From a923fb4f51ad2a81566f3b647525f7bb3e499a98 Mon Sep 17 00:00:00 2001
From: Orkeliot <eliot.ragueneau@etu.u-bordeaux.fr>
Date: Tue, 20 Nov 2018 09:44:17 +0100
Subject: [PATCH] clean new 16S

---
 .idea/workspace.xml                           | 230 +++++----------
 .../cleaned_protein_sequence_rooted.fasta     | 265 ++++++++++++++++++
 Phe t-RNA/raw_protein_sequence_rooted.fasta   | 265 ++++++++++++++++++
 cure.py                                       |   4 +-
 4 files changed, 602 insertions(+), 162 deletions(-)
 create mode 100644 Phe t-RNA/cleaned_protein_sequence_rooted.fasta
 create mode 100644 Phe t-RNA/raw_protein_sequence_rooted.fasta

diff --git a/.idea/workspace.xml b/.idea/workspace.xml
index 0cd1075..1bdc6db 100644
--- a/.idea/workspace.xml
+++ b/.idea/workspace.xml
@@ -1,7 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <project version="4">
   <component name="ChangeListManager">
-    <list default="true" id="3cb3f4f1-56e1-4d7a-b2e3-1fa71be88fbd" name="Default Changelist" comment="" />
+    <list default="true" id="3cb3f4f1-56e1-4d7a-b2e3-1fa71be88fbd" name="Default Changelist" comment="">
+      <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
+    </list>
     <option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" />
     <option name="SHOW_DIALOG" value="false" />
     <option name="HIGHLIGHT_CONFLICTS" value="true" />
@@ -12,36 +14,39 @@
     <session id="-775274785">
       <usages-collector id="statistics.lifecycle.project">
         <counts>
-          <entry key="project.closed" value="2" />
+          <entry key="project.closed" value="3" />
           <entry key="project.open.time.1" value="2" />
+          <entry key="project.open.time.10" value="1" />
           <entry key="project.open.time.11" value="1" />
-          <entry key="project.opened" value="3" />
+          <entry key="project.open.time.8" value="1" />
+          <entry key="project.opened" value="5" />
         </counts>
       </usages-collector>
       <usages-collector id="statistics.file.extensions.open">
         <counts>
-          <entry key="fasta" value="8" />
+          <entry key="fasta" value="9" />
+          <entry key="newick" value="1" />
           <entry key="py" value="1" />
           <entry key="txt" value="3" />
         </counts>
       </usages-collector>
       <usages-collector id="statistics.file.types.open">
         <counts>
-          <entry key="PLAIN_TEXT" value="11" />
+          <entry key="PLAIN_TEXT" value="13" />
           <entry key="Python" value="1" />
         </counts>
       </usages-collector>
       <usages-collector id="statistics.file.extensions.edit">
         <counts>
           <entry key="fasta" value="12" />
-          <entry key="py" value="132" />
+          <entry key="py" value="168" />
           <entry key="txt" value="94" />
         </counts>
       </usages-collector>
       <usages-collector id="statistics.file.types.edit">
         <counts>
           <entry key="PLAIN_TEXT" value="106" />
-          <entry key="Python" value="132" />
+          <entry key="Python" value="168" />
         </counts>
       </usages-collector>
     </session>
@@ -51,43 +56,44 @@
       <file pinned="false" current-in-tab="false">
         <entry file="file://$PROJECT_DIR$/cure.py">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="60">
-              <caret line="4" column="15" selection-start-line="4" selection-start-column="15" selection-end-line="4" selection-end-column="15" />
+            <state relative-caret-position="75">
+              <caret line="5" column="33" selection-start-line="5" selection-start-column="33" selection-end-line="5" selection-end-column="33" />
             </state>
           </provider>
         </entry>
       </file>
       <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/16S/cleaned_new_16s.fasta">
+        <entry file="file://$PROJECT_DIR$/Phe t-RNA/cleaned_DNA_pheT.fasta">
+          <provider selected="true" editor-type-id="text-editor" />
+        </entry>
+      </file>
+      <file pinned="false" current-in-tab="true">
+        <entry file="file://$PROJECT_DIR$/Phe t-RNA/dna.newick">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="-7417" />
+            <state relative-caret-position="150">
+              <caret line="10" column="53" lean-forward="true" selection-start-line="10" selection-start-column="53" selection-end-line="10" selection-end-column="53" />
+            </state>
           </provider>
         </entry>
       </file>
-      <file pinned="false" current-in-tab="true">
-        <entry file="file://$PROJECT_DIR$/Phe t-RNA/DNA_pheT.fasta">
+      <file pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/16S/cleaned_new_16s.fasta">
           <provider selected="true" editor-type-id="text-editor" />
         </entry>
       </file>
       <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/OBIRapport.txt">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="-1652" />
-          </provider>
+        <entry file="file://$PROJECT_DIR$/Phe t-RNA/DNA_pheT.fasta">
+          <provider selected="true" editor-type-id="text-editor" />
         </entry>
       </file>
       <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/16S/news_16S.fasta">
+        <entry file="file://$PROJECT_DIR$/OBIRapport.txt">
           <provider selected="true" editor-type-id="text-editor" />
         </entry>
       </file>
       <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/Phe t-RNA/cleaned_protein_sequence.fasta">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="1425">
-              <caret line="95" column="68" selection-start-line="95" selection-start-column="68" selection-end-line="95" selection-end-column="68" />
-            </state>
-          </provider>
+        <entry file="file://$PROJECT_DIR$/16S/news_16S.fasta">
+          <provider selected="true" editor-type-id="text-editor" />
         </entry>
       </file>
       <file pinned="false" current-in-tab="false">
@@ -98,7 +104,7 @@
       <file pinned="false" current-in-tab="false">
         <entry file="file://$PROJECT_DIR$/16S/cleaned_16S_alignement.fasta">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="4513">
+            <state relative-caret-position="6195">
               <caret line="413" column="17" selection-start-line="413" selection-start-column="17" selection-end-line="413" selection-end-column="17" />
             </state>
           </provider>
@@ -107,7 +113,7 @@
       <file pinned="false" current-in-tab="false">
         <entry file="file://$PROJECT_DIR$/Phe t-RNA/raw_protein_sequence.fasta">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="478">
+            <state relative-caret-position="2490">
               <caret line="166" column="34" selection-start-line="166" selection-start-column="34" selection-end-line="166" selection-end-column="34" />
             </state>
           </provider>
@@ -130,6 +136,7 @@
         <option value="$PROJECT_DIR$/cleaned_protein_sequence.fasta" />
         <option value="$PROJECT_DIR$/16S/cleaned_16S_alignement.fasta" />
         <option value="$PROJECT_DIR$/cure.py" />
+        <option value="$PROJECT_DIR$/Phe t-RNA/dna.newick" />
       </list>
     </option>
   </component>
@@ -177,116 +184,6 @@
       <recent name="$PROJECT_DIR$/16S" />
     </key>
   </component>
-  <component name="RestoreUpdateTree" date="Moments ago" ActionInfo="_Update">
-    <UpdatedFiles>
-      <FILE-GROUP>
-        <option name="myUpdateName" value="Updated from server" />
-        <option name="myStatusName" value="Changed on server" />
-        <option name="mySupportsDeletion" value="false" />
-        <option name="myCanBeAbsent" value="false" />
-        <option name="myId" value="CHANGED_ON_SERVER" />
-        <FILE-GROUP>
-          <option name="myUpdateName" value="Updated" />
-          <option name="myStatusName" value="Changed" />
-          <option name="mySupportsDeletion" value="false" />
-          <option name="myCanBeAbsent" value="false" />
-          <option name="myId" value="UPDATED" />
-        </FILE-GROUP>
-        <FILE-GROUP>
-          <option name="myUpdateName" value="Created" />
-          <option name="myStatusName" value="Created" />
-          <option name="mySupportsDeletion" value="false" />
-          <option name="myCanBeAbsent" value="false" />
-          <option name="myId" value="CREATED" />
-          <PATH vcs="Git" revision="">$PROJECT_DIR$/Phe t-RNA/DNA_pheT.fasta</PATH>
-        </FILE-GROUP>
-        <FILE-GROUP>
-          <option name="myUpdateName" value="Deleted" />
-          <option name="myStatusName" value="Deleted" />
-          <option name="mySupportsDeletion" value="false" />
-          <option name="myCanBeAbsent" value="true" />
-          <option name="myId" value="REMOVED_FROM_REPOSITORY" />
-        </FILE-GROUP>
-        <FILE-GROUP>
-          <option name="myUpdateName" value="Restored" />
-          <option name="myStatusName" value="Will be restored" />
-          <option name="mySupportsDeletion" value="false" />
-          <option name="myCanBeAbsent" value="false" />
-          <option name="myId" value="RESTORED" />
-        </FILE-GROUP>
-      </FILE-GROUP>
-      <FILE-GROUP>
-        <option name="myUpdateName" value="Modified" />
-        <option name="myStatusName" value="Modified" />
-        <option name="mySupportsDeletion" value="false" />
-        <option name="myCanBeAbsent" value="false" />
-        <option name="myId" value="MODIFIED" />
-      </FILE-GROUP>
-      <FILE-GROUP>
-        <option name="myUpdateName" value="Skipped" />
-        <option name="myStatusName" value="Skipped" />
-        <option name="mySupportsDeletion" value="false" />
-        <option name="myCanBeAbsent" value="false" />
-        <option name="myId" value="SKIPPED" />
-      </FILE-GROUP>
-      <FILE-GROUP>
-        <option name="myUpdateName" value="Merged with conflicts" />
-        <option name="myStatusName" value="Will be merged with conflicts" />
-        <option name="mySupportsDeletion" value="false" />
-        <option name="myCanBeAbsent" value="false" />
-        <option name="myId" value="MERGED_WITH_CONFLICTS" />
-      </FILE-GROUP>
-      <FILE-GROUP>
-        <option name="myUpdateName" value="Merged with tree conflicts" />
-        <option name="myStatusName" value="Merged with tree conflicts" />
-        <option name="mySupportsDeletion" value="false" />
-        <option name="myCanBeAbsent" value="false" />
-        <option name="myId" value="MERGED_WITH_TREE_CONFLICT" />
-      </FILE-GROUP>
-      <FILE-GROUP>
-        <option name="myUpdateName" value="Merged with property conflicts" />
-        <option name="myStatusName" value="Will be merged with property conflicts" />
-        <option name="mySupportsDeletion" value="false" />
-        <option name="myCanBeAbsent" value="false" />
-        <option name="myId" value="MERGED_WITH_PROPERTY_CONFLICT" />
-      </FILE-GROUP>
-      <FILE-GROUP>
-        <option name="myUpdateName" value="Merged" />
-        <option name="myStatusName" value="Will be merged" />
-        <option name="mySupportsDeletion" value="false" />
-        <option name="myCanBeAbsent" value="false" />
-        <option name="myId" value="MERGED" />
-      </FILE-GROUP>
-      <FILE-GROUP>
-        <option name="myUpdateName" value="Not in repository" />
-        <option name="myStatusName" value="Not in repository" />
-        <option name="mySupportsDeletion" value="true" />
-        <option name="myCanBeAbsent" value="false" />
-        <option name="myId" value="UNKNOWN" />
-      </FILE-GROUP>
-      <FILE-GROUP>
-        <option name="myUpdateName" value="Locally added" />
-        <option name="myStatusName" value="Locally added" />
-        <option name="mySupportsDeletion" value="false" />
-        <option name="myCanBeAbsent" value="false" />
-        <option name="myId" value="LOCALLY_ADDED" />
-      </FILE-GROUP>
-      <FILE-GROUP>
-        <option name="myUpdateName" value="Locally removed" />
-        <option name="myStatusName" value="Locally removed" />
-        <option name="mySupportsDeletion" value="false" />
-        <option name="myCanBeAbsent" value="false" />
-        <option name="myId" value="LOCALLY_REMOVED" />
-      </FILE-GROUP>
-      <FILE-GROUP>
-        <option name="myUpdateName" value="Switched" />
-        <option name="myStatusName" value="Switched" />
-        <option name="mySupportsDeletion" value="false" />
-        <option name="myCanBeAbsent" value="false" />
-        <option name="myId" value="SWITCHED" />
-      </FILE-GROUP>
-    </UpdatedFiles>
-  </component>
   <component name="RunDashboard">
     <option name="ruleStates">
       <list>
@@ -422,13 +319,20 @@
       <option name="project" value="LOCAL" />
       <updated>1542631568913</updated>
     </task>
-    <option name="localTasksCounter" value="13" />
+    <task id="LOCAL-00013" summary="clean new 16S">
+      <created>1542638711627</created>
+      <option name="number" value="00013" />
+      <option name="presentableId" value="LOCAL-00013" />
+      <option name="project" value="LOCAL" />
+      <updated>1542638711627</updated>
+    </task>
+    <option name="localTasksCounter" value="14" />
     <servers />
   </component>
   <component name="ToolWindowManager">
     <frame x="67" y="27" width="1853" height="1053" extended-state="6" />
     <layout>
-      <window_info active="true" content_ui="combo" id="Project" order="0" visible="true" weight="0.255119" />
+      <window_info active="true" content_ui="combo" id="Project" order="0" visible="true" weight="0.26065302" />
       <window_info id="Structure" order="1" side_tool="true" weight="0.25" />
       <window_info id="Favorites" order="2" side_tool="true" />
       <window_info anchor="bottom" id="Message" order="0" />
@@ -471,9 +375,6 @@
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/16S/raw_16s_alignment.fasta">
-      <provider selected="true" editor-type-id="text-editor" />
-    </entry>
     <entry file="file://$PROJECT_DIR$/16S/Newick.txt">
       <provider selected="true" editor-type-id="text-editor">
         <state relative-caret-position="270">
@@ -481,42 +382,51 @@
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/16S/cleaned_16S_alignement.fasta">
+    <entry file="file://$PROJECT_DIR$/cure.py">
       <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="4513">
-          <caret line="413" column="17" selection-start-line="413" selection-start-column="17" selection-end-line="413" selection-end-column="17" />
+        <state relative-caret-position="75">
+          <caret line="5" column="33" selection-start-line="5" selection-start-column="33" selection-end-line="5" selection-end-column="33" />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/Phe t-RNA/raw_protein_sequence.fasta">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="478">
-          <caret line="166" column="34" selection-start-line="166" selection-start-column="34" selection-end-line="166" selection-end-column="34" />
-        </state>
-      </provider>
+    <entry file="file://$PROJECT_DIR$/Phe t-RNA/cleaned_DNA_pheT.fasta">
+      <provider selected="true" editor-type-id="text-editor" />
+    </entry>
+    <entry file="file://$PROJECT_DIR$/16S/cleaned_new_16s.fasta">
+      <provider selected="true" editor-type-id="text-editor" />
+    </entry>
+    <entry file="file://$PROJECT_DIR$/Phe t-RNA/DNA_pheT.fasta">
+      <provider selected="true" editor-type-id="text-editor" />
     </entry>
     <entry file="file://$PROJECT_DIR$/OBIRapport.txt">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-1652" />
-      </provider>
+      <provider selected="true" editor-type-id="text-editor" />
     </entry>
     <entry file="file://$PROJECT_DIR$/16S/news_16S.fasta">
       <provider selected="true" editor-type-id="text-editor" />
     </entry>
-    <entry file="file://$PROJECT_DIR$/cure.py">
+    <entry file="file://$PROJECT_DIR$/16S/raw_16s_alignment.fasta">
+      <provider selected="true" editor-type-id="text-editor" />
+    </entry>
+    <entry file="file://$PROJECT_DIR$/16S/cleaned_16S_alignement.fasta">
       <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="60">
-          <caret line="4" column="15" selection-start-line="4" selection-start-column="15" selection-end-line="4" selection-end-column="15" />
+        <state relative-caret-position="6195">
+          <caret line="413" column="17" selection-start-line="413" selection-start-column="17" selection-end-line="413" selection-end-column="17" />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/16S/cleaned_new_16s.fasta">
+    <entry file="file://$PROJECT_DIR$/Phe t-RNA/raw_protein_sequence.fasta">
       <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="-7417" />
+        <state relative-caret-position="2490">
+          <caret line="166" column="34" selection-start-line="166" selection-start-column="34" selection-end-line="166" selection-end-column="34" />
+        </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/Phe t-RNA/DNA_pheT.fasta">
-      <provider selected="true" editor-type-id="text-editor" />
+    <entry file="file://$PROJECT_DIR$/Phe t-RNA/dna.newick">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="150">
+          <caret line="10" column="53" lean-forward="true" selection-start-line="10" selection-start-column="53" selection-end-line="10" selection-end-column="53" />
+        </state>
+      </provider>
     </entry>
   </component>
 </project>
\ No newline at end of file
diff --git a/Phe t-RNA/cleaned_protein_sequence_rooted.fasta b/Phe t-RNA/cleaned_protein_sequence_rooted.fasta
new file mode 100644
index 0000000..747c3cf
--- /dev/null
+++ b/Phe t-RNA/cleaned_protein_sequence_rooted.fasta	
@@ -0,0 +1,265 @@
+>Aquifex aeolicus
+MKVPYSWLSEFVELSDVSPEEIAEKLSLRSVEATVETFGIDLDGVVFGKVVEVKEHPTKKKLAVVKVQVQ
+EHIFIDVVTVDKSVREGDGVIVALPNAKVGNMCVTEREFDGVVSKGLLLSAQELGLEEKSEGVLKIHEDF
+KPGTDANEILGFGEKIIEIDITPNRGDMLSVRGVARDLSAIFRLPKKKPEEPTYEETGEFFIEIEDEDCK
+RYRGVVIEGVEIKESPLYIKKRLWQCGIKSINNVVDITNYVMLRDGQPLHAFDLSKVEGGIIVRSAKKGE
+KIITLDGEERELDEDILVIADREKPLAVAGVIGGLESGIKENTKDILLESAYFNPFRVRKASKKLGIQTE
+SSYRFERNVDIERVDRAQDYAVYLILKHAGGKVKVVKDVYREKYKPKKVFLPQGKYIRYAGESYKNEEVK
+EILDALEIPNEIMRCGVEVLVPSHRSFDIQRDVDLIEEIMRVKGYEHYTSETLKLPSIANLWKDNLLEVK
+KYLRDKGLTEVINFSFEDSKLYELLNLPLPELEVINPLNPTQRYMRNTLITSLLRTAVYNDRNYNYDQAV
+FELGKVFFKEGEENRLGILLKGNKPRTLKEEKWEPYDLTEIIAGIFALFGLEPEFRNAKRNFLHPYVQGE
+VYLEGEFVGFFGKLHPKIAKELELKGEPFVAEIEIERVLSKKRLPHYREVAKFPPVVRDIALVMDKELDV
+NKLLIDTKSQIGELLEEVRVFDVYTGEKVGEGKKSVAVRLVLRSKTGSLKDEEANELVNKLVNYLKEKYG
+VELRT
+
+>Aeropyrum pernix
+MPVIRVRRERLESLTGLSIGELEELLFRLKCEVEEPEEGVLEVEVNPDRPDMYIGEGIARAVKGIAGVEE
+GWDPPELADTPLSLRVERVPQRPYIAAAVVYGVNVDELFLEELIQFQEKLHDSLGRRRAKIAIGFHDLAK
+LPSASVEYRLMTLDTRMKPLGYGGSEMSFREFLLADEKGSLYGGLATKDNSHPFLLSGGEVIAAPPVINS
+EITRVEPGTRDLFIDVTGTSAELVAKTLDIIVASLAEREGARVGRVRLEGPGAVWASTPLLSEAAAKLDP
+GTVSKALGVDLTPEEAALHLRRMRHNASPAGGLVNVRVPPFRVDILGEVDLVEDIAISIGYEALGPRWPG
+KFHGGSLRWETHVYRAVKDLLVGLGFTEVLQLVLTSPRLVEAAGFSSMAVEVLNPVQQEYSVLRPTLLIT
+LLQTLRENQHRRKPVKVFEAGNAVYLEDGEPRDEEKLALGVLDEEAGFEDVQAPLYAVLRIMGVDFEVEE
+ASHPMFMEGRTAAVKVGGERLGYIGEVKPEVLEAFGLEYPVAAAEISLEVLARWTSRT
+
+>Bacillus halodurans
+MLVSYQWLKQYVDLDGISAEEVAEKLTRGGIEVDIIHDLNQGATGVVVGHVLECRQHPNADKLNLCQVEI
+GEEEPVQIVCGAPNVAAGQKVAVAKVGAVLPGNFKIKKAKLRGELSQGMICSLQELGVENKFVQKEFADG
+IYVFSDDVEIGSDALEALNRYDQVLELDLTPNRSDCLNMYGVAYEVAALFDKEVHWPTAESSGTDGQASD
+YVSVEIEDIEKNPYYGATIIKNVKVGPSPLWLQNRLIAAGIRPISNVVDVTNYVLLEYGQPLHAFDYDRL
+GSNKVVTRLAKEGEKMVTLDDVERTLQADHLLITNGRDPVAIAGVMGGATSEVQEDTTTVLLEAAYFDPA
+TVRKASRDLGLRSDSSSRFEKGVDPKRVREAAARAATLIAEVAGGTVVGGVVEAGELAIEEPVVSLNLPH
+MNQRLGMELSHDEVAAIFDRLGFAYTVENDTFEVTAPSRRGDIRIEEDLFEEVARLYGYDNIPTTFPVGG
+TTRGGLTDYQQKRRKIRRYLEGAGLFEVMTYSLTSEEKEKGLQGENEDYLPIRVAMPMSEERSTMRTSLV
+PHLLDVVQYNLNRKQEALFIYELGSVFLSKEETLTKQPEEREMLAGALTGFWTEHLWQGEKKAVDFFVVK
+GILEGMFAELGLSEKVTFERGEQPGMHPGRTANVKVNGRAVGFAGQIHPERQSELDLKETYVFQLDVESL
+LTEEGTEVAYEPLPRFPAISRDIALVVDENVTAAQLQQVIEANGGEWLKHVYLFDLYEGEHMEAGKKSIA
+FSLTYFDPERTLTDEEVTAVHEQILKELEASTGAVLRG
+
+>Bacillus subtilis
+MFVSYKWLEDYVDIKGMDPAVLAEKITRAGIEVEGIEYKGEGIKGVVIGHVLEREQHPNADKLNKCLVDI
+GADAPVQIICGAPNVEKGQKVAVATVGAVLPGNFKIKKAKLRGEESNGMICSLQELGIESKLVAKEYAEG
+IFVFPNDAETGRDALAALQLDDAILELGLTPNRADAMNMLGVAYEVAAILDTEVKLPQTDYPAASEQASD
+YIAVKVEDQEANPLYTAKIIKNVTIAPSPLWMQTKLMNAGIRPHNNVVDITNFVLLEYGQPLHAFDYDRF
+GSKEVVVRKAAENETIVTLDDQERKLSADHLVITNGTKAQAVAGVMGGAESEVQEDTKTILLEAAYFNGQ
+TVRKASKDLGLRSESSVRFEKGIDPARVRLAAERAAQLIHLYAGGEVLTGTVEEDHLTIEANNIHVSADK
+VSSVLGMTISKEELISIYKRLGFTVGEANDLLVVTVPSRRGDITIEEDLIEEAARLYGYDNIPSTLPETA
+GTTGGLTPYQAKRRKVRRFLEGAGLSQAITYSLTNEKKAAAFAIEKSLNTVLALPMSEERSILRHSLVPN
+LLESVSYNLARQADSVALYEVGSVFLTKEEDTKPVETERVAGAVTGLWRKQLWQGEKKPVDFFVAKGIVE
+GLLDKLNVLDSIEFVQSERKQLHPGRTANILLNGSLIGFIGQVHPSLEKELDIKETYVFELDLHALLAAD
+TAPLVYTAIPKYPSVTRDIALVTDKSVTSGQLESVIKEAGGQLLKEVSVFDVYEGEHMEEGKKSVAFSLQ
+YVNPEQTLTEEEVTKAHSKVLKALEDTYQAVLRG
+
+
+>Helicobacter pylori
+MKLSVNDLSVFVDASKDITKLCEDLSCLGLEVESCIPCIAPKNVVVGKVLEKAPHKNAEKLSVCQVDVGKEVLQIVCGAK
+NVASNQFVPVALKGAIIGSTTIAKTELRGVESHGMICSSSELGFPKINDGILELDESVGELVLGKELHEYAPFNTHVLEI
+SLTPNRGDCLSVLGIAREISAFYNTPLKPIKALNFTPTSDSIALHADENIESHLAYYLICNHSLKTPLNIKLSLAHNNAL
+SENDLNNFIEFSAHFSGVIMNAYSLNTTPMDLSVKNDENNLESVYINHQKRSTIAIKHQDQKDLSECLLLEASYIDPVSL
+SLKLHALKDKTLQKDNALIYRSARGSNPNLSDGLNFLSAQLKATILESKQTKHSLKDRTLTFQLEDITEILGLAVEKEKI
+QSILKNLGFKVSAKEPNSKPPILEVVAPSFRHDIKTIQDIAEEILRFVGIDNLVSKPLNCVSSKNSNPHYDTHRFFENLK
+HKALACGFKEVIHYVFYSKEKQQKLGFEVLEDPLELQNPITTELNTLRTSLVCGLLDASLRNKNLGFKSIALYEKGSVYN
+SKREEVQKLGFLASGLQKKESYPDAKGKAWDFYSFAECVSKVIGDFSLEKLTTQAPINHPYQSAKIIQNHEIIGVIAKIH
+PKVIQELDLFESYYAEIDASKLKRPAMLLKPFSIYPSSVRDLTLIIDENTAFSGIKKALKDAQIPNLSEILPLDIFKESH
+NSIALSVRCVIHSLEKTLNDEEVNSAVQKALEILEKEFNARLKG
+
+>Chlamydia trachomatis
+MLVSYKWLNEYVNLSNVTPQELADKMSVTGIEVEGVAVPEEGLKKIVVGEVKECVPHPNSDHLSICQVDIGEEELSQIVC
+GAPNVKAGIKVIVALPGSRIAGNQKIKKGKMRGEVSNGMICSLEELGYSDNVVPKAYAEGIYYLPQEAVNGTPVFPYLDM
+DDAIIELSITPNRADALSMRGVAYEVGAIYRQTPQFNDPELKEDASDNVGNYVTVTVEDSQDAPAYQIRVIKDVTIAESP
+QWLQNRLMNEGIRPINNVVDVTNYILLLFGQPLHAFDYQKLDSKEILVRRATAAEELITLDGETRQLTEENIVITNGKTP
+VGLAGVMGGANSEISQETTTVALEAALFNPLSIRKTSKQFNLRSESSSRFEKGINQATVGLACDVAAAMIAELANGTVVS
+GTAVGSEVAVKEAQVAVTLERINQYLGTALDEATVNEIFEALGFAYEVNQGAYEITIPPRRWDIAIEADIIEEVARIYGY
+DHLPSTLPSGETVAGSLTKAQHVTRQLKSLLEGHGTSEAISYALTTEEKSRQFMMKESQTTRLQWPMSEERSVLRMNLIS
+GLLDDVAYNVARKNNNIAFYEVGRVFYQTEDPTKNLPTEENHLALALTGNTMVKDWQTKATAVDFYTVKGLVESIVAVLG
+LTEKISYQATTAIPEMHPGRTAWIYLEDEVVGFVGQVHPTTAKAYDIPETYVAELNLQQLVATEAGGVTYEAVSKFPAVS
+RDIALLVDETVTNQELVKTISDNAGKYLKEIHLFDVYQGEKLGAGKKSMAYSLTFVNAEATLVDEEINRSMEKVEKALIE
+KHQVEVR
+
+>Deinococcus radiodurans
+MKLPYSWLKELIPDLPPVADLEPTFAHLGLPLEGVEDVPAPVGGVLLVAVKAAEPMEGTQLTKLTLDTGENGEKTIASGA
+PNAVGLPAGTMVALVTPGTTLGGITYGVRPMQGVESWGMAASAKELGIGESNAGILTFPAGTAAPGTPLRELWPADSVLD
+VEVTPNRADVLSALGLARDLAAYLNLELKEPQIPAAPTQPGEIRVSLPDRGRVLDRDPQGKLRFGCDHFAARAVSGLQNG
+PAPLWMQRRVSLAGMRSIDLIVDTSNYVMLELGQPTALYDRRDVAGDGLVVAFGLREGETVKDLLGNTHQVGPEDLLILD
+AGMSDEPVMTVAEAFASAGQPKEGSHVLGIAGIMGGDHGHVRADTRDVVIESAHFDPVLLRRTSTRLGLKTDAVYRYERG
+VDPLLAPKAAVRVAELLRAAGGTPEAGQTVVGTPEVPQTITTTGEQIRALLGMHIGTAEMRESLTRLGCTVTGDGDSLTV
+TPPSWRVDMVIWQDLAEEVARLHGFTELPETLPTLRVHESNIGASAQSEARAELRRTLAGLGFQEVVTYTFTSDEEAQKA
+RAEAPGVRLRNPMTTDRTGMRTALYPSLLRAAGAHPKGERALLFEIGRIFPAAGEQERLGLLMRGDLAARTYQDGVRGDF
+SVFKGLVQGFAGAVGASFALEQLRGDDVPAALHPGVAGAVVWNGERVGWLGALHPEIAQEFGLKGDTFLMEAALPLPGRD
+WAFRDPSRAPAAWRDLAVIAPQGVSYGDIVGVLKGAGGELLESVEPFDVFTGEQVGAGNRSVAVRLTYRGAKTLTDEEVD
+PVFNAQIDAVKARGWAIREK
+
+>Chlamydia pneumoniae
+MRIPITLLQTYFSEPLSTKEILEACDHIGIEAEIENTTLYSFTSVITAKILHTIPHPNADKLRVATLTDGEKEHQVVCGA
+PNCEAGLIVALALPGAKLFDSEGKAYTIKKSKLRGVESQGMCCGADELGLDELQIQERALLELPEATPLGEDLATVLGNT
+SLEISLTPNLGHCASLLGLAREICHVTQANLVIPKEFSFENLPTTALDMGNDPDICPFFSYVVITGISAQPSPIKLQESL
+QALKQKPINAIVDITNYIMLSLGQPLHAYDASHVALDSLRVEKLSTPESLTLLNGETVLLPSGVPVVRDDHSLLGLGGVM
+GAKAPSFQETTTTTVIEAAYFLPEALRASQKLLPIPSESAYRFTRGIDPQNVVPALQAAIHYILEIFPEATISPIYSSGE
+ICRELKEVALRPKTLQRILGKSFSIEILSQKLQSLGFSTTPQETSLLVKVPSYRHDINEEIDLVEEICRTESWNIETQNP
+VSCYTPIYKLKRETAGFLANAGLQEFFTPDLLDPETAALTRKEKEEISLQGSKHTTVLRSSLLPGLLKSAATNLNRQAPS
+VQAFEIGTVYAKHGEQYQETQTLAILLTEDGESRSWLPKPSLSFYSLKGWVERLLYHHHLSIDALTLESSALCEFHPYQQ
+GVLRIHKQSFATLGQVHPELAKKAQIKHPVFFAELNLDLLCKMLKKTTKLYKPYAIYPSSFRDLTLTVPEDIPANLLRQK
+LLHEGSKWLESVTIISIYQDKSLETRNKNVSLRLVFQDYERTLSNQDIEEEYCRLVALLNELLTDTKGTINS
+
+>Campylobacter jejuni
+MIITKSWLSEWLELEDKNLDDIAKTLNSIGIEVDRICSLRVPDKIVVGFVKEKVKHENSDKLSICQVDIGSEILQIVCGA
+VNVEIGQFVAVALKGALMPNGMEIKEAKLRGVDSCGMLCSSTELGFEKINEGIILLDESIGKLELGKALNSYEIFNDGLI
+EVELTPNRGDCLSVYGIARDLAVALNLNLKESASFKEGENVLGIGRILRLATQKELNSLYNYRAIELQEKIQTSLLISLR
+LAQIENLGKNSIENFLNYATHSTGVIFNAYDLSEISKENEEITLNLSKENYGETKILCQDKLLSVSGIYQEERFKCKEDS
+KIVIIEANYTDPMIIADAKIAYEKQDEKIIYRSFRGSEPRLNLGMDFLLNVLEKIPNLIIYSSSQQILTDKELPTISVSI
+EGISNIIGQNVDKDEVLKILKKLGFELILSGDGLINVKAPIHRPDIKNLADICEEVVRIIGIDNITSKGLEFIEKNRLNS
+TYKNYKELVELRKKAVENGYFESLHYVLDSEEELKMLGFNPTKLKIINPITAELNTLRTTLLNHLLNAASLNAKNAKKTI
+KLFELGIVFGANNEELNHIAFVYSGYKEEAKISNKAKPEFVNFYDFLLELKNIIGDFKLKASKYSILSPYEQADVYIGEL
+KIGFVGRLHLKIENERDLLKTYICELDLNLIKPKFKTAKAYSRFPSISRDLSVLIPKGFAYEKIRSCIEELGLEILENFR
+LVDLYSDENLKESYSLTMSFIFRDMNKTLEENQVAECMDRILQNLNNLGLELR
+
+>Escherichia coli
+MKFSELWLREWVNPAIDSDALANQITMAGLEVDGVEPVAGSFHGVVVGEVVECAQHPNAD
+KLRVTKVNVGGDRLLDIVCGAPNCRQGLRVAVATIGAVLPGDFKIKAAKLRGEPSEGMLC
+SFSELGISDDHSGIIELPADAPIGTDIREYLKLDDNTIEISVTPNRADCLGIIGVARDVA
+VLNQLPLVQPEIVPVGATIDDTLPITVEAPEACPRYLGRVVKGINVKAPTPLWMKEKLRR
+CGIRSIDAVVDVTNYVLLELGQPMHAFDKDRIEGGIVVRMAKEGETLVLLDGTEAKLNAD
+TLVIADHNKALAMGGIFGGEHSGVNDETQNVLLECAFFSPLSITGRARRHGLHTDASHRY
+ERGVDPALQHKAMERATRLLIDICGGEAGPVIDITNEATLPKRATITLRRSKLDRLIGHH
+IADEQVTDILRRLGCEVTEGKDEWQAVAPSWRFDMEIEEDLVEEVARVYGYNNIPDEPVQ
+ASLIMGTHREADLSLKRVKTLLNDKGYQEVITYSFVDPKVQQMIHPGVEALLLPSPISVE
+MSAMRLSLWTGLLATVVYNQNRQQNRVRIFESGLRFVPDTQAPLGIRQDLMLAGVICGNR
+YEEHWNLAKETVDFYDLKGDLESVLDLTGKLNEVEFRAEANPALHPGQSAAIYLKGERIG
+FVGVVHPELERKLDLNGRTLVFELEWNKLADRVVPQAREISRFPANRRDIAVVVAENVPA
+ADILSECKKVGVNQVVGVNLFDVYRGKGVAEGYKSLAISLILQDTSRTLEEEEIAATVAK
+CVEALKERFQASLRD
+
+>Methanothermobacter thermautotrophicus
+MPVITFDYDDLKELGIDIDREKLLDVLPMMGSDIEDFDDESIKVEFFPNRPDLLSVEGVARSLRGFLGIEKGMPSYDVHD
+SGVEVTVDESVLDVRPYLGMAVIEDVQFTDKKLKQVMEFQEDLHWVIGRDRRKVAIGIHDLDRVEPPFLYSGVEPEGVTF
+TPLDSVCEMTPHEILEEHPKGVSYAHLLRDHDRYPLITDKNGDVLSMPPIINGELTKLTVNTRRILVDVTGTDDRAVRQT
+LNIICTSFAEAGGRIGSVRVKRPDGELHLPDLTPREMRVSVSEASRITGLELSADEVMDLLMKARMDARRTSDDEVVAVI
+PAYRVDILHEVDLVENIAVQHCIGRIEPELPDIATIAEEDTWSRADASIREVMVGLGFQEVMSLMLTSEESHYRRMRLEE
+DERVEVAQPISQDRTMIRKSLLNGLLEFFEDNKHEDLPQKIFEVGDVVYINPESETRSRVVTKLACAVTHSSAGFTEIKS
+LAAAVVENLGYEFRIEPLEHPSFIEGRCAAIESEGKSSAIGGFFGEVHPEVVTNFNLEYPVIALEIEFK
+
+>Mycobacterium tuberculosis
+MKFSELWLREWVNPAVSSDALSDQITMAGLEVDGTEAVAGQFNGVVIGEVVECGQHPNADKLRVTKVNTGGDRLLDIVCG
+APNCRQGLRVAVATVGAVLPGDFKIKAAKLRGEPSEGMLCSFSELGISADHSGIIELPADAPIGTDLRDYMKLDDTAIEI
+SITPNRADCLSIRGVARDVAVLNKMDYQAPDMSPVAAVHQDTFPIRVDAPQACPRFTGRVIKNVDVTAKTPLWMVEKLRR
+GGIRSIDPVVDITNYVLLELGQPQHAYDLDTLEGELIVRMAEQGEKLTLLDGNEVTLTDNILVIADRRGALGMAGIFGGE
+HSGVSDTTKNILLETAFFNPLAITGRARQYGLHTDASHRFERGVDPQLQRIAAERTTRLILDICGGEPGEIIEVVSEADL
+PKTATIILTRNKLDRLIGHHVDDAQVTDILTRLGCDVKMSQDQWLVTAPSWRFDMEIEEDLVEEVARIYGYNNIPDVPLR
+ADLIMTSRHEAHLPLKRVKTLLVDRGFQEAITYSFVDPKIQTLLHPGQDAIILPNPISADMSAMRLSLLTGLLSTVVYNQ
+NRQQSRVRLFESGLRFVPDAAADLGIRQETMLAGVIAGNRNEEHWSSEKQVVDFYDLKGDLEAILELTGKLDRVSFKATT
+NPALHPGQGAEIYLEDEHIGYIGVVHPELEKKLDLNGRTVVFEIRWDALTNRIIPEAEAISRFPANRRDIAIVVPENVAA
+QDILNECKKVGVNQLVGINLFDVYCGKGVAEGYKSLAISLTLQDTERTLEEDEIAATVNKCVAALQQRFKASLRD
+
+>Neisseria meningitidis
+MQFSYSWLKTQANPDLSADKLEHLLTMAGLEVEEIDTAAPAFSGVVVAEVKSVEKHPDADRLNVTQVDAG
+TGELVQIVCGAPNVKPGIKVPCSLPGAVLPGNFKIKPTKMRGVPSNGMLCSTNELGLPDDGVDGLHILPE
+DAPVGTNIREYLDLDDTLFTLKITPNRADCLSVKGIAREVSALTQCAFTPVEIQTASIGSEKKQAVRIDA
+PADCGRFISRVIENVNAEAATPDWMKQRLERSGIRSISALVDIGNYVMLEIGQPMHVFDADKLSGSLIVR
+RAQNGETLACLNEKTVTLADNTLVVADEKGVLSLAGLMGGEASAVSDDTQNIVLEAAWFAPEIIAGKSRQ
+YGFGSDSSFRFERGVDYRLQADAIERATELVVQICGGAAGEMVEAQGKLPEAKQVELRLGRLKTVLGVEI
+SAEQVEIILQHLGLQPEKTAEGFRVTSPSFRFDIEIEADLIEEIGRVYGYENIPDDYTSGRLKMLALPET
+KRPRFAVYNEMAARGYREVVSYAFVDEQWEQDFAANTNPIRLQNPLAAQYAVMRSTLIGGLVEVLQNNLN
+RKQNRVRVFEIARVFSKDSADQFVQNERIGGLWYGSVLPEQWGEKTRNVDFYDIKADVESLLKNKEVSFV
+KTEHPALHPGRAANIVSDGRVVGFVGELHPKWLQKYDLPQAPLVFEIDMDAVLGREKTRYQSVSKFQAAR
+RDLAFVMPEAVTHDDLLNALKAAANKLVQEISVFDVYRGTGVPEGMKSVAVKIILQDMENTLTDEVIEPL
+VAKMIKAAAEKDAQLRA
+
+>Pseudomonas aeruginosa
+MKFSEKWLRSWANPQVSHDELVARLSMVGLEVDADLPVAGAFSGVVVGEVLSTEQHPDADKLRVCQVSNGSETFQVVCGA
+PNVRAGLKIPFAMIGAELPGDFKIKKAKLRGVESFGMLCSAKELQISEENAGLLELPADAPVGQDVRTYLELDDYTIEVG
+LTPNRGDCLSLAGLAREVSAIYDVPLAPVAVDAVAAQHDETRPVELAAPAACPRYLGRVIRNVDLSRPTPLWMVERLRRS
+DIRSIDPVVDVTNYVMIELGQPMHAFDLAEINGGVRVRMAEDGEKLVLLDGQEITLRADTLVIADHQRALAIAGVMGGEH
+SGVSDSTRDLFLEAAFFDTIALAGKARSYGLHTDSSHRFERGVDSQLARKAMERATRLILDIVGGEPGPIVEQVSEAHLP
+KVAPITLRAERVTQMLGMPLDAAEIVRLLQALELTVVADGEGQWSVGVPSHRFDISLEVDLIEELARLYGYNRLPVRYPQ
+ARLAPNNKPEARAALPLLRHLLVARGYQEAITFSFIDPVLFELFDPGTQPLTLANPISADMSAMRSSLWPGLVKALQHNL
+NRQQSRVRLFESGLRFVGQLEGLKQEAMLAGAICGKRLPEGWANGRDGVDFFDAKADVEAVLASAGALADFSFVPGEHPA
+LHPGQTGRIERDGRLVGYLGALHPELAKKLDLEQPVFLFELLLAEVVDGHLPKFRELSRFPEVRRDLALLVDQDVPAQDI
+LTQIRAAAGEWLTDLRLFDVYHGKGIDPHRKSLAVGLTWQHPSRTLNDDEVNSTTQNIVTSLEERFNATLRK
+
+>Rickettsia prowazekii
+MKFTLSWLKQFLEISASVTEIAEALTDIGLEVEEVIDKSKELQKFEVAYIRNIKPHPSADKLKLCDVETK
+NGILQIVCGASNVRADIKVVLANIGIEIPKGNLKIKESVIRGQKSYGMLCSEEELLLSSNSDGIIELPKD
+AVVGDNFTKYYGLDDPIFVINVTPNRGDVLGVYGIARDLSAKGLGTLKELELSEIKSTFFSKIKLNVHDK
+EACPLFTFREIRNLKNKPSPNWLQQLLKNVGIKTISSLVDVTNYISHSFGQPIHAYDADKIYGGISVDCY
+IRSDKVISCKNHEMATAVLQFSNDSANFYAINGKGYLLTENDLVIKDESGIQGLAGIIGGAKSSCNDSTT
+NVILEAACFNAKMVAASGRRLKIDTDARYRNERNIDRNFTEKALNIATNLILSICGNCEVSEVVKVGEQE
+PQKKPLDFSVYFLEKITGIKLSIQEIEDILNKLGFITDVKGDIIKVIAPSWRHDINILEDIAEEIVRIYG
+YDKIESIKLPELYQNNNLREYKRISSFKRILASKGYDEVVTNSFMSSEDAKLFAELKEGLFLLNPMSIEE
+NYMRPTVLPNLISIVSKNLARDVKDMAFFEVGPSFVNLNIESTYLTAIISGAFNNKNPHSFGRNYDIFDI
+KGDLEQVIEYAGLSLDKCIVIDETVLPQYYHPTRAINIRLGKNLLGHFGQIHPKILKYYDINQEIFAFEL
+NITNLPLIKAKFGKRDEFTVSDYQANFRDYSFIVDQDHKVGEIISYIKNFNKKLVKSVMLFDIYSGDKLP
+EGKKSIAIKIKLQADDRTLSETDLNSFSEDLVASISQKFQGILRE
+
+>WP_010873010.1 MULTISPECIES: phenylalanine--tRNA ligase subunit beta [Synechocystis]
+MRISVNWLQSLVELNLSPEELGELLTIAGLEVEEIEDRRSWAAGVVLGRVISREKHPNADKLSVCVVDIG
+TEEPSTIVCGAANVRADILVPVATLGSYLPKVDLKIKPAKLRGVKSSGMICSLAELGLSKESEGIHIFPD
+LDLPSGSPVGPLLGLDDVILEISPTANRADALSMVGVAREVAALTGGKLSLPEIKAVSVSDQDLPISVTE
+PQACPTYVGTVIRGVKVGPSPDWLQQRLLAAGTRPINNVVDVTNYVLLEWGQPLHSFDQDKLQTLVGPEG
+FALGVRFAEEGEKLITLDDQERTLQPQNLLVTANDQPVAIAGVMGGAATEVDENTQNIVLETALFDGVTI
+RKSSKAINLRSESSTRYERGVNRCELEVALHRAIALMTELAGGTVVRQGKADQRQDRGEAIINLRLERLQ
+QLLGKVNTPTGIGNITAEDVERILTDLGCGLTRQSDSDTPVWAVTVPSYRQRDIEREIDLIEEVARLYGY
+DHFCEQLPSNTIAGGLSPSYQAELALREACRGVGLTEVVHYSLVKPHGSEVMLANPLFAEYSALRTNLLD
+GLITAFANNQAQNNGALNAFEVGRVFWQNEGDIGEADHLAGICGGSQITEGTWPQGGKPQPMSWYDAKGL
+LEAIFQRLGATVTYSGDHQDPRLHPGRTALLSCNGTVLGRFGQLHPQLRREKGLIDEVYAFEITLTPLYQ
+AMETQILGTPDFRPYSPYPAVARDLALYAPLELTVAELTQAMVKAGGDLLEQVELFDEYRGQSVPAGQRS
+LAFSLAYRVGDRTLTDADVEPLHNQIREALTKQFAVSLRS
+
+>Xylella fastidiosa
+MKFSENWLRNHVPIQANRDVLVATLTAIGLEVENVAVLGEALDLIVVARIVNVVPHPESDLLQICQVDVAQDNLLQIVCG
+ASNVRPGLVVPLALLGAKIGALTIKSTTLRGVESNGMLCSAKELGLDTEASGLMELPEDAPIGTPLADYLALPDASIEIK
+LTPNRADCFSVRGIAFDVAAACASEVTPFHIDEIPAVSARTLPVELHAGANAPRYCGCVIEGIDSAAPTPVWMAERLRRS
+GIRPVSLLVDITQYVMLELGQPMHAFDVDTLRGPIGVRLSRNDEALKLLDGRTVVLDNDFLVVTDADQPIALAGLIGGWE
+TRITDTTVNVFLEAAHFAPAAIMGRGRKLGLHTDASHRFERGVDPALPPQAIAFATRLILELAGGKPGSLIHVELPEYLP
+APASILLRRTRIARLLGIVIDDAEVERILQALGMQVTTQAEGWRVVAPSRRFDIAIEEDLIEELVRIRGYEHLPTALPVG
+ASHIAMPSETRLDMTSVRRQLIARELQETINYAFIDAELLRRWQLNTGQVMLMNPLSAELAVMRPRLLPGLVAALGRNIA
+RQLERVRLFELGNVFTASDEAGVAPLETRHVAAAVCGDAFALQWGEQVRKVDFYDLKGDLESLAAASGAVLTFHSSAQPW
+GHPGRSADVWCDDMCIGWIGQLHPALTQTLEINVDVIAFELALEPLVRRALPRAHALSRFPFVRRDLACVVPEHVTWSEL
+AITVRDVIGPLLRDVKLFDRYVGKGIEPGFKSLAIGLILQDDTRTLIDRDVDDIMTKVVMAIQQRHDVRIRS
+
+>Thermotoga maritima
+MRVPESWLREFVDLDWDIEQIAERLTFSGTSVEDILRPFNVSGEIITARVIERFDHPASEKLIVCKVDTGKRIYTVITAD
+KTVNEGDYVILALEGATLNNGLKIEPREFKGVISEGMLCSLEELGLEEKSDRVYRFPDPVELGVNVVEEYGLNERVLDIE
+ITPNRPDCLSIIGVARELSALSGRPLNKPQPDVSFVDEDVQFDVEIEDVEGCPRYSARIMKGVTVKDSPLWMKARLVAAG
+VRSLNNVVDATNYVMIELGHPVHAFDLNRLKNKRIVVKSAKGGERVLLLDEKEYELKGGEVLITDGENVLALGGIMGGME
+SGVYDDTRDLVLEVAYFDPVRIRKAAKALGISSESSYRFERGVDPNDVELVSLRLAELIQKLAGGYVLRKFWDVYPRKIE
+PKKVMLRKARIEKILGTKVEEPGDILRRLEFQVEDRGDSYEVLVPTFRPDVEREIDLIEEIGRIYGYEKVESKVISVPAV
+NRGWGEKQLFRREISQFMKGMGFDEVVTFSFVDSQKVKKWPLVDREPIALSNPIASDMDVMRTSQFYSLIQVLAENFKRQ
+NRDLKLFEIGKIYFKENGNFREIETLSAMSCGLENPGDYTDKRSVSFYTIKGVLDELFFRLGVNVVYRAAEIPGLFPTRS
+ARIYVENREIGFIGMVDPKLLDEYDVKEDTYFFEIDMELLRKYASKRPAYRPTPRFPAVRRDISFLLPKGFESVKIIELF
+KKSGGDLVEEVGVFDIYEGKGIPENMVSVTLYVVFRHPERTLTDEEVNKIFEEMVQKAEREFGIRRRF
+
+>Ureaplasma urealyticum
+MILSLNLLHKISPKLKKISLNELCTALMDLGCEVETINTIKPSTNLVFAKVLEKTKHPNANHLNLVKVKANQEVYEIVCG
+ADNFNVNNWVVLAKINAELANGLKITPRELRGYVSNGMLCAYSEINPEVAHFLGQTDSDGILVLHDSYDHYKTPNQIFNL
+DDVILDLSIPSNRNDLNGYFWMAKELCAYFDLEYVIDATINHRSHKEIVNVRILSDDVNSYGMIEVKNIQNYTLKWNTKS
+VLVNNQIKIVNNFADNMNFLTLLTANPLHAFDAHKISGQIIVKNAEEDSILLGLDQKEYAIKKGDLIIVDDQKILALAGI
+IGSNDSKIDNNTTTAYIECANFNPLLIANTARRLKINTTAAMRFSKPLTNYVTKATLKKLLAHFKLDAKLICYFKHLVHN
+VIKNKIDQVSDFVGTKINLDTAHTFLKRLGYKINKTNLITPSHRYDVLNEFDVYEDIMKKFSIQQIKPQPINFDILSFKN
+NIAYDFEKKVSDFLVDQGLFECKTYNLKSQTQAYEFDFFNFQQAYEINNPISNIRSHLKLNNLNSLLEVLEYNQNQKNEL
+ENIFEISKINPINSNQQTILSIVLCKPLINAKLNDSIVVNNFVTTKALLHVLLTKLNISYVYDTNHIVNELYENNQLALV
+NENKQVFGFIGQLKNQIKKTYGLNNDIFVINLNLTSYLNQEQAITKVIKPSVYHDIVRDVSVKLASNVDLNDVMDNIEKI
+KNIRKVEISDLYVKDDEIIYTFKYYINDYSSNLSSEQIAVIEQEVNNYLKQF
+
+>Vibrio cholerae
+MKFSESWLREWVNPAITTDELTHQITMAGLEVDDVLAVAGVFDGVKVGHVVECAQHPDADKLRVTKVDVGEEELLDIVCG
+AANCRQGLKVAVATVGATLPGDFKIKKAKLRGQPSHGMLCSFSELGIDVESNGIMELAENAPIGMDFRDFLSLNDVTIDV
+DLTSNRADCFSIRGLAREVGVLNRADVTAPAVNAIAATINDTIAIDVKAPAACPRYLGRIVKNVNVQAQTPLWMQEKLRR
+CGIRSIDPVVDITNFVMLEQGQPMHAFDLAKIEGGIVVRLAEQDEKLTLLDGSEAKLNADTLVIADQQKALAIAGVFGGE
+HSGVSTETKDVLLECAFFAPDHIRGRARSYGLHTDSSMRFERGVDYALQHAAMERATQLLVEICGGDVAPVVAAESAADL
+PKPNQVTLRRTKLDKLLGHAIPDADVVEILERLGMQVATTAEGWQATAPTWRFDIAIEQDLVEEVGRIYGYNNIPNQAPV
+AALNMNLHNEAKLPLKRVRDLLVDRGYQEAITYSFVEPEQQKLVVPGVDALILPNPISAEMSAMRLSLIQGLLNTVVHNQ
+KRQQPRVRLFEYGLRFIPDAAAENGMRQEPMLAGVISGARGEEHWNMETATVDFFDMKGDLEAVLELTAKGKAYSFAATK
+HPALHPGQAAAIMVDGKAIGVIGTVHPELERKFGLNGRTIVFEIEWNAINTRVIPEAAAISKFPANRRDIALVVDGNIAS
+GDIVEACRVAGGELLKDAKLFDVYVGKGVEEGKKSLAIALTLQSVERTLEEADIAAAVEAIVQAVSAQFGAALRD
+
+>Puccinia sorghi (Fungi)
+MPTITVEKERFFKDLGKTFRDEKEFDGILFDYGLELDEDTQLTTPEEKPYKLKIEVPANRYDLLCHQGLV
+LALRTYMGTSPAPNYSLSIPPPEHQWKAYVRKETSQIRPFFASAILRGIHFDEQRYKDFIDLQDKLHGNL
+CRKRTLVAIGTHDLSTLDHSNKIISYEARPPQDIKFIPLNKQSEYDATQLMTLYESIRRTNDFHLINWTC
+TRINSNKTKITLDTKDVFIDVTATDQTKLGIVINIIITMFSQYCSKPFTVEPVDIIYEHDVGSSYRSPNI
+EPLIFATRQSYINSVTGLSLTREATMALLGKMGHQASKGASANKPAINASTSVVLQNAPHDDLLNVAVPP
+TRPDILHECDLVEDVAISYGFNNLKKTFPSTNTVAKPYPINKLSDLVRKECAFAGWLEVLPLTLCSHDEN
+FRFLGKEDDGREAVILSNPATIEFQVVRTSLLPGLLKTIRENRKQPLPMKVFEVSDVVKKDSSLERKARN
+TRRLGAVFVGKKSAGFEVVHGLLDRILAMLDIHWIGLTSDPSSRKSFRGQYQIEESNHPTFFPGRSARIL
+FQPSVLIKKEGQEEGWTEIGRLGIVHPDVLQHFALDFPCSALEIDLLPFL
+
diff --git a/Phe t-RNA/raw_protein_sequence_rooted.fasta b/Phe t-RNA/raw_protein_sequence_rooted.fasta
new file mode 100644
index 0000000..9c4a4d4
--- /dev/null
+++ b/Phe t-RNA/raw_protein_sequence_rooted.fasta	
@@ -0,0 +1,265 @@
+>WP_010881123.1 phenylalanine--tRNA ligase subunit beta [Aquifex aeolicus]
+MKVPYSWLSEFVELSDVSPEEIAEKLSLRSVEATVETFGIDLDGVVFGKVVEVKEHPTKKKLAVVKVQVQ
+EHIFIDVVTVDKSVREGDGVIVALPNAKVGNMCVTEREFDGVVSKGLLLSAQELGLEEKSEGVLKIHEDF
+KPGTDANEILGFGEKIIEIDITPNRGDMLSVRGVARDLSAIFRLPKKKPEEPTYEETGEFFIEIEDEDCK
+RYRGVVIEGVEIKESPLYIKKRLWQCGIKSINNVVDITNYVMLRDGQPLHAFDLSKVEGGIIVRSAKKGE
+KIITLDGEERELDEDILVIADREKPLAVAGVIGGLESGIKENTKDILLESAYFNPFRVRKASKKLGIQTE
+SSYRFERNVDIERVDRAQDYAVYLILKHAGGKVKVVKDVYREKYKPKKVFLPQGKYIRYAGESYKNEEVK
+EILDALEIPNEIMRCGVEVLVPSHRSFDIQRDVDLIEEIMRVKGYEHYTSETLKLPSIANLWKDNLLEVK
+KYLRDKGLTEVINFSFEDSKLYELLNLPLPELEVINPLNPTQRYMRNTLITSLLRTAVYNDRNYNYDQAV
+FELGKVFFKEGEENRLGILLKGNKPRTLKEEKWEPYDLTEIIAGIFALFGLEPEFRNAKRNFLHPYVQGE
+VYLEGEFVGFFGKLHPKIAKELELKGEPFVAEIEIERVLSKKRLPHYREVAKFPPVVRDIALVMDKELDV
+NKLLIDTKSQIGELLEEVRVFDVYTGEKVGEGKKSVAVRLVLRSKTGSLKDEEANELVNKLVNYLKEKYG
+VELRT
+
+>Q9Y9I3.1 Phenylalanine--tRNA ligase beta subunit [Aeropyrum pernix]
+MPVIRVRRERLESLTGLSIGELEELLFRLKCEVEEPEEGVLEVEVNPDRPDMYIGEGIARAVKGIAGVEE
+GWDPPELADTPLSLRVERVPQRPYIAAAVVYGVNVDELFLEELIQFQEKLHDSLGRRRAKIAIGFHDLAK
+LPSASVEYRLMTLDTRMKPLGYGGSEMSFREFLLADEKGSLYGGLATKDNSHPFLLSGGEVIAAPPVINS
+EITRVEPGTRDLFIDVTGTSAELVAKTLDIIVASLAEREGARVGRVRLEGPGAVWASTPLLSEAAAKLDP
+GTVSKALGVDLTPEEAALHLRRMRHNASPAGGLVNVRVPPFRVDILGEVDLVEDIAISIGYEALGPRWPG
+KFHGGSLRWETHVYRAVKDLLVGLGFTEVLQLVLTSPRLVEAAGFSSMAVEVLNPVQQEYSVLRPTLLIT
+LLQTLRENQHRRKPVKVFEAGNAVYLEDGEPRDEEKLALGVLDEEAGFEDVQAPLYAVLRIMGVDFEVEE
+ASHPMFMEGRTAAVKVGGERLGYIGEVKPEVLEAFGLEYPVAAAEISLEVLARWTSRT
+
+>WP_010899254.1 phenylalanine--tRNA ligase subunit beta [Bacillus halodurans]
+MLVSYQWLKQYVDLDGISAEEVAEKLTRGGIEVDIIHDLNQGATGVVVGHVLECRQHPNADKLNLCQVEI
+GEEEPVQIVCGAPNVAAGQKVAVAKVGAVLPGNFKIKKAKLRGELSQGMICSLQELGVENKFVQKEFADG
+IYVFSDDVEIGSDALEALNRYDQVLELDLTPNRSDCLNMYGVAYEVAALFDKEVHWPTAESSGTDGQASD
+YVSVEIEDIEKNPYYGATIIKNVKVGPSPLWLQNRLIAAGIRPISNVVDVTNYVLLEYGQPLHAFDYDRL
+GSNKVVTRLAKEGEKMVTLDDVERTLQADHLLITNGRDPVAIAGVMGGATSEVQEDTTTVLLEAAYFDPA
+TVRKASRDLGLRSDSSSRFEKGVDPKRVREAAARAATLIAEVAGGTVVGGVVEAGELAIEEPVVSLNLPH
+MNQRLGMELSHDEVAAIFDRLGFAYTVENDTFEVTAPSRRGDIRIEEDLFEEVARLYGYDNIPTTFPVGG
+TTRGGLTDYQQKRRKIRRYLEGAGLFEVMTYSLTSEEKEKGLQGENEDYLPIRVAMPMSEERSTMRTSLV
+PHLLDVVQYNLNRKQEALFIYELGSVFLSKEETLTKQPEEREMLAGALTGFWTEHLWQGEKKAVDFFVVK
+GILEGMFAELGLSEKVTFERGEQPGMHPGRTANVKVNGRAVGFAGQIHPERQSELDLKETYVFQLDVESL
+LTEEGTEVAYEPLPRFPAISRDIALVVDENVTAAQLQQVIEANGGEWLKHVYLFDLYEGEHMEAGKKSIA
+FSLTYFDPERTLTDEEVTAVHEQILKELEASTGAVLRG
+
+>WP_072566655.1 phenylalanine--tRNA ligase subunit beta [Bacillus subtilis]
+MFVSYKWLEDYVDIKGMDPAVLAEKITRAGIEVEGIEYKGEGIKGVVIGHVLEREQHPNADKLNKCLVDI
+GADAPVQIICGAPNVEKGQKVAVATVGAVLPGNFKIKKAKLRGEESNGMICSLQELGIESKLVAKEYAEG
+IFVFPNDAETGRDALAALQLDDAILELGLTPNRADAMNMLGVAYEVAAILDTEVKLPQTDYPAASEQASD
+YIAVKVEDQEANPLYTAKIIKNVTIAPSPLWMQTKLMNAGIRPHNNVVDITNFVLLEYGQPLHAFDYDRF
+GSKEVVVRKAAENETIVTLDDQERKLSADHLVITNGTKAQAVAGVMGGAESEVQEDTKTILLEAAYFNGQ
+TVRKASKDLGLRSESSVRFEKGIDPARVRLAAERAAQLIHLYAGGEVLTGTVEEDHLTIEANNIHVSADK
+VSSVLGMTISKEELISIYKRLGFTVGEANDLLVVTVPSRRGDITIEEDLIEEAARLYGYDNIPSTLPETA
+GTTGGLTPYQAKRRKVRRFLEGAGLSQAITYSLTNEKKAAAFAIEKSLNTVLALPMSEERSILRHSLVPN
+LLESVSYNLARQADSVALYEVGSVFLTKEEDTKPVETERVAGAVTGLWRKQLWQGEKKPVDFFVAKGIVE
+GLLDKLNVLDSIEFVQSERKQLHPGRTANILLNGSLIGFIGQVHPSLEKELDIKETYVFELDLHALLAAD
+TAPLVYTAIPKYPSVTRDIALVTDKSVTSGQLESVIKEAGGQLLKEVSVFDVYEGEHMEEGKKSVAFSLQ
+YVNPEQTLTEEEVTKAHSKVLKALEDTYQAVLRG
+
+
+>WP_079307819.1 phenylalanine--tRNA ligase subunit beta [Helicobacter pylori]
+MKLSVNDLSVFVDASKDITKLCEDLSCLGLEVESCIPCIAPKNVVVGKVLEKAPHKNAEKLSVCQVDVGKEVLQIVCGAK
+NVASNQFVPVALKGAIIGSTTIAKTELRGVESHGMICSSSELGFPKINDGILELDESVGELVLGKELHEYAPFNTHVLEI
+SLTPNRGDCLSVLGIAREISAFYNTPLKPIKALNFTPTSDSIALHADENIESHLAYYLICNHSLKTPLNIKLSLAHNNAL
+SENDLNNFIEFSAHFSGVIMNAYSLNTTPMDLSVKNDENNLESVYINHQKRSTIAIKHQDQKDLSECLLLEASYIDPVSL
+SLKLHALKDKTLQKDNALIYRSARGSNPNLSDGLNFLSAQLKATILESKQTKHSLKDRTLTFQLEDITEILGLAVEKEKI
+QSILKNLGFKVSAKEPNSKPPILEVVAPSFRHDIKTIQDIAEEILRFVGIDNLVSKPLNCVSSKNSNPHYDTHRFFENLK
+HKALACGFKEVIHYVFYSKEKQQKLGFEVLEDPLELQNPITTELNTLRTSLVCGLLDASLRNKNLGFKSIALYEKGSVYN
+SKREEVQKLGFLASGLQKKESYPDAKGKAWDFYSFAECVSKVIGDFSLEKLTTQAPINHPYQSAKIIQNHEIIGVIAKIH
+PKVIQELDLFESYYAEIDASKLKRPAMLLKPFSIYPSSVRDLTLIIDENTAFSGIKKALKDAQIPNLSEILPLDIFKESH
+NSIALSVRCVIHSLEKTLNDEEVNSAVQKALEILEKEFNARLKG
+
+>CRH74160.1 phenylalanyl-tRNA synthetase subunit beta [Chlamydia trachomatis]
+MLVSYKWLNEYVNLSNVTPQELADKMSVTGIEVEGVAVPEEGLKKIVVGEVKECVPHPNSDHLSICQVDIGEEELSQIVC
+GAPNVKAGIKVIVALPGSRIAGNQKIKKGKMRGEVSNGMICSLEELGYSDNVVPKAYAEGIYYLPQEAVNGTPVFPYLDM
+DDAIIELSITPNRADALSMRGVAYEVGAIYRQTPQFNDPELKEDASDNVGNYVTVTVEDSQDAPAYQIRVIKDVTIAESP
+QWLQNRLMNEGIRPINNVVDVTNYILLLFGQPLHAFDYQKLDSKEILVRRATAAEELITLDGETRQLTEENIVITNGKTP
+VGLAGVMGGANSEISQETTTVALEAALFNPLSIRKTSKQFNLRSESSSRFEKGINQATVGLACDVAAAMIAELANGTVVS
+GTAVGSEVAVKEAQVAVTLERINQYLGTALDEATVNEIFEALGFAYEVNQGAYEITIPPRRWDIAIEADIIEEVARIYGY
+DHLPSTLPSGETVAGSLTKAQHVTRQLKSLLEGHGTSEAISYALTTEEKSRQFMMKESQTTRLQWPMSEERSVLRMNLIS
+GLLDDVAYNVARKNNNIAFYEVGRVFYQTEDPTKNLPTEENHLALALTGNTMVKDWQTKATAVDFYTVKGLVESIVAVLG
+LTEKISYQATTAIPEMHPGRTAWIYLEDEVVGFVGQVHPTTAKAYDIPETYVAELNLQQLVATEAGGVTYEAVSKFPAVS
+RDIALLVDETVTNQELVKTISDNAGKYLKEIHLFDVYQGEKLGAGKKSMAYSLTFVNAEATLVDEEINRSMEKVEKALIE
+KHQVEVR
+
+>WP_010888983.1 phenylalanine--tRNA ligase subunit beta [Deinococcus radiodurans]
+MKLPYSWLKELIPDLPPVADLEPTFAHLGLPLEGVEDVPAPVGGVLLVAVKAAEPMEGTQLTKLTLDTGENGEKTIASGA
+PNAVGLPAGTMVALVTPGTTLGGITYGVRPMQGVESWGMAASAKELGIGESNAGILTFPAGTAAPGTPLRELWPADSVLD
+VEVTPNRADVLSALGLARDLAAYLNLELKEPQIPAAPTQPGEIRVSLPDRGRVLDRDPQGKLRFGCDHFAARAVSGLQNG
+PAPLWMQRRVSLAGMRSIDLIVDTSNYVMLELGQPTALYDRRDVAGDGLVVAFGLREGETVKDLLGNTHQVGPEDLLILD
+AGMSDEPVMTVAEAFASAGQPKEGSHVLGIAGIMGGDHGHVRADTRDVVIESAHFDPVLLRRTSTRLGLKTDAVYRYERG
+VDPLLAPKAAVRVAELLRAAGGTPEAGQTVVGTPEVPQTITTTGEQIRALLGMHIGTAEMRESLTRLGCTVTGDGDSLTV
+TPPSWRVDMVIWQDLAEEVARLHGFTELPETLPTLRVHESNIGASAQSEARAELRRTLAGLGFQEVVTYTFTSDEEAQKA
+RAEAPGVRLRNPMTTDRTGMRTALYPSLLRAAGAHPKGERALLFEIGRIFPAAGEQERLGLLMRGDLAARTYQDGVRGDF
+SVFKGLVQGFAGAVGASFALEQLRGDDVPAALHPGVAGAVVWNGERVGWLGALHPEIAQEFGLKGDTFLMEAALPLPGRD
+WAFRDPSRAPAAWRDLAVIAPQGVSYGDIVGVLKGAGGELLESVEPFDVFTGEQVGAGNRSVAVRLTYRGAKTLTDEEVD
+PVFNAQIDAVKARGWAIREK
+
+>CRI42712.1 Phenylalanine--tRNA ligase beta subunit [Chlamydia pneumoniae]
+MRIPITLLQTYFSEPLSTKEILEACDHIGIEAEIENTTLYSFTSVITAKILHTIPHPNADKLRVATLTDGEKEHQVVCGA
+PNCEAGLIVALALPGAKLFDSEGKAYTIKKSKLRGVESQGMCCGADELGLDELQIQERALLELPEATPLGEDLATVLGNT
+SLEISLTPNLGHCASLLGLAREICHVTQANLVIPKEFSFENLPTTALDMGNDPDICPFFSYVVITGISAQPSPIKLQESL
+QALKQKPINAIVDITNYIMLSLGQPLHAYDASHVALDSLRVEKLSTPESLTLLNGETVLLPSGVPVVRDDHSLLGLGGVM
+GAKAPSFQETTTTTVIEAAYFLPEALRASQKLLPIPSESAYRFTRGIDPQNVVPALQAAIHYILEIFPEATISPIYSSGE
+ICRELKEVALRPKTLQRILGKSFSIEILSQKLQSLGFSTTPQETSLLVKVPSYRHDINEEIDLVEEICRTESWNIETQNP
+VSCYTPIYKLKRETAGFLANAGLQEFFTPDLLDPETAALTRKEKEEISLQGSKHTTVLRSSLLPGLLKSAATNLNRQAPS
+VQAFEIGTVYAKHGEQYQETQTLAILLTEDGESRSWLPKPSLSFYSLKGWVERLLYHHHLSIDALTLESSALCEFHPYQQ
+GVLRIHKQSFATLGQVHPELAKKAQIKHPVFFAELNLDLLCKMLKKTTKLYKPYAIYPSSFRDLTLTVPEDIPANLLRQK
+LLHEGSKWLESVTIISIYQDKSLETRNKNVSLRLVFQDYERTLSNQDIEEEYCRLVALLNELLTDTKGTINS
+
+>WP_087724745.1 phenylalanine--tRNA ligase subunit beta [Campylobacter jejuni]
+MIITKSWLSEWLELEDKNLDDIAKTLNSIGIEVDRICSLRVPDKIVVGFVKEKVKHENSDKLSICQVDIGSEILQIVCGA
+VNVEIGQFVAVALKGALMPNGMEIKEAKLRGVDSCGMLCSSTELGFEKINEGIILLDESIGKLELGKALNSYEIFNDGLI
+EVELTPNRGDCLSVYGIARDLAVALNLNLKESASFKEGENVLGIGRILRLATQKELNSLYNYRAIELQEKIQTSLLISLR
+LAQIENLGKNSIENFLNYATHSTGVIFNAYDLSEISKENEEITLNLSKENYGETKILCQDKLLSVSGIYQEERFKCKEDS
+KIVIIEANYTDPMIIADAKIAYEKQDEKIIYRSFRGSEPRLNLGMDFLLNVLEKIPNLIIYSSSQQILTDKELPTISVSI
+EGISNIIGQNVDKDEVLKILKKLGFELILSGDGLINVKAPIHRPDIKNLADICEEVVRIIGIDNITSKGLEFIEKNRLNS
+TYKNYKELVELRKKAVENGYFESLHYVLDSEEELKMLGFNPTKLKIINPITAELNTLRTTLLNHLLNAASLNAKNAKKTI
+KLFELGIVFGANNEELNHIAFVYSGYKEEAKISNKAKPEFVNFYDFLLELKNIIGDFKLKASKYSILSPYEQADVYIGEL
+KIGFVGRLHLKIENERDLLKTYICELDLNLIKPKFKTAKAYSRFPSISRDLSVLIPKGFAYEKIRSCIEELGLEILENFR
+LVDLYSDENLKESYSLTMSFIFRDMNKTLEENQVAECMDRILQNLNNLGLELR
+
+>P07395 Phenylalanine--tRNA ligase beta subunit [Escherichia coli]
+MKFSELWLREWVNPAIDSDALANQITMAGLEVDGVEPVAGSFHGVVVGEVVECAQHPNAD
+KLRVTKVNVGGDRLLDIVCGAPNCRQGLRVAVATIGAVLPGDFKIKAAKLRGEPSEGMLC
+SFSELGISDDHSGIIELPADAPIGTDIREYLKLDDNTIEISVTPNRADCLGIIGVARDVA
+VLNQLPLVQPEIVPVGATIDDTLPITVEAPEACPRYLGRVVKGINVKAPTPLWMKEKLRR
+CGIRSIDAVVDVTNYVLLELGQPMHAFDKDRIEGGIVVRMAKEGETLVLLDGTEAKLNAD
+TLVIADHNKALAMGGIFGGEHSGVNDETQNVLLECAFFSPLSITGRARRHGLHTDASHRY
+ERGVDPALQHKAMERATRLLIDICGGEAGPVIDITNEATLPKRATITLRRSKLDRLIGHH
+IADEQVTDILRRLGCEVTEGKDEWQAVAPSWRFDMEIEEDLVEEVARVYGYNNIPDEPVQ
+ASLIMGTHREADLSLKRVKTLLNDKGYQEVITYSFVDPKVQQMIHPGVEALLLPSPISVE
+MSAMRLSLWTGLLATVVYNQNRQQNRVRIFESGLRFVPDTQAPLGIRQDLMLAGVICGNR
+YEEHWNLAKETVDFYDLKGDLESVLDLTGKLNEVEFRAEANPALHPGQSAAIYLKGERIG
+FVGVVHPELERKLDLNGRTLVFELEWNKLADRVVPQAREISRFPANRRDIAVVVAENVPA
+ADILSECKKVGVNQVVGVNLFDVYRGKGVAEGYKSLAISLILQDTSRTLEEEEIAATVAK
+CVEALKERFQASLRD
+
+>WP_010876408.1 phenylalanine--tRNA ligase subunit beta [Methanothermobacter thermautotrophicus]
+MPVITFDYDDLKELGIDIDREKLLDVLPMMGSDIEDFDDESIKVEFFPNRPDLLSVEGVARSLRGFLGIEKGMPSYDVHD
+SGVEVTVDESVLDVRPYLGMAVIEDVQFTDKKLKQVMEFQEDLHWVIGRDRRKVAIGIHDLDRVEPPFLYSGVEPEGVTF
+TPLDSVCEMTPHEILEEHPKGVSYAHLLRDHDRYPLITDKNGDVLSMPPIINGELTKLTVNTRRILVDVTGTDDRAVRQT
+LNIICTSFAEAGGRIGSVRVKRPDGELHLPDLTPREMRVSVSEASRITGLELSADEVMDLLMKARMDARRTSDDEVVAVI
+PAYRVDILHEVDLVENIAVQHCIGRIEPELPDIATIAEEDTWSRADASIREVMVGLGFQEVMSLMLTSEESHYRRMRLEE
+DERVEVAQPISQDRTMIRKSLLNGLLEFFEDNKHEDLPQKIFEVGDVVYINPESETRSRVVTKLACAVTHSSAGFTEIKS
+LAAAVVENLGYEFRIEPLEHPSFIEGRCAAIESEGKSSAIGGFFGEVHPEVVTNFNLEYPVIALEIEFK
+
+>SGC91367.1 phenylalanyl-tRNA synthetase subunit beta [Mycobacterium tuberculosis]
+MKFSELWLREWVNPAVSSDALSDQITMAGLEVDGTEAVAGQFNGVVIGEVVECGQHPNADKLRVTKVNTGGDRLLDIVCG
+APNCRQGLRVAVATVGAVLPGDFKIKAAKLRGEPSEGMLCSFSELGISADHSGIIELPADAPIGTDLRDYMKLDDTAIEI
+SITPNRADCLSIRGVARDVAVLNKMDYQAPDMSPVAAVHQDTFPIRVDAPQACPRFTGRVIKNVDVTAKTPLWMVEKLRR
+GGIRSIDPVVDITNYVLLELGQPQHAYDLDTLEGELIVRMAEQGEKLTLLDGNEVTLTDNILVIADRRGALGMAGIFGGE
+HSGVSDTTKNILLETAFFNPLAITGRARQYGLHTDASHRFERGVDPQLQRIAAERTTRLILDICGGEPGEIIEVVSEADL
+PKTATIILTRNKLDRLIGHHVDDAQVTDILTRLGCDVKMSQDQWLVTAPSWRFDMEIEEDLVEEVARIYGYNNIPDVPLR
+ADLIMTSRHEAHLPLKRVKTLLVDRGFQEAITYSFVDPKIQTLLHPGQDAIILPNPISADMSAMRLSLLTGLLSTVVYNQ
+NRQQSRVRLFESGLRFVPDAAADLGIRQETMLAGVIAGNRNEEHWSSEKQVVDFYDLKGDLEAILELTGKLDRVSFKATT
+NPALHPGQGAEIYLEDEHIGYIGVVHPELEKKLDLNGRTVVFEIRWDALTNRIIPEAEAISRFPANRRDIAIVVPENVAA
+QDILNECKKVGVNQLVGINLFDVYCGKGVAEGYKSLAISLTLQDTERTLEEDEIAATVNKCVAALQQRFKASLRD
+
+>WP_049344098.1 phenylalanine--tRNA ligase subunit beta [Neisseria meningitidis]
+MQFSYSWLKTQANPDLSADKLEHLLTMAGLEVEEIDTAAPAFSGVVVAEVKSVEKHPDADRLNVTQVDAG
+TGELVQIVCGAPNVKPGIKVPCSLPGAVLPGNFKIKPTKMRGVPSNGMLCSTNELGLPDDGVDGLHILPE
+DAPVGTNIREYLDLDDTLFTLKITPNRADCLSVKGIAREVSALTQCAFTPVEIQTASIGSEKKQAVRIDA
+PADCGRFISRVIENVNAEAATPDWMKQRLERSGIRSISALVDIGNYVMLEIGQPMHVFDADKLSGSLIVR
+RAQNGETLACLNEKTVTLADNTLVVADEKGVLSLAGLMGGEASAVSDDTQNIVLEAAWFAPEIIAGKSRQ
+YGFGSDSSFRFERGVDYRLQADAIERATELVVQICGGAAGEMVEAQGKLPEAKQVELRLGRLKTVLGVEI
+SAEQVEIILQHLGLQPEKTAEGFRVTSPSFRFDIEIEADLIEEIGRVYGYENIPDDYTSGRLKMLALPET
+KRPRFAVYNEMAARGYREVVSYAFVDEQWEQDFAANTNPIRLQNPLAAQYAVMRSTLIGGLVEVLQNNLN
+RKQNRVRVFEIARVFSKDSADQFVQNERIGGLWYGSVLPEQWGEKTRNVDFYDIKADVESLLKNKEVSFV
+KTEHPALHPGRAANIVSDGRVVGFVGELHPKWLQKYDLPQAPLVFEIDMDAVLGREKTRYQSVSKFQAAR
+RDLAFVMPEAVTHDDLLNALKAAANKLVQEISVFDVYRGTGVPEGMKSVAVKIILQDMENTLTDEVIEPL
+VAKMIKAAAEKDAQLRA
+
+>WP_059349576.1 phenylalanine--tRNA ligase subunit beta [Pseudomonas aeruginosa]
+MKFSEKWLRSWANPQVSHDELVARLSMVGLEVDADLPVAGAFSGVVVGEVLSTEQHPDADKLRVCQVSNGSETFQVVCGA
+PNVRAGLKIPFAMIGAELPGDFKIKKAKLRGVESFGMLCSAKELQISEENAGLLELPADAPVGQDVRTYLELDDYTIEVG
+LTPNRGDCLSLAGLAREVSAIYDVPLAPVAVDAVAAQHDETRPVELAAPAACPRYLGRVIRNVDLSRPTPLWMVERLRRS
+DIRSIDPVVDVTNYVMIELGQPMHAFDLAEINGGVRVRMAEDGEKLVLLDGQEITLRADTLVIADHQRALAIAGVMGGEH
+SGVSDSTRDLFLEAAFFDTIALAGKARSYGLHTDSSHRFERGVDSQLARKAMERATRLILDIVGGEPGPIVEQVSEAHLP
+KVAPITLRAERVTQMLGMPLDAAEIVRLLQALELTVVADGEGQWSVGVPSHRFDISLEVDLIEELARLYGYNRLPVRYPQ
+ARLAPNNKPEARAALPLLRHLLVARGYQEAITFSFIDPVLFELFDPGTQPLTLANPISADMSAMRSSLWPGLVKALQHNL
+NRQQSRVRLFESGLRFVGQLEGLKQEAMLAGAICGKRLPEGWANGRDGVDFFDAKADVEAVLASAGALADFSFVPGEHPA
+LHPGQTGRIERDGRLVGYLGALHPELAKKLDLEQPVFLFELLLAEVVDGHLPKFRELSRFPEVRRDLALLVDQDVPAQDI
+LTQIRAAAGEWLTDLRLFDVYHGKGIDPHRKSLAVGLTWQHPSRTLNDDEVNSTTQNIVTSLEERFNATLRK
+
+>WP_015508578.1 phenylalanine--tRNA ligase subunit beta [Rickettsia prowazekii]
+MKFTLSWLKQFLEISASVTEIAEALTDIGLEVEEVIDKSKELQKFEVAYIRNIKPHPSADKLKLCDVETK
+NGILQIVCGASNVRADIKVVLANIGIEIPKGNLKIKESVIRGQKSYGMLCSEEELLLSSNSDGIIELPKD
+AVVGDNFTKYYGLDDPIFVINVTPNRGDVLGVYGIARDLSAKGLGTLKELELSEIKSTFFSKIKLNVHDK
+EACPLFTFREIRNLKNKPSPNWLQQLLKNVGIKTISSLVDVTNYISHSFGQPIHAYDADKIYGGISVDCY
+IRSDKVISCKNHEMATAVLQFSNDSANFYAINGKGYLLTENDLVIKDESGIQGLAGIIGGAKSSCNDSTT
+NVILEAACFNAKMVAASGRRLKIDTDARYRNERNIDRNFTEKALNIATNLILSICGNCEVSEVVKVGEQE
+PQKKPLDFSVYFLEKITGIKLSIQEIEDILNKLGFITDVKGDIIKVIAPSWRHDINILEDIAEEIVRIYG
+YDKIESIKLPELYQNNNLREYKRISSFKRILASKGYDEVVTNSFMSSEDAKLFAELKEGLFLLNPMSIEE
+NYMRPTVLPNLISIVSKNLARDVKDMAFFEVGPSFVNLNIESTYLTAIISGAFNNKNPHSFGRNYDIFDI
+KGDLEQVIEYAGLSLDKCIVIDETVLPQYYHPTRAINIRLGKNLLGHFGQIHPKILKYYDINQEIFAFEL
+NITNLPLIKAKFGKRDEFTVSDYQANFRDYSFIVDQDHKVGEIISYIKNFNKKLVKSVMLFDIYSGDKLP
+EGKKSIAIKIKLQADDRTLSETDLNSFSEDLVASISQKFQGILRE
+
+>WP_010873010.1 MULTISPECIES: phenylalanine--tRNA ligase subunit beta [Synechocystis]
+MRISVNWLQSLVELNLSPEELGELLTIAGLEVEEIEDRRSWAAGVVLGRVISREKHPNADKLSVCVVDIG
+TEEPSTIVCGAANVRADILVPVATLGSYLPKVDLKIKPAKLRGVKSSGMICSLAELGLSKESEGIHIFPD
+LDLPSGSPVGPLLGLDDVILEISPTANRADALSMVGVAREVAALTGGKLSLPEIKAVSVSDQDLPISVTE
+PQACPTYVGTVIRGVKVGPSPDWLQQRLLAAGTRPINNVVDVTNYVLLEWGQPLHSFDQDKLQTLVGPEG
+FALGVRFAEEGEKLITLDDQERTLQPQNLLVTANDQPVAIAGVMGGAATEVDENTQNIVLETALFDGVTI
+RKSSKAINLRSESSTRYERGVNRCELEVALHRAIALMTELAGGTVVRQGKADQRQDRGEAIINLRLERLQ
+QLLGKVNTPTGIGNITAEDVERILTDLGCGLTRQSDSDTPVWAVTVPSYRQRDIEREIDLIEEVARLYGY
+DHFCEQLPSNTIAGGLSPSYQAELALREACRGVGLTEVVHYSLVKPHGSEVMLANPLFAEYSALRTNLLD
+GLITAFANNQAQNNGALNAFEVGRVFWQNEGDIGEADHLAGICGGSQITEGTWPQGGKPQPMSWYDAKGL
+LEAIFQRLGATVTYSGDHQDPRLHPGRTALLSCNGTVLGRFGQLHPQLRREKGLIDEVYAFEITLTPLYQ
+AMETQILGTPDFRPYSPYPAVARDLALYAPLELTVAELTQAMVKAGGDLLEQVELFDEYRGQSVPAGQRS
+LAFSLAYRVGDRTLTDADVEPLHNQIREALTKQFAVSLRS
+
+>WP_038211244.1 phenylalanine--tRNA ligase subunit beta [Xylella fastidiosa]
+MKFSENWLRNHVPIQANRDVLVATLTAIGLEVENVAVLGEALDLIVVARIVNVVPHPESDLLQICQVDVAQDNLLQIVCG
+ASNVRPGLVVPLALLGAKIGALTIKSTTLRGVESNGMLCSAKELGLDTEASGLMELPEDAPIGTPLADYLALPDASIEIK
+LTPNRADCFSVRGIAFDVAAACASEVTPFHIDEIPAVSARTLPVELHAGANAPRYCGCVIEGIDSAAPTPVWMAERLRRS
+GIRPVSLLVDITQYVMLELGQPMHAFDVDTLRGPIGVRLSRNDEALKLLDGRTVVLDNDFLVVTDADQPIALAGLIGGWE
+TRITDTTVNVFLEAAHFAPAAIMGRGRKLGLHTDASHRFERGVDPALPPQAIAFATRLILELAGGKPGSLIHVELPEYLP
+APASILLRRTRIARLLGIVIDDAEVERILQALGMQVTTQAEGWRVVAPSRRFDIAIEEDLIEELVRIRGYEHLPTALPVG
+ASHIAMPSETRLDMTSVRRQLIARELQETINYAFIDAELLRRWQLNTGQVMLMNPLSAELAVMRPRLLPGLVAALGRNIA
+RQLERVRLFELGNVFTASDEAGVAPLETRHVAAAVCGDAFALQWGEQVRKVDFYDLKGDLESLAAASGAVLTFHSSAQPW
+GHPGRSADVWCDDMCIGWIGQLHPALTQTLEINVDVIAFELALEPLVRRALPRAHALSRFPFVRRDLACVVPEHVTWSEL
+AITVRDVIGPLLRDVKLFDRYVGKGIEPGFKSLAIGLILQDDTRTLIDRDVDDIMTKVVMAIQQRHDVRIRS
+
+>WP_004080832.1 phenylalanine--tRNA ligase subunit beta [Thermotoga maritima]
+MRVPESWLREFVDLDWDIEQIAERLTFSGTSVEDILRPFNVSGEIITARVIERFDHPASEKLIVCKVDTGKRIYTVITAD
+KTVNEGDYVILALEGATLNNGLKIEPREFKGVISEGMLCSLEELGLEEKSDRVYRFPDPVELGVNVVEEYGLNERVLDIE
+ITPNRPDCLSIIGVARELSALSGRPLNKPQPDVSFVDEDVQFDVEIEDVEGCPRYSARIMKGVTVKDSPLWMKARLVAAG
+VRSLNNVVDATNYVMIELGHPVHAFDLNRLKNKRIVVKSAKGGERVLLLDEKEYELKGGEVLITDGENVLALGGIMGGME
+SGVYDDTRDLVLEVAYFDPVRIRKAAKALGISSESSYRFERGVDPNDVELVSLRLAELIQKLAGGYVLRKFWDVYPRKIE
+PKKVMLRKARIEKILGTKVEEPGDILRRLEFQVEDRGDSYEVLVPTFRPDVEREIDLIEEIGRIYGYEKVESKVISVPAV
+NRGWGEKQLFRREISQFMKGMGFDEVVTFSFVDSQKVKKWPLVDREPIALSNPIASDMDVMRTSQFYSLIQVLAENFKRQ
+NRDLKLFEIGKIYFKENGNFREIETLSAMSCGLENPGDYTDKRSVSFYTIKGVLDELFFRLGVNVVYRAAEIPGLFPTRS
+ARIYVENREIGFIGMVDPKLLDEYDVKEDTYFFEIDMELLRKYASKRPAYRPTPRFPAVRRDISFLLPKGFESVKIIELF
+KKSGGDLVEEVGVFDIYEGKGIPENMVSVTLYVVFRHPERTLTDEEVNKIFEEMVQKAEREFGIRRRF
+
+>WP_016829299.1 phenylalanine--tRNA ligase subunit beta [Ureaplasma urealyticum]
+MILSLNLLHKISPKLKKISLNELCTALMDLGCEVETINTIKPSTNLVFAKVLEKTKHPNANHLNLVKVKANQEVYEIVCG
+ADNFNVNNWVVLAKINAELANGLKITPRELRGYVSNGMLCAYSEINPEVAHFLGQTDSDGILVLHDSYDHYKTPNQIFNL
+DDVILDLSIPSNRNDLNGYFWMAKELCAYFDLEYVIDATINHRSHKEIVNVRILSDDVNSYGMIEVKNIQNYTLKWNTKS
+VLVNNQIKIVNNFADNMNFLTLLTANPLHAFDAHKISGQIIVKNAEEDSILLGLDQKEYAIKKGDLIIVDDQKILALAGI
+IGSNDSKIDNNTTTAYIECANFNPLLIANTARRLKINTTAAMRFSKPLTNYVTKATLKKLLAHFKLDAKLICYFKHLVHN
+VIKNKIDQVSDFVGTKINLDTAHTFLKRLGYKINKTNLITPSHRYDVLNEFDVYEDIMKKFSIQQIKPQPINFDILSFKN
+NIAYDFEKKVSDFLVDQGLFECKTYNLKSQTQAYEFDFFNFQQAYEINNPISNIRSHLKLNNLNSLLEVLEYNQNQKNEL
+ENIFEISKINPINSNQQTILSIVLCKPLINAKLNDSIVVNNFVTTKALLHVLLTKLNISYVYDTNHIVNELYENNQLALV
+NENKQVFGFIGQLKNQIKKTYGLNNDIFVINLNLTSYLNQEQAITKVIKPSVYHDIVRDVSVKLASNVDLNDVMDNIEKI
+KNIRKVEISDLYVKDDEIIYTFKYYINDYSSNLSSEQIAVIEQEVNNYLKQF
+
+>WP_069216494.1 phenylalanine--tRNA ligase subunit beta [Vibrio cholerae]
+MKFSESWLREWVNPAITTDELTHQITMAGLEVDDVLAVAGVFDGVKVGHVVECAQHPDADKLRVTKVDVGEEELLDIVCG
+AANCRQGLKVAVATVGATLPGDFKIKKAKLRGQPSHGMLCSFSELGIDVESNGIMELAENAPIGMDFRDFLSLNDVTIDV
+DLTSNRADCFSIRGLAREVGVLNRADVTAPAVNAIAATINDTIAIDVKAPAACPRYLGRIVKNVNVQAQTPLWMQEKLRR
+CGIRSIDPVVDITNFVMLEQGQPMHAFDLAKIEGGIVVRLAEQDEKLTLLDGSEAKLNADTLVIADQQKALAIAGVFGGE
+HSGVSTETKDVLLECAFFAPDHIRGRARSYGLHTDSSMRFERGVDYALQHAAMERATQLLVEICGGDVAPVVAAESAADL
+PKPNQVTLRRTKLDKLLGHAIPDADVVEILERLGMQVATTAEGWQATAPTWRFDIAIEQDLVEEVGRIYGYNNIPNQAPV
+AALNMNLHNEAKLPLKRVRDLLVDRGYQEAITYSFVEPEQQKLVVPGVDALILPNPISAEMSAMRLSLIQGLLNTVVHNQ
+KRQQPRVRLFEYGLRFIPDAAAENGMRQEPMLAGVISGARGEEHWNMETATVDFFDMKGDLEAVLELTAKGKAYSFAATK
+HPALHPGQAAAIMVDGKAIGVIGTVHPELERKFGLNGRTIVFEIEWNAINTRVIPEAAAISKFPANRRDIALVVDGNIAS
+GDIVEACRVAGGELLKDAKLFDVYVGKGVEEGKKSLAIALTLQSVERTLEEADIAAAVEAIVQAVSAQFGAALRD
+
+>KNZ59753.1 phenylalanine--tRNA ligase, beta subunit [Puccinia sorghi]
+MPTITVEKERFFKDLGKTFRDEKEFDGILFDYGLELDEDTQLTTPEEKPYKLKIEVPANRYDLLCHQGLV
+LALRTYMGTSPAPNYSLSIPPPEHQWKAYVRKETSQIRPFFASAILRGIHFDEQRYKDFIDLQDKLHGNL
+CRKRTLVAIGTHDLSTLDHSNKIISYEARPPQDIKFIPLNKQSEYDATQLMTLYESIRRTNDFHLINWTC
+TRINSNKTKITLDTKDVFIDVTATDQTKLGIVINIIITMFSQYCSKPFTVEPVDIIYEHDVGSSYRSPNI
+EPLIFATRQSYINSVTGLSLTREATMALLGKMGHQASKGASANKPAINASTSVVLQNAPHDDLLNVAVPP
+TRPDILHECDLVEDVAISYGFNNLKKTFPSTNTVAKPYPINKLSDLVRKECAFAGWLEVLPLTLCSHDEN
+FRFLGKEDDGREAVILSNPATIEFQVVRTSLLPGLLKTIRENRKQPLPMKVFEVSDVVKKDSSLERKARN
+TRRLGAVFVGKKSAGFEVVHGLLDRILAMLDIHWIGLTSDPSSRKSFRGQYQIEESNHPTFFPGRSARIL
+FQPSVLIKKEGQEEGWTEIGRLGIVHPDVLQHFALDFPCSALEIDLLPFL
+
diff --git a/cure.py b/cure.py
index f874f81..7707875 100644
--- a/cure.py
+++ b/cure.py
@@ -2,8 +2,8 @@
 import re
 
 specie = re.compile(r'[A-Z][a-z]+\s[a-z]{2,}')
-with open("Phe t-RNA/DNA_pheT.fasta") as input_file:
-    with open("Phe t-RNA/cleaned_DNA_pheT.fasta", 'w') as output_file:
+with open("/home/eliot/ProjetOBIS1/Phe t-RNA/raw_protein_sequence_rooted.fasta") as input_file:
+    with open("/home/eliot/ProjetOBIS1/Phe t-RNA/cleaned_protein_sequence_rooted.fasta", 'w') as output_file:
         for line in input_file.readlines():
             if line[0] == '>':
                 if specie.search(line):