<?xml version="1.0" encoding="utf-8"?>
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  <notes>
    <stats ortholog_groups="201" inparalogs="559"/>
    <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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    <notes>
      <additionalInformation abbreviation="C.trachomatis" link="http://www.uniprot.org/taxonomy/272561"/>
    </notes>
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        <gene id="195" protId="H3AEC4" geneId="SDHA"/>
        <gene id="197" protId="H2ZYK7" geneId="METAP1D"/>
        <gene id="199" protId="H3ARG3" geneId="uncharacterized_H3ARG3"/>
        <gene id="201" protId="H3APP7" geneId="CBR4"/>
        <gene id="203" protId="H3ARK4" geneId="DIS3"/>
        <gene id="204" protId="H3AHD4" geneId="DIS3L"/>
        <gene id="205" protId="H3AY08" geneId="DIS3L2"/>
        <gene id="207" protId="H3AP55" geneId="GBE1"/>
        <gene id="209" protId="H3A5H3" geneId="PET112"/>
        <gene id="211" protId="H3A9S8" geneId="GTPBP3"/>
        <gene id="213" protId="H3ATZ8" geneId="HTRA2"/>
        <gene id="215" protId="M3XHU7" geneId="TKT"/>
        <gene id="216" protId="H3AYY5" geneId="uncharacterized_H3AYY5"/>
        <gene id="218" protId="H3AD61" geneId="YARS2"/>
        <gene id="220" protId="H3B406" geneId="PRDX3"/>
        <gene id="221" protId="H2ZYG0" geneId="PRDX4"/>
        <gene id="223" protId="H3B5X8" geneId="GTPBP10"/>
        <gene id="225" protId="H3B3Y2" geneId="RSAD1"/>
        <gene id="227" protId="H3B1F6" geneId="uncharacterized_H3B1F6"/>
        <gene id="228" protId="H2ZV24" geneId="uncharacterized_H2ZV24"/>
        <gene id="229" protId="H2ZTN3" geneId="uncharacterized_H2ZTN3"/>
        <gene id="231" protId="H3AD82" geneId="METTL15"/>
        <gene id="233" protId="H3A886" geneId="DHDDS"/>
        <gene id="235" protId="H3AXX3" geneId="GTPBP6"/>
        <gene id="237" protId="H3BAF3" geneId="TXNRD2"/>
        <gene id="238" protId="H3B6J5" geneId="TXNRD3"/>
        <gene id="240" protId="H3AG86" geneId="uncharacterized_H3AG86"/>
        <gene id="241" protId="H3B2Y8" geneId="SLC6A4"/>
        <gene id="242" protId="H3B302" geneId="SLC6A2"/>
        <gene id="243" protId="H2ZYV9" geneId="SLC6A3"/>
        <gene id="244" protId="H3AZL2" geneId="SLC6A5"/>
        <gene id="245" protId="H3BIB7" geneId="SLC6A1"/>
        <gene id="246" protId="H2ZRV4" geneId="uncharacterized_H2ZRV4"/>
        <gene id="247" protId="H3A4N3" geneId="uncharacterized_H3A4N3"/>
        <gene id="248" protId="H3BDU1" geneId="uncharacterized_H3BDU1"/>
        <gene id="249" protId="H3BI94" geneId="SLC6A11"/>
        <gene id="250" protId="H2ZWC3" geneId="uncharacterized_H2ZWC3"/>
        <gene id="251" protId="H3A4J1" geneId="SLC6A9"/>
        <gene id="252" protId="H2ZX72" geneId="uncharacterized_H2ZX72"/>
        <gene id="253" protId="H3B921" geneId="uncharacterized_H3B921"/>
        <gene id="254" protId="H3AUR4" geneId="uncharacterized_H3AUR4"/>
        <gene id="255" protId="H3AQG6" geneId="uncharacterized_H3AQG6"/>
        <gene id="256" protId="H3B6Q8" geneId="uncharacterized_H3B6Q8"/>
        <gene id="257" protId="H3AB15" geneId="SLC6A6"/>
        <gene id="258" protId="H3AHW6" geneId="SLC6A15"/>
        <gene id="259" protId="H2ZZZ4" geneId="SLC6A20"/>
        <gene id="260" protId="H3ADK3" geneId="SLC6A16"/>
        <gene id="261" protId="H3A1D8" geneId="SLC6A19"/>
        <gene id="263" protId="H3BD09" geneId="UAP1L1"/>
        <gene id="264" protId="H3B049" geneId="UAP1"/>
        <gene id="266" protId="H3A0Q6" geneId="ATP4A"/>
        <gene id="267" protId="H2ZW56" geneId="ATP1A1"/>
        <gene id="268" protId="H3AXY8" geneId="ATP1A3"/>
        <gene id="269" protId="H2ZT16" geneId="uncharacterized_H2ZT16"/>
        <gene id="270" protId="H3BDY4" geneId="ATP2A3"/>
        <gene id="271" protId="M3XI19" geneId="ATP2A2"/>
        <gene id="272" protId="H3ANB8" geneId="uncharacterized_H3ANB8"/>
        <gene id="273" protId="H3AHX2" geneId="ATP2C1"/>
        <gene id="274" protId="H2ZU49" geneId="uncharacterized_H2ZU49"/>
        <gene id="275" protId="H3BI64" geneId="ATP2B2"/>
        <gene id="276" protId="H3A9B9" geneId="ATP2B1"/>
        <gene id="277" protId="H3ADK4" geneId="ATP2B3"/>
        <gene id="278" protId="H3AEX1" geneId="ATP2C2"/>
        <gene id="280" protId="H3B391" geneId="BPGM"/>
        <gene id="281" protId="H3B5R5" geneId="PGAM2"/>
        <gene id="282" protId="H3BB55" geneId="uncharacterized_H3BB55"/>
        <gene id="284" protId="H3B2Z7" geneId="OSGEPL1"/>
        <gene id="286" protId="H3B2U7" geneId="TSTD2"/>
        <gene id="288" protId="H3AAV8" geneId="TPI1"/>
        <gene id="290" protId="H3BHP5" geneId="NFS1"/>
        <gene id="292" protId="H3BGA5" geneId="uncharacterized_H3BGA5"/>
        <gene id="294" protId="H3AWZ8" geneId="uncharacterized_H3AWZ8"/>
        <gene id="295" protId="H3AT42" geneId="RRM2"/>
        <gene id="297" protId="H3A0F4" geneId="RPE"/>
        <gene id="299" protId="H3A9M3" geneId="WARS2"/>
        <gene id="301" protId="H3B1G7" geneId="TRIT1"/>
        <gene id="303" protId="H3ARW6" geneId="GUK1"/>
        <gene id="305" protId="M3XJ87" geneId="PMS2"/>
        <gene id="307" protId="H3B6G4" geneId="MRPL2"/>
        <gene id="309" protId="H3BE21" geneId="SLC26A11"/>
        <gene id="310" protId="H3A6G7" geneId="SLC26A4"/>
        <gene id="311" protId="H3A5I1" geneId="SLC26A5"/>
        <gene id="312" protId="H3BG44" geneId="SLC26A10"/>
        <gene id="313" protId="H3AYL5" geneId="uncharacterized_H3AYL5"/>
        <gene id="314" protId="H3AX38" geneId="SLC26A2"/>
        <gene id="316" protId="H3ARI0" geneId="UROD"/>
        <gene id="318" protId="H3AKB8" geneId="TOP3A"/>
        <gene id="319" protId="H3B0D1" geneId="TOP3B"/>
        <gene id="321" protId="H3A640" geneId="AK3"/>
        <gene id="322" protId="H2ZV67" geneId="AK4"/>
        <gene id="323" protId="M3XK55" geneId="AK2"/>
        <gene id="325" protId="H3BGB3" geneId="MRPS12"/>
        <gene id="327" protId="H3B4S8" geneId="TRUB1"/>
        <gene id="329" protId="H3B2C3" geneId="C12orf10"/>
        <gene id="331" protId="H3BEM9" geneId="NME4"/>
        <gene id="332" protId="H3AA08" geneId="uncharacterized_H3AA08"/>
        <gene id="333" protId="H3AYT5" geneId="NME3"/>
        <gene id="335" protId="H3A0K1" geneId="ADAT2"/>
        <gene id="337" protId="H3AVX1" geneId="TACO1"/>
        <gene id="339" protId="H3A182" geneId="MRPS7"/>
        <gene id="341" protId="H3BAY6" geneId="QTRT1"/>
        <gene id="344" protId="H3AZG3" geneId="TRNT1"/>
        <gene id="346" protId="H3AKI6" geneId="RMND1"/>
        <gene id="348" protId="H3BDC6" geneId="TRMT2A"/>
        <gene id="349" protId="H3B9R3" geneId="TRMT2B"/>
        <gene id="351" protId="H3A5P1" geneId="XPNPEP3"/>
        <gene id="353" protId="H3B9L6" geneId="uncharacterized_H3B9L6"/>
        <gene id="355" protId="H3AFM8" geneId="MRPS11"/>
        <gene id="357" protId="H3A3Z4" geneId="PPOX"/>
        <gene id="359" protId="H3B7H7" geneId="uncharacterized_H3B7H7"/>
        <gene id="360" protId="H3AX93" geneId="HINT1"/>
        <gene id="361" protId="H3AZZ9" geneId="HINT2"/>
        <gene id="363" protId="H3BFQ5" geneId="COQ5"/>
        <gene id="365" protId="H3B6I7" geneId="OAT"/>
        <gene id="366" protId="H3A3S4" geneId="AGXT2"/>
        <gene id="367" protId="H3B5G2" geneId="AGXT2L1"/>
        <gene id="369" protId="H3AXD8" geneId="TFB1M"/>
        <gene id="371" protId="H3B142" geneId="MRPS9"/>
        <gene id="373" protId="H2ZSB7" geneId="GCAT"/>
        <gene id="374" protId="H3B343" geneId="ALAS2"/>
        <gene id="375" protId="H3B216" geneId="SPTLC2"/>
        <gene id="376" protId="H3B3N8" geneId="SPTLC3"/>
        <gene id="378" protId="H3AZL8" geneId="NDOR1"/>
        <gene id="379" protId="H3BGP9" geneId="POR"/>
        <gene id="380" protId="H3AFP6" geneId="MTRR"/>
        <gene id="381" protId="H3BE24" geneId="NOS2"/>
        <gene id="383" protId="H3BBW9" geneId="MCAT"/>
        <gene id="385" protId="H2ZZA0" geneId="GPD1"/>
        <gene id="386" protId="H3ATR1" geneId="uncharacterized_H3ATR1"/>
        <gene id="387" protId="H3B379" geneId="GPD1L"/>
        <gene id="389" protId="H3BB46" geneId="FECH"/>
        <gene id="391" protId="H3BAV5" geneId="PTRH1"/>
        <gene id="393" protId="H3AJV4" geneId="PDF"/>
        <gene id="395" protId="H2ZY23" geneId="uncharacterized_H2ZY23"/>
        <gene id="396" protId="M3XI97" geneId="uncharacterized_M3XI97"/>
        <gene id="398" protId="H3ATN4" geneId="ISPD"/>
        <gene id="400" protId="H3BHR6" geneId="MRPS2"/>
        <gene id="402" protId="H3B8R6" geneId="SDHB"/>
        <gene id="404" protId="H3A4A6" geneId="ACSL3"/>
        <gene id="405" protId="H3A108" geneId="ACSL4"/>
        <gene id="406" protId="H3AXU8" geneId="uncharacterized_H3AXU8"/>
        <gene id="407" protId="H3AJJ4" geneId="ACSL1"/>
        <gene id="408" protId="H3AAB0" geneId="ACSL6"/>
        <gene id="409" protId="H3ARP6" geneId="ACSL5"/>
        <gene id="411" protId="H3A7H2" geneId="TATDN3"/>
        <gene id="413" protId="H3BB44" geneId="MTFMT"/>
        <gene id="415" protId="H3BGZ0" geneId="RFC2"/>
        <gene id="416" protId="H3BBL3" geneId="RFC5"/>
        <gene id="417" protId="H3BEI1" geneId="RFC4"/>
        <gene id="419" protId="H3APX0" geneId="uncharacterized_H3APX0"/>
        <gene id="421" protId="H3AHH1" geneId="PGLS"/>
        <gene id="423" protId="H3ARE2" geneId="GRPEL1"/>
        <gene id="424" protId="H3ABV3" geneId="GRPEL2"/>
        <gene id="426" protId="H2ZWW5" geneId="uncharacterized_H2ZWW5"/>
        <gene id="427" protId="H3A060" geneId="uncharacterized_H3A060"/>
        <gene id="429" protId="H3BFF6" geneId="uncharacterized_H3BFF6"/>
        <gene id="431" protId="H3BIR9" geneId="MRPL20"/>
        <gene id="433" protId="H2ZWC2" geneId="DCAKD"/>
        <gene id="435" protId="H3AMF2" geneId="MRPS14"/>
        <gene id="437" protId="H3AR72" geneId="YRDC"/>
        <gene id="439" protId="H3AS95" geneId="RPUSD4"/>
        <gene id="441" protId="H3BHM1" geneId="PUSL1"/>
        <gene id="443" protId="H3AK91" geneId="RPUSD1"/>
        <gene id="445" protId="H3A5R1" geneId="RPL23"/>
        <gene id="446" protId="H3ADD1" geneId="uncharacterized_H3ADD1"/>
        <gene id="448" protId="H3AAB6" geneId="DUS2L"/>
        <gene id="450" protId="H3B6D7" geneId="HSPE1"/>
        <gene id="452" protId="H3AEH1" geneId="PDSS1"/>
        <gene id="453" protId="H3AJS1" geneId="PDSS2"/>
        <gene id="455" protId="H3A9L9" geneId="GCSH"/>
        <gene id="457" protId="H3AQH4" geneId="HOGA1"/>
        <gene id="459" protId="H3B6N8" geneId="MRPL13"/>
        <gene id="461" protId="H3B668" geneId="MRPL17"/>
        <gene id="463" protId="H3A981" geneId="SLC7A8"/>
        <gene id="464" protId="H3APS3" geneId="SLC7A10"/>
        <gene id="465" protId="H3ATR4" geneId="uncharacterized_H3ATR4"/>
        <gene id="467" protId="H3A703" geneId="GMPPB"/>
        <gene id="468" protId="H3AGB5" geneId="GMPPA"/>
        <gene id="470" protId="H2ZY36" geneId="MRPL16"/>
        <gene id="472" protId="H3B460" geneId="MTIF3"/>
        <gene id="474" protId="H3A827" geneId="SLC7A6"/>
        <gene id="475" protId="H3ALS9" geneId="SLC7A11"/>
        <gene id="476" protId="H3A009" geneId="SLC7A7"/>
        <gene id="477" protId="H3A9F1" geneId="uncharacterized_H3A9F1"/>
        <gene id="478" protId="H3B3X6" geneId="SLC7A5"/>
        <gene id="479" protId="H3AHW9" geneId="uncharacterized_H3AHW9"/>
        <gene id="480" protId="H3AUZ7" geneId="uncharacterized_H3AUZ7"/>
        <gene id="481" protId="H2ZXM3" geneId="uncharacterized_H2ZXM3"/>
        <gene id="482" protId="H3AEZ9" geneId="uncharacterized_H3AEZ9"/>
        <gene id="483" protId="H3A3I2" geneId="SLC7A13"/>
        <gene id="484" protId="H3A5L8" geneId="SLC7A2"/>
        <gene id="485" protId="H3AGX9" geneId="SLC7A1"/>
        <gene id="487" protId="H3AMZ6" geneId="CCBL2"/>
        <gene id="488" protId="H3B744" geneId="CCBL1"/>
        <gene id="490" protId="H3AS40" geneId="COQ2"/>
        <gene id="492" protId="H2ZUS7" geneId="uncharacterized_H2ZUS7"/>
        <gene id="493" protId="H3AQY8" geneId="PGM5"/>
        <gene id="495" protId="H3ALI4" geneId="MRPL4"/>
        <gene id="497" protId="H3ASZ1" geneId="uncharacterized_H3ASZ1"/>
        <gene id="499" protId="M3XJB9" geneId="uncharacterized_M3XJB9"/>
        <gene id="500" protId="H3AEG5" geneId="GRINA"/>
        <gene id="501" protId="H3ACW5" geneId="uncharacterized_H3ACW5"/>
        <gene id="502" protId="H3BF52" geneId="FAIM2"/>
        <gene id="503" protId="H3AAX5" geneId="uncharacterized_H3AAX5"/>
        <gene id="504" protId="H2ZZK8" geneId="uncharacterized_H2ZZK8"/>
        <gene id="506" protId="H3A519" geneId="RPS20"/>
        <gene id="508" protId="H3AB87" geneId="uncharacterized_H3AB87"/>
        <gene id="510" protId="H2ZXI1" geneId="BBS4"/>
        <gene id="516" protId="H2ZTC7" geneId="PLD6"/>
        <gene id="518" protId="H3AI35" geneId="MRPL1"/>
        <gene id="520" protId="H3AMK4" geneId="RPS15"/>
        <gene id="522" protId="H3AAY7" geneId="N6AMT1"/>
        <gene id="524" protId="H3AHK3" geneId="HSPA13"/>
        <gene id="526" protId="H3ADL5" geneId="uncharacterized_H3ADL5"/>
        <gene id="527" protId="H3AFF7" geneId="uncharacterized_H3AFF7"/>
        <gene id="529" protId="H3ARX8" geneId="RPS18"/>
        <gene id="531" protId="H3BIT2" geneId="MRPS16"/>
        <gene id="533" protId="H3BDW3" geneId="HMBS"/>
        <gene id="535" protId="H3AA50" geneId="MRPL11"/>
        <gene id="537" protId="H3AB04" geneId="uncharacterized_H3AB04"/>
        <gene id="538" protId="H2ZZA5" geneId="PPM1K"/>
        <gene id="539" protId="H3ACF2" geneId="PPM1L"/>
        <gene id="540" protId="H3BH13" geneId="PPM1A"/>
        <gene id="541" protId="H3AUD4" geneId="PPM1N"/>
        <gene id="542" protId="H3B1C5" geneId="PPM1F"/>
        <gene id="543" protId="H3AWP3" geneId="ILKAP"/>
        <gene id="544" protId="H3AW71" geneId="PPM1B"/>
        <gene id="546" protId="H3ABJ5" geneId="uncharacterized_H3ABJ5"/>
        <gene id="548" protId="H3AD65" geneId="uncharacterized_H3AD65"/>
        <gene id="550" protId="H3ATC3" geneId="LYPLA2"/>
        <gene id="551" protId="H3B980" geneId="LYPLA1"/>
        <gene id="552" protId="H3A7T1" geneId="LYPLAL1"/>
        <gene id="555" protId="H2ZU14" geneId="TREX2"/>
        <gene id="557" protId="H3ASZ4" geneId="MRPS18C"/>
        <gene id="559" protId="H3A2N8" geneId="HDHD1"/>
      </genes>
    </database>
    <notes>
      <additionalInformation abbreviation="L.chalumnae" link="http://www.uniprot.org/taxonomy/7897"/>
    </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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      <score id="bit" value="931"/>
      <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="706"/>
      <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>
      <geneRef id="5">
        <score id="inparalog" value="0.349"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="3">
      <score id="bit" value="646"/>
      <geneRef id="6">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="7">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.97"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="4">
      <score id="bit" value="617"/>
      <geneRef id="8">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="9">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="10">
        <score id="inparalog" value="0.406"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="5">
      <score id="bit" value="595"/>
      <geneRef id="11">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="12">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.99"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="6">
      <score id="bit" value="589"/>
      <geneRef id="13">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="14">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="7">
      <score id="bit" value="531"/>
      <geneRef id="15">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="16">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="8">
      <score id="bit" value="530"/>
      <geneRef id="17">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="18">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.78"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="9">
      <score id="bit" value="505"/>
      <geneRef id="19">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="20">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="21">
        <score id="inparalog" value="0.309"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="10">
      <score id="bit" value="495"/>
      <geneRef id="22">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="23">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="11">
      <score id="bit" value="487"/>
      <geneRef id="24">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="25">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="26">
        <score id="inparalog" value="0.62"/>
      </geneRef>
      <geneRef id="27">
        <score id="inparalog" value="0.251"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="12">
      <score id="bit" value="487"/>
      <geneRef id="28">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="29">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
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