<?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="310" inparalogs="910"/>
    <parameters scoreCutoff="40" confidenceCutoff="0.05" overlapCutoff="0.5" mergingCutoff="0.5" matrix="BLOSUM62"/>
  </notes>
  <species name="Bos taurus " NCBITaxId="9913">
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        <gene id="905" protId="F1MKG1" geneId="uncharacterized_F1MKG1"/>
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    <notes>
      <additionalInformation abbreviation="B.taurus" link="http://www.uniprot.org/taxonomy/9913"/>
    </notes>
  </species>
  <species name="Thermotoga maritima " NCBITaxId="243274">
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        <gene id="214" protId="Q9X2I8" geneId="gltX2"/>
        <gene id="216" protId="Q9WYC9" geneId="proA"/>
        <gene id="218" protId="Q9X199" geneId="serS"/>
        <gene id="220" protId="Q9X0U3" geneId="TM_1216"/>
        <gene id="222" protId="Q9X0Z7" geneId="TM_1270"/>
        <gene id="227" protId="P16115" geneId="ldh"/>
        <gene id="229" protId="P56838" geneId="galK"/>
        <gene id="231" protId="Q9WZF9" geneId="clpP"/>
        <gene id="233" protId="Q9WZU7" geneId="TM_0843"/>
        <gene id="235" protId="Q9WYA4" geneId="mnmE"/>
        <gene id="238" protId="Q9WZM7" geneId="TM_0769"/>
        <gene id="240" protId="Q9X100" geneId="gatB"/>
        <gene id="242" protId="Q9WYJ1" geneId="TM_0356"/>
        <gene id="244" protId="Q9X1S1" geneId="TM_1585"/>
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        <gene id="248" protId="Q9WZD3" geneId="TM_0665"/>
        <gene id="250" protId="Q9WZV3" geneId="dnaJ"/>
        <gene id="252" protId="Q9X1C0" geneId="TM_1400"/>
        <gene id="254" protId="Q9X248" geneId="fabG"/>
        <gene id="260" protId="Q9X2I6" geneId="TM_1873"/>
        <gene id="262" protId="Q9WZX6" geneId="rsmH"/>
        <gene id="264" protId="Q9WZ18" geneId="TM_0548"/>
        <gene id="268" protId="Q9WZI1" geneId="rnr"/>
        <gene id="286" protId="Q9X0A2" geneId="TM_1009"/>
        <gene id="288" protId="Q9X260" geneId="TM_1738"/>
        <gene id="291" protId="Q9WY44" geneId="TM_0201"/>
        <gene id="292" protId="G4FFG1" geneId="TM_1426"/>
        <gene id="295" protId="Q9X1T9" geneId="TM_1603"/>
        <gene id="297" protId="Q9WZC2" geneId="speE"/>
        <gene id="300" protId="Q9X1S9" geneId="TM_1593"/>
        <gene id="302" protId="Q9WZ24" geneId="leuC2"/>
        <gene id="303" protId="Q9WYC7" geneId="leuC1"/>
        <gene id="305" protId="Q9WY54" geneId="gcvT"/>
        <gene id="307" protId="Q9S5Y2" geneId="TM_1840"/>
        <gene id="309" protId="Q9WYW2" geneId="trpS"/>
        <gene id="312" protId="Q9X1I7" geneId="TM_1478"/>
        <gene id="314" protId="Q9WXZ2" geneId="gcp"/>
        <gene id="316" protId="Q9WYG0" geneId="TM_0325"/>
        <gene id="321" protId="Q9WZ41" geneId="TM_0571"/>
        <gene id="326" protId="Q9WYE4" geneId="TM_0308"/>
        <gene id="328" protId="O33836" geneId="galT"/>
        <gene id="329" protId="Q9WZZ8" geneId="TM_0896"/>
        <gene id="331" protId="Q9X1I8" geneId="adk"/>
        <gene id="333" protId="Q9X0X6" geneId="purH"/>
        <gene id="335" protId="Q9WZX0" geneId="TM_0866"/>
        <gene id="349" protId="Q9X051" geneId="rbsA2"/>
        <gene id="350" protId="Q9WXX0" geneId="rbsA1"/>
        <gene id="351" protId="Q9WXV8" geneId="TM_0103"/>
        <gene id="353" protId="Q9WZS1" geneId="TM_0814"/>
        <gene id="355" protId="G4FH33" geneId="TM_0118"/>
        <gene id="357" protId="Q9WYZ0" geneId="mnmA"/>
        <gene id="359" protId="Q9X2J1" geneId="TM_1878"/>
        <gene id="361" protId="P38510" geneId="rplB"/>
        <gene id="367" protId="Q9WY03" geneId="TM_0156"/>
        <gene id="371" protId="Q9WZ26" geneId="leuB"/>
        <gene id="374" protId="Q9X288" geneId="folD"/>
        <gene id="376" protId="Q9WYS2" geneId="TM_0441"/>
        <gene id="377" protId="Q9WYD3" geneId="TM_0297"/>
        <gene id="379" protId="Q9WYT7" geneId="TM_0466"/>
        <gene id="381" protId="Q9WYX9" geneId="TM_0509"/>
        <gene id="383" protId="Q9X0L5" geneId="TM_1131"/>
        <gene id="388" protId="Q9X1E3" geneId="glpF"/>
        <gene id="390" protId="Q9X1B8" geneId="uppS"/>
        <gene id="392" protId="Q9X0P9" geneId="TM_1166"/>
        <gene id="394" protId="Q9WXW6" geneId="TM_0111"/>
        <gene id="395" protId="Q9WZS7" geneId="TM_0820"/>
        <gene id="397" protId="Q9X1L7" geneId="TM_1531"/>
        <gene id="399" protId="Q9WYU8" geneId="tyrS"/>
        <gene id="401" protId="Q9X1N3" geneId="TM_1547"/>
        <gene id="403" protId="Q9WY13" geneId="TM_0166"/>
        <gene id="406" protId="Q9X0Y2" geneId="aspC"/>
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        <gene id="412" protId="Q9WZS8" geneId="pheS"/>
        <gene id="414" protId="Q9X1X8" geneId="TM_1645"/>
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        <gene id="420" protId="Q9WZ08" geneId="TM_0538"/>
        <gene id="422" protId="Q9WZV2" geneId="TM_0848"/>
        <gene id="432" protId="Q9X079" geneId="TM_0984"/>
        <gene id="435" protId="Q9WYW0" geneId="cobB"/>
        <gene id="437" protId="Q9WZR4" geneId="TM_0807"/>
        <gene id="439" protId="Q9X055" geneId="TM_0960"/>
        <gene id="441" protId="Q9WYK0" geneId="nth"/>
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        <gene id="450" protId="Q9WYM6" geneId="TM_0395"/>
        <gene id="451" protId="Q9WYL1" geneId="TM_0379"/>
        <gene id="453" protId="P46799" geneId="topA"/>
        <gene id="454" protId="O51934" geneId="rgy"/>
        <gene id="456" protId="P38516" geneId="rplD"/>
        <gene id="458" protId="Q9X1A4" geneId="apt"/>
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        <gene id="464" protId="Q9WZQ5" geneId="TM_0798"/>
        <gene id="466" protId="Q9X1L4" geneId="TM_1528"/>
        <gene id="468" protId="Q9X215" geneId="gmk"/>
        <gene id="471" protId="O33832" geneId="suhB"/>
        <gene id="473" protId="Q9WZV0" geneId="TM_0846"/>
        <gene id="475" protId="P36205" geneId="glnA"/>
        <gene id="478" protId="Q9WXP9" geneId="TM_0042"/>
        <gene id="481" protId="Q9X0H5" geneId="hisS"/>
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        <gene id="490" protId="Q9WZI9" geneId="dtd"/>
        <gene id="492" protId="Q9X1X1" geneId="rad50"/>
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        <gene id="499" protId="Q9X264" geneId="TM_1742"/>
        <gene id="501" protId="P74925" geneId="mutL"/>
        <gene id="503" protId="Q9S5X7" geneId="TM_1424"/>
        <gene id="504" protId="Q9WXM7" geneId="TM_0012"/>
        <gene id="510" protId="Q9WYR7" geneId="TM_0436"/>
        <gene id="513" protId="Q9X0H8" geneId="argS"/>
        <gene id="515" protId="Q9X0U1" geneId="TM_1214"/>
        <gene id="517" protId="Q9X1J3" geneId="rpsL"/>
        <gene id="519" protId="P38526" geneId="rpsG"/>
        <gene id="521" protId="Q9WY58" geneId="TM_0215"/>
        <gene id="523" protId="Q9X249" geneId="TM_1726"/>
        <gene id="525" protId="Q9WZK7" geneId="TM_0748"/>
        <gene id="527" protId="Q9WYC6" geneId="TM_0290"/>
        <gene id="534" protId="Q9WZS6" geneId="TM_0819"/>
        <gene id="536" protId="P38515" geneId="rplC"/>
        <gene id="540" protId="Q9X167" geneId="TM_1346"/>
        <gene id="542" protId="P29395" geneId="rplK"/>
        <gene id="547" protId="Q9WZU9" geneId="TM_0845"/>
        <gene id="549" protId="Q9WZD5" geneId="TM_0667"/>
        <gene id="554" protId="Q9WY49" geneId="TM_0206"/>
        <gene id="556" protId="Q9WZV1" geneId="era"/>
        <gene id="558" protId="Q9WZL2" geneId="ubiE"/>
        <gene id="560" protId="Q9X243" geneId="TM_1718"/>
        <gene id="562" protId="Q9X1U6" geneId="atpG"/>
        <gene id="564" protId="Q9WYT3" geneId="TM_0462"/>
        <gene id="565" protId="Q9X038" geneId="TM_0940"/>
        <gene id="567" protId="Q9WXX4" geneId="TM_0120"/>
        <gene id="569" protId="Q9X1L8" geneId="TM_1532"/>
        <gene id="571" protId="Q9X1H7" geneId="engB"/>
        <gene id="573" protId="Q9X0Y0" geneId="nadE2"/>
        <gene id="575" protId="Q9X1K9" geneId="dapA"/>
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        <gene id="580" protId="Q9X0T9" geneId="TM_1212"/>
        <gene id="582" protId="Q9X1R0" geneId="truA"/>
        <gene id="584" protId="Q9WYP3" geneId="TM_0412"/>
        <gene id="586" protId="Q9X1G5" geneId="rplM"/>
        <gene id="588" protId="Q9X253" geneId="TM_1731"/>
        <gene id="590" protId="Q9WZ52" geneId="TM_0583"/>
        <gene id="592" protId="Q9X0Y1" geneId="TM_1254"/>
        <gene id="594" protId="Q9WYN2" geneId="tdk"/>
        <gene id="596" protId="Q9X1I4" geneId="rpsK"/>
        <gene id="600" protId="Q9WZF2" geneId="TM_0686"/>
        <gene id="603" protId="Q9WZS2" geneId="norM"/>
        <gene id="606" protId="Q9WY40" geneId="TM_0197"/>
        <gene id="608" protId="Q9WYV8" geneId="prmC"/>
        <gene id="610" protId="Q9WZM1" geneId="rpsB"/>
        <gene id="612" protId="Q9WZM6" geneId="rbgA"/>
        <gene id="614" protId="Q9X034" geneId="mtaD"/>
        <gene id="616" protId="Q9X1B3" geneId="ispD"/>
        <gene id="618" protId="Q9X024" geneId="nnr"/>
        <gene id="620" protId="Q9WYZ8" geneId="fmt"/>
        <gene id="622" protId="Q9WZV6" geneId="TM_0852"/>
        <gene id="626" protId="Q9WZ12" geneId="TM_0542"/>
        <gene id="628" protId="Q9X1B9" geneId="frr"/>
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        <gene id="649" protId="Q9X0L2" geneId="TM_1128"/>
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        <gene id="661" protId="Q9WZK3" geneId="TM_0744"/>
        <gene id="662" protId="Q9WZ90" geneId="TM_0622"/>
        <gene id="664" protId="Q9X1W1" geneId="pth"/>
        <gene id="666" protId="Q9WYD1" geneId="tal"/>
        <gene id="670" protId="G4FEX7" geneId="TM_1021"/>
        <gene id="672" protId="Q9WXV1" geneId="TM_0096"/>
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        <gene id="680" protId="Q9X0U0" geneId="TM_1213"/>
        <gene id="683" protId="Q9WZI0" geneId="upp"/>
        <gene id="686" protId="Q9X219" geneId="TM_1693"/>
        <gene id="688" protId="Q9X263" geneId="TM_1741"/>
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        <gene id="693" protId="Q9WY28" geneId="glmM"/>
        <gene id="695" protId="Q9WY06" geneId="TM_0159"/>
        <gene id="699" protId="Q9WZV4" geneId="grpE"/>
        <gene id="702" protId="Q56313" geneId="ruvB"/>
        <gene id="704" protId="Q9X2H9" geneId="nfi"/>
        <gene id="706" protId="P96113" geneId="def"/>
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        <gene id="710" protId="Q9WYX5" geneId="groS"/>
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        <gene id="752" protId="Q9WYG8" geneId="pyrD"/>
        <gene id="754" protId="Q9X0R3" geneId="TM_1181"/>
        <gene id="757" protId="P38508" geneId="rplN"/>
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        <gene id="767" protId="Q9WYF4" geneId="TM_0318"/>
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        <gene id="826" protId="Q9WY65" geneId="ecfA2"/>
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        <gene id="829" protId="Q9WXS9" geneId="TM_0074"/>
        <gene id="830" protId="Q9WY34" geneId="TM_0191"/>
        <gene id="831" protId="Q9X0M3" geneId="TM_1139"/>
        <gene id="832" protId="Q9WYD9" geneId="TM_0303"/>
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        <gene id="834" protId="Q9X150" geneId="TM_1327"/>
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        <gene id="836" protId="Q9WXN5" geneId="TM_0028"/>
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        <gene id="838" protId="Q9X0U7" geneId="TM_1220"/>
        <gene id="839" protId="Q9WYX0" geneId="TM_0500"/>
        <gene id="840" protId="Q9WXT3" geneId="TM_0078"/>
        <gene id="842" protId="P29393" geneId="rplA"/>
        <gene id="844" protId="Q9X0P5" geneId="TM_1162"/>
        <gene id="846" protId="P38518" geneId="rpsJ"/>
        <gene id="851" protId="P36203" geneId="recA"/>
        <gene id="853" protId="Q9X1X6" geneId="nadX"/>
        <gene id="855" protId="Q9X036" geneId="TM_0938"/>
        <gene id="857" protId="Q9X1J7" geneId="ybeY"/>
        <gene id="859" protId="Q9WZX9" geneId="TM_0876"/>
        <gene id="861" protId="Q9WYJ8" geneId="TM_0363"/>
        <gene id="863" protId="Q9WYB9" geneId="TM_0283"/>
        <gene id="866" protId="Q9X1Q0" geneId="acyP"/>
        <gene id="868" protId="Q9X1A9" geneId="TM_1389"/>
        <gene id="878" protId="P38511" geneId="rplV"/>
        <gene id="881" protId="P38519" geneId="rpsQ"/>
        <gene id="883" protId="Q9WZW8" geneId="TM_0864"/>
        <gene id="885" protId="Q9X192" geneId="nifU"/>
        <gene id="888" protId="Q9X1I1" geneId="rplQ"/>
        <gene id="890" protId="Q9X1Q2" geneId="rpsP"/>
        <gene id="892" protId="Q9X0G5" geneId="TM_1076"/>
        <gene id="894" protId="Q9X017" geneId="rnhB"/>
        <gene id="896" protId="Q9X107" geneId="TM_1280"/>
        <gene id="898" protId="Q9X027" geneId="trmB"/>
        <gene id="900" protId="Q9WZ73" geneId="ssb"/>
        <gene id="908" protId="Q9X0C1" geneId="TM_1031"/>
        <gene id="910" protId="Q9X1K4" geneId="TM_1516"/>
      </genes>
    </database>
    <notes>
      <additionalInformation abbreviation="T.maritima" link="http://www.uniprot.org/taxonomy/243274"/>
    </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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      <geneRef id="1">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="2">
        <score id="inparalog" value="0.298"/>
      </geneRef>
      <geneRef id="3">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="2">
      <score id="bit" value="635"/>
      <geneRef id="4">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="5">
        <score id="inparalog" value="0.261"/>
      </geneRef>
      <geneRef id="6">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="3">
      <score id="bit" value="631"/>
      <geneRef id="7">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="8">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="4">
      <score id="bit" value="617"/>
      <geneRef id="9">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="10">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="5">
      <score id="bit" value="602"/>
      <geneRef id="11">
        <score id="inparalog" value="1"/>
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