<?xml version="1.0" encoding="utf-8"?>
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  <notes>
    <stats ortholog_groups="327" inparalogs="834"/>
    <parameters scoreCutoff="40" confidenceCutoff="0.05" overlapCutoff="0.5" mergingCutoff="0.5" matrix="BLOSUM62"/>
  </notes>
  <species name="Schizophyllum commune " NCBITaxId="578458">
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    <notes>
      <additionalInformation abbreviation="S.commune" link="http://www.uniprot.org/taxonomy/578458"/>
    </notes>
  </species>
  <species name="Thermodesulfovibrio yellowstonii " NCBITaxId="289376">
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        <gene id="715" protId="B5YIB4" geneId="hisA"/>
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        <gene id="730" protId="B5YIS2" geneId="THEYE_A2007"/>
        <gene id="739" protId="B5YHY0" geneId="THEYE_A0196"/>
        <gene id="741" protId="B5YG18" geneId="pheT"/>
        <gene id="744" protId="B5YJG1" geneId="recA"/>
        <gene id="746" protId="B5YJL0" geneId="rimI"/>
        <gene id="771" protId="B5YJX3" geneId="recG"/>
        <gene id="786" protId="B5YGK5" geneId="THEYE_A1608"/>
        <gene id="788" protId="B5YJN4" geneId="groS"/>
        <gene id="790" protId="B5YKC7" geneId="THEYE_A0853"/>
        <gene id="796" protId="B5YHQ6" geneId="THEYE_A1852"/>
        <gene id="797" protId="B5YJH0" geneId="pyrK"/>
        <gene id="800" protId="B5YJH6" geneId="THEYE_A0548"/>
        <gene id="803" protId="B5YHY2" geneId="THEYE_A0198"/>
        <gene id="805" protId="B5YK94" geneId="rpsP"/>
        <gene id="807" protId="B5YGD9" geneId="rpsB"/>
        <gene id="809" protId="B5YI02" geneId="THEYE_A0219"/>
        <gene id="811" protId="B5YHC8" geneId="lepB"/>
        <gene id="813" protId="B5YHB2" geneId="THEYE_A0082"/>
        <gene id="819" protId="B5YKZ7" geneId="cas3_1"/>
        <gene id="820" protId="B5YIV2" geneId="cas3_2"/>
        <gene id="823" protId="B5YHI4" geneId="aroB"/>
        <gene id="825" protId="B5YL76" geneId="THEYE_A1168"/>
        <gene id="827" protId="B5YHG2" geneId="THEYE_A0133"/>
        <gene id="829" protId="B5YK67" geneId="nadD"/>
        <gene id="832" protId="B5YL16" geneId="THEYE_A1107"/>
        <gene id="834" protId="B5YJG8" geneId="acpS"/>
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    </database>
    <notes>
      <additionalInformation abbreviation="T.yellowstonii" link="http://www.uniprot.org/taxonomy/289376"/>
    </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>
  <groups>
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      <geneRef id="1">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="2">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="2">
      <score id="bit" value="763"/>
      <geneRef id="3">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.78"/>
      </geneRef>
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