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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

Microme data

  • Compounds
  • Reactions
  • Pathways
  • Genes / Genomes
  • Polypeptides / Proteins
  • Metabolic networks
compounds reactions

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

compounds reactions issues

Compounds / Reactions issues

Done:

Rhea – UniProt xrefs available (rel 23)

(Still) under development

Bulk submission tools (ChEBI, Rhea)

Reactions with macromolecules

Polymerization reactions

genes proteins

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)

slide5

Microme species

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

pathways

Pathways

In its first release, Microme will focuse on EcoCyc / MetaCyc pathways

 Microme/Reactome pathways

metabolic networks

Metabolic networks

E.coli iAF1260

B.subtilis iBsu1103

A.baylyiiBaylyi

P.aeruginosa iMO1056 paonew (WP3)

P.putidappunew (WP3)

iaf1260 metabolic network e coli

iAF1260 metabolic network E.coli

1’359 biochemical reactions

ppunew100629 metabolic network pseudomonas putida kt24401

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

pseudomonas putida kt2440 mage pathologic

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

pseudomonas putida kt2440 tobin mage uniprot proteome 5 313 entries pseudogenes new predictions

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

microme databases
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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