Loman Labs

Research group at the University of Birmingham, fusing cutting-edge sequencing with microbial genomics.

Human DNA in bacterial genomes? Yes? No? Maybe?

16 Feb 2011

Astronomer Carl Sagan once said that “extraordinary claims require
extraordinary evidence” and that basis I was primed for scepticism when
I first glanced at <a
href="http://mbio.asm.org/content/2/1/e00005-11.full">this paper in
mBio</a>, which reports apparently human DNA sequences (specifically
from the Line 1 retrotransposon) within a bacterial genome (that of the
obligate human pathogen, Neisseria gonorrhoeae). But the most exciting
scientific reports are those that overturn one’s assumptions and force
one to realise that “there are more things in heaven and Earth than were
ever dreamt of in your philosophy”. Examples for me include the
discovery of reverse transcriptase in bacteria, group II introns in
bacteria, the non-essentiality of the ATPase in flagellar protein export
and evidence of Neanderthal admixture in non-African human genomes.
After careful reading of the paper, I cannot find any obvious flaws, so
I have to accept that human DNA does sometimes get incorporated into
bacterial genomes.

But as a professional sceptic, I wanted to check whether these authors
had not told the whole story, so I had a look for myself at the evidence
for Line 1-like sequences in bacteria. The easiest place to start is to
look for homology at the protein level. There are two CDSs within <a
href="http://www.ncbi.nlm.nih.gov/nuccore/U09116">Line 1</a>. Let’s
start with ORF1. A BlastP search of the NR database does indeed find the
gonococcal sequences:

<div class=MsoNormal style=’mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none’><span lang=EN-US style=’font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US’> </span></div> <div class=MsoNormal style=’mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none’><span lang=EN-US style=’font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US’> </span></div> <div class=MsoNormal style=’mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none’><span lang=EN-US style=’font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US’>><a
href=”http://www.ncbi.nlm.nih.gov/protein/240014458?report=genbank&log$=protalign&blast_rank=23&RID=NR7PEHFH01R”><span
class=GramE>ref</span><span
style=’color:#32508C’>|ZP_04721371.1|</span></a>  hypothetical protein NgonD_07408 [<span class=SpellE>Neisseria</span>
<span class=SpellE>gonorrhoeae</span> DGI18]</span></div> <div class=MsoNormal style=’mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none’><span lang=EN-US style=’font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US’><span
style=”mso-spacerun: yes”> </span><a
href=”http://www.ncbi.nlm.nih.gov/protein/240016904?report=genbank&log$=protalign&blast_rank=23&RID=NR7PEHFH01R”><span
class=GramE>ref</span><span
style=’color:#32508C’>|ZP_04723444.1|</span></a>  hypothetical protein NgonFA_07006 [<span class=SpellE>Neisseria</span>
<span class=SpellE>gonorrhoeae</span> FA6140]</span></div> <div class=MsoNormal style=’mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none’><span lang=EN-US style=’font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US’><span
style=”mso-spacerun: yes”> </span><a
href=”http://www.ncbi.nlm.nih.gov/protein/240120980?report=genbank&log$=protalign&blast_rank=23&RID=NR7PEHFH01R”><span
class=GramE>ref</span><span
style=’color:#32508C’>|ZP_04733942.1|</span></a>  hypothetical protein NgonPI_04276 [<span class=SpellE>Neisseria</span></p>

<span class=SpellE>gonorrhoeae</span> PID24-1]</span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US'>Length=147</span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US'> </span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US'><span
style="mso-spacerun: yes"> </span>Score <span class=GramE>=<span
style="mso-spacerun: yes">  </span>259</span> bits (661),<span
style="mso-spacerun: yes">  </span>Expect = 5e-67</span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US'><span
style="mso-spacerun: yes"> </span>Identities = 128/130 (99%), Positives =
128/130 (99%), Gaps = 0/130 (0%)</span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US'> </span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span class=GramE><span lang=EN-US style='font-size:10.0pt;
font-family:Courier;mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:
EN-US'>Query  35</span></span><span
lang=EN-US style='font-size:10.0pt;font-family:Courier;mso-bidi-font-family:
Courier;color:#1A1A1A;mso-ansi-language:EN-US'>  
MENDFDELREEGFRRSNYSELREDIQTKGKEVENFEKNLEECITRITNTEKCLKELMELK<span
style="mso-spacerun: yes">  </span>94</span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US'><span
style="mso-spacerun:
yes">           
</span>MENDFDELREEGFRRSNYSELREDIQTKGKEVENFEKNLEECITRITNTEKCLKELMELK</span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span class=SpellE><span class=GramE><span lang=EN-US
style='font-size:10.0pt;font-family:Courier;mso-bidi-font-family:Courier;
color:#1A1A1A;mso-ansi-language:EN-US'>Sbjct</span></span></span><span
class=GramE><span lang=EN-US style='font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US'><span
style="mso-spacerun: yes">  </span>1</span></span><span lang=EN-US
style='font-size:10.0pt;font-family:Courier;mso-bidi-font-family:Courier;
color:#1A1A1A;mso-ansi-language:EN-US'>    MENDFDELREEGFRRSNYSELREDIQTKGKEVENFEKNLEECITRITNTEKCLKELMELK<span
style="mso-spacerun: yes">  </span>60</span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US'> </span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span class=GramE><span lang=EN-US style='font-size:10.0pt;
font-family:Courier;mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:
EN-US'>Query  95</span></span><span
lang=EN-US style='font-size:10.0pt;font-family:Courier;mso-bidi-font-family:
Courier;color:#1A1A1A;mso-ansi-language:EN-US'>  
TKARELREECRSLRSRCDQLEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVK<span
style="mso-spacerun: yes">  </span>154</span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US'><span
style="mso-spacerun:
yes">           
</span>TKAREL EECRSLRSRCD LEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVK</span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span class=SpellE><span class=GramE><span lang=EN-US
style='font-size:10.0pt;font-family:Courier;mso-bidi-font-family:Courier;
color:#1A1A1A;mso-ansi-language:EN-US'>Sbjct</span></span></span><span
class=GramE><span lang=EN-US style='font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US'><span
style="mso-spacerun: yes">  </span>61</span></span><span lang=EN-US
style='font-size:10.0pt;font-family:Courier;mso-bidi-font-family:Courier;
color:#1A1A1A;mso-ansi-language:EN-US'>  
TKARELHEECRSLRSRCDPLEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVK<span
style="mso-spacerun: yes">  </span>120</span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US'> </span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span class=GramE><span lang=EN-US style='font-size:10.0pt;
font-family:Courier;mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:
EN-US'>Query  155</span></span><span
lang=EN-US style='font-size:10.0pt;font-family:Courier;mso-bidi-font-family:
Courier;color:#1A1A1A;mso-ansi-language:EN-US'>  RPNLRLIGVP  164</span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US'><span
style="mso-spacerun:
yes">           
</span>RPNLRLIGVP</span></div> <div class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none'><span class=SpellE><span class=GramE><span lang=EN-US
style='font-size:10.0pt;font-family:Courier;mso-bidi-font-family:Courier;
color:#1A1A1A;mso-ansi-language:EN-US'>Sbjct</span></span></span><span
class=GramE><span lang=EN-US style='font-size:10.0pt;font-family:Courier;
mso-bidi-font-family:Courier;color:#1A1A1A;mso-ansi-language:EN-US'><span
style="mso-spacerun: yes">  </span>121</span></span><span lang=EN-US
style='font-size:10.0pt;font-family:Courier;mso-bidi-font-family:Courier;
color:#1A1A1A;mso-ansi-language:EN-US'> 
RPNLRLIGVP  130</span></div> <div class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:Courier;
mso-ansi-language:EN-US'> </span></div> <div class=MsoNormal> </div>

But when the search results are limited to bacterial sequences, one also
finds these

<div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_02004867.1| 
hypothetical protein BGP_6678 [<span class=SpellE>Beggiatoa</span> sp.
PS]</span></div> <div class=MsoNormal>Length=100</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score <span class=GramE>=<span
style="mso-spacerun: yes">  </span>179</span> bits (453),<span
style="mso-spacerun: yes">  </span>Expect = 6e-43</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 88/97 (91%), Positives =
92/97 (95%), Gaps = 0/97 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  114</span><span
style='font-size:10.0pt;font-family:Courier'> 
LEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESDVENGTK<span
style="mso-spacerun: yes">  </span>173</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
+EERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESD ENGTK</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  1</span></span>   </p>

</span>MEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESDGENGTK<span
style="mso-spacerun: yes">  </span>60</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  174</span><span
style='font-size:10.0pt;font-family:Courier'>  LENTLQDIIQENFPNLARQANVQIQEIQRTPQRYSSR<span
style="mso-spacerun: yes">  </span>210</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           </p>

</span>LENTLQDIIQENFPNLARQAN+QIQEIQR PQ 
+ +</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  61</span></span>  
LENTLQDIIQENFPNLARQANIQIQEIQRMPQEKAGK  97</div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_02871253.1| 
hypothetical protein cdivTM_13371 [candidate division TM7 single-cell </span></div> <div class=MsoNormal><span class=GramE>isolate</span>
TM7a]</div> <div class=MsoNormal>Length=109</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score <span class=GramE>=<span
style="mso-spacerun: yes">  </span>175</span> bits (444),<span
style="mso-spacerun: yes">  </span>Expect = 7e-42</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 92/109 (85%), Positives =
95/109 (88%), Gaps = 0/109 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  230</span><span
style='font-size:10.0pt;font-family:Courier'>  MLRAAREKGRVTLKGKPIRLTADLSAETLQARREWGPIFNILKEKNFQPRISFPAKLSFI<span
style="mso-spacerun: yes">  </span>289</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
MLRAARE G+VT KGKPIRLTADL <span class=GramE>AETLQARREWGPIFNILKEKNFQ<span
style="mso-spacerun: yes">  </span>IS</span> PAKLSFI</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  1</span></span>   
MLRAARETGQVTHKGKPIRLTADLLAETLQARREWGPIFNILKEKNFQLIISCPAKLSFI<span
style="mso-spacerun: yes">  60</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  290</span><span
style='font-size:10.0pt;font-family:Courier'>  SEGERKYFTDKQMLRDFVTTRPTLKELLKEALNMERNNRYQPLQNHAKM<span
style="mso-spacerun: yes">  </span>338</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
SEG+ <span class=GramE>K 
TDKQMLRD</span> VT RP LKELLKEALNMERNN YQPLQ HAK+</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  61</span></span>  
SEGKIKSSTDKQMLRDSVTARPALKELLKEALNMERNNWYQPLQKHAKL<span
style="mso-spacerun: yes">  109</span></div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_02871255.1| </p>

</span>hypothetical protein cdivTM_13381 [candidate division TM7 single-cell </span></div> <div class=MsoNormal><span class=GramE>isolate</span>
TM7a]</div> <div class=MsoNormal>Length=68</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score = 80.1 bits (196)<span
class=GramE>,  Expect</span> =
4e-13</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 41/67 (62%), Positives =
48/67 (72%), Gaps = 2/67 (2%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  1</span><span
style='font-size:10.0pt;font-family:Courier'>  
MGKKQNRKTGNSKTQSASPPPKERSSSPATEQSWMENDFDELREEGFRRS--NYSELRED<span
style="mso-spacerun: yes">  </span>58</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           MG+ Q <span
class=GramE>RK  NSK</span> QSAS
PPK+ SSSPA +QSWME  F +L E
GFRRS  N+SEL+E </span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  1</span></span>  
MGRNQGRKVENSKNQSASSPPKDHSSSPAVDQSWMEKGFQKLIEVGFRRSVINFSELKEH<span
style="mso-spacerun: yes">  60</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  59</span><span
style='font-size:10.0pt;font-family:Courier'>  IQTKGKE  65</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           + <span
class=GramE>T  KE</span></span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  61</span></span>  VLTHCKE<span
style="mso-spacerun: yes">  67</span></div> <div class=MsoNormal> </div>

Which at first glance provides additional evidence that Line-1-like
sequences have found their way into other bacterial genome sequences.
However, given that Beggiatoa is not intimately associated with humans
and the sequence sits in its own little contig, one has to assume that
contamination of the sequencing library is the most likely explanation.
Ditto for the TM7 sequences.

What if we try similar searches with the second Line 1 CDS, the one that
encodes reverse transcriptase. Well, here we turn up a dozen or more
hits to bacterial proteins:

<div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_02544188.1| 
hypothetical protein cdiviTM7_00470 [candidate division TM7 single-cell </span></div> <div class=MsoNormal><span class=GramE>isolate</span>
TM7c]</div> <div class=MsoNormal>Length=316</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score <span class=GramE>=<span
style="mso-spacerun: yes">  </span>610</span> bits (1574),<span
style="mso-spacerun: yes">  </span>Expect = 4e-172</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 308/316 (98%), Positives =
312/316 (99%), Gaps = 0/316 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  570</span><span
style='font-size:10.0pt;font-family:Courier'> 
MQGWFNIRKSINVIQHINRAKDKNHMIISIDAEKAFDKIQQPFMLKTLNKLGIDGTYFKI<span
style="mso-spacerun: yes">  </span>629</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes">       <span
style="mso-spacerun:
yes">     </span>MQGWFNIRKSINVIQHINRAKDKNHMIISIDAEKAFDKIQQPFMLKTLNKLGIDGTYFKI</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  1</span></span>   </p>

</span>MQGWFNIRKSINVIQHINRAKDKNHMIISIDAEKAFDKIQQPFMLKTLNKLGIDGTYFKI<span
style="mso-spacerun: yes">  </span>60</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  630</span><span
style='font-size:10.0pt;font-family:Courier'> 
IRAIYDKPTANIILNGQKLEAFPLKTGTRQGCPLSPLLFNIVLEVLARAIRQEKEIKGIQ<span
style="mso-spacerun: yes">  </span>689</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">            </p>

</span>RAIYDKPTANIILNGQKLEAFPLKTGTRQGCPLSPLLFN+VLEVLARAIR+EKE+KGIQ</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  61</span></span>  
TRAIYDKPTANIILNGQKLEAFPLKTGTRQGCPLSPLLFNVVLEVLARAIRREKEVKGIQ<span
style="mso-spacerun: yes">  120</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  690</span><span
style='font-size:10.0pt;font-family:Courier'> </p>

</span>LGKEEVKLSLFADDMIVYLENPIVSAQNLLKLISNFSKVSGYKINVQKSQAFLYTNNRQT<span
style="mso-spacerun: yes">  </span>749</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
LGKEEVKLSLFADDMIVYLENPIVSAQNLLKLISNFSKVSGYKINVQKSQAFLYTNNRQT</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  121</span></span> 
LGKEEVKLSLFADDMIVYLENPIVSAQNLLKLISNFSKVSGYKINVQKSQAFLYTNNRQT<span
style="mso-spacerun: yes">  180</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  750</span><span
style='font-size:10.0pt;font-family:Courier'> 
ESQIMGELPFTIASKRIKYLGIQLTRDVKDLFKENYKPLLKEIKEDTNKWKNIPCSWVGR<span
style="mso-spacerun: yes">  </span>809</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
ESQIM ELPFTIASKRIKYLGIQLTRDVKDLFKENYKPLLKEIKEDTNKWKNIPCSWVGR</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  181</span></span>  ESQIMSELPFTIASKRIKYLGIQLTRDVKDLFKENYKPLLKEIKEDTNKWKNIPCSWVGR<span
style="mso-spacerun: yes">  240</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  810</span><span
style='font-size:10.0pt;font-family:Courier'> 
INIVKMAILPKVIYRFNAIPIKLPMTFFTELEKTTLKFIWNQKRARIAKSILSQKNKAGG<span
style="mso-spacerun: yes">  </span>869</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
INIVKMAILPKVIYRFNAIPIKLPMTFFTELEKTTLKF+WNQKRA IAKSILSQKNKAGG</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  241</span></span> </p>

</span>INIVKMAILPKVIYRFNAIPIKLPMTFFTELEKTTLKFMWNQKRACIAKSILSQKNKAGG<span
style="mso-spacerun: yes">  </span>300</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  870</span><span
style='font-size:10.0pt;font-family:Courier'>  ITLPYFKLYYKATVTK 
885</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           </p>

</span>ITLP FKLYYKATVTK</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  301</span></span>  ITLPDFKLYYKATVTK<span
style="mso-spacerun: yes">  316</span></div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_04563087.1| </p>

</span>conserved hypothetical protein [<span class=SpellE>Mollicutes</span>
bacterium D7]</span></div> <div class=MsoNormal>Length=131</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score <span class=GramE>=<span
style="mso-spacerun: yes">  </span>211</span> bits (536),<span
style="mso-spacerun: yes">  </span>Expect = 8e-52</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 104/121 (86%), Positives =
112/121 (93%), Gaps = 0/121 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  945</span><span
style='font-size:10.0pt;font-family:Courier'>  
RKLKLDLFLTPYTKINSRWIKDLNVKPKTIKTLEENLGITIQDIGVGKDFMSKTPKAMAT<span
style="mso-spacerun: yes">  </span>1004</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">            
+K <span class=GramE>+  </p>

</span>FLTPYTKI</span>+SRWIKDL+V+PKTIKTLEENLGITIQDI +GKDFMSKTPKAMAT</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  2</span></span>    <span
style="mso-spacerun:
yes"> QKTETGPFLTPYTKIHSRWIKDLHVRPKTIKTLEENLGITIQDIXMGKDFMSKTPKAMAT<span
style="mso-spacerun: yes">  </span>61</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  1005</span><span
style='font-size:10.0pt;font-family:Courier'> </p>

</span>KDKIDKWDLIKLKSFCTAKETTIRVNRQPTTWEKIFATYSSDKGLISRIYNELKQIYKKK<span
style="mso-spacerun: yes">  </span>1064</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">            
K KIDKWDLIKLKSFCTA+ETTIRVNRQPT <span class=GramE>WEKIFATYSSDKGLISRI<span
style="mso-spacerun: yes">  </span>ELKQIY</span>+KK</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  62</span></span>   </p>

</span>KAKIDKWDLIKLKSFCTAEETTIRVNRQPTEWEKIFATYSSDKGLISRICKELKQIYRKK<span
style="mso-spacerun: yes">  </span>121</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  1065</span><span
style='font-size:10.0pt;font-family:Courier'>  T  1065</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">            </p>

</span>T</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  122</span></span>   T<span
style="mso-spacerun: yes">  122</span></div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_04563088.1| </p>

</span>conserved hypothetical protein [<span class=SpellE>Mollicutes</span>
bacterium D7]</span></div> <div class=MsoNormal>Length=91</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score <span class=GramE>=<span
style="mso-spacerun: yes">  </span>206</span> bits (524),<span
style="mso-spacerun: yes">  </span>Expect = 2e-50</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 90/91 (99%), Positives =
91/91 (100%), Gaps = 0/91 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  1104</span><span
style='font-size:10.0pt;font-family:Courier'> 
MQIKTTMRYHLTPVRMAIIKKSGNNRCWRGCGEIGTLLHCWWDCKLVQPLWKSVWRFLRD<span
style="mso-spacerun: yes">  </span>1163</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">            
MQIKTTMRYHLTPVRMAIIKKSGNNRCWRGCGEIGTLLHCWWDCKLVQPLWKSVWRFLRD</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  1</span></span>    
MQIKTTMRYHLTPVRMAIIKKSGNNRCWRGCGEIGTLLHCWWDCKLVQPLWKSVWRFLRD<span
style="mso-spacerun: yes">  60</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  1164</span><span
style='font-size:10.0pt;font-family:Courier'>  LELEIPFDPAIPLLGIYPEDYKSCCYKDTCT  1194</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">            
LELEIPFDPAIPLLGIYP+DYKSCCYKDTCT</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  61</span></span>   
LELEIPFDPAIPLLGIYPKDYKSCCYKDTCT 
91</div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_02004659.1| 
conserved hypothetical protein [<span class=SpellE>Beggiatoa</span> sp.
PS]</span></div> <div class=MsoNormal>Length=95</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score <span class=GramE>=<span
style="mso-spacerun: yes">  </span>179</span> bits (455),<span
style="mso-spacerun: yes">  </span>Expect = 2e-42</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 91/92 (99%), Positives =
91/92 (99%), Gaps = 0/92 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  595</span><span
style='font-size:10.0pt;font-family:Courier'> 
MIISIDAEKAFDKIQQPFMLKTLNKLGIDGTYFKIIRAIYDKPTANIILNGQKLEAFPLK<span
style="mso-spacerun: yes">  </span>654</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
MIISIDAEKAFDKIQQPFMLKTLNKLGIDGTY KIIRAIYDKPTANIILNGQKLEAFPLK</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  1</span></span>   
MIISIDAEKAFDKIQQPFMLKTLNKLGIDGTYLKIIRAIYDKPTANIILNGQKLEAFPLK<span
style="mso-spacerun: yes">  60</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  655</span><span
style='font-size:10.0pt;font-family:Courier'>  TGTRQGCPLSPLLFNIVLEVLARAIRQEKEIK  686</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
TGTRQGCPLSPLLFNIVLEVLARAIRQEKEIK</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  61</span></span>  
TGTRQGCPLSPLLFNIVLEVLARAIRQEKEIK 
92</div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_02544187.1| 
hypothetical protein cdiviTM7_00465 [candidate division TM7 single-cell </span></div> <div class=MsoNormal><span class=GramE>isolate</span>
TM7c]</div> <div class=MsoNormal>Length=84</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score <span class=GramE>=<span
style="mso-spacerun: yes">  </span>167</span> bits (424),<span
style="mso-spacerun: yes">  </span>Expect = 8e-39</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 83/84 (99%), Positives =
83/84 (99%), Gaps = 0/84 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  466</span><span
style='font-size:10.0pt;font-family:Courier'>  PTKKSPGPDGFTAEFYQRYKEELVPFLLKLFQSIEKEGILPNSFYEASIILIPKPGRDTT<span
style="mso-spacerun: yes">  </span>525</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
PTKKSPGPDGFTAEFYQRYKEELV FLLKLFQSIEKEGILPNSFYEASIILIPKPGRDTT</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  1</span></span>   
PTKKSPGPDGFTAEFYQRYKEELVQFLLKLFQSIEKEGILPNSFYEASIILIPKPGRDTT<span
style="mso-spacerun: yes">  60</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  526</span><span
style='font-size:10.0pt;font-family:Courier'>  KKENFRPISLMNIDAKILNKILAN  549</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
KKENFRPISLMNIDAKILNKILAN</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  61</span></span>  
KKENFRPISLMNIDAKILNKILAN  84</div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_02532187.1| 
hypothetical protein Epers_00800 [<span class=SpellE>Endoriftia</span> <span
class=SpellE>persephone</span> 'Hot96_1+Hot96_2']</span></div> <div class=MsoNormal>Length=89</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score <span class=GramE>=<span
style="mso-spacerun: yes">  </span>166</span> bits (419),<span
style="mso-spacerun: yes">  </span>Expect = 3e-38</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 85/89 (96%), Positives =
86/89 (97%), Gaps = 0/89 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  595</span><span
style='font-size:10.0pt;font-family:Courier'> </p>

</span>MIISIDAEKAFDKIQQPFMLKTLNKLGIDGTYFKIIRAIYDKPTANIILNGQKLEAFPLK<span
style="mso-spacerun: yes">  </span>654</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
MIISIDAEKAFDKIQQ FMLKTLNKL IDGTY KIIRAIYDKPTANIILNG+KLEAFPLK</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  1</span></span>   
MIISIDAEKAFDKIQQHFMLKTLNKLYIDGTYLKIIRAIYDKPTANIILNGKKLEAFPLK<span
style="mso-spacerun: yes">  60</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  655</span><span
style='font-size:10.0pt;font-family:Courier'>  TGTRQGCPLSPLLFNIVLEVLARAIRQEK  683</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
TGTRQGCPLSPLLFNIVLEVLARAIRQEK</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  61</span></span>  </p>

</span>TGTRQGCPLSPLLFNIVLEVLARAIRQEK 
89</span></div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_01265305.1| 
hypothetical protein PU1002_07017 [<span class=SpellE>Candidatus</span> <span
class=SpellE>Pelagibacter</span> <span class=SpellE>ubique</span> </span></div> <div class=MsoNormal>HTCC1002]</div> <div class=MsoNormal>Length=120</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score <span class=GramE>=<span
style="mso-spacerun: yes">  </span>152</span> bits (385),<span
style="mso-spacerun: yes">  </span>Expect = 3e-34</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 83/122 (69%), Positives =
94/122 (78%), Gaps = 2/122 (1%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  943</span><span
style='font-size:10.0pt;font-family:Courier'>  
ICRKLKLDLFLTPYTKINSRWIKDLNVKPKTIKTLEENLGITIQDIGVGKDFMSKTPKAM<span
style="mso-spacerun: yes">  </span>1002</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">            
+CRKLKLD FLT YTKINSRWI++LNVK KTIK LEENLG TI+ IG+GK FM K+PKA+</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  1</span></span>     MCRKLKLDPFLTLYTKINSRWIQNLNVKSKTIKILEENLGNTIKGIGMGKYFMIKSPKAI<span
style="mso-spacerun: yes">  60</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  1003</span><span
style='font-size:10.0pt;font-family:Courier'> 
ATKDKIDKWDLIKLKSFCTAKETTIRVNRQPTTWEKIFATYSSDKGLISRIYNELKQIYK<span
style="mso-spacerun: yes">  </span>1062</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">            
ATK KIDKWDLIKLKSFCTA+ET<span class=GramE>+          E</span>
+     +DK LISRIY
ELKQI K</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  61</span></span>    ATKAKIDKWDLIKLKSFCTAEETSQHKQTIYRMGENV--CNLTDKSLISRIYKELKQIKK<span
style="mso-spacerun: yes">  118</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  1063</span><span
style='font-size:10.0pt;font-family:Courier'>  KK  1064</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">            
KK</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  119</span></span>   KK<span
style="mso-spacerun: yes">  120</span></div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_02873580.1| 
hypothetical protein cdivTM_25184 [candidate division TM7 single-cell </span></div> <div class=MsoNormal><span class=GramE>isolate</span>
TM7a]</div> <div class=MsoNormal>Length=58</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score <span class=GramE>=<span
style="mso-spacerun: yes">  </span>101</span> bits (251),<span
style="mso-spacerun: yes">  </span>Expect = 9e-19</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 50/58 (87%), Positives =
52/58 (90%), Gaps = 0/58 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  109</span><span
style='font-size:10.0pt;font-family:Courier'> 
LTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSILDRSTRQKVNKDTQ<span
style="mso-spacerun: yes">  </span>166</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
LTILNIYAPNTGAPRFIKQVL DLQRDLDS T+I+GD NTPLSI DRS RQKVNKD Q</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  1</span></span>   </p>

</span>LTILNIYAPNTGAPRFIKQVLRDLQRDLDSRTIIVGDINTPLSISDRSMRQKVNKDIQ<span
style="mso-spacerun: yes">  </span>58</span></div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_07929653.1| 
LOW QUALITY PROTEIN: conserved hypothetical protein [<span class=SpellE>Fusobacterium</span>
</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>ulcerans</span></span> ATCC 49185]</div> <div class=MsoNormal><span
style="mso-spacerun: yes"> <span class=GramE>gb</span>|EFS27679.1|<span
style="mso-spacerun: yes">  </span>LOW QUALITY PROTEIN: conserved
hypothetical protein [<span class=SpellE>Fusobacterium</span> </span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>ulcerans</span></span> ATCC 49185]</div> <div class=MsoNormal>Length=57</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score <span class=GramE>=<span
style="mso-spacerun: yes">  </span>100</span> bits (250),<span
style="mso-spacerun: yes">  </span>Expect = 1e-18</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 48/57 (85%), Positives =
51/57 (90%), Gaps = 0/57 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  214</span><span
style='font-size:10.0pt;font-family:Courier'> 
LSKCKRTEIITNYLSDHSAIKLELRIKNLTQSRSTTWKLNNLLLNDYWVHNEMKAEI<span
style="mso-spacerun: yes">  </span>270</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">            LSKCKRTEIITN
LSDHS IKLEL+IK LTQ+ S TW+LNNLLLNDYWVHNEM AEI</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  1</span></span>   </p>

</span>LSKCKRTEIITNCLSDHSEIKLELKIKKLTQNCSATWRLNNLLLNDYWVHNEMNAEI<span
style="mso-spacerun: yes">  </span>57</span></div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_02873206.1| 
hypothetical protein cdivTM_23289 [candidate division TM7 single-cell </span></div> <div class=MsoNormal><span class=GramE>isolate</span></p>

TM7a]</span></div> <div class=MsoNormal>Length=82</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score = 97.1 bits (240)<span
class=GramE>,  Expect</span> =
2e-17</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 43/60 (72%), Positives =
51/60 (85%), Gaps = 0/60 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  1204</span><span
style='font-size:10.0pt;font-family:Courier'> 
IAKTWNQPKCPTMIDWIKKMWHIYTMEYYAAIKNDEFISFVGTWMKLETIILSKLSQEQK<span
style="mso-spacerun: yes">  </span>1263</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">            
+AKTWNQPKCP+++D IKKMW IYTMEY AA+K +E + F GTWM+LE IILSKL QEQK</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  1</span></span>    </p>

</span>MAKTWNQPKCPSVVDCIKKMWFIYTMEYNAAMKKNEIMFFAGTWMELEAIILSKLMQEQK<span
style="mso-spacerun: yes">  </span>60</span></div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_02873863.1| 
hypothetical protein cdivTM_26611 [candidate division TM7 single-cell </span></div> <div class=MsoNormal><span class=GramE>isolate</span></p>

TM7a]</span></div> <div class=MsoNormal>Length=54</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score = 95.1 bits (235)<span
class=GramE>,  Expect</span> =
6e-17</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 47/52 (91%), Positives =
50/52 (97%), Gaps = 0/52 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  61</span><span
style='font-size:10.0pt;font-family:Courier'>  
KIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTIL<span
style="mso-spacerun: yes">  </span>112</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
+IYQANGK+KKAG+AILVSDKTDFKPTKIKRDKE H IMVKGSIQQEELTIL</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  3</span></span>   </p>

</span>EIYQANGKEKKAGIAILVSDKTDFKPTKIKRDKERHDIMVKGSIQQEELTIL<span
style="mso-spacerun: yes">  </span>54</span></div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_04563056.1| 
conserved hypothetical protein [<span class=SpellE>Mollicutes</span>
bacterium D7]</span></div> <div class=MsoNormal>Length=44</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score = 87.8 bits (216)<span
class=GramE>,  Expect</span> =
1e-14</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 42/42 (100%), Positives =
42/42 (100%), Gaps = 0/42 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  61</span><span
style='font-size:10.0pt;font-family:Courier'>   KIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKG<span
style="mso-spacerun: yes">  </span>102</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
KIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKG</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  3</span></span>   </p>

</span>KIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKG  44</span></div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>ref|ZP_02871216.1| 
hypothetical protein cdivTM_13184 [candidate division TM7 single-cell </span></div> <div class=MsoNormal><span class=GramE>isolate</span></p>

TM7a]</span></div> <div class=MsoNormal>Length=78</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score = 83.2 bits (204)<span
class=GramE>,  Expect</span> =
3e-13</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 42/72 (59%), Positives =
50/72 (70%), Gaps = 0/72 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  971</span><span
style='font-size:10.0pt;font-family:Courier'>  
PKTIKTLEENLGITIQDIGVGKDFMSKTPKAMATKDKIDKWDLIKLKSFCTAKETTIRVN<span
style="mso-spacerun: yes">  </span>1030</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">            
P  +KT <span class=GramE>+<span
style="mso-spacerun: yes">  </span>LG</span>  I  <span
class=SpellE>I</span> +GKDFM K PKA+A K K++KWDLI+ KS CTAKET<span
style="mso-spacerun: yes">  </span>RVN</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  1</span></span>    
PSLLKTWKTILGNIILGIEMGKDFMMKMPKAIAKKGKVEKWDLIEQKSLCTAKETINRVN<span
style="mso-spacerun: yes">  60</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  1031</span><span
style='font-size:10.0pt;font-family:Courier'>  RQPTTWEKIFAT </p>

</span>1042</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">            
+<span class=GramE>QPT  EKI</span><span
style="mso-spacerun: yes">  </span>T</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  61</span></span>   
KQPTEGEKILQT  72</div> <div class=MsoNormal> </div> <div class=MsoNormal> </div> <div class=MsoNormal>><span
class=GramE>gb|ADV08625.1| 
hypothetical protein NGTW08_1668 [<span class=SpellE>Neisseria</span> <span
class=SpellE>gonorrhoeae</span> TCDC-NG08107]</span></div> <div class=MsoNormal>Length=58</div> <div class=MsoNormal> </div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Score = 76.3 bits (186)<span
class=GramE>,  Expect</span> =
3e-11</span></div> <div class=MsoNormal><span
style="mso-spacerun: yes"> Identities = 35/52 (68%), Positives =
46/52 (89%), Gaps = 0/52 (0%)</span></div> <div class=MsoNormal> </div> <div class=MsoNormal><span class=GramE>Query  333</span><span
style='font-size:10.0pt;font-family:Courier'>  KASRRQEITKIRAELKEIETQKTLQKINESRSWFFERINKIDRPLARLIKKK<span
style="mso-spacerun: yes">  </span>384</span></div> <div class=MsoNormal><span
style="mso-spacerun:
yes">           
+ SRR+EI KIRAE<span class=GramE>+   ET</span>++T+ KIN+++SWFFERINKID+PLARLIKK+</span></div> <div class=MsoNormal><span class=SpellE><span class=GramE>Sbjct</span></span><span class=GramE><span
style='font-size:10.0pt;font-family:Courier'>  5</span></span>   
RVSRRKEILKIRAEINAKETKETIAKINKAKSWFFERINKIDKPLARLIKKQ<span
style="mso-spacerun: yes">  56</span></div>

All of these are in dinky little contigs, again suggesting contamination
of the bacterial DNA with human DNA rather then genuine HGT.

All that is, apart from the gonococcal Line-1 RT sequence!! This sits
slap bang in the middle of the TCDC-NG08107 <a
href="http://www.ncbi.nlm.nih.gov/nuccore/317163438">gonococcal
chromosome</a>, next to an invertase-related gene (just like in the
paper!), providing clear evidence that there is more going on here than
the authors report.

Now, I was prepared to leave it there, but for some reason, I decided to
look for hits to the RT CDS just in Neisseria and then discovered over
a dozen matches to the Line-1 RT among proteins from the Neisseria
polysaccharea ATCC 43768 genome. These all appear to be in small
contigs, so look like contamination!

So the take away message is that, yes, it seems plausible that Line-1
DNA has made its way into gonococcal genomes, but given that Line-1 DNA
has also contaminated many bacterial genomes, I think we should say that
the verdict is so far rests on the balance of probabilities, rather than
being beyond all reasonable doubt.

P.S. Oh, and I just checked and the marine metagenome in the
environmental DNA archive is also chock full of Line 1 sequences!

<div class=MsoNormal> </div>

ResearchBlogging.org

Mark T. Anderson, & H. Steven Seifert (2001). Opportunity and Means: Horizontal Gene Transfer from the Human Host to a Bacterial Pathogen mBio, 2 (1)

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