuse on EcoCyc / MetaCyc pathways  Microme/Reactome pathways

  7. Metabolic networks E.coli iAF1260 B.subtilis iBsu1103 A.baylyiiBaylyi P.aeruginosa iMO1056 paonew (WP3) P.putidappunew (WP3)

  8. iAF1260 metabolic network E.coli 1’359 biochemical reactions

  9. TOBIN compounds / reactions mapped to KEGG Ppunew100629 metabolic network Pseudomonas putida KT2440 TOBIN compounds / KEGG compounds / ChEBI compounds

  10. Reaction mapping from Ppunew100629 network: TOBIN / KEGG / Rhea 651 TOBIN reactions mapped to KEGG among them : 492 reactions are cross-referenced in Rhea full mapping : under progress  Microme DB TOBIN / KEGG / Rhea / MetaCyc MaGE DB Ppunew100629 metabolic network Pseudomonas putida KT2440

  11. Pseudomonas putida KT2440MaGE - PathoLogic 1’299 (gene,reaction) pairs 1’119 distinct reactions (MetaCyc) 632 / 1’119 reactions are cross-referenced in Rhea 647 Rhea reactions [NAD(P)] 487 MetaCyc reactions not mapped

  12. Pseudomonas putida KT2440TOBIN – MaGEUniProt proteome: 5’313 entries(pseudogenes – new predictions) 694 genes with links toMaGe& TOBIN 265 genes with links to TOBIN but not Mage 540 genes with links to MaGE but not TOBIN

  13. Microme databases 3 Microme/Reactomedbs: microme_prerelease_eco_meta_cyc_14_5_iaf1260 EcoCyc+ MetaCyc + curated data (met. networks) microme_prerelease_eco_meta_cyc_14_5   EcoCyc+ MetCyc microme_prerelease_ecocyc_14_5_jamboree EcoCycplus initial projections

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