Merge pull request #1258 from nextstrain/feat/aa-ancestral

feat: allow reconstruction of amino acid sequences

CHANGES.md

@@ -2,6 +2,12 @@
 
 ## __NEXT__
 
+### Features
+
+* ancestral: add functionality to reconstruct ancestral amino acid sequences and add inferred mutations to the `node_data_json` with output equivalent to `augur translate`. `ancestral` now takes an annotation (`--annotation`), a list of genes (`--genes`), and a file name pattern for amino acid alignments (`--translations`). Mutations for each of these genes will be inferred and added to the output JSON to each node as a list at `['aa_muts'][gene]`. The annotations will be added to the `annotation` field in the output JSON. Inferred amino acids sequences can be saved with the new `--output-translations` argument. [#1258][] (@rneher, @huddlej)
+* ancestral: add the ability to report mutations relative to a sequence other than the inferred root of the tree. This sequence can be specified via `--root-sequence` and difference between this sequence and the inferred root of the tree will be added as mutations to the root node for nucleotides and amino acids. All differences between the specified `root-sequence` and the inferred sequence of the root node of the tree will be added as mutations to the root node. This was previously already possible for `vcf` input via `--vcf-reference`. [#1258][] (@rneher)
+
+[#1258]: https://github.com/nextstrain/augur/pull/1258
 
 ## 22.2.0 (31 July 2023)
 

tests/builds/zika/results/nt_muts.json

@@ -3,7 +3,8 @@
     "nuc": {
       "end": 10769,
       "start": 1,
-      "strand": "+"
+      "strand": "+",
+      "type": "source"
     }
   },
   "generated_by": {

tests/functional/ancestral/cram/_setup.sh

@@ -0,0 +1 @@
+export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"

tests/functional/ancestral/cram/default-nucleotide-reconstruction.t

@@ -0,0 +1,26 @@
+Setup
+
+  $ source "$TESTDIR"/_setup.sh
+
+Infer ancestral sequences for the given tree and alignment.
+The default is to infer ambiguous bases, so there should not be N bases in the inferred output sequences.
+
+  $ ${AUGUR} ancestral \
+  >  --tree $TESTDIR/../data/tree.nwk \
+  >  --alignment $TESTDIR/../data/aligned.fasta \
+  >  --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" \
+  >  --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" > /dev/null
+
+  $ grep "^N" "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta"
+  [1]
+
+Check that the reference length was correctly exported as the nuc annotation
+
+  $ grep -A 6 'annotations' "$CRAMTMP/$TESTFILE/ancestral_mutations.json"
+    "annotations": {
+      "nuc": {
+        "end": 10769,
+        "start": 1,
+        "strand": "+",
+        "type": "source"
+      }

tests/functional/ancestral/cram/infer-ambiguous-nucleotides.t

@@ -0,0 +1,16 @@
+Setup
+
+  $ source "$TESTDIR"/_setup.sh
+
+Infer ancestral sequences for the given tree and alignment, explicitly requesting that ambiguous bases are inferred.
+There should not be N bases in the inferred output sequences.
+
+  $ ${AUGUR} ancestral \
+  >  --tree $TESTDIR/../data/tree.nwk \
+  >  --alignment $TESTDIR/../data/aligned.fasta \
+  >  --infer-ambiguous \
+  >  --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" \
+  >  --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" > /dev/null
+
+  $ grep "^N" "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta"
+  [1]

tests/functional/ancestral/cram/infer-amino-acid-sequences-with-missing-arguments.t

@@ -0,0 +1,15 @@
+Setup
+
+  $ source "$TESTDIR"/_setup.sh
+
+Try to infer ancestral amino acid sequences without all required arguments.
+This should fail.
+
+  $ ${AUGUR} ancestral \
+  >  --tree $TESTDIR/../data/tree.nwk \
+  >  --alignment $TESTDIR/../data/aligned.fasta \
+  >  --annotation $TESTDIR/../data/zika_outgroup.gb \
+  >  --genes ENV PRO \
+  >  --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" > /dev/null
+  ERROR: For amino acid sequence reconstruction, you must provide an annotation file, a list of genes, and a template path to amino acid sequences.
+  [2]

tests/functional/ancestral/cram/infer-amino-acid-sequences-with-root-sequence.t

@@ -0,0 +1,26 @@
+Setup
+
+  $ source "$TESTDIR"/_setup.sh
+
+Infer ancestral nucleotide and amino acid sequences using a root sequence that
+was used for alignment. This additional argument allows the ancestral command to
+assign mutations on the branch leading to the inferred root (differences between
+the "root" used as an alignment reference and the inferred most recent common
+ancestor).
+
+  $ ${AUGUR} ancestral \
+  >  --tree $TESTDIR/../data/tree.nwk \
+  >  --alignment $TESTDIR/../data/aligned.fasta \
+  >  --annotation $TESTDIR/../data/zika_outgroup.gb \
+  >  --root-sequence $TESTDIR/../data/zika_outgroup.gb \
+  >  --genes ENV PRO \
+  >  --translations $TESTDIR/../data/aa_sequences_%GENE.fasta \
+  >  --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" > /dev/null
+
+Check that the reference length was correctly exported as the nuc annotation
+
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
+  >   --exclude-regex-paths "['seqid']" -- \
+  >   "$TESTDIR/../data/ancestral_mutations_with_root_sequence.json" \
+  >   "$CRAMTMP/$TESTFILE/ancestral_mutations.json"
+  {}

tests/functional/ancestral/cram/infer-amino-acid-sequences.t

@@ -0,0 +1,27 @@
+Setup
+
+  $ source "$TESTDIR"/_setup.sh
+
+Infer ancestral nucleotide and amino acid sequences.
+
+  $ ${AUGUR} ancestral \
+  >  --tree $TESTDIR/../data/tree.nwk \
+  >  --alignment $TESTDIR/../data/aligned.fasta \
+  >  --annotation $TESTDIR/../data/zika_outgroup.gb \
+  >  --genes ENV PRO \
+  >  --translations $TESTDIR/../data/aa_sequences_%GENE.fasta \
+  >  --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" \
+  >  --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" \
+  >  --output-translations "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_%GENE.fasta" > /dev/null
+
+Check that the reference length was correctly exported as the nuc annotation
+
+  $ grep -E "\"(ENV|PRO|nuc)\": {" "$CRAMTMP/$TESTFILE/ancestral_mutations.json"
+      "ENV": {
+      "PRO": {
+      "nuc": {
+
+Check that internal nodes have ancestral amino acid sequences.
+
+  $ grep "NODE" "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_ENV.fasta" | wc -l
+  \s*8 (re)

tests/functional/ancestral/cram/keep-ambiguous-nucleotides.t

@@ -0,0 +1,16 @@
+Setup
+
+  $ source "$TESTDIR"/_setup.sh
+
+Infer ancestral sequences for the given tree and alignment, explicitly requesting that ambiguous bases are NOT inferred.
+There should be N bases in the inferred output sequences.
+
+  $ ${AUGUR} ancestral \
+  >  --tree $TESTDIR/../data/tree.nwk \
+  >  --alignment $TESTDIR/../data/aligned.fasta \
+  >  --keep-ambiguous \
+  >  --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" \
+  >  --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" > /dev/null
+
+  $ grep "^N" "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" | head -n 1
+  NNNNNNNNNNNNGACAGTTCGAGTTTGAAGCGAAAGCTAGCAACAGTATCAACAGGTTTT

tests/functional/ancestral/data/aa_sequences_2K.fasta

@@ -0,0 +1,20 @@
+>BRA/2016/FC_6706
+SPQDNQMAIIIMVAVGLLGLITA
+>COL/FLR_00008/2015
+SPQDNQMAIIIMVAVGLLGLITA
+>Colombia/2016/ZC204Se
+SPQDNQMAIIIMVAVGLLGLITA
+>DOM/2016/BB_0183
+SPQDNQMAIIIMVAVGLLGLITA
+>EcEs062_16
+SPQDNQMAIIIMVAVGLLGLITA
+>HND/2016/HU_ME59
+SPQDNQMAIIIMVAVGLLGLITA
+>PAN/CDC_259359_V1_V3/2015
+SPQDNQMAIIIMVAVGLLGLITA
+>PRVABC59
+SPQDNQMAIIIMVAVGLLGLITA
+>VEN/UF_1/2016
+SPQDNQMAIIIMVAVGLLGLITA
+>ZKC2/2016
+SPQDNQMAIIIMVAVGLLGLITA

tests/functional/ancestral/data/aa_sequences_CA.fasta

@@ -0,0 +1,40 @@
+>BRA/2016/FC_6706
+MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK
+PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLTTA
+MA
+>COL/FLR_00008/2015
+MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK
+PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGAETSVGIVGLLLTTA
+MA
+>Colombia/2016/ZC204Se
+MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK
+PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGAETSVGIVGLLLTTA
+MA
+>DOM/2016/BB_0183
+MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK
+PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLTTA
+MA
+>EcEs062_16
+MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK
+PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLTTA
+MA
+>HND/2016/HU_ME59
+MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK
+PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLTTA
+MA
+>PAN/CDC_259359_V1_V3/2015
+MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK
+PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGAETSVGIVGLLLTTA
+MA
+>PRVABC59
+MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK
+PSLGLINRWGSVGKKEAMETIKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLTTA
+MA
+>VEN/UF_1/2016
+MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK
+PSLGLINRWGSVGKKDAMEIIKKFKKDLAAMLRIINARKEKKRRGAETSVGIVGLLLTTA
+MA
+>ZKC2/2016
+MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK
+PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGADTNVGIVGLLLTTA
+MA

tests/functional/ancestral/data/aa_sequences_ENV.fasta

@@ -0,0 +1,100 @@
+>BRA/2016/FC_6706
+IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC
+YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA
+CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL
+GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE
+ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL
+KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT
+ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR
+MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK
+NGSISLMCLALGGVLIFLSTAVSA
+>COL/FLR_00008/2015
+IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC
+YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA
+CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL
+GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE
+ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL
+KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT
+ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR
+MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK
+NGSISLMCLALGGVLIFLSTAVSA
+>Colombia/2016/ZC204Se
+IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC
+YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA
+CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL
+GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE
+ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL
+KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT
+ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR
+MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK
+NGSISLMCLALGGVLIFLSTAVSA
+>DOM/2016/BB_0183
+IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC
+YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA
+CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL
+GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE
+ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL
+KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT
+ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR
+MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK
+NGSISLMCLALGGVLIFLSTAVSA
+>EcEs062_16
+IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC
+YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA
+CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL
+GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE
+ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL
+KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT
+ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR
+MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK
+NGSISLMCLALGGVLIFLSTAVSA
+>HND/2016/HU_ME59
+IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC
+YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA
+CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL
+GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE
+ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL
+KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT
+ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR
+MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK
+NGSISLMCLALGGVLIFLSTAVSA
+>PAN/CDC_259359_V1_V3/2015
+IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC
+YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA
+CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL
+GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE
+ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL
+KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT
+ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR
+MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK
+NGSISLMCLALGGVLIFLSTAVSA
+>PRVABC59
+IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC
+YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA
+CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL
+GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE
+ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL
+KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT
+ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR
+MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK
+NGSISLMCLALGGVLIFLSTAVSA
+>VEN/UF_1/2016
+IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC
+YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA
+CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL
+GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE
+ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL
+KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT
+ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR
+MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK
+NGSISLMCLALGGVLIFLSTAVSA
+>ZKC2/2016
+IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC
+YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA
+CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL
+GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE
+ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL
+KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT
+ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGARR
+MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK
+NGSISLMCLALGGVLIFLSTAVSA