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    <stats ortholog_groups="205" inparalogs="591"/>
    <parameters scoreCutoff="40" confidenceCutoff="0.05" overlapCutoff="0.5" mergingCutoff="0.5" matrix="BLOSUM62"/>
  </notes>
  <species name="Chlamydia trachomatis " NCBITaxId="272561">
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    <notes>
      <additionalInformation abbreviation="C.trachomatis" link="http://www.uniprot.org/taxonomy/272561"/>
    </notes>
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    </database>
    <notes>
      <additionalInformation abbreviation="L.africana" link="http://www.uniprot.org/taxonomy/9785"/>
    </notes>
  </species>
  <scores>
    <scoreDef id="bit" desc="BLAST score in bits of seed orthologs"/>
    <scoreDef id="inparalog" desc="Inparalog similarity relative to seed ortholog similarity"/>
    <scoreDef id="bootstrap" desc="Reliability of seed orthologs"/>
  </scores>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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    </orthologGroup>
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      <score id="bit" value="854"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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      <geneRef id="4">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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      <geneRef id="5">
        <score id="inparalog" value="0.659"/>
      </geneRef>
      <geneRef id="6">
        <score id="inparalog" value="0.227"/>
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    </orthologGroup>
    <orthologGroup id="3">
      <score id="bit" value="712"/>
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        <score id="bootstrap" value="1"/>
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      <geneRef id="8">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.99"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="4">
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      <geneRef id="9">
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        <score id="bootstrap" value="1"/>
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      <geneRef id="10">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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    </orthologGroup>
    <orthologGroup id="5">
      <score id="bit" value="623"/>
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        <score id="bootstrap" value="1"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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        <score id="inparalog" value="0.435"/>
      </geneRef>
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