Menu ▾ ▴

Compound kegg annotation issues and some notes

General Discussion
mabawsa
2016-05-11
2016-05-21

  • mabawsa

    mabawsa - 2016-05-11

    Some things I found while looking at version 7.6 of the model

    Missing
    I cannot see L-glutamine in the mitochondria. Is this correct. There are a number of sources that suggest otherwise.
    e.g: http://www.ymdb.ca/proteins/P33893
    No mitochondrial H2S, is this correct, it is a volatile and reacts with electron transport
    Always thought that D-glucose-6-phosphate was a combination between beta-D-glucose-6-phosphate and alpha-D-glucose-6-phosphate then YBR196C converts between the alpha and beta (and fructose-6-P)

    KEGG Annotation (chebi not checked)
    1-pyrroline-5-carboxylate C04322 > C03912
    glyceraldehyde-3-phosphate C00661 > C00118
    Ornathine C01602 > C00077
    Ammonium C01342 > C00014

    Yours

    Dougie

     

  • mabawsa

    mabawsa - 2016-05-21

    Additionally this is incorrect:
    <species metaid="meta_s_0765" sboTerm="SBO:0000247" id="s_0765" name="glycerol &lt;span&gt;[cytoplasm]&lt;/span&gt;" compartment="c_03" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
    <notes>
    <body xmlns="http://www.w3.org/1999/xhtml">

    FORMULA:C3H8O3


    CHARGE:0


    CARBONS:3


    </body>
    </notes>
    <annotation>
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
    <rdf:Description rdf:about="#meta_s_0765">
    <bqbiol:is>
    <rdf:Bag>
    <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:17754"/>
    <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00118"/>
    </rdf:Bag>
    </bqbiol:is>
    </rdf:Description>
    </rdf:RDF>
    </annotation>
    </species>

    should be:
              <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:17754"/>
              <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00116"/>
     

Log in to post a comment.