<?xml version="1.0" encoding="utf-8"?>
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  <notes>
    <stats ortholog_groups="222" inparalogs="525"/>
    <parameters scoreCutoff="40" confidenceCutoff="0.05" overlapCutoff="0.5" mergingCutoff="0.5" matrix="BLOSUM62"/>
  </notes>
  <species name="Leishmania braziliensis " NCBITaxId="5660">
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        <gene id="504" protId="A4H7P8" geneId="LBRM_14_0920"/>
        <gene id="506" protId="A4HIG3" geneId="LBRM_30_2260"/>
        <gene id="508" protId="A4HK43" geneId="LBRM_32_0710"/>
        <gene id="510" protId="A4H5Y8" geneId="LBRM_10_0060"/>
        <gene id="512" protId="A4HNX6" geneId="LBRM_35_1290"/>
        <gene id="514" protId="A4HNQ5" geneId="LBRM_35_0560"/>
        <gene id="516" protId="A4HPY0" geneId="LBRM_35_4880"/>
        <gene id="518" protId="A4HGE5" geneId="LBRM_28_1080"/>
        <gene id="520" protId="A4HCN4" geneId="LBRM_23_0220"/>
        <gene id="522" protId="A4HBW5" geneId="LBRM_21_1280"/>
        <gene id="524" protId="A4H750" geneId="LBRM_13_0430"/>
      </genes>
    </database>
    <notes>
      <additionalInformation abbreviation="L.braziliensis" link="http://www.uniprot.org/taxonomy/5660"/>
    </notes>
  </species>
  <species name="Thermotoga maritima " NCBITaxId="243274">
    <database name="UniProt" version="UniProt_Complete_Proteomes_2013_06" protLink="http://www.uniprot.org/uniprot/">
      <genes>
        <gene id="2" protId="Q9WYA9" geneId="TM_0272"/>
        <gene id="4" protId="Q9WZ27" geneId="carB"/>
        <gene id="6" protId="Q9X2D7" geneId="valS"/>
        <gene id="8" protId="Q9X1B1" geneId="TM_1391"/>
        <gene id="9" protId="Q9WY41" geneId="TM_0198"/>
        <gene id="11" protId="Q9X112" geneId="metE"/>
        <gene id="15" protId="Q9WYK6" geneId="dnaK"/>
        <gene id="17" protId="O50550" geneId="atpD"/>
        <gene id="19" protId="Q9WZH5" geneId="TM_0716"/>
        <gene id="23" protId="Q9WYX6" geneId="groL"/>
        <gene id="25" protId="Q9X287" geneId="fhs"/>
        <gene id="27" protId="Q9WZJ9" geneId="thrS"/>
        <gene id="29" protId="P38525" geneId="fusA"/>
        <gene id="30" protId="Q9X1Y4" geneId="TM_1651"/>
        <gene id="32" protId="Q9S5X0" geneId="hppA"/>
        <gene id="34" protId="Q9X1B6" geneId="alaS"/>
        <gene id="36" protId="Q9X0N2" geneId="TM_1148"/>
        <gene id="38" protId="Q9X1E4" geneId="glpK2"/>
        <gene id="39" protId="Q9X049" geneId="glpK1"/>
        <gene id="41" protId="P13537" geneId="tuf"/>
        <gene id="43" protId="Q9X1U7" geneId="atpA"/>
        <gene id="45" protId="Q9X168" geneId="guaB"/>
        <gene id="47" protId="Q9X1Y8" geneId="metK"/>
        <gene id="49" protId="O33925" geneId="metG"/>
        <gene id="51" protId="Q9WZ49" geneId="ftsH"/>
        <gene id="53" protId="Q9WYZ2" geneId="hslU"/>
        <gene id="55" protId="Q9WZR0" geneId="pyrG"/>
        <gene id="57" protId="Q9X1V8" geneId="lepA"/>
        <gene id="59" protId="P36204" geneId="pgk/tpi"/>
        <gene id="61" protId="P46213" geneId="ileS"/>
        <gene id="64" protId="Q9WZH9" geneId="glyA"/>
        <gene id="66" protId="Q9WYF3" geneId="TM_0317"/>
        <gene id="68" protId="Q9X231" geneId="lysS"/>
        <gene id="70" protId="Q9WXZ5" geneId="glmS"/>
        <gene id="72" protId="P42848" geneId="eno"/>
        <gene id="74" protId="Q9X0N9" geneId="zwf"/>
        <gene id="76" protId="Q9WY70" geneId="TM_0228"/>
        <gene id="77" protId="Q9WXM5" geneId="TM_0010"/>
        <gene id="78" protId="G4FFG0" geneId="TM_1425"/>
        <gene id="80" protId="P17721" geneId="gap"/>
        <gene id="82" protId="Q9WYL2" geneId="TM_0381"/>
        <gene id="84" protId="Q9WZH8" geneId="cysS"/>
        <gene id="86" protId="Q9WYR9" geneId="TM_0438"/>
        <gene id="88" protId="Q9WYA5" geneId="TM_0268"/>
        <gene id="90" protId="Q9X218" geneId="TM_1692"/>
        <gene id="92" protId="Q9WZD3" geneId="TM_0665"/>
        <gene id="95" protId="O51933" geneId="ahcY"/>
        <gene id="97" protId="Q9X0R4" geneId="smc"/>
        <gene id="100" protId="P36252" geneId="rpoC"/>
        <gene id="104" protId="Q9X1W3" geneId="prs"/>
        <gene id="106" protId="Q9X199" geneId="serS"/>
        <gene id="111" protId="Q9WY99" geneId="TM_0261"/>
        <gene id="113" protId="Q9X0W7" geneId="TM_1240"/>
        <gene id="115" protId="Q9WZN3" geneId="infB"/>
        <gene id="117" protId="Q9X2E0" geneId="guaA"/>
        <gene id="121" protId="Q9WY51" geneId="pyk"/>
        <gene id="123" protId="Q9WZY4" geneId="TM_0882"/>
        <gene id="125" protId="Q9X013" geneId="mtnA"/>
        <gene id="128" protId="Q9X0A2" geneId="TM_1009"/>
        <gene id="130" protId="Q9WYC9" geneId="proA"/>
        <gene id="132" protId="Q9X1P7" geneId="tgt"/>
        <gene id="134" protId="Q9WYC4" geneId="TM_0288"/>
        <gene id="135" protId="Q9WYC3" geneId="TM_0287"/>
        <gene id="136" protId="Q9WXQ0" geneId="TM_0043"/>
        <gene id="138" protId="P74926" geneId="mutS"/>
        <gene id="141" protId="P29398" geneId="rpoB"/>
        <gene id="143" protId="Q9WXV3" geneId="obg"/>
        <gene id="145" protId="Q9WZV3" geneId="dnaJ"/>
        <gene id="147" protId="Q9X1Q1" geneId="ffh"/>
        <gene id="150" protId="Q9WZQ7" geneId="TM_0800"/>
        <gene id="152" protId="Q9WYI7" geneId="TM_0352"/>
        <gene id="154" protId="Q9X024" geneId="nnr"/>
        <gene id="156" protId="Q9WZQ9" geneId="TM_0802"/>
        <gene id="160" protId="O33833" geneId="bfrA"/>
        <gene id="162" protId="P96110" geneId="gdhA"/>
        <gene id="164" protId="Q9WZM7" geneId="TM_0769"/>
        <gene id="166" protId="Q9X1P5" geneId="deoC"/>
        <gene id="168" protId="Q9X1C1" geneId="TM_1401"/>
        <gene id="171" protId="Q9X1S9" geneId="TM_1593"/>
        <gene id="173" protId="Q9WZI1" geneId="rnr"/>
        <gene id="175" protId="Q9WYE4" geneId="TM_0308"/>
        <gene id="177" protId="Q9WY54" geneId="gcvT"/>
        <gene id="179" protId="Q9X0Z7" geneId="TM_1270"/>
        <gene id="181" protId="Q9X1E3" geneId="glpF"/>
        <gene id="183" protId="Q9WYB8" geneId="TM_0282"/>
        <gene id="185" protId="Q9X265" geneId="TM_1743"/>
        <gene id="187" protId="Q9X1F8" geneId="der"/>
        <gene id="189" protId="Q9WXW6" geneId="TM_0111"/>
        <gene id="190" protId="Q9WZS7" geneId="TM_0820"/>
        <gene id="193" protId="P77993" geneId="gyrB"/>
        <gene id="195" protId="Q9X2I6" geneId="TM_1873"/>
        <gene id="197" protId="Q9X183" geneId="prfA"/>
        <gene id="198" protId="Q9X1R5" geneId="prfB"/>
        <gene id="200" protId="Q9WZC2" geneId="speE"/>
        <gene id="202" protId="Q9WYZ1" geneId="hslV"/>
        <gene id="204" protId="Q9X0W5" geneId="TM_1238"/>
        <gene id="206" protId="P46799" geneId="topA"/>
        <gene id="208" protId="Q9X288" geneId="folD"/>
        <gene id="210" protId="Q9WYJ1" geneId="TM_0356"/>
        <gene id="212" protId="Q9X1I7" geneId="TM_1478"/>
        <gene id="214" protId="P56838" geneId="galK"/>
        <gene id="216" protId="Q9WZX0" geneId="TM_0866"/>
        <gene id="218" protId="Q9X017" geneId="rnhB"/>
        <gene id="222" protId="Q9X1I8" geneId="adk"/>
        <gene id="224" protId="Q9X1L7" geneId="TM_1531"/>
        <gene id="226" protId="Q9X0Y2" geneId="aspC"/>
        <gene id="229" protId="Q9X1F4" geneId="aspS"/>
        <gene id="232" protId="Q9WYD0" geneId="proB"/>
        <gene id="234" protId="Q9X283" geneId="TM_1762"/>
        <gene id="236" protId="Q9X0H5" geneId="hisS"/>
        <gene id="238" protId="Q9X055" geneId="TM_0960"/>
        <gene id="242" protId="Q9WZR4" geneId="TM_0807"/>
        <gene id="245" protId="Q9X1N3" geneId="TM_1547"/>
        <gene id="247" protId="Q9X0G9" geneId="TM_1080"/>
        <gene id="249" protId="G4FH33" geneId="TM_0118"/>
        <gene id="251" protId="Q9WY13" geneId="TM_0166"/>
        <gene id="253" protId="Q9WZV6" geneId="TM_0852"/>
        <gene id="255" protId="Q9WYK0" geneId="nth"/>
        <gene id="257" protId="Q9X1F1" geneId="rsmA"/>
        <gene id="259" protId="Q9X248" geneId="fabG"/>
        <gene id="260" protId="Q9WYG0" geneId="TM_0325"/>
        <gene id="261" protId="Q9WYD3" geneId="TM_0297"/>
        <gene id="262" protId="Q9WYS2" geneId="TM_0441"/>
        <gene id="263" protId="Q56318" geneId="TM_0019"/>
        <gene id="265" protId="Q9X215" geneId="gmk"/>
        <gene id="267" protId="Q9WZW6" geneId="TM_0862"/>
        <gene id="269" protId="Q9WZ47" geneId="TM_0578"/>
        <gene id="271" protId="Q9WXZ2" geneId="gcp"/>
        <gene id="273" protId="Q9WY40" geneId="TM_0197"/>
        <gene id="275" protId="Q9WZ18" geneId="TM_0548"/>
        <gene id="277" protId="Q9WY55" geneId="gcvH"/>
        <gene id="279" protId="Q9WYC5" geneId="TM_0289"/>
        <gene id="281" protId="Q9WZG8" geneId="rsmI"/>
        <gene id="283" protId="O33832" geneId="suhB"/>
        <gene id="285" protId="Q9WZS8" geneId="pheS"/>
        <gene id="287" protId="Q9X085" geneId="TM_0990"/>
        <gene id="289" protId="Q9WYT3" geneId="TM_0462"/>
        <gene id="290" protId="Q9X038" geneId="TM_0940"/>
        <gene id="292" protId="Q9X1B8" geneId="uppS"/>
        <gene id="295" protId="Q9X264" geneId="TM_1742"/>
        <gene id="299" protId="Q9WZU9" geneId="TM_0845"/>
        <gene id="304" protId="Q9X1K4" geneId="TM_1516"/>
        <gene id="306" protId="Q9WYX9" geneId="TM_0509"/>
        <gene id="307" protId="Q9WZ98" geneId="TM_0630"/>
        <gene id="309" protId="Q9X1L8" geneId="TM_1532"/>
        <gene id="311" protId="Q9WZI9" geneId="dtd"/>
        <gene id="313" protId="Q9WZL2" geneId="ubiE"/>
        <gene id="315" protId="Q9X0H8" geneId="argS"/>
        <gene id="318" protId="Q9X243" geneId="TM_1718"/>
        <gene id="320" protId="Q9WXP9" geneId="TM_0042"/>
        <gene id="322" protId="Q9WXV8" geneId="TM_0103"/>
        <gene id="324" protId="P38510" geneId="rplB"/>
        <gene id="326" protId="Q9WYW0" geneId="cobB"/>
        <gene id="328" protId="Q9X1L6" geneId="TM_1530"/>
        <gene id="334" protId="P16115" geneId="ldh"/>
        <gene id="336" protId="Q9X0U1" geneId="TM_1214"/>
        <gene id="338" protId="Q9WZ15" geneId="thrB"/>
        <gene id="340" protId="Q9WZ26" geneId="leuB"/>
        <gene id="342" protId="Q9X171" geneId="TM_1350"/>
        <gene id="344" protId="Q9X253" geneId="TM_1731"/>
        <gene id="347" protId="Q9WY49" geneId="TM_0206"/>
        <gene id="349" protId="Q9X1E6" geneId="TM_1432"/>
        <gene id="351" protId="Q9WZW0" geneId="truB"/>
        <gene id="353" protId="Q9X2H9" geneId="nfi"/>
        <gene id="355" protId="Q9WZI0" geneId="upp"/>
        <gene id="357" protId="Q9X1A5" geneId="pgi"/>
        <gene id="359" protId="Q9WYJ9" geneId="apeA"/>
        <gene id="362" protId="Q9WZ12" geneId="TM_0542"/>
        <gene id="364" protId="P96111" geneId="pyrBI"/>
        <gene id="369" protId="Q9WZF2" geneId="TM_0686"/>
        <gene id="371" protId="Q9WZN6" geneId="TM_0779"/>
        <gene id="373" protId="Q9X1C0" geneId="TM_1400"/>
        <gene id="375" protId="Q9WZX6" geneId="rsmH"/>
        <gene id="377" protId="Q9WYH0" geneId="pyrC"/>
        <gene id="379" protId="Q9WZB3" geneId="nadE1"/>
        <gene id="382" protId="Q9WYC6" geneId="TM_0290"/>
        <gene id="385" protId="Q9WZB9" geneId="TM_0651"/>
        <gene id="387" protId="Q9WYN2" geneId="tdk"/>
        <gene id="390" protId="Q9X1J2" geneId="rpsE"/>
        <gene id="392" protId="Q9WYD1" geneId="tal"/>
        <gene id="394" protId="Q9WYY4" geneId="proS"/>
        <gene id="396" protId="Q9X1I4" geneId="rpsK"/>
        <gene id="398" protId="Q9X178" geneId="TM_1357"/>
        <gene id="400" protId="Q9X1M1" geneId="TM_1535"/>
        <gene id="401" protId="Q9WY08" geneId="TM_0161"/>
        <gene id="403" protId="Q9X1G5" geneId="rplM"/>
        <gene id="406" protId="Q9X1Z4" geneId="TM_1666"/>
        <gene id="408" protId="Q9X0I0" geneId="purB"/>
        <gene id="410" protId="Q9WYR7" geneId="TM_0436"/>
        <gene id="412" protId="Q9WYP3" geneId="TM_0412"/>
        <gene id="414" protId="Q9WYG8" geneId="pyrD"/>
        <gene id="416" protId="Q9X1A4" geneId="apt"/>
        <gene id="418" protId="P38508" geneId="rplN"/>
        <gene id="421" protId="Q9WZD5" geneId="TM_0667"/>
        <gene id="424" protId="Q9WZM6" geneId="rbgA"/>
        <gene id="426" protId="Q9X034" geneId="mtaD"/>
        <gene id="428" protId="Q9WXX0" geneId="rbsA1"/>
        <gene id="429" protId="Q9X051" geneId="rbsA2"/>
        <gene id="431" protId="Q9WZS1" geneId="TM_0814"/>
        <gene id="433" protId="Q9WZV0" geneId="TM_0846"/>
        <gene id="435" protId="Q9X0N8" geneId="pgl"/>
        <gene id="437" protId="Q9S5X7" geneId="TM_1424"/>
        <gene id="438" protId="Q9WXM7" geneId="TM_0012"/>
        <gene id="440" protId="Q9WZK1" geneId="TM_0742"/>
        <gene id="443" protId="Q9X2G1" geneId="TM_1846"/>
        <gene id="445" protId="Q9X213" geneId="TM_1687"/>
        <gene id="447" protId="Q9X219" geneId="TM_1693"/>
        <gene id="449" protId="Q9WY44" geneId="TM_0201"/>
        <gene id="450" protId="G4FFG1" geneId="TM_1426"/>
        <gene id="452" protId="Q9WYK7" geneId="TM_0374"/>
        <gene id="454" protId="Q9WZ08" geneId="TM_0538"/>
        <gene id="455" protId="Q9WZX9" geneId="TM_0876"/>
        <gene id="458" protId="Q9WZV4" geneId="grpE"/>
        <gene id="460" protId="Q9WZV1" geneId="era"/>
        <gene id="462" protId="Q9X1I5" geneId="rpsM"/>
        <gene id="464" protId="Q9WZL3" geneId="TM_0754"/>
        <gene id="465" protId="Q9WYM6" geneId="TM_0395"/>
        <gene id="466" protId="Q9WYL1" geneId="TM_0379"/>
        <gene id="469" protId="P36203" geneId="recA"/>
        <gene id="472" protId="Q9WYX5" geneId="groS"/>
        <gene id="474" protId="Q9WYU6" geneId="TM_0475"/>
        <gene id="476" protId="Q9WZD0" geneId="acpP"/>
        <gene id="478" protId="P36205" geneId="glnA"/>
        <gene id="480" protId="Q9X121" geneId="TM_1295"/>
        <gene id="485" protId="G4FEX6" geneId="TM_1022"/>
        <gene id="487" protId="Q9X194" geneId="TM_1374"/>
        <gene id="489" protId="P38520" geneId="rpsS"/>
        <gene id="491" protId="Q9X249" geneId="TM_1726"/>
        <gene id="494" protId="P38526" geneId="rpsG"/>
        <gene id="496" protId="Q9X1T2" geneId="TM_1596"/>
        <gene id="497" protId="Q9X259" geneId="TM_1737"/>
        <gene id="499" protId="P38517" geneId="rplE"/>
        <gene id="501" protId="Q9WY27" geneId="TM_0183"/>
        <gene id="503" protId="Q9X1J3" geneId="rpsL"/>
        <gene id="505" protId="P38509" geneId="rplP"/>
        <gene id="507" protId="Q9X223" geneId="TM_1697"/>
        <gene id="509" protId="Q9X1N7" geneId="TM_1551"/>
        <gene id="511" protId="Q9X0I3" geneId="tmk"/>
        <gene id="513" protId="Q9WXU2" geneId="TM_0087"/>
        <gene id="515" protId="Q9WXV1" geneId="TM_0096"/>
        <gene id="517" protId="Q9WY06" geneId="TM_0159"/>
        <gene id="519" protId="P38518" geneId="rpsJ"/>
        <gene id="521" protId="Q9WY58" geneId="TM_0215"/>
        <gene id="523" protId="Q9ZAE4" geneId="rplF"/>
        <gene id="525" protId="Q9X244" geneId="TM_1720"/>
      </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>
  <groups>
    <orthologGroup id="1">
      <score id="bit" value="958"/>
      <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="753"/>
      <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="667"/>
      <geneRef id="5">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="6">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="4">
      <score id="bit" value="641"/>
      <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>
      <geneRef id="9">
        <score id="inparalog" value="0.15"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="5">
      <score id="bit" value="566"/>
      <geneRef id="10">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="11">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="6">
      <score id="bit" value="546"/>
      <geneRef id="12">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.77"/>
      </geneRef>
      <geneRef id="13">
        <score id="inparalog" value="0.968"/>
      </geneRef>
      <geneRef id="14">
        <score id="inparalog" value="0.098"/>
      </geneRef>
      <geneRef id="15">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="7">
      <score id="bit" value="541"/>
      <geneRef id="16">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="17">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="8">
      <score id="bit" value="533"/>
      <geneRef id="18">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="19">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="9">
      <score id="bit" value="531"/>
      <geneRef id="20">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.99"/>
      </geneRef>
      <geneRef id="21">
        <score id="inparalog" value="0.835"/>
      </geneRef>
      <geneRef id="22">
        <score id="inparalog" value="0.151"/>
      </geneRef>
      <geneRef id="23">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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