[WIP] Dark proteome

DARK/README.md

@@ -0,0 +1,16 @@
+## Contents of this folder
+
+### [coronavirus.fasta.CAST_thr20_4hackathon.tab](./coronavirus.fasta.CAST_thr20_4hackathon.tab)
+Compositionally biased regions detected by the CAST algorithm (Promponas et al., 2000). 
+CAST v2.2 (Ioannides et al., in preparation) tab-separated output, reformatted to be in line with the Swiss-Model annotation format. 
+Regions are colored according to amino acid type, following the Rasmol color scheme as described in 
+http://life.nthu.edu.tw/~fmhsu/rasframe/SHAPELY.HTM.
+
+### [casttab2swmodel.pl](./casttab2swmodel.pl)
+Perl code to reformat CAST output for input to Swiss-Model portal. Tested with perl v5.16.2 on MacOS, should work fine on Linux/Windows as well. No external dependencies.
+
+On the command line simply run:
+$perl casttab2swmodel.pl path/to/cast_tab_file > path/to/hackathon.tab
+
+### [coronavirus.fasta.CASTV2.2.thr20](./coronavirus.fasta.CASTV2.2.thr20)
+Raw tab output from CAST v2.2 to be used for Perl script above.

DARK/casttab2swmodel.pl

@@ -0,0 +1,65 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+
+# Description
+# -----------
+# Code to reformat CAST output for the covid-19-Annotations-on-Structures
+# project https://github.com/gtauriello/covid-19-Annotations-on-Structures
+
+#
+# Author: Vasilis J Promponas 
+# Contact: [email protected]; [email protected]
+#
+
+my %colorscheme = getColorScheme();
+
+my @annot = ();
+open(CASTTAB, $ARGV[0]) or die "Could not open CAST tab ($ARGV[0])";
+my $entry = <CASTTAB>; # Read header line
+
+while($entry = <CASTTAB>)
+{
+# Input format (tab separated):
+# >sp|P0DTD3|Y14_WCPV Uncharacterized protein 14 OS=Wuhan seafood market pneumonia virus OX=2697049 GN=ORF14 PE=3 SV=1    C       68      70      27
+	chomp($entry);
+	next if $entry eq '';
+	my @tmp = split(/\t/,$entry);
+	my $aatype = $tmp[1]. '-rich region (' . $tmp[4]. ')';
+	my $from = $tmp[2];
+	my $to  = $tmp[3];
+	my @tmp2 = split(/\|/, $tmp[0]);
+	my $uniprot_id = $tmp2[1];
+	my $color = $colorscheme{$tmp[1]};
+	my $out = join("\t", ($uniprot_id,  $from, $to, $color, $aatype,)) . "\n";
+	push @annot, $out;
+}
+close(CASTTAB);
+
+
+foreach my $annotation (@annot)
+{
+	print $annotation;
+}
+
+
+sub getColorScheme
+{
+	# Return a hash mapping the Rasmol color scheme
+	# See http://life.nthu.edu.tw/~fmhsu/rasframe/SHAPELY.HTM
+	my %colors=();
+	$colors{'D'} = $colors{'E'} = '#E60A0A';
+	$colors{'C'} = $colors{'M'} = '#E6E600';
+	$colors{'K'} = $colors{'R'} = '#145AFF';
+	$colors{'S'} = $colors{'T'} = '#FA9600';
+	$colors{'F'} = $colors{'Y'} = '#3232AA';
+	$colors{'N'} = $colors{'Q'} = '#00DCDC';
+	$colors{'G'} = '#EBEBEB';
+	$colors{'L'} = $colors{'V'} = $colors{'I'} = '#0F820F';
+	$colors{'A'} = '#C8C8C8';
+	$colors{'W'} = '#B45AB4';
+	$colors{'H'} = '#8282D2';
+	$colors{'P'} = '#DC9682';
+
+	return(%colors);
+}

DARK/coronavirus.fasta.CASTV2.2.thr20

@@ -0,0 +1,261 @@
+>sp|P0DTD1|R1AB_WCPV Replicase polyprotein 1ab OS=Wuhan seafood market pneumonia virus OX=2697049 GN=rep PE=1 SV=1
+MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGV
+LPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRK
+VLLRKNXNKXAXXHSYXADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG
+AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW
+YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI
+RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL
+PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC
+AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF
+SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA
+ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY
+ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV
+GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC
+VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG
+TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVN
+ITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEW
+SMATYYLFDESGEFKLASHMYCSFYPPDXDXXXGDCXXXXFXPSTQYXYGTXDDYQGKPL
+XFGATSAALQPXXXQXXDWLXXXSQQTVGQQXGSXXNQTTTIQTIVXVQPQLXMXLTPVV
+QTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHXXXVAXALNKATN
+NAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQ
+HEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLXMXSXXQVX
+QXIAXIPXXXVXPFITXSXPSVXQRXQDDXXIXACVXXVTTTLXXTKFLTENLLLYIDIN
+GNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKV
+PTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLA
+HAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDXGARFXFXXSKXXVASLINXLND
+LNEXLVXMPLGYVTHGLNLEEAARYMRSLKVPATVXVXXPDAVTAYNGYLTXXXKTPEEH
+FIETIXLAGXYKDWXYXGQXTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLL
+SLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV
+LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATAL
+LTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHAN
+LDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQ
+ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYK
+GPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPY
+PNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFK
+KGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLA
+CEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAAYV
+DNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSXXXNIVXRC
+LNRVCXNYMPYFFXLLLQLCXFXRSXNSRIKASMPXXIAKNXVKSVGKFCLEASFNYLKS
+PNFSKXINIIIWFXXXSVCXGSXIYSTAAXGVXMSNLGMPSYCTGYREGYLNSTNVTIAT
+YCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWXLAYILXTRXXYV
+LGLAAIMQLXXSYXAVHXISNSWLXWLIINLVQXAPISAXVRXXIFFASFXXVWKSXVHV
+VDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCA
+GSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSH
+FVNLDNLRANNTKGSLPINVIVFDGKXKCEEXXAKXAXVYYSQLMCQPILLLDQALVSDV
+GDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQG
+FVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHIN
+AQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQXXNXXTTKIAL
+KGGKIXNNWLKQLIKXTLXFLFXAAIFYLITPXHXMSKHTDFSSEIIGYKAIDGGVTRDI
+ASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGD
+FLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLE
+GSVAYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVST
+SGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCL
+AYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVXSFLPGVXSVIXLXLTFXLTNDV
+SFLAHIQWMVMFTPLVPFWITIAYIICISTKHFXWFFSNXLKRRVVFNGVSFSTFEEAAL
+CTFLLNKEMYLKLRSDVLLPLTQXNRXLALXNKXKXFSGAMDTTSYREAACCHLAKALND
+FSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVY
+CPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPK
+TPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCV
+SFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQXAQAAGXDXXIXVNVLAWLYAAVINGDR
+WFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMN
+GRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWXXXTIXTSXXVXVQSTQW
+SLXXXLYENAXLPXAXGIIAXSAFAXXFVKHKHAFLCLFLLPSLATVAYFNXVYXPASWV
+XRIXTWLDXVDTSLSGFKLKDCVXYASAVVLLILXTARTVYDDGARRVWTLMNVLTLVYK
+VYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIM
+LVYCXLGYXCTCYXGLXCLLNRYXRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKL
+NIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILL
+AKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRXTLQXIXSEFSSLPSYXXFXTX
+QEXYEQXVXNGDSEVVLXXLXXSLNVAXSEFDRDAAMQRXLEXMADQAMTQMYXQARSED
+XRAXVTSAMQTMLFTMLRKLDXDALXXIIXXARDGCVPLNIIPLTTAAKLMVVIPDYNTY
+KNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ
+NNELSPVALRQMSCAAGXXQXACXDDNALAYYNXXKGGRFVLALLSDLQDLKWARFPKSD
+GTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLXXTVRLQXGNXTEV
+PXNSTVLSFCXFXVDXXKXYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQES
+FGGASXXLYXRXHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYG
+CSCDQLREPMLQSADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKF
+LKTNCCRFQEKXEXXNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDG
+DMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVEN
+PDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPG
+SGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRXFK
+XWDQTXHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHF
+RELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQ
+TVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDXDXXRXNLPTMCDIRQ
+LLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALF
+AYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVV
+IGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSL
+SHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALL
+STDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNS
+TYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVY
+LPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYI
+RKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGAXVLXNSQTSLRX
+GAXIRRPFLXXKXXYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHK
+PPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAE
+TLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIG
+EYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTL
+NISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDA
+LCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEI
+SMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDM
+FLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVV
+REFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSC
+NVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVI
+TGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFIT
+REEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSR
+VSAKXXXGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSM
+KYFVKIGPERTXXLXDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQS
+NHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHM
+VVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSD
+KFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSA
+FVNLKQLPFFXXSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYL
+DAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSIIN
+NTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDY
+KRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSV
+KGLQPSVGPKQASLNGVTLIGEAVKTQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQ
+MEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPFELEDF
+IPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEIS
+FMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMM
+NVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLND
+FVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLA
+LGGSVAIKITEHSWNADLYKLMGHFAXXTAFVTNVNASSSEAFLIGCNYLGKPREQIDGY
+VMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLII
+RENNRVVISSDVLVNN
+>sp|P0DTC1|R1A_WCPV Replicase polyprotein 1a OS=Wuhan seafood market pneumonia virus OX=2697049 PE=3 SV=1
+MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGV
+LPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRK
+VLLRKNXNKXAXXHSYXADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG
+AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW
+YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI
+RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL
+PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC
+AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF
+SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA
+ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY
+ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV
+GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC
+VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG
+TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVN
+ITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEW
+SMATYYLFDESGEFKLASHMYCSFYPPDXDXXXGDCXXXXFXPSTQYXYGTXDDYQGKPL
+XFGATSAALQPXXXQXXDWLXXXSQQTVGQQXGSXXNQTTTIQTIVXVQPQLXMXLTPVV
+QTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHXXXVAXALNKATN
+NAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQ
+HEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLXMXSXXQVX
+QXIAXIPXXXVXPFITXSXPSVXQRXQDDXXIXACVXXVTTTLXXTKFLTENLLLYIDIN
+GNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKV
+PTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLA
+HAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDXGARFXFXXSKXXVASLINXLND
+LNEXLVXMPLGYVTHGLNLEEAARYMRSLKVPATVXVXXPDAVTAYNGYLTXXXKTPEEH
+FIETIXLAGXYKDWXYXGQXTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLL
+SLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV
+LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATAL
+LTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHAN
+LDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQ
+ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYK
+GPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPY
+PNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFK
+KGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLA
+CEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAAYV
+DNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSXXXNIVXRC
+LNRVCXNYMPYFFXLLLQLCXFXRSXNSRIKASMPXXIAKNXVKSVGKFCLEASFNYLKS
+PNFSKXINIIIWFXXXSVCXGSXIYSTAAXGVXMSNLGMPSYCTGYREGYLNSTNVTIAT
+YCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWXLAYILXTRXXYV
+LGLAAIMQLXXSYXAVHXISNSWLXWLIINLVQXAPISAXVRXXIFFASFXXVWKSXVHV
+VDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCA
+GSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSH
+FVNLDNLRANNTKGSLPINVIVFDGKXKCEEXXAKXAXVYYSQLMCQPILLLDQALVSDV
+GDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQG
+FVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHIN
+AQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQXXNXXTTKIAL
+KGGKIXNNWLKQLIKXTLXFLFXAAIFYLITPXHXMSKHTDFSSEIIGYKAIDGGVTRDI
+ASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGD
+FLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLE
+GSVAYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVST
+SGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCL
+AYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVXSFLPGVXSVIXLXLTFXLTNDV
+SFLAHIQWMVMFTPLVPFWITIAYIICISTKHFXWFFSNXLKRRVVFNGVSFSTFEEAAL
+CTFLLNKEMYLKLRSDVLLPLTQXNRXLALXNKXKXFSGAMDTTSYREAACCHLAKALND
+FSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVY
+CPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPK
+TPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCV
+SFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQXAQAAGXDXXIXVNVLAWLYAAVINGDR
+WFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMN
+GRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWXXXTIXTSXXVXVQSTQW
+SLXXXLYENAXLPXAXGIIAXSAFAXXFVKHKHAFLCLFLLPSLATVAYFNXVYXPASWV
+XRIXTWLDXVDTSLSGFKLKDCVXYASAVVLLILXTARTVYDDGARRVWTLMNVLTLVYK
+VYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIM
+LVYCXLGYXCTCYXGLXCLLNRYXRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKL
+NIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILL
+AKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRXTLQXIXSEFSSLPSYXXFXTX
+QEXYEQXVXNGDSEVVLXXLXXSLNVAXSEFDRDAAMQRXLEXMADQAMTQMYXQARSED
+XRAXVTSAMQTMLFTMLRKLDXDALXXIIXXARDGCVPLNIIPLTTAAKLMVVIPDYNTY
+KNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ
+NNELSPVALRQMSCAAGXXQXACXDDNALAYYNXXKGGRFVLALLSDLQDLKWARFPKSD
+GTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLXXTVRLQXGNXTEV
+PXNSTVLSFCXFXVDXXKXYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQES
+FGGASXXLYXRXHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYG
+CSCDQLREPMLQSADAQSFLNGFAV
+>sp|P0DTC2|SPIKE_WCPV Spike glycoprotein OS=Wuhan seafood market pneumonia virus OX=2697049 GN=S PE=3 SV=1
+MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
+NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
+NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
+GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
+LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
+CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
+CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
+YNYKLPDDFTGCVIAWXSXXLDSKVGGXYXYLYRLFRKSNLKPFERDISTEIYQAGSTPC
+NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN
+FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
+GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY
+ECDIPIGAGICAXYQTQTNXPRRARXVAXQXIIAYTMXLGAENXVAYXNNXIAIPXNFXI
+XVXXEILPVXMXKXXVDCXMYICGDXTECXNLLLQYGSFCTQLNRALTGIAVEQDKNTQE
+VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
+LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
+QMAYRFNGIGVTQNVLYENQKLIANQFNXAIGKIQDXLXXTAXALGKLQDVVNQNAQALN
+TLVKQLXXNFGAIXXVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
+SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
+ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP
+LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
+QELGKYEQYIKXPXYIXLGFIAGLXAXVMVTXMLXXMTSXXSXLKGXXSXGSXXKFXEXX
+SEPVLKGVKLHYT
+>sp|P0DTC3|AP3A_WCPV Protein 3a OS=Wuhan seafood market pneumonia virus OX=2697049 GN=3a PE=3 SV=1
+MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQASLPFGWLIVGVALLAVFQSAS
+KIITLKKRWQLALSKGVHFVCNXXXXFVTVYSHXXXVAAGXEAPFXXXXAXVXFXQSINF
+VRIIMRXWXCWKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPIS
+EHDYQIGGYTEKWESGVKDCVVLHSXFTSDXXQLXSTQLSTDTGVEHVTFFIYNKIVDEP
+EEHVQIHTIDGSSGVVNPVMEPIYDEPXXXXSVPL
+>sp|P0DTC4|VEMP_WCPV Envelope small membrane protein OS=Wuhan seafood market pneumonia virus OX=2697049 GN=E PE=3 SV=1
+MYSFVSEETGTXIVNSVXXFXAFVVFXXVTXAIXTAXRXXAYXXNIVNVSLVKPSFYVYS
+RVKNLNSSRVPDLLV
+>sp|P0DTC5|VME1_WCPV Membrane protein OS=Wuhan seafood market pneumonia virus OX=2697049 PE=3 SV=1
+MADSNGTITVEELKKLLEQWNXVIGFXFXTWICXXQFAYANRNRFXYIIKXIFXWXXWPV
+TXACFVXAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILL
+NVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYK
+LGASQRVAGDSGFAAYSRYRIGXYKLXTDHSSSSDXIALLVQ
+>sp|P0DTC6|NS6_WCPV Non-structural protein 6 OS=Wuhan seafood market pneumonia virus OX=2697049 GN=6 PE=3 SV=1
+MFHLVDFQVTXAEXLLXXMRTFKVSXWNLDYXXNLXXKNLSKSLTENKYSQLDEEQPMEI
+D
+>sp|P0DTC7|NS7A_WCPV Protein 7a OS=Wuhan seafood market pneumonia virus OX=2697049 GN=7a PE=3 SV=1
+MKIIXFXAXITXATCELYHYQECVRGTTVLLKEPCSSGTYEGNSPFHPLADNKFALTCFS
+TQFAFACPDGVKHVYQLRARSVSPKLFIRQEEVQELYSPXFLXVAAXVFXTLCFTLKRKT
+E
+>sp|P0DTD8|NS7B_WCPV Protein non-structural 7b OS=Wuhan seafood market pneumonia virus OX=2697049 PE=3 SV=1
+MIEXSXIDXYXCXXAXXXXXVXIMXIIXWXSXEXQDHNETCHA
+>sp|P0DTC8|NS8_WCPV Non-structural protein 8 OS=Wuhan seafood market pneumonia virus OX=2697049 PE=3 SV=1
+MKFLVFLGIITTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGARKSAPLIEL
+CVDEAGSKSPIQYIDIGNYTVSCLPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVLDF
+I
+>sp|P0DTC9|NCAP_WCPV Nucleoprotein OS=Wuhan seafood market pneumonia virus OX=2697049 GN=N PE=3 SV=1
+MSDXGPQXQRXAPRITFGGPSDSTGSXQXGERSGARSKQRRPQGLPXXTASWFTALTQHG
+KEDLKFPRGQGVPINTNSSPDDQIGYYXXATXXIXGGDGKMKDLSPRWXFXXLGTGPEAG
+LPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGXRGGX
+QAXXRXXXRXRNXXRNXTPGXXRGTXPARMAGNGGDAALALLLLDRLNXLEXKMXGKGXX
+XXGXTVTXXXAAEAXXXPRXXRTATXAYNVTXAFGRRGPEXTXGNFGDXELIRXGTDYKH
+WPXIAXFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAY
+KTFPPTEPXXDXXXXADETXALPXRXXXXXTVTLLPAADLDDFSKXLXXSMSSADSTXA
+>tr|A0A663DJA2|A0A663DJA2_9BETC ORF10 protein OS=Wuhan seafood market pneumonia virus OX=2697049 GN=ORF10 PE=2 SV=1
+MGYINVFAFPFTIYSLLLCRMNSRNYIAQVDVVNFNLT
+>sp|P0DTD2|ORF9B_WCPV Protein 9b OS=Wuhan seafood market pneumonia virus OX=2697049 PE=3 SV=1
+MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT
+LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK
+>sp|P0DTD3|Y14_WCPV Uncharacterized protein 14 OS=Wuhan seafood market pneumonia virus OX=2697049 GN=ORF14 PE=3 SV=1
+MLQSCYNFLKEQHCQKASTQKGAEAAVKPLLVPHHVVATVQEIQLQAAVGEXXXXEWXAM
+AVMXXXXXXXXTD