<?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="131" inparalogs="294"/>
    <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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        <gene id="13" protId="O84591" geneId="eno"/>
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        <gene id="17" protId="P0CE09" geneId="rpoB"/>
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        <gene id="23" protId="O84834" geneId="nrdA"/>
        <gene id="25" protId="P0CE13" geneId="gap"/>
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        <gene id="41" protId="O84373" geneId="aroC"/>
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        <gene id="141" protId="O84599" geneId="ycfH"/>
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        <gene id="172" protId="O84139" geneId="ywlC"/>
        <gene id="174" protId="O84690" geneId="CT_684"/>
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        <gene id="204" protId="O84284" geneId="gcvH"/>
        <gene id="206" protId="O84094" geneId="ychF"/>
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        <gene id="212" protId="O84778" geneId="ldh"/>
        <gene id="214" protId="O84073" geneId="CT_070"/>
        <gene id="216" protId="O84375" geneId="aroE"/>
        <gene id="218" protId="P0CE02" geneId="rpsJ"/>
        <gene id="220" protId="P0CD81" geneId="rplN"/>
        <gene id="222" protId="O84320" geneId="rplA"/>
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        <gene id="228" protId="P28539" geneId="secY"/>
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        <gene id="232" protId="O84860" geneId="CT_852"/>
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        <gene id="236" protId="O84379" geneId="aaxC"/>
        <gene id="242" protId="O84366" geneId="dapA"/>
        <gene id="245" protId="O84557" geneId="fmu"/>
        <gene id="247" protId="O84685" geneId="pyrH"/>
        <gene id="249" protId="P0CE01" geneId="rplF"/>
        <gene id="251" protId="P66480" geneId="rpsS"/>
        <gene id="253" protId="P0CD80" geneId="recA"/>
        <gene id="256" protId="O84191" geneId="tmk"/>
        <gene id="258" protId="O84393" geneId="CT_388"/>
        <gene id="260" protId="P0CE05" geneId="rpsQ"/>
        <gene id="262" protId="O84160" geneId="CT_158"/>
        <gene id="263" protId="O84159" geneId="CT_157"/>
        <gene id="264" protId="O84156" geneId="CT_154"/>
        <gene id="265" protId="O84086" geneId="CT_084"/>
        <gene id="266" protId="O84157" geneId="CT_155"/>
        <gene id="268" protId="O84863" geneId="fumC"/>
        <gene id="270" protId="P66370" geneId="rpsL"/>
        <gene id="272" protId="O84219" geneId="ydaO"/>
        <gene id="275" protId="O84435" geneId="ubiE"/>
        <gene id="277" protId="O84217" geneId="fbaB"/>
        <gene id="279" protId="O84011" geneId="rnhC"/>
        <gene id="281" protId="O84044" geneId="ruvB"/>
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        <gene id="285" protId="O84469" geneId="truA"/>
        <gene id="287" protId="O84756" geneId="amn"/>
        <gene id="289" protId="O84127" geneId="rplM"/>
        <gene id="291" protId="O84743" geneId="yycJ"/>
        <gene id="293" protId="P0CE07" geneId="rpsH"/>
      </genes>
    </database>
    <notes>
      <additionalInformation abbreviation="C.trachomatis" link="http://www.uniprot.org/taxonomy/272561"/>
    </notes>
  </species>
  <species name="Korarchaeum cryptofilum " NCBITaxId="374847">
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        <gene id="6" protId="B1L630" geneId="Kcr_1163"/>
        <gene id="8" protId="B1L4A4" geneId="Kcr_0530"/>
        <gene id="10" protId="B1L6G7" geneId="atpA"/>
        <gene id="12" protId="B1L733" geneId="glmS"/>
        <gene id="14" protId="B1L7C2" geneId="eno"/>
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        <gene id="18" protId="B1L740" geneId="Kcr_1523"/>
        <gene id="20" protId="B1L5G4" geneId="cysS"/>
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        <gene id="159" protId="B1L638" geneId="Kcr_1171"/>
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        <gene id="252" protId="B1L708" geneId="rps19"/>
        <gene id="254" protId="B1L679" geneId="radA"/>
        <gene id="255" protId="B1L6V3" geneId="Kcr_1436"/>
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        <gene id="261" protId="B1L652" geneId="rps17p"/>
        <gene id="267" protId="B1L3J9" geneId="Kcr_0268"/>
        <gene id="269" protId="B1L394" geneId="argH"/>
        <gene id="271" protId="B1L736" geneId="rps12"/>
        <gene id="273" protId="B1L682" geneId="Kcr_1215"/>
        <gene id="274" protId="B1L3E1" geneId="Kcr_0210"/>
        <gene id="276" protId="B1L512" geneId="Kcr_0794"/>
        <gene id="278" protId="B1L3I0" geneId="Kcr_0249"/>
        <gene id="280" protId="B1L614" geneId="Kcr_1147"/>
        <gene id="282" protId="B1L6Y9" geneId="Kcr_1472"/>
        <gene id="284" protId="B1L779" geneId="rpl5p"/>
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        <gene id="288" protId="B1L3L3" geneId="Kcr_0284"/>
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        <gene id="292" protId="B1L7H5" geneId="Kcr_0042"/>
        <gene id="294" protId="B1L781" geneId="rps8"/>
      </genes>
    </database>
    <notes>
      <additionalInformation abbreviation="K.cryptofilum" link="http://www.uniprot.org/taxonomy/374847"/>
    </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>
    <orthologGroup id="1">
      <score id="bit" value="599"/>
      <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="475"/>
      <geneRef id="3">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="4">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="3">
      <score id="bit" value="416"/>
      <geneRef id="5">
        <score id="inparalog" value="1"/>
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