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  <notes>
    <stats ortholog_groups="311" inparalogs="888"/>
    <parameters scoreCutoff="40" confidenceCutoff="0.05" overlapCutoff="0.5" mergingCutoff="0.5" matrix="BLOSUM62"/>
  </notes>
  <species name="Loxodonta africana " NCBITaxId="9785">
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    <notes>
      <additionalInformation abbreviation="L.africana" link="http://www.uniprot.org/taxonomy/9785"/>
    </notes>
  </species>
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        <gene id="221" protId="Q9X199" geneId="serS"/>
        <gene id="223" protId="Q9S5X9" geneId="TM_1653"/>
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        <gene id="231" protId="Q9X013" geneId="mtnA"/>
        <gene id="234" protId="Q9WZM7" geneId="TM_0769"/>
        <gene id="237" protId="Q9WZI1" geneId="rnr"/>
        <gene id="239" protId="Q9WZD3" geneId="TM_0665"/>
        <gene id="241" protId="Q9WYA4" geneId="mnmE"/>
        <gene id="243" protId="Q9WZT7" geneId="mtaB"/>
        <gene id="245" protId="Q9X266" geneId="TM_1744"/>
        <gene id="247" protId="Q9X248" geneId="fabG"/>
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        <gene id="251" protId="Q9WZ18" geneId="TM_0548"/>
        <gene id="253" protId="P56838" geneId="galK"/>
        <gene id="257" protId="Q9X2I6" geneId="TM_1873"/>
        <gene id="261" protId="Q9X2A5" geneId="argD"/>
        <gene id="263" protId="Q9WZC2" geneId="speE"/>
        <gene id="266" protId="Q9X1T9" geneId="TM_1603"/>
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        <gene id="270" protId="G4FFG1" geneId="TM_1426"/>
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        <gene id="274" protId="Q9WYC7" geneId="leuC1"/>
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        <gene id="288" protId="Q9X0A2" geneId="TM_1009"/>
        <gene id="290" protId="Q9WYW2" geneId="trpS"/>
        <gene id="294" protId="Q9WYG0" geneId="TM_0325"/>
        <gene id="296" protId="Q9WY54" geneId="gcvT"/>
        <gene id="298" protId="Q9X1S1" geneId="TM_1585"/>
        <gene id="300" protId="Q9X1S9" geneId="TM_1593"/>
        <gene id="303" protId="Q9X1I7" geneId="TM_1478"/>
        <gene id="305" protId="Q9X1C0" geneId="TM_1400"/>
        <gene id="307" protId="Q9WXZ2" geneId="gcp"/>
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        <gene id="318" protId="Q9WYE4" geneId="TM_0308"/>
        <gene id="320" protId="Q9X1I8" geneId="adk"/>
        <gene id="322" protId="Q9X0L5" geneId="TM_1131"/>
        <gene id="324" protId="G4FH33" geneId="TM_0118"/>
        <gene id="326" protId="Q9WY52" geneId="pfkA"/>
        <gene id="330" protId="Q9WZ26" geneId="leuB"/>
        <gene id="334" protId="Q9WZX0" geneId="TM_0866"/>
        <gene id="336" protId="Q9WZS1" geneId="TM_0814"/>
        <gene id="338" protId="Q9X1B8" geneId="uppS"/>
        <gene id="340" protId="Q9S5Y2" geneId="TM_1840"/>
        <gene id="341" protId="P80099" geneId="mgtA"/>
        <gene id="343" protId="Q9WYX9" geneId="TM_0509"/>
        <gene id="348" protId="Q9X051" geneId="rbsA2"/>
        <gene id="349" protId="Q9WXX0" geneId="rbsA1"/>
        <gene id="352" protId="Q9X288" geneId="folD"/>
        <gene id="355" protId="Q9WY03" geneId="TM_0156"/>
        <gene id="357" protId="Q9WZX6" geneId="rsmH"/>
        <gene id="359" protId="Q9X0P9" geneId="TM_1166"/>
        <gene id="361" protId="Q9X1L7" geneId="TM_1531"/>
        <gene id="374" protId="Q9WXV8" geneId="TM_0103"/>
        <gene id="378" protId="Q9X1E3" geneId="glpF"/>
        <gene id="380" protId="O33836" geneId="galT"/>
        <gene id="381" protId="Q9WZZ8" geneId="TM_0896"/>
        <gene id="383" protId="Q9WYT7" geneId="TM_0466"/>
        <gene id="385" protId="Q9X0I0" geneId="purB"/>
        <gene id="387" protId="Q9WZS8" geneId="pheS"/>
        <gene id="389" protId="Q9WZW0" geneId="truB"/>
        <gene id="391" protId="Q9WYU8" geneId="tyrS"/>
        <gene id="393" protId="P38516" geneId="rplD"/>
        <gene id="396" protId="Q9WYM0" geneId="TM_0389"/>
        <gene id="397" protId="Q9X1C3" geneId="TM_1403"/>
        <gene id="399" protId="Q9WY13" geneId="TM_0166"/>
        <gene id="401" protId="Q9X1X8" geneId="TM_1645"/>
        <gene id="403" protId="Q9X1N3" geneId="TM_1547"/>
        <gene id="405" protId="Q9WYK0" geneId="nth"/>
        <gene id="407" protId="Q9WYZ5" geneId="miaA"/>
        <gene id="409" protId="Q9X1A4" geneId="apt"/>
        <gene id="412" protId="P46799" geneId="topA"/>
        <gene id="413" protId="O51934" geneId="rgy"/>
        <gene id="415" protId="Q9WYM6" geneId="TM_0395"/>
        <gene id="416" protId="Q9WYL1" geneId="TM_0379"/>
        <gene id="418" protId="Q9WY55" geneId="gcvH"/>
        <gene id="420" protId="Q9WZQ5" geneId="TM_0798"/>
        <gene id="425" protId="Q9WZ08" geneId="TM_0538"/>
        <gene id="427" protId="Q9WXW6" geneId="TM_0111"/>
        <gene id="428" protId="Q9WZS7" geneId="TM_0820"/>
        <gene id="429" protId="Q9X022" geneId="TM_0920"/>
        <gene id="432" protId="Q9X0Y2" geneId="aspC"/>
        <gene id="433" protId="Q9X224" geneId="TM_1698"/>
        <gene id="436" protId="Q9X0H5" geneId="hisS"/>
        <gene id="439" protId="Q9WYW0" geneId="cobB"/>
        <gene id="448" protId="Q9X079" geneId="TM_0984"/>
        <gene id="450" protId="Q9WYZ0" geneId="mnmA"/>
        <gene id="452" protId="Q9WZR4" geneId="TM_0807"/>
        <gene id="454" protId="Q9X1L4" geneId="TM_1528"/>
        <gene id="459" protId="Q9WZ47" geneId="TM_0578"/>
        <gene id="462" protId="Q9WXP9" geneId="TM_0042"/>
        <gene id="464" protId="Q9WZV0" geneId="TM_0846"/>
        <gene id="466" protId="Q9X215" geneId="gmk"/>
        <gene id="468" protId="P36205" geneId="glnA"/>
        <gene id="470" protId="Q9X1F1" geneId="rsmA"/>
        <gene id="472" protId="Q9X055" geneId="TM_0960"/>
        <gene id="474" protId="Q9X1E6" geneId="TM_1432"/>
        <gene id="477" protId="O33832" geneId="suhB"/>
        <gene id="479" protId="Q9X264" geneId="TM_1742"/>
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        <gene id="483" protId="P38510" geneId="rplB"/>
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        <gene id="489" protId="Q9X1L6" geneId="TM_1530"/>
        <gene id="496" protId="Q9WYR7" geneId="TM_0436"/>
        <gene id="499" protId="Q9X0H8" geneId="argS"/>
        <gene id="501" protId="Q9S5X7" geneId="TM_1424"/>
        <gene id="502" protId="Q9WXM7" geneId="TM_0012"/>
        <gene id="504" protId="Q9WZV1" geneId="era"/>
        <gene id="506" protId="P38515" geneId="rplC"/>
        <gene id="508" protId="Q9WYC6" geneId="TM_0290"/>
        <gene id="511" protId="Q9WY58" geneId="TM_0215"/>
        <gene id="513" protId="Q9X0U1" geneId="TM_1214"/>
        <gene id="515" protId="Q9X1J3" geneId="rpsL"/>
        <gene id="517" protId="P38526" geneId="rpsG"/>
        <gene id="522" protId="Q9WZS6" geneId="TM_0819"/>
        <gene id="524" protId="Q9WZL2" geneId="ubiE"/>
        <gene id="526" protId="Q9WZD5" geneId="TM_0667"/>
        <gene id="531" protId="Q9WZU9" geneId="TM_0845"/>
        <gene id="535" protId="Q9X167" geneId="TM_1346"/>
        <gene id="538" protId="Q9WZW6" geneId="TM_0862"/>
        <gene id="540" protId="Q9WYP3" geneId="TM_0412"/>
        <gene id="542" protId="P29395" geneId="rplK"/>
        <gene id="544" protId="Q9X1M1" geneId="TM_1535"/>
        <gene id="546" protId="Q9WY49" geneId="TM_0206"/>
        <gene id="551" protId="Q9WZF2" geneId="TM_0686"/>
        <gene id="553" protId="Q9WZI9" geneId="dtd"/>
        <gene id="555" protId="Q9X1A5" geneId="pgi"/>
        <gene id="557" protId="Q9X1L8" geneId="TM_1532"/>
        <gene id="559" protId="Q9WYT3" geneId="TM_0462"/>
        <gene id="560" protId="Q9X038" geneId="TM_0940"/>
        <gene id="562" protId="Q9X1H7" geneId="engB"/>
        <gene id="564" protId="Q9X1R0" geneId="truA"/>
        <gene id="566" protId="Q9X1G5" geneId="rplM"/>
        <gene id="568" protId="Q9X1U6" geneId="atpG"/>
        <gene id="570" protId="Q9X1K9" geneId="dapA"/>
        <gene id="572" protId="Q9WXX4" geneId="TM_0120"/>
        <gene id="576" protId="Q9WZS2" geneId="norM"/>
        <gene id="580" protId="Q9X0T9" geneId="TM_1212"/>
        <gene id="582" protId="Q9X1I4" geneId="rpsK"/>
        <gene id="584" protId="Q9WYZ8" geneId="fmt"/>
        <gene id="587" protId="Q9WXV1" geneId="TM_0096"/>
        <gene id="589" protId="Q9X1B3" geneId="ispD"/>
        <gene id="591" protId="Q9X253" geneId="TM_1731"/>
        <gene id="593" protId="Q9WZ52" geneId="TM_0583"/>
        <gene id="595" protId="Q9X0N8" geneId="pgl"/>
        <gene id="597" protId="Q9WYN2" geneId="tdk"/>
        <gene id="599" protId="Q9X0Y1" geneId="TM_1254"/>
        <gene id="602" protId="Q9X0H9" geneId="TM_1094"/>
        <gene id="604" protId="Q9WZV6" geneId="TM_0852"/>
        <gene id="606" protId="Q9X1P5" geneId="deoC"/>
        <gene id="608" protId="Q9WYJ9" geneId="apeA"/>
        <gene id="610" protId="Q9X0X0" geneId="purC"/>
        <gene id="612" protId="Q9X0Y0" geneId="nadE2"/>
        <gene id="625" protId="Q9X0L2" geneId="TM_1128"/>
        <gene id="627" protId="Q9X1B9" geneId="frr"/>
        <gene id="629" protId="Q9WZM6" geneId="rbgA"/>
        <gene id="633" protId="Q9WZ12" geneId="TM_0542"/>
        <gene id="635" protId="Q9WZK3" geneId="TM_0744"/>
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        <gene id="639" protId="Q9WZM1" geneId="rpsB"/>
        <gene id="641" protId="Q9WYD1" geneId="tal"/>
        <gene id="645" protId="G4FEX7" geneId="TM_1021"/>
        <gene id="647" protId="Q9X024" geneId="nnr"/>
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        <gene id="651" protId="Q9X171" geneId="TM_1350"/>
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        <gene id="663" protId="Q9X034" geneId="mtaD"/>
        <gene id="665" protId="Q9WZI0" geneId="upp"/>
        <gene id="674" protId="Q9X085" geneId="TM_0990"/>
        <gene id="677" protId="Q9X219" geneId="TM_1693"/>
        <gene id="690" protId="Q9X2G1" geneId="TM_1846"/>
        <gene id="692" protId="P96113" geneId="def"/>
        <gene id="694" protId="Q9WY28" geneId="glmM"/>
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        <gene id="698" protId="Q9X2H9" geneId="nfi"/>
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        <gene id="704" protId="Q9X0R3" geneId="TM_1181"/>
        <gene id="707" protId="Q9WYX5" geneId="groS"/>
        <gene id="709" protId="Q9WY06" geneId="TM_0159"/>
        <gene id="712" protId="Q9X1B7" geneId="cdsA"/>
        <gene id="715" protId="Q9X1Q8" geneId="TM_1572"/>
        <gene id="717" protId="Q9WYP5" geneId="TM_0414"/>
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        <gene id="724" protId="P38508" geneId="rplN"/>
        <gene id="728" protId="Q9X2C3" geneId="TM_1803"/>
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        <gene id="733" protId="Q9WYF4" geneId="TM_0318"/>
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        <gene id="738" protId="Q9WXU2" geneId="TM_0087"/>
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        <gene id="745" protId="Q9X0I9" geneId="TM_1105"/>
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        <gene id="764" protId="Q9X1G4" geneId="rpsI"/>
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        <gene id="788" protId="Q9X0E4" geneId="TM_1054"/>
        <gene id="789" protId="Q9WXN4" geneId="TM_0027"/>
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        <gene id="812" protId="Q9WXN5" geneId="TM_0028"/>
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        <gene id="815" protId="Q9WYX0" geneId="TM_0500"/>
        <gene id="816" protId="Q9WXT3" geneId="TM_0078"/>
        <gene id="818" protId="P38509" geneId="rplP"/>
        <gene id="820" protId="P38511" geneId="rplV"/>
        <gene id="822" protId="P38518" geneId="rpsJ"/>
        <gene id="826" protId="P36203" geneId="recA"/>
        <gene id="828" protId="Q9WYB9" geneId="TM_0283"/>
        <gene id="830" protId="Q9X0P5" geneId="TM_1162"/>
        <gene id="832" protId="Q9X0Q9" geneId="TM_1177"/>
        <gene id="834" protId="Q9X0M7" geneId="mcp2"/>
        <gene id="835" protId="Q9X1E2" geneId="mcp4"/>
        <gene id="836" protId="Q9X0N0" geneId="mcp3"/>
        <gene id="837" protId="Q9WXN0" geneId="TM_0023"/>
        <gene id="838" protId="Q9X020" geneId="TM_0918"/>
        <gene id="839" protId="Q9WYR0" geneId="mcp1"/>
        <gene id="841" protId="Q9WZ90" geneId="TM_0622"/>
        <gene id="842" protId="Q9WZ95" geneId="TM_0627"/>
        <gene id="845" protId="Q9X1N7" geneId="TM_1551"/>
        <gene id="847" protId="Q9X1Q2" geneId="rpsP"/>
        <gene id="849" protId="Q9X1A9" geneId="TM_1389"/>
        <gene id="851" protId="Q9X1G9" geneId="rplU"/>
        <gene id="853" protId="Q9X1J7" geneId="ybeY"/>
        <gene id="855" protId="Q9X017" geneId="rnhB"/>
        <gene id="859" protId="Q9X194" geneId="TM_1374"/>
        <gene id="861" protId="Q9X192" geneId="nifU"/>
        <gene id="864" protId="Q9X0G5" geneId="TM_1076"/>
        <gene id="866" protId="P38519" geneId="rpsQ"/>
        <gene id="868" protId="Q9WZ73" geneId="ssb"/>
        <gene id="870" protId="Q9X036" geneId="TM_0938"/>
        <gene id="872" protId="Q9WZF5" geneId="TM_0691"/>
        <gene id="874" protId="Q9X1I1" geneId="rplQ"/>
        <gene id="876" protId="Q9WZW8" geneId="TM_0864"/>
        <gene id="878" protId="G4FEX6" geneId="TM_1022"/>
        <gene id="880" protId="P38517" geneId="rplE"/>
        <gene id="884" protId="Q9WY41" geneId="TM_0198"/>
        <gene id="885" protId="Q9X1B1" geneId="TM_1391"/>
        <gene id="888" protId="Q9X1Q0" geneId="acyP"/>
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    </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>
  <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="0.297"/>
      </geneRef>
      <geneRef id="3">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="2">
      <score id="bit" value="639"/>
      <geneRef id="4">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="5">
        <score id="inparalog" value="0.194"/>
      </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="619"/>
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