<?xml version="1.0" encoding="utf-8"?>
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  <notes>
    <stats ortholog_groups="528" inparalogs="1994"/>
    <parameters scoreCutoff="40" confidenceCutoff="0.05" overlapCutoff="0.5" mergingCutoff="0.5" matrix="BLOSUM62"/>
  </notes>
  <species name="Caenorhabditis brenneri " NCBITaxId="135651">
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        <gene id="1960" protId="G0PI47" geneId="CAEBREN_07846"/>
        <gene id="1961" protId="G0N116" geneId="Cbn-gst-38"/>
        <gene id="1962" protId="G0MPX8" geneId="CAEBREN_13946"/>
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        <gene id="1968" protId="G0PML5" geneId="CAEBREN_30082"/>
        <gene id="1969" protId="G0NHR4" geneId="CAEBREN_25113"/>
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        <gene id="1971" protId="G0PJB6" geneId="CAEBREN_13249"/>
        <gene id="1972" protId="G0P5T3" geneId="CAEBREN_24163"/>
        <gene id="1973" protId="G0NB07" geneId="Cbn-gst-1"/>
        <gene id="1974" protId="G0PML4" geneId="CAEBREN_30539"/>
        <gene id="1979" protId="G0MK79" geneId="CAEBREN_05677"/>
        <gene id="1981" protId="G0MPM9" geneId="CAEBREN_04854"/>
        <gene id="1983" protId="G0M8Q7" geneId="Cbn-bus-8"/>
        <gene id="1984" protId="G0NAY8" geneId="CAEBREN_13902"/>
        <gene id="1985" protId="G0PDG2" geneId="CAEBREN_25681"/>
        <gene id="1987" protId="G0MT13" geneId="Cbn-kin-2"/>
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    <notes>
      <additionalInformation abbreviation="C.brenneri" link="http://www.uniprot.org/taxonomy/135651"/>
    </notes>
  </species>
  <species name="Pseudomonas aeruginosa " NCBITaxId="208964">
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        <gene id="1874" protId="Q9I4P0" geneId="PA1089"/>
        <gene id="1876" protId="Q9I6B3" geneId="trmB"/>
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        <gene id="1922" protId="Q9HXE3" geneId="dauA"/>
        <gene id="1924" protId="Q9I0H2" geneId="PA2666"/>
        <gene id="1926" protId="Q9HWF7" geneId="rpsM"/>
        <gene id="1929" protId="P08280" geneId="recA"/>
        <gene id="1932" protId="Q9I2J7" geneId="PA1907"/>
        <gene id="1934" protId="Q9HX22" geneId="rsfS"/>
        <gene id="1936" protId="Q9HXJ1" geneId="hscB"/>
        <gene id="1975" protId="Q9I030" geneId="PA2813"/>
        <gene id="1976" protId="Q9I2K7" geneId="PA1890"/>
        <gene id="1977" protId="Q9I370" geneId="PA1655"/>
        <gene id="1978" protId="Q9HZH3" geneId="PA3035"/>
        <gene id="1980" protId="Q9HXJ2" geneId="pilF"/>
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        <gene id="1986" protId="Q9HUG1" geneId="PA5004"/>
        <gene id="1988" protId="Q9HV93" geneId="cbpA"/>
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        <gene id="1994" protId="Q9HWE9" geneId="rpsH"/>
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    </database>
    <notes>
      <additionalInformation abbreviation="P.aeruginosa" link="http://www.uniprot.org/taxonomy/208964"/>
    </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="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="2">
        <score id="inparalog" value="0.127"/>
      </geneRef>
      <geneRef id="3">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="2">
      <score id="bit" value="1029"/>
      <geneRef id="4">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="5">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="6">
        <score id="inparalog" value="0.157"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="3">
      <score id="bit" value="1028"/>
      <geneRef id="7">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="8">
        <score id="inparalog" value="0.897"/>
      </geneRef>
      <geneRef id="9">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="4">
      <score id="bit" value="911"/>
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