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Microme data

The Microme databases provide extensive resources on various metabolic networks, highlighting compounds, reactions, and pathways relevant to microbial systems. The databases feature detailed mappings of biochemical reactions associated with Escherichia coli and Pseudomonas putida, integrating data from sources such as ChEBI, Rhea, EcoCyc, and MetaCyc. Highlighting 1,359 biochemical reactions and an array of 3,667 chemical entities, Microme emphasizes cross-referenced reactions and comprehensive gene associations essential for metabolic studies and research in microbial genomics.

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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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