<?xml version="1.0" encoding="utf-8"?>
<orthoXML xmlns="http://orthoXML.org/2011/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="0.3" origin="InParanoid" originVersion="8.0" xsi:schemaLocation="http://orthoXML.org/2011/ http://www.orthoxml.org/0.3/orthoxml.xsd">
  <notes>
    <stats ortholog_groups="333" inparalogs="1172"/>
    <parameters scoreCutoff="40" confidenceCutoff="0.05" overlapCutoff="0.5" mergingCutoff="0.5" matrix="BLOSUM62"/>
  </notes>
  <species name="Rattus norvegicus " NCBITaxId="10116">
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        <gene id="4" protId="D4A8A0" geneId="Cad"/>
        <gene id="6" protId="P48721" geneId="Hspa9"/>
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        <gene id="10" protId="P10719" geneId="Atp5b"/>
        <gene id="12" protId="D3ZHF8" geneId="Guf1"/>
        <gene id="14" protId="Q04462" geneId="Vars"/>
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        <gene id="17" protId="P15999" geneId="Atp5a1"/>
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        <gene id="20" protId="Q3MIB4" geneId="Lonp2"/>
        <gene id="22" protId="P63039" geneId="Hspd1"/>
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        <gene id="24" protId="M0RBL5" geneId="uncharacterized_M0RBL5"/>
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        <gene id="27" protId="P50137" geneId="Tkt"/>
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        <gene id="29" protId="M0RB43" geneId="uncharacterized_M0RB43"/>
        <gene id="31" protId="Q64566" geneId="Atp2c1"/>
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        <gene id="73" protId="Q5XI17" geneId="Tarsl2"/>
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        <gene id="85" protId="P82808" geneId="Gfpt1"/>
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        <gene id="163" protId="P14408" geneId="Fh"/>
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        <gene id="167" protId="P52873" geneId="Pc"/>
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        <gene id="171" protId="P04797" geneId="Gapdh"/>
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    <notes>
      <additionalInformation abbreviation="R.norvegicus" link="http://www.uniprot.org/taxonomy/10116"/>
    </notes>
  </species>
  <species name="Thermodesulfovibrio yellowstonii " NCBITaxId="289376">
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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>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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        <score id="bootstrap" value="1"/>
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      <geneRef id="4">
        <score id="inparalog" value="0.297"/>
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      <geneRef id="5">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
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    <orthologGroup id="3">
      <score id="bit" value="767"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.99"/>
      </geneRef>
      <geneRef id="7">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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    </orthologGroup>
    <orthologGroup id="4">
      <score id="bit" value="701"/>
      <geneRef id="8">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.92"/>
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      <geneRef id="9">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
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    <orthologGroup id="5">
      <score id="bit" value="642"/>
      <geneRef id="10">
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        <score id="bootstrap" value="1"/>
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      <geneRef id="11">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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    <orthologGroup id="6">
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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