From 68caa594724e280f31ba52407dec16f5b6b13ee5 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Fri, 10 Nov 2017 11:20:51 -0500 Subject: [PATCH 01/27] first commit --- exercise 11 Question 1 | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 exercise 11 Question 1 diff --git a/exercise 11 Question 1 b/exercise 11 Question 1 new file mode 100644 index 0000000..adea56b --- /dev/null +++ b/exercise 11 Question 1 @@ -0,0 +1,16 @@ +#Import Packages +#Question 1 +import pandas +import numpy +from scipy.optimize import minimize +from scipy.stats import norm +import scipy.integrate as spi +from scipy.integrate import odeint +import matplotlib.pyplot as plt +import re +import os +from plotnine import * + +os.chdir("/Users/madelinebuynak/Exercise11_files/Problem1") +#Sequence alignment +./Exercise11_files -in "Arthrobacter.fasta" -out "Bacillus.fasta" \ No newline at end of file From 382499b7c11bf960ae9ef6ccba13dcd4d073583a Mon Sep 17 00:00:00 2001 From: yunluyingying Date: Fri, 10 Nov 2017 12:45:20 -0500 Subject: [PATCH 02/27] Add files via upload Problem 2 --- Exercise11.py | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 Exercise11.py diff --git a/Exercise11.py b/Exercise11.py new file mode 100644 index 0000000..78cb847 --- /dev/null +++ b/Exercise11.py @@ -0,0 +1,38 @@ +#!/usr/bin/env python2 +# -*- coding: utf-8 -*- +""" +Created on Fri Nov 10 10:44:24 2017 + +@author: chenyingying +""" + +import re as re +import pandas as pd + +reg1='AKKPRVZE' +reg2='AAQWWRNYGG' + +vcffile = open("motifsort.fasta","r") +outfile1= open("Motif1.fasta","w") +outfile2= open("Motif2.fasta","w") +outfile3= open("Motifno.fasta","w") +for line in vcffile: + line=line.strip() + if line.startswith('>'): + seqid=line + elif re.search(reg1,line): + motif1=line + outfile1.write(seqid+'\n') + outfile1.write(line+'\n') + elif re.search(reg2,line): + motif2=line + outfile2.write(seqid+'\n') + outfile2.write(line+'\n') + else: + outfile3.write(seqid+'\n') + outfile3.write(line+'\n') + +outfile1.close() +outfile2.close() +outfile3.close() +vcffile.close() \ No newline at end of file From 2be7aca10b935e14e14592844b7f53d5b14cde31 Mon Sep 17 00:00:00 2001 From: yunluyingying Date: Fri, 10 Nov 2017 12:48:39 -0500 Subject: [PATCH 03/27] File for Problem 2 --- Motif1.fasta | 22 +++++++++ Motif2.fasta | 26 ++++++++++ Motifno.fasta | 132 ++++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 180 insertions(+) create mode 100644 Motif1.fasta create mode 100644 Motif2.fasta create mode 100644 Motifno.fasta diff --git a/Motif1.fasta b/Motif1.fasta new file mode 100644 index 0000000..e062bf0 --- /dev/null +++ b/Motif1.fasta @@ -0,0 +1,22 @@ +>sequence2 +MSLKPFTYPFPETRFLHSGSSVYKFKIRYGDSIRGEDIENKEVIVQELEDSIRVVLGNLDSLQPFATEHFVVFPYKSKWERVSHLKFKHGEIVLIPYPFVLTLYVAKKPRVZEDELKWFNENLSTGKPIDDSPLGLVPAERKAARAMKKKRKRMELSVSPSRPGLDRAKMRTSSQGPSKKKFLMETSRNMERNTQQKCQETPAFDGTDVQEQGSRWEDNLAGEITPPVQQSNPPPPAGPTDLGTSGFFGF +>sequence11 +MSLKPFTYPFPETRFLHAGPNVYKFKIRYGNNIRGEEIEDKEVIVQELEDSIRVVLGNLDSLQPFATEHFIIFPYKSKWESISHLKFKHGEIVLVPYPFVFTLYVAKKPRVZEDEMKWFHESLSAGKPIKDSPLGLVLTERKAAGAMMRKRKQVEVLSSPSRPGLDRAKIGISSQSPSKKKPLMETRRNREGKTHQEWQETPAFNITDVQEQDSKSEDSPAGQIIPPLQQNNPLPPKGPTELATGGFFGF +>sequence12 +MSLKPFTYPFPETRFLHAGPNVYKFKIRYGNSIRGEEIQDKEVIVQELEDSIRVVLGNLDNLQPFATEHFVVFPYKSRWERVAHLKFKHGEIVLVPYPFVFTLYVAKKPRVZEDEMKWIHEDLSPGKPVNDCPLGLVLPERTAAGAMLRKRKRGQVPSSPGRPGLDRTGKEKPSRNGRRLQRLISPMSRTRVGSGNREGCQGRLSHQCRRTIHLHLKDPQSWEPVASLGF +>sequence35 +MSLKPFTYPFPETRFLHAGPSVYKFKIRYGHSVRAEEITDKEVIIQELEDSIRAVLGNLDNLQPFITEHFIVFPYKSKWERVSHLKFKHEEVVLIPYPFVFTLYVAKKPRVZEDEMKWFHENLPPGKPINDSPLGSAVAEKKAAGDAGKKRKLVEEHGSPRGTALPRSVAEGKAESQSTEATLKKDQNRKKTQQETWKTVTSDTTDVQTQDSKRGHNLPGAMVPALQQSSSPPPQEPGTRSFFGF +>sequence38 +MSLKPFTYPFPETRFLHAGPNVYKFKIRYGNNIRGEEIEDKEVIVQELEDSIRVVLGNLDSLQPFATEHFIIFPYKSKWESISHLKFKHGEIVLVPYPFVFTLYVAKKPRVZEDEMKWFHESLSAGKPIKDSPLGLVLTERKAAGAMMRKRKQVEVLSSPSRPGLDRTGKEKPIRNGKRPQHLISLMSRNRILSQRTAQQGRSFPHCSKTIHFHLKDPQSWQLVASLGF +>sequence46 +MSLKPFTYPFPETRFLHAGPNVYKFKIRYGNSIRGEEIENKEVIIQELEDSIRVVLGNLDNLQPFATEHFIVFPYKSKWERVSHLKFKHGEIILIPYPFVFTLYVAKKPRVZEDEMKWFHENLSPGKPISDSPLGLVPAEKKAVGAVMRKRKHMDEPSSPSRPGLDRTGKEKPNKDCRRLWPLISLVSRNKILSGGTACQGQLSHPCSTTHLHLRSEQPAASLGF +>sequence59 +MSLKPFTYPFPETRFLHAGPSVYKFKIRYGHSIRTVATLLKSFQIYLFQDSIRAVLENLDNLQPFVTEHFIVFPYKSKWERVSHLKFKHEDVVLIPYPFVFTLYVAKKPRVZEDEMKWFHENLSPGRPINDSPLGLVVVEKKAAGASKKQKRKLVEQHSSPGGARQPRDKMRSSSQRPSTKKPPMGTRRNRERKPQQERQKTVASDTTDVQEQHSKWGHNLPGAIVPPLQQNNSPPPKELGIRSFFGF +>sequence64 +MSLKPFTYPFPETRFLHAGPNVYKFKIRYGNSIRGEEIEDKEVIVQELEDSIRAVLANMDSLQPFVTEHFIVFPYKSKWERVSHLKFKHGESILTPYPFVFTLYIAKKPRVZEDEMKWFAEDLPSGKPADDIPLELVLAETEAEEATMRKWKRKLMEEPSSPSRQGPHRAKMETSSEASSNKKPLKESKRSTDEEAQQEYQDTPASNAIAVKEQDAALGHGLQGLVVPPLQHSSPPPPKEPGARGFLGF +>sequence66 +MSLKAFTYPLPETRFLHAGSSVYKFKIRYGSSVRGEEIEDKKIVSQELEDSIRAVLGNLDNLQPFTTDHFVIFPYKSKWERVSHLRFKHGAALLEPYPFVCTLYVAKKPRVZEDEMKWAPAGGNGGPTNSAPLHLHKTQKEQDRPGTETSRKKEPPAPPSRGGERRTSLEQSWKELADSPELLLQLTRNWTGESASEKGEAEDSDISFLKDHGSGSSLRHQQKSPPKPSSPPSEGPPKQKHAGFLGF +>sequence78 +MSLKPFTYPFPETRFLHAGPNVYKFKIRYGNSIRGEEVENKEVIVRELEDSIRVVLGNLDNLQPFTTEHFIIFPYKSKWERVSHLKFKHGEVVLVPYPFVFTLYVAKKPRVZEDEMKWFHENLSPGKLINDSPLGLVSAEKKSAEAMMRKRRHTEVPSSPRKSGRFFPHLRAKVETSSEAPSKKKPPMETRRTWNDNEQQETPAFDATDVQEQGPKWGDSLAGQMAPSLQWNNPPPPKGPKELGTTGFFGF +>sequence81 +MSLKPFTYPFPETRFLHAGPNVYKFKIRYGNSIRGEEVENKEVIVQELEDSIRAVLGNLDNLQPFATEHFIVFPYKSKWERVSHLKFKHGEAVLVPYPFVFTLYVAKKPRVZEDEMKCFHENLSPGKSMNSSPLGLVLAERKTAEAVLKKRKRGEVPSSPARPGLDRAEMGTSSQGLSKKKPPMETRRNRERKTQQECQKTPAFDVTDVQDQDSKWEDSLVGKTIPPSQQNNPPPAEGPTELGTSGFFGF diff --git a/Motif2.fasta b/Motif2.fasta new file mode 100644 index 0000000..d0190ab --- /dev/null +++ b/Motif2.fasta @@ -0,0 +1,26 @@ +>sequence1 +DEFIALMHGSDPVRVELTRLENELRDKERELGEAQTEIRALRLSERAREKAVEELTDELEKMFEKLKLTESLLDSKNLEVKKINDEKKAAMAAQFAAEATLRRVHAAQKDDDMPPIEAILAPLEAELKLARQEIAKLQDDNRALDRLTKQKEAALLDAERTVEIAMAKAAMVDDLQNKNQELMKQIEICHEENKILDKLQRQKVAEVKKLSLTVKELEEAVLRGGATANVVRDYQRQVQEVNDQKKTLECELAAQWWRNYGGARAKVTANRVAVVVANEWKDSNDKVMPVKQWLEERRFLQGEMQQLRDKLAVAERTARSEAQLKEKYQLRLKVLEDGLRGPPSGSSRLPTEGKSFSNGPSRRLSLGGADNMSKLSPNGLLARRSPSFHSRSSLSSSSSLVLKHAKGTSKSFDGGTRSLDRSKINGNGAHLLNRSTDAVRDCETNDSWKGNADEGTIENTNSNTDESNKETANNKSAEMVSGFLYDMLQKEVISLRKACHEKDQSLKDKDDAIEMLAKKVDTLTKAMEVEAKKMRREVAAMEKEVAAMRVDKEQEVKARRLGSSKGTGSSQV +>sequence22 +LAHSDPIVLEFNRLQNQLKEKDRELGVASSEIKALRATIVLKDKALEQFRNEVNKLDERLGVIENLLKQKDLEIKKLTSEKKDALAAQFAAEAALRRVHANQKDDDTVPIEDVIAPLEADIKMYKIEIGRLQEDNKALERHIKSKESALLEAERILRSALERALIVEEVQNQNFELKRQIEICQEENKILDKTNRQKVLEVEKLSQTIQELEEAILAGGVAANAIRDYRRQISELNEEKRTLERELAAQWWRNYGGARVKVSANRVATVVANEWKDENDKVMPIKQWLEERRLLQAETQRLRDKLAISERTAKAEAQLKDKLKLRLKTLEEGLKQVSSFSENPYLSCRSPKPEKSNHILGFLSGNGGLKRRSTSQPRGSCIGKTSPLMPPNVENGAADAAGELKGVNSLKKKYASGENMLRKSLWASRSKVADIGGKENTEMKSNTDMHIDKFNNDTAVSADAKIKGGAKEETQNVGSAGFDSEDMVSAFLYDRLQREVINLRKSCEVKNNTLTAKDDEIKMLMRKVDALSKAIEVESKKIKREAAAREKEAISTKADENKKIRNTDSSKRRVA +>sequence24 +SSDPIVLELNRLENHLKDNDRELGIAHAEIKALKVTERLKEKAVEELNDDLKKLDEKLRFTENLLEDKNLEIKKLVSERRDALAAQFAAEATLRRVHANQKDEDYIPLDAVLAPMESEIRMCRNEISVLQEDKKALERLTKSKELALLETERMLKIAIERALLVEDLQNQNLELKRQIDICQEENRILDKANRQKVAEVEKLSQTIHELEESILAGGAAANAVRDYQRQILEMNEERRTLERELAAQWWRNYGGARVKILANRVATVVANEWKDDNDKVMPVKQWLEERKVLQGEIQRLRDKLNVSERTAKAESQLKDKFKLRLKTLEEGLKQVTTSSPNTEGSHLKQTVKPEPVLGYLSSNMGPRKRSQSQPRASFNAEQSTVQQRPNVTSENSNSNRTLEHVNSLKYKYISGKNLVKKNLWAPRNKLVDDVGKENSERKEDVGLEEFASVGPEVSKDFSAEAHSMQSTPEKDDLNVDCEDIVSGFLYDKLQKEVLNLRKSSQEKDGLLTAKDEEIKMLVKKIDTLTKAMETELKKMRRESASKERELTPRRVQKDPLHKSSTMIISKRAVKSV +>sequence28 +EDIIHLLHGSDPIKVELNRLENEVRDKDRELCEAHAEIKALRQTERLKEKAVEELFDEREKLQEKLKAMEIALENKNLDLKRTNDERKSALAAQAAAEATLRRLHASQKDEDLLPLEAILAPVEAELKSTRNDFLKLQDDNKALDRLTKSKEAALLEAERAVQIAEAKASLVDDLQNRNQELLKQIEICQEENKILDKMHRQKVAEVEKLSTTVAELEEALLAGGAAANAARDFERQVHHLMEEKRTLERELAAQWWRNYGGARAKVTANRVAVVVANEWKDANDKVMPVKQWLEERRFMQGEMQQLRDKLATTERTARSEAQLKEKLQVRLKVLEEGLRTSTNGSTRKHDDFLRSGTNGASVRRQSTGGSDIGNGVARRRPSMSSASQMRGSVSGSTILKNGKFGSKAFDGSKSLDAGRFKAYANGCEEPRKVSSAASGAGGGGGGGGGGGDVKPEAGKVEGATVAAADDNVSVLFYDMLQKEVVTLRKLGHEKDQSLKDKDDAIEMLSKKVDTLTKAMEVEAKKMRREVAAMEKEVAAMRVDKEQENRARRLSIAKGSVNSSHA +>sequence40 +EDLLNLLHGSDPVKVELNRLENEVRDKDRKLAEATAECKVLKQRERLREKAVEELAEELDKVDEKLKAAEDLLESKNLELKKLNDEKKAALAAQFAAEATLRRVHAAQKDEQLPSIEEILSPLEAELKIARQEIAKLQDTNRALDRLTKSKEAALLEIERAIDAAEAKASQVDDLLNRNQELMKQIEICQEENKIMDKMHRQKTAEIEKLSSTVAELEEAVLAGGAAVNAARDYQRQAHELLEGKKTLERELAAQWWRNYGGARAKITANRVAVVVANEWKDANDKVMPVKQWLDERRFMQGEMQQLRDKLASAERTAKNESQLKDKFQMRLKVLEESLKPVTNGAPRRTEEVRSSSTTRRSTSGSEEASKLLANGSRRQRSAVTQVRASMASQTLMRATNGRMTSKSFDGGRSLDAGTTRLRAFSNGFEEVPVKPDSVEAKSEVEAVKSENGTTNQVSGSSSSVEDPVSGVLYDLLQKEVVNLRKASYEKDQSLKDKDDAIEMLSKKVDTLSKALEVEGKKMRREVQAMEKEVATLRAEKDQTRNPRRLSSGTGTVNSSSK +>sequence42 +NEFITLLHGSDPVKVELNRLENEVRDKDRELGEAQAEIKALRLSERLREKAVEELTDELSKVEEKLKLTESLLESKNLEIKKINDEKKASMAAQFAAEATLRRVHAAQKDDDMPPIEAILAPLEAELKLARQEIAKLQDDNKALDRLTKSKEAALLEAERTVQVALAKASMVDDLQNKNQELMKQIEICQEENKILDKMHRQKVAEVEKLTQTVRELEEAVLAGGAAANAVRDYQRKVQEMNEERKTLDRELAAQWWRNYGGARAKVTANRVATVVANEWKDANDKVMPVKQWLEERRFLQGEMQQLRDKLAITERAAKSEAQLKEKYHLRLKVLEESLRGSSSNTRSMPEGRSTSNGPSRRQSLGGADNFSKFTSNGFLSKRTPTSQLRSSLSSNSVLKHAKGTSKSFDGGTRSLDRGSRALLNGSSPNCSFNQPCDETKDTEAANMWKGNSDEKPVEFPVTETEDTVPGVLYDLLQKEVVALRKAGHEKDQSLKDKDDAIEMLAKKVETLTKAMEVEAKKMRREVAAMEKEVAAMRVEKEHENRAKRFGSSKGPVGAAQL +>sequence55 +DLMNHFNGSDPVRLELTRLENEVRDKSRVLAEAQAEIKSLRLSDRQKQKAVDELSDKLEKVDEKLKGTLILLDNKNLEMKKLNDERKAALAAQTAAEATLRRVHASQKDNDMPSLEVILAPLEAELKIARDSAVVVVTLQISKLQETNRALDRLTKSKEAALIESERVIKAAEAKASMVDDLQNRNQELLKQIEICQEENKILDKMHRSKVNEVEKLSATVRDLEEAVLAGGAAVNAARDYQRQVHELMEIKRTLERELAAQWWRNYGGARAKISANRVATVVANDWKDESEKVMPVKQWLEERRFLQGEMQQLREKLASAERTCKSEAQLKEKVQLRLKVLEEGLKSGNGTVRRGAGAGGTVEAKRSSSVTSNGSVRKGSGSEEGAKVLANGSRARRSAVSQLRAMGGPLVKNGRLTSKSFDGGGGGRSSSGGSYDAGGMAALKPFTNGFEELRAGIKTESRSCSGEAAGDAGEGAGDTVSGVLYDMLQKEVISLRRASQEKDQSLKDKDNAIEMLSKKVDTLGKAMEVEAKKMRREVTVMEKEVASMRVDKDQERRMRRLSMMKEPVNSSQR +>sequence61 +EDVINLLHGSDPVRVELNRLENEVRDKDRELGDAHAEIKALKYSERLKEKAVEELTDELQKVDGKLKATEALLESKNLEIKKINDERKAALAAQFAAEATLRRVHAAQKDDEMPPIEAIIAPLEAELKLARLEAAKLQDDNRALDRLTKSKETALLEAERTVEIALAKASLVDDLQNKNQELMKQIEICQEENKILDKMHRQKVAEVKKLTQTVCELEEAVLAGGAAANAVRDYRRKVQEMNDERKILDRELAAQWWRNYGGSRAKVTANRVAVVVANEWKDANDKVMPVKQWLEERKFFQGEMQLLRDKLAVAERTAKAEAQLKEKYQLRFKVLEERLRASPSGNLRTTSEGRSISNGPSRRQSLGGAENLSRSASNGFALRRTANSQSGSIRSNSASVLLRNAKISSRSFDGGSRSLDRDKVIPNAARKHEVLTDTNDQIQNAKTIGTHEASTNGNRSEKTKSELDDSVSGVLYDMLQKEVITLRRACHEKDQSLKDKDDAIEMLAKKVDTLNKAMGVEAKKMRREVAAMEKEVAAMRVSKEHDPRARRPSAPRGSQ +>sequence62 +DDFISLFHGSDPVRVELTRLQNELREKDRELGDALAEIKSLRNSERLKEKGVEELTDELIKVDEKLKAAEALLESKNLEIKKINEEKRAALAAQFAAEATLRRVHAAQKDDEMPPIEAIIAPLEAELKLARMEVAKLQDDNRALGRLTKSKEAALLEAERTVQIALAKASLVDDLQNKNQELMKQIEICQEENKILDKMLRQKVAEVEKLTQTVRELEEAVLAGGAAANAVRDYQRKVQEMNDERKILEREVAAQWWRNYGGARAKVTANRVATVVANEWKDANDKVMPVKQWLEERKFFQGEMQQLRDKLAIAERTAKAEAQMKEKYQLRFKVLEERVKTSNGNSKFTVSDGRNIATGPSRRQSFGGAESLSASSSNGYQSRKTSISRPGSLRSNSANVLLKHAKLSSRSFDGGSRNLERERPTSDANGLDNMPRNSNIQTITSETITTHEESANGTPVKKSKSENEDYVSGMLYDMLQKEVISLRKACHEKDLTLKDKDDAIEMLAKKVDTLSKAMEVEARKMRREVASMEKEVAAMRISKEHDHRARRASAPRGAVNSQSI +>sequence69 +EEFINMLHGSDPVRVELCRLENEVRDRDRELSEAQAEIKALRLSERAREKAVEELTEEVNKMDEKLKLTESLLENRNLEIKKINDEKKAALAAQFAAEATLRRVHAAQKDDDMPPIEAILAPLEAELKLARQEIAKLQDDNRALDRLTKSKEAALLEAERTVQIALAKASMVDDLQNKNQELMKQIEICQEENKILDKMHRQKVAEVEKLSQTVRELEEAVLAGGAAANAVRDYQRKVQEMNDEMKTLDRELAAQWWRNYGGSRAKVSANRVAVVVANEWKDSNDKVMPVKQWLEERRFMQGEMQQLRDKLVIAERTARSEAQLKEKFQLRLKVLEDGSRMSASGTYRTTIEGKSVSNGPSRRQSLGGADNVPKSVNGFLSKRPSFQMRSSVSSSTVLKHAKGASKSFDGGTRSLDRSKVLLTGAGLSLNRSSDATGDGVTHESWKKIPDEKTNDFPNVDSDDCVSGLLYDMLQKEVITLRKACHEKDQSLKDKDDAIEMLAKKVDMLTKAMEVEAKKMRREVAAMEKEVAAMRVEKEQDNKSKRLGGSKGLANSSQL +>sequence80 +DDFINLLHGSDPVKVELNRLENEVKDKDRELGEAQAEIKALKLSERLREKAVEELTDELQKVDEKLKAAGALIESKNLEIKKINDEKKASLAAQYAAEATLRRVHAAQKDDEMPPIEAIIAPLEAELRLARLEGAGSPYQVKGAALLEAERTVQVALAKAALVDDLQNKNQELMKQIEICQEENKILDKLHRQKVAEVEKLSQTVRELEEAVLAGGAAANAVRDYQRKFMEMNEEKKILDRELAAQWWRNYGGARTKVTANRVAVVVANEWKDANDKVMPVRQWLEERRFLQGEMQQLRDKLAIAERTAKSEAQLKERYHLRLKVLEDGLKASPSGHIRPSEVRSVSNGRSRRQSLGGAENFSRLSSNGLSRRTPASSPSNNISTVLKHAKGSSRSFDGGNRLSEKNKVCLNNGVVPNSSLNTAVEEHRRTENSNTCKENQDVKQSDTSKADADDYVSGLLYDMLQKEVIALRKASHEKDQSLKDKDDAIEMLAKKVDTLTKAMEVEAKKMRREVATMEKEVAAMRVGKGHDLRTKRLSNSKVTSQL +>sequence84 +NEFITLLHGSDPVKVELNRLENDVRDKDRELSESQAEIKALRLSERQREKAVEELTEELGKMSEKLKLTENLLDSKNLEIKKINEEKRASMAAQFAAEATLRRVHAAQKDDDMPPIEAILAPLEAELKLARHEIVKLQDDNRALDRLTKSKEAALLDAERTVQSALAKASMVDDLQNKNQELMKQIEICQEENRILDKLHRQKVAEVEKFTQTVRELEEAVLAGGTAANAVRDYQRKFQEMNEERRILDRELAAQWWRNYGGARAKVSASRVATVVANEWKDGSDKVMPVKQWLEERRFLQGEMQQLRDKLAIADRAAKSEAQLKEKFQLRLRVLEESLRGPSSSGNRSTPEGRSMSNGPSRRQSLGGADIIPKLTSNGFFSKRSPSSQFRSLNASTSTILKHAKGTSRSFDGGSRSLDRSKVLTNEPRSKFPLNQSSEGTSGGGSPNSTKQGDSEKAAGTNNDSVPGVLHDLLQKEVITLRKAANDKDQSLRDKDEAIEMLAKKVETLTKAMEVEAKKMRREVAAMEKEVSAMRVDNKGSDSRTRRHSTNSKGASTTAQL +>sequence88 +DDFVNFLHGSDPVKIELNRLQNEVIDKNRELVDAQAEIKALKLTDRIKEKALEELTEELRKMVEKFQASEAALENKNLEIKRVVDEKKAALAAQFAAEATLRRVHAAQKDEELPPLEAILSPLEAEIKQLRQEVSKLQDDNRALERLTKSKEAALLEAERDVQSAYFKASLVDELQNRNQELMKQIEISLEENKILDKINRQKIAEVEKLGQTVRDLEEALLSGAAAANAVRDYQRQVSELKGEKRTLERTLAAQWWRNYGGSRAKVVENRVAVVVANEWKDSDGKVMPVKQWLEERRFLMGEMQQLRDKLSIAERTAKTEAQLKEKFQLRLKVVEDGLRSSFNGGVRSSELQNCSNGVSRRLSLGGFENSTKLSSNSFGTKKVPSLTRSSTMSSTSSSALLKHAKGASKSFDGSKSSSEGQSIDGNKSFSNGLDDPCFGNNTDESSMNTINNSGREICCNKQSEFAEPTSTDLVSGILYDMLQKEVIVLRKASHEKDQSLKDKDDAIEMLAKKVDTLTKAMEVEAKKMRREVAAMEKEVASMRADNEHGQRGRRLSGSSKGLLNNAHM diff --git a/Motifno.fasta b/Motifno.fasta new file mode 100644 index 0000000..f7bd658 --- /dev/null +++ b/Motifno.fasta @@ -0,0 +1,132 @@ +>sequence3 +GAFNAMFDYHGCWHKDAAATGSLCFDGRFIELYAVEAPRAHLALLDRVKRDVPPFWDPAALAEFIDKYGTHVIAGVKMGGKDVVCIKQLKGSNLTQSDVQSRLKKLSDDKLAQDSPESLTARDDKFLLGLNGSLLLGPGSAAWRSFRPSVVSHKDDILSIHIRRGGVDNGQGHSNWLSTISGSPDVISMAFVPITSLLTGVRGCGFLNHAVNLY +>sequence4 +GLFNSCFDFGSDSWASDAGDTRCLAFDGYFISLLDLRLDCRPLALAGHVVADVPAAWDPSAIASFIEKYGTHIIVGLSMGGQDVVYVKQDKSSPLSPSVIKEHLDKLGDQLFTGTCTLPPSHCKSRDHKFKVPEAFNVFDAQMTRQRIEGMTAPMSCKEGVTVIYSKRGGDTAASNHSEWLPTVPLMPDAINFKLVPITSLLKGVAGVGFLSHAINLY +>sequence5 +KAITNDIYIPAEFAACEFSLKSGKSSLYSSHINPGQLIFGQGSDTLHHTSNTHQLPLPPNALGEANIGKLYVSIVEYLRGCQDGAGQPNEPLVVFTSTELVPVVRGCFRYLESDSDELQENIEVYDIQYLFYVLKKEVMDIADLPNEHINKSITDNLFVNDFFEYHSGISCQFHEDNDRGKYCTQSKVARWCYMFSDYMCGDLAIKPLPGKHMPPKQEP +>sequence6 +KLAEYSMEKTKNDKFSFASQSTSCVFYRSYRLSSSPTLSQEFRKAVRGLPKTYSPENKLKFYRLIDTFGTHYITKVKLGGEVQSVTSIRQCQASLQGLSTEEVQMCLEAEASATIKATVKTELKHCKKDTEKMESKSSFSSLFNDRFTEIKGGQTTEPDLLFSSDKDPSAYKEWLNTLPLIPDIISYSLNSLHELLPTSCPVRKDLRSAIRHY +>sequence7 +NPFSASIPYKGYFTDLEIKKRKYIVAENTCLHSYATYSLRESIKNINSDFLLDTENLPILSKSITEKTCSKLIYMYNSKNDQCIKFIKPWIDFFRKYGTHVIVSAHFGGKTINTLEVPIHKFEELKIYNYKYPIENNRYLNVFKDRLLLQKILKIEKGEYAYRGGSQDNYMEDEQAEKNNDNLEKKANDVLNKYENSTSNKINLDIKGGTKLNEDWKQLTYEKWRNSIYTNIAPIYLDLFSLSSFMHIEKKESYNNALLYY +>sequence8 +YSFSASAGYKNALKKLKIQNSIIFMMKIYCLRYYTGISTTTNTWEFTNNFRNALNKLPNTFDGLKEDNECTYEYYITKSHSPQCEKNVNKWMTFFKLHGTHVAHEMYLGGKIIIKVNIEKEEYNKMKETNLDMKTVFDFYFHKMGLSARKNRRIQKFINKMHGSKTVSILGGHPGLNIDDPSFFEKWINSIDKNSMPIRTKLLPFSFFMDDPNMIKAYNDALMFY +>sequence9 +QFSEKIFPIEIGISSYSLKENKEIASYHKLLYPGKFKNVFARTQMIHGIDARDPRLEQNYSLVCIELIKYIEQFPGLAFFVSKEESLAGDKKCIDEIFLRGNVPIPKQIRFITHIQLFDYWCSIQHIELHEKSSFILNHIFKQLECAERCEYHKKINQKYHCALSDARHTSLMELICMKSYGATIIGSDTLPSVKFV +>sequence10 +AKYSKSVKKLRRVSGKSYSFVRAKAQLELAQYMLKSNDLMLHPEFLHRLRALPLSYVYGEYRQIFQDYGTHYITEAALGGEFEYTIILNKERLEQSDYTLEDYKKCAQAGLKVGANIYGVYVSAGVHGGSCNGLLNEMGENTARGSMVEDFVSVVRGGTSESITALLSKKLPTPELMRLWGEGVQFNPDFIRRTTQPLYELVTSRDFSQASTLKRNLKRALSEY +>sequence13 +VLGGSRSDLAKFARSQHSVDKATFAIHEISCTYYSYRLADHPQLSAEFTKYLRRLPQRVQTKQDRGPYRRLIDTYGTHYIHQVQLGGKVRRITAFRTCLATLKGFAETDVKTCLNAELRMSLGFLPANVTLSNKCDNLLKGNMSMGFYQGFMTHKIEVIGGERYFPDILYQQDPSEAYDSWMNSLHDNPDVISYAIFPLHQLVPDSQIAANLRDAITEY +>sequence14 +YSKNKSVQRLRQYSETKDKTYMRVSGTVQLASFQMRTRGAMLSPTFIEDIKSLPRDYDKAEYFSILEMYGTHYTVSGTVGGKYDLVYVLDSIVMKSLDITTEDVTDCLKLNAGANIGGTENGAKVDVNPNVKTDICNKGGGETETEPRRTQKPVIESIISFVDGGSVEYVTALEEKLNKKEPVADVDDYIQWASSLKDSPTVINSKSNPIISLIPTDIKDAYIKTRNLERAIEEY +>sequence15 +GSQESEFFHNVTHYKSTDLGFVRLWSKVETAHFKMRSDKLMLHEDFYISLMDLPEQYDFGMYSRFFNTYGTHYVTQGTMGGTLEYALVLNKTKMAESKLQGEQAGRCFSASIGLSYPIGQGASVDLKLGVNPCSKDGTFNQGSDASSVMVEDIITLVKGGILDSTSGVMVVRNPETYRTWGASLKYNPTLIEHEIMPIYELVRFSTAADHVGARLANLRRAWDEY +>sequence16 +TDICTVPVEICIKPTLLNGTINIECFQTIINQPIPIQHFLNSKHYTDFEHGISQENNPVPQTDFDFLWKKINTFIKSNMSKYSDSSMLPIIICTPFISSVQCVEFLASQAKVSDVRRSIFNTMFSVDDFVECVNRFKEIIPNTNAIYNFYKPLVCWTCNNDFKCDFHKSNGTRTFCCSKTNSEYLASTLCDLYKTIKSKIFVASMPSQV +>sequence17 +DRRKFHKTVTESRAHRLIILKNKVELAQFQNTAPEYLTLAEGFWRALSSLPTTYDYAAYRQLFQTYGTHYFSEGSLGGEYQALLELTQHALATTSTTSREYERCWRKVKRRFLRKKVKTVCEKLTSSTAASYVTPWSPGTSMRNVPIKVDVVGGNPGLKRFLSILDLENPEENGRKYDDWASSVKDFPQIIEQKVRPLYELVKEVECAGLKKLHMKQALEEY +>sequence18 +VNYEHKLENKSLNKLLTKNNLSIKKINCSIHTSGMIISYQWKLKKSISILLNDIQNKLVKDSGHTSNSNPQKNQKNIEKDWYNIFNTYGTHVLTKITLGGKIIEINAVEGGQNITENTSIFGSKLDINFFKMSLNSNSKDKLHDLDKNKSEKIIILGGNAMTTDRKTTNNNGEINYDKKLDKQKWVETIKYNPVPIKFELTPLSYFIYQNFSDENLVNSFHYF +>sequence19 +HGDMPSLCEQRYVPCEIACVRYSLREGILGSFHDFIDPGELPRGFRYHCQSGSASTHQIPISGFELANSDYHNMFRKLCSFVCPTPCPVVPVYTKANDIYRVDWCLQWLANKAGMENHFRVQEVETLIIKFYQDKLQEEPSRPTVSRLLDVVQWDYSSNTRCKWHEDNDMWCCALASCKKIAYCISKALASVYGVTLTPAHLPNPERS +>sequence20 +VSLSGEYVPAELAIIKYSLNDGVMDSLNVLINPTDLPLGMALDAKTHSSSTHQLPVPPDALGEANYEKILRQILKFFKNTSGSKVVPPIFTWNKDIPMVDSILRGILEATDLDYVKFSILPLIDFFYNLKLATEDYGLDIKTFPSIHLAKALLEKDVYAYTAGIACDVHEQLNNQVACALSRVVRWAYVISDSCCLDVGIEMEKGRHLPHNMTT +>sequence21 +FSFSASTGYKNFVKSTATNKVRTYITKTYCLRYVGGIVDYHSLDTTDEFKKAVEALPDKFDSHSCTIETFKSNEDDSICAETVLPWMQFIKMFGTHFTTIVHLGGKITHQVQIDKSDVLHMQQNGINVDAAVKASISPVMVDSLQGGFASTSEKASLSQSNNLKYDKQVLVIGGDGLVDSKNANSLNNWAKELYKRPMPIKIKLESIKSLLGKKRELFDEALKFY +>sequence23 +SHSRSSQFASSHSRKDKFSFTTHNLKCSYYTFRIHSRPPLSKEFEESLKNLPSTYDHKNTSAFTQFLSVYGTHFIRRVRLGGHVNSITAIRTCQASMSQMSVQTVSNCLSVEAQANIKGVTVSAATQFCKTKSSKLKTGATFRQAFSDRSIEVLGGDGDVGDVLFNSNGVAGFKKWLASIKRVPGLVWYQISPLHLLVPDNPVLQETLSKAISHY +>sequence25 +KAIGNDIYMPAEFAACKFSLRSGRGPVYSSHINPGQLIFGQASDAQHHTSTTHQLPLPPKAMGESNMGSLYVNIVKYLRDCQGAGNPLVVFTTAELMPVVSGCFRYLQSDSDEVGEQIHVYDILYLFYVLKKEVMDIADLPHANINKCITDNFFFNDFFEYYSNIACQFHEDNDRGKYCTHSMVSRWCYTFCDYMCGDLAIKPLAGKHMPPVQEQ +>sequence26 +ASFSASADFKQMKDTLSQKDTQCIQSHATCTAFDLSFYNDINSLPLLSLQLVDKIQQLYSYSNYTNEKEYYYDFFDSWGTHVATSVRLGSLFGYQFKMSSSSVQQQSSLGFDASVGASLYGVKGKVSTSYAQQQLNSFQQSLKSWSSYSLGATPNANLDAAQWATQTLDTPMPIKTELTPIYTFISQYQNNADIPLNSTTMAYVVNAMQNY +>sequence27 +FSASATNEFSDSSLRKSENEFSRCQQSFDLWSISIPADIARLQNYVSDDFIKLINAINPESKDSIATVFNVYGSHVLMSGVMGGKAHVSASANKLTLTQKFEMSTIVQAKYEQLTSQLSVEDKLKYSEAFDSFSESGSYTYDILGGSPSLGALVFKNNSQGSSDDNLKNWIQSISSMPVLTKFIDQTSLMPVWLLCEDKTKADALKKY +>sequence29 +GSFSASTGYKKFINEVSKRTSKTYFIKSNCIKYTIGLPPYVPWEQTTAYMNAVGILPKEFTGLNEDSCAPDVYEQKKMTKQCKNVHQWIQFFKTYGTHIIVEAQLGGKITKIINVSNTAVNQMKKDGVSVKAQIQAQFGFASVGGSTSVSSDNSSKNDNSSYDMSEKLVVIGGNPIKDVTKEENLYEWSKTVSSNPMPIHIKLLPIYKSFDSEELKESYEQAVLYY +>sequence30 +KYNINRLLCYPAEIAITTFNMKEGIIYSDSKFVEFDERWAFGQDERDHRTMSERVNENEDLDELMHQLSSTIGIDHLSTDHNPESPFGVFEWLRSRIDIYPYAKILVDMNQFRFVYNGLKNIAKYHGFTGQTYFNENIKFNMVSIQDFTDVLLDYCSLLVARRWSDQDINNQYLRPNLVPNRDKNTICEYHETVPCPTRYNCMKAHNSRLVHHFFTIMKAHRLQNFRYSPPVHEPCIEDM +>sequence31 +NGKFSTENQRMKIHQVKDSSVTTRVQIRNFIYKVKVFPDFSLDVRFAQQAKEIADAIENNQSRYADYLSERMVMDFGTHVITSVDAGASLVEEDYLNSKYVSDNVSQSSSISAQAGLNFFDKLKFDISSHNSQQSSTLQGYQSNIRYSLIQSHGGGIPFYPGMTLQKWQESTRNNLVAIDRSGLPLQYFISPNMLPDLPQPTVRKVSHLVRSAIERY +>sequence32 +ISLGINHELDQFHQEITQNNKAVSVSQSYWAQYSLTTAPAFLMPLNPMFKQSLDALNRMAKEPTTDTQQTIYNQVINSFGTHYVTSAIMGGAAKIYTTLDQNYLKTVDIEQTKTQIGINFSYNVFQFKFGFNSTDLAQKLDENFKKNSNDIIIFSPEVDHISDPKAWSTWESTVPEKPQPVNTTVSYISDLAYEFPEVQAHLRKTIEFY +>sequence33 +KAVNTDIYIPAEFSACEFSLKTGVNSLYSTMIDPSQLIFGQTCDAMLYAAATHQLPLPPAALGESKMTKLYHSIQDYLRSRLERTDKNLKSLVVFTKTDDIDMVKSCFRFIKSGYHDEQSKRYDDDNDEENDQFKFFEAAASKFLPIVVYDIQYLFLALKLAAMDIGGLTLPKPNLYITDAFFSRDFYEFQDGIACWFHEDMDRSKYCTQSKVKRWAYTFCDYMCADLAIKMQPGKHMPPSYKA +>sequence34 +KALTGDIYVPAEFSACRYSLKGGISSNYSTMINPGHIIYGQSRDAQDHSKTTHKLPLPPQAFGETNMGKLYIDIFNWLSVRNEEKLDQDPVIVYTTPELMPVVKSCFRYLASEAEIDEDERKIMVFDIHHLFYTLKKSVLDVAGVTNDRINFHVTNNFFVKDFFEYTEGISCDYHEKIDRSKYCTNSMVKRWGFTFSDYMCADLAIPLQPGKHIPLKVKP +>sequence36 +NSFTGSLEYKNALMNFKSKRQKIYNKTEQCVRYQVGIPLNLKWGYTEYFNRTLSRLPILSSKVIKNCNIDNKLNLSDEECKSIKPWIKFFEVFGTHFNNQLTLGGKINQTMVFDSSTLEELKKKGIDIEAEVRTELGSGNVKLNLDMGGKKSRLDEIGQKKMSVLGGKMPNFPMDDNEFAHWAETVAENPMPIGVVSTSLKTLMHPAMHQSYDQALHQY +>sequence37 +VNGKFSTEFQRMKTLQVKDQAVTTRVQVRNRIYTVKTTPTSELSLGFTKALMDICDQLEKNQTKMATYLAELLILNYGTHVITSVDAGAALVQEDHVRSSFLLDNQNSQNTVTASAGIAFLNIVNFKVETDYISQTSLTKDYLSNRTNSRVQSFGGVPFYPGITLETWQKGITNHLVAIDRAGLPLHFFIKPDKLPGLPGPLVKKLSKTVETAVRHY +>sequence39 +SSHNSAFKQAIQASHKKDSSFIRIHKVIKVLNFTMKTKDLQLSDVFLKALNHLPLEYNAALYSRIFDDFGTHYFTSGSLGGVYDLLYQFSNEELKNSGLTQEEAKNCIRIETKKRYFIVTKTKVEHRCTTNRMSEKYEGSFLQGSEKSISLVKGGRSEYAAALAWEKGSSGPGEKTYSEWLESVKENPAVIDFELAPITDLVRNIPCAVTRRNNLRRAFREY +>sequence41 +YSGYNNDEYTHDDMLHNLNKHNKLLIKSYKCIVYKANLTSLNFLKNKNNDEIGLNFNGMLILNVLKKLNKNCNSEFDNQKCPISMFRNDPFDANCIRCIMPWMEFFKDYGTFMTKEITMGGVINKFYNIKKYEGSMRKEYKKKTIKQSSTFFHLSKSRSESLNEKKSGETNKEELEELYTLTIGPEPPGNVSNSKVISDWLEKVVHNPTPIDLELVPIKQIIPEKYLKIYENALKYY +>sequence43 +SGSRESAFLNKLSKYNEKKYSFIRIFTKVQTASFKMRRDNIMLDEVMLQSLMELPEQYNYGMYAKFIDDYGTHYITSGSMGGVYEYILVLNKENMTKSGVTSDDVTSCFGGSFGIDYDYTDNLQITGSLSGKHCKKLGGGHREDEESNMAVEDIISRVRGGSSGWGGGLTQNGSIITYRAWGRSLKYNPAVIDFEMKPIYEILRHTNLGPLEAKCQNLRRALDQY +>sequence44 +KALTTDVYVPAEFSASEYSFNEGIMSVYSTLIDPGQIIFGQGSDAQHHSSTTHNLPLPPNALGEKNMGKLYRNILEYLSKIQEGKDATKPFVVFTKTDMVPVVKSCFRYLACENQDGSYENGDQIQVLDIQYLLFILKKEVLDIAGVSDEKINLYVTDAYFLKDFFEFTPEISCQYHEENDRSKYCTQSLVMRWAYTFSDYMCSDLAISVQPGKHIPPKTKP +>sequence45 +SVAGSHSKVANFAAEKTYQDQYNFNSDTVECRMYSFRLVQKPPLHLDFKKALRALPRNFNSSTEHAYHRLISSYGTHFITAVDLGGRISVLTALRTCQLTLNGLTADEVGDCLNVEAQVSIGAQASVSSEYKACEEKKKQHKMATSFHQTYRERHVEVLGGPLDSTHDLLFGNQATPEQFSTWTASLPSNPGLVDYSLEPLHTLLEEQNPKREALRQAISHY +>sequence47 +KALTTDVYVPAEFAACEYSLKEGIRSIYSTMIDPGQIIFGQGSDALLHSSTTHDLPLPPNALGEKNMTKLYRNIVDYLSKCQGKGKTLVVFTPAENITMVKSCFRYLECDDDFRDGGEKIQVFDIQYLLFILKKEVMNVADLNDEKINKFATDAFFKKDFFEFTAGIACQYHEDNDRTKYCTQSMVTRWAYTFTDFMCGDLAITVQPGKHIPAQTK +>sequence48 +AKFSLSTNYSEISDLLKNNDNKLYVDKSYCFLLEAALPIHNSLKMTRSFATAMSKLTRDFKKHTKDCNAIKYSINKNNKDCKEIKNWMELFDQFGTHFSYNIKLGGRITFITQEEGSKDERGNEKSVDVGVGGKFEKDNKGVGIEGNVKFVFGNKRGESKNLSFKYTNILGGLPVSDISKESEYVKWIKSVYKYPMPIRTQFAPISKIFKSKALKDSYDEAFRFY +>sequence49 +GSFSASVGYASASNTISKKKFRMFILKSYCFKYVASLSQYSQWKLSDQFLRAINLLPSYFNSLEHDGKYCNAEELRDNKTGMDSCGKSVESWLYFFKNFGTHVSTVIHLGGKITQQVKISKNEYKSLSESGLSTSVSASVGFGLFKANASSSTDSKESSNEESSNSSIEKETVIIGGTTIYDPNDPSNFEKWADSIKNNPMPIKGQYEPLSRILPERLTKIYDEALSFY +>sequence50 +NIDGECMLAEMAMNEFSLFSGIVEKFHAIVGPWMPESESHRRRASRHALETHRIPLQNNFATITKKRLVEEILGRVEPSIACHQGVKVGLYSDACNEKTKIDLNIKNNFKDPGMLCDKNDRRFILVLQSELDLMVDSMKHLANNVGFHYDGFPVTPNCFVIVEAFVEAISDIMNEKIDVETMRWFSLLGQKVDAEDSVSPWETGTDFHCARHSEPKSNFCASVTVGRTCCIVYHVIGSFFRRYHLKKIPTAHQPSSSNS +>sequence51 +KALNGDVYQPAELSACRFSLKGGISSNYSTMINPGHIIFGQTSDAQDHSRTTHKLPLPPNAMGEKNLGNLYSDTLKWLSASNDEEDEQYDHPVIVYTTPELMPVVKSCFRYLACEGDTDKHAKKIIVYDICYLFLTLKKTVLDLVGVPSDHMNIHVTNSFFRRDFFEFSSGIACDYHEEVDRTKYCTKSMVLRWGYMISHYICGDLAIPLQPRKHVPIEVKH +>sequence52 +RTNTGVHLPAELAVVRYSLEGGVKDKLHMFINPGRLPIGMAYDAQRHAEEDHQLPLPPNAMGVSDYGDVAMRLFSFLLQNDDMPLLFTDETDVPRVESMLEHILSDHLSEIELRICPLAELFFRLKQNVELYMMDQTTFPSVYIAQQIITKDVYDYTKGISCDYHEEKDNVLYCPLSRCIRWAYIISDNCCQDMGIEPIPGKHVPLNANT +>sequence53 +FSGSLTCEFVKKSTQHAKNTVTCSTAAHSLYTLKEDDSSNPSEKRLDSCFRNWIENKLSANSPDSWSAFIQKFGTHYIASATFGGIGFQVLKLSFEQVEDLHSKKISLETAAANSLLKGSVSSSTESGYSSYSSTSSSHTVFLGGTVLPSVHDERLDFKDWSESVHLEPVPIQVSLQPITNLLVPLHFPNIGAAELSNKRESLQQAIRVY +>sequence54 +WAFTASSEFNHMQQKIEQTSATFVISMATCQIAQITQVPELAEFHQSFIDQLSALPVEYSAPQYLEFLSNFGTHYATDIILGSKVGYVYTLPPAIVDDFDQKKFKEIDLKQAATITSALLKGVIGQQILPKEQEAKAYSDVSKLSTQSFTIEIGPQSTENTPKDWLRETELEPTPIRYTLKSISELVSEGKGQLSSVKEYQKIGQNLKKALTDY +>sequence56 +VTSGGTYIPAEMGLVRYSLKDGVMDKLHMFIDPGKLPLGMAYDAKQHSESDHQLPIPPDAKGEKDNDEIILKLFSFLSQQEKMPPLFTETNDIRMVENILKGILNQGSMDENTLLVCPLSELFYQLKRATESFGLDIKTFPSVHIAQAIIQKDVYEYTKDISCEFHEDQGNGKYCPLSRCVRWAYIISDSCCLDLSIEMKPGRHLPMNADT +>sequence57 +KSMTNDIYIPAEFSACQFSLKSGICSMYSSHIDPGQLIFGQGSETMHHTKHTHQLPLPPNAMGESDIGRLYANIVEYLRACNPDAKPNDPLVVFATPEFMPIVKGCFRYLESDSEEPLATIHIYDIQYLLYVLKLEVLDSVDIRNVTVNRTATDSLFINDYFCYHLGISCQYHEDIDRCQYCTQSIISRWCYVFSDFMCGDLAITPLPGKHMPPKQEP +>sequence58 +SSSRSYTSHTNEIHKGKSYQLLVVENTVEVAQFINNNPEFLQLAEPFWKELSHLPSLYDYSAYRRLIDQYGTHYLQSGSLGGEYRVLFYVDSEKLKQNDFNSVEEKKCKSSGWHFVVKFSSHGCKELENALKAASGTQNNVLRGEPFIRGGGAGFISGLSYLELDNPAGNKRRYSAWAESVTNLPQVIKQKLTPLYELVKEVPCASVKKLYLKWALEEY +>sequence60 +KDACTPAELAVVQFTLKHGMRNIYHTLINPDGSQYATQEHVRATHQYPNALGNDDLEGILADLLEFVRLECGPEAELSPMFTLESQISVVNNALEFLNGGVASQLKVHPIEYLFYVLKKATCAAGILPPPASFHITNAQFNLDPHEFLSDIGCEFHKQRDLTAHCAKSYVTRWAFAFADYMCSDLAIKMLPNRHMPNRLDT +>sequence63 +IDLANEPLYREAVKASQQKDSVFYRVHQVIATSTFKVKSSDLYLSDPFLQFLNSLPLEYNYALYRHIFQLFGTHYFSSGTLGGKYDLLFQFDREELKTFGLKESDSEYCLSDDDTLVTFFYNRHKQRNTCGNISMKTKYEGSMVKASERCITSVQGGRTEFAAALAWEKKGVSPQSTVYTDWIKSTIENPVVINYELLPLVNLVRGISCAVTKRRHFHRALEEY +>sequence65 +HPFNDSNYYKMLVKRINRGDSIIIEKKLCSKYFSFINDINKNDLDTFFLTTLNELGDNYQNIKDDTYKCSLQYYKMNNMNKYSENCLKTITPWISFFNMYGTHVISGVYYGGKIIHNLYFENNNLKKKEYKIRMYKSRLNPFSTINSNLYFGSSLSKEKIIYIRERNLIMDGGVHINPYNINEVNMENKKKNIYVNNVEKNLYDQKKKYRNYYNFYELKDDVRKRNYYNSWKDTIEWEQAKPVKLNLVPLSEFINSEEGKSAYYMALEFY +>sequence67 +CEQRFLPCEIGCVKYSLQEGIMADFHSFINPGEIPRGFRFHCQAASDSSHKIPISNFERGHNQATVLQNLYRFIHPNPGNWPPIYCKSDDRTRVNWCLKHMAKASEIRQDLQLLTVEDLVVGIYQQKFLKEPSKTWIRSLLDVAMWDYSSNTRCKWHEENDILFCALAVCKKIAYCISNSLATLFGIQLTEAHVPLQ +>sequence68 +GKFSEENTRMKIHQVRGNSVTTRVQVRNHLYTVNAYPDFTLDSRFSQQISELADAIENNQTRQAMYLSEKVILEYGTHVITSIDAGATLVQEDYIKRSYVSDTNSERSSVSASAGINFFNMVNFNFGSKETEQTSETLTYQQNITYSLVQSHGGALFYQGITMQKWQESTQNHLVAIDRSGLPIHYFLNPAVFPDLPVPTLHKLAFSVQKAAERY +>sequence70 +GMFNNMFAFSKCWPKDASSVKTLAYDGWFISLYSVEIVRKQLTLRDEVKREVPSSWDSAALAGFIEKYGTHVVVGVTMGGKDVIHVKQMRKSNHEPEEIQKMLKHWGDERFCVDPVESKSPASVYSGKPKEENLLQWGLQPFGTSVSSAVVMHTKNEEIMRVCIRRGGVDLGQSHERWLSTVSQAPNVISMCFVPITSLLSGLPGTGFLSHAVNLY +>sequence71 +GNFNATFGFQSGSWATDAANVKSLGLDASVVTLFNLHIHNPNRLRLTDRVRNAVPSSWDPQLLARFIERYGTHVITGVSVGGQDVVVVRQDKSSDLDNDLLRHHLYDLGDQLFTGSCLLSTRRLNKAYHHSHSQPKFPEAFNVFDDKQTVAFNNFSINSQNGITVICAKRGGDGRAKSHSEWLITVPDKPDAINFNFIPITSLLKDVPGSGLLSHAMSLY +>sequence72 +KPFSASMPYKSYFADLEIKKKKYALAQNMCVLNYATYDLKESGNNINKDFVLDIEKLPILTKNQMKLCTKVLYMNNNLHCSEGIKSWMKFFEKYGTHVVLSAHFGGMSFNTMEITKRKIEEIKIYKYKYSLWNNPYLNIFKSGSLFQDLSINVDGHKENKKNNSNNNINIDEKKKNDAYIKNDVLIEQYRDNINLEIRGGNNFDEKWRNLTYLVWKNSIYSNIVPIHLDLYSLNTFMPIEKKESYDMALLFY +>sequence73 +EFSAEFMFLNNISKYTNKEMGFVQLMSKIQTSQFKMRSKDLVLDEDMLWALSDLPDHYHFGAYSQFFNEYGTHYVTEGTMGGLMDYVAVVNINEMEENQMTGQMIGSCIGGSFGLVFMEKIKATVKGKSCGKFTSNEKTSDESHSAIKDVFGFVKGGNTASSAGSLGIKDAKSYKDWGKSLKYNPALIEFEILPIYELLRLSTAAEQLSSKLPHVKMAWEEY +>sequence74 +ELPDDMGYMPCEIGVVEYSLQEGITREFHRFIQPGKPPLGYRYLCQSTSDNTHQIPIEGFELAEGDYHRLWTDLCKFTSPNGRDFPPLYVQVTHTSMCEWCLDWLSEMAGEYNRFHVYELDSLVKDLYEHGEGHAPSLSMIASILNTSVFDYEDGSSCEYHASKEVKYCALGAVKRFCFSISDSMAQVYDLQLTARHLPERPEN +>sequence75 +FKFSASAKFKKLQDVSKSGKSKMFINKSYCFKYVAGISTSLKWDFTLGFQSSLGRLSDFKGLEKDSICKPFIYREDPKNENCQELGISDWMELFNTFGTHVATKIYLGGKIFTTLEIKKSQEKKLSDQGLDVRAILSAKIKDTDIDSNVEVSTIKSKNAGDFLLDTKKSTFVLGGDIYGHGKTIEFAEWARSVADHAMPIKAEFTPISHFIDKNLRDAYNKAYLYY +>sequence76 +HPFNSSNYYRMLVERIEKGYSIIIDKKICSRYFVALKNVDSSKLDPFFINMLNDLEKNYKNININKYKCSVHSYKKNKYDQNCLRTITPWITFFNLYGTHLVSEVYYGGKIINILYSEYYNNIYNSEQVQIYKKRLNPFTSGSKLGSFYFGSIISKKQNSTNQKDNDNMLTYIKEKNTIYDGGEDIKEYKDGEGKVLMINGMEDEWEKTINGKYAKPIKLILKPFSDFIKTNDGKVAYYKALEYY +>sequence77 +GRFRASVDYQNMQNDMASGTYQYIVSNSRCSVFQLDLIDSPTYHPQFSNDILLNLQQLALNQNNANNTEANAYYDFFDNWGTHVVTSVDLGSLFGYKFKMLKTDVQSMQNQGIDVSASATLFNVRGRTNTQLEQNSLNSFSQSIQSWTSYSIGATPDLNNDPANWATQTLTKPMPIKSSITPYHEALKIFTQGGNNILSSTQILQLYSKLRMY +>sequence79 +FLGEIENRFDMSDDKSSKRTNEYISYDINNTLYRITLKGNVPLSEQFQEDLNSLDATTLFEKYGTHYLKSTWIGGRISFSTTIDTYGMTDDMRKKFAFVTKRKVGNWTGTSDVELTREEKDISEKMKSNSIVRVWGGDPKLGRDIERAIQGHTVSDIYQQWGQTVEERPYISDFDHGQGLVPIYELATGTRKEQLKEQWEAY +>sequence82 +GKFSASSDYQEVQDGLNSANIQYIESQARCSIFQLDVYNSPSQNAQLTPQLQQALFTLAFNQTSQNDYYDFIDTWGTHVVTSVNLGSRFGYKYQMDKYQSNQLTQQGVNLSVSASYFSSSGSASGAYNQTQIQNFTQAMTSWSSYSIGATPDANQDPLSWAQQTLDTPMPINISILSFDDFLNKFSFSVNGLTSSQLNTVISNLSQY +>sequence83 +SQSRMTHEVIESAQKIDSKYFKVVNTVELAQFKMRRNGLNPSDIFLRRMKDLPVYYNYLDYSFLIEDFGTHYFSSGSLGGQYEYVYRYSRADLSHSGLTEEEQKSCLSAEAKASFFSFSGSSSGSRCKENALSQRNSGSFTLSASESFSHVKGGSSESAGQLAFANGPNPQKYEAWIQDVKRNPAIISYEITPISELLVGIPYADIKRRNMEKALVEY +>sequence85 +YYPTEDKYFICEIAIAAVSLKNGVEDVFHRIVKPGKLPLGYYGGALTHSKETHQMLELVQDEPYENNTREVFNEMTSFLKLWRGKGSDSIVYADEKTHEMITKVIDNFCQEFNYPDEIKVYNFQYLFFALRNSVAARTVWPTETYSSTELEKDLYSYTPDISCEFHEMSDISVYCSKSIVTRYCYTLCDHCCTDLNIQLVAGFHVPKNSRI +>sequence86 +ISAEVKSKFSKESLDVKVGKEVYLTSSVSVPRLEFCINPLKVKLSDEFYSKLNNVETHGELIKVFKEYGEFYPKRYILGGMITNHETQKFTTIENLESKLLSLSAGVNAAIGPVKVGGSVGGESATDEKKSKQNEENSSKKDVIGGDPSKTGSEWVSSLSDINNWGIIGIDVYPIMDLIKKNDNTLYKKLEKIKNS +>sequence87 +KTSTEAFVPAEIALIKYNLELGVLDKLHELINPVRLPLGLAHEALTYSEQTHELPTPPNAMGETDFYTVLQKILSFTDYNSKPHKKLAIMTDAKEVPVIESLLSQLNDDVKLEYQFLVIPLGEFFFHLKRATEKYGLDICTFPTKTVADILLKKDAYEYTSGIACDFHEKLGNQRFCALSKVVRWSYIISDNCCLDLSIDLIAGRHLPSNADT +>sequence89 +GFFNAMFEFTGCWQKDASITKSLAFDGWCITLYTVALSKAHIILKDHVKQAVPSTWEPAALARFIKKFGTHIVVGVKMGGKDVIYLKQQHSSSLQAVDVQKRLKEMSDQRFLDANGHSDISLADSYAKDNKVEAREQRLRFVESNPLNSYSSNEELVMMPKRRGGRDKDIISHSEWLNTVQAEPDVISMSFIPITSLLNGVPGCGFLNHAINLY +>sequence90 +SFSASTGYRDFAKEVSKKDTRTYMLKNYCMRYEAGVAQSNHLKWNVTLAFAAGVSQLPDVFDAHNPECACSAEQWRQDQNAEACTKTNVPIWISFIEQFGTHFLVRLFAGGKMTYQVTAKRSEVEKMRNMGIDVKTQLKMQLGGVSGGAGQGTSSKKNQSSSEYQMNVQKETLVIGGRPPGNVSDPAALAAWADTVEELPMPVKFEVQPLYHLLPVEKQEAFKQAVTFY From a50826a3eba07605059daae48c69114f454ed40b Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 19:08:16 -0500 Subject: [PATCH 04/27] Create Alignment 1 --- Alignment 1 | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 Alignment 1 diff --git a/Alignment 1 b/Alignment 1 new file mode 100644 index 0000000..ac04af2 --- /dev/null +++ b/Alignment 1 @@ -0,0 +1,15 @@ +Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Bacillus.fasta -out Bacillus.align + +MUSCLE v3.8.31 by Robert C. Edgar + +http://www.drive5.com/muscle +This software is donated to the public domain. +Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. + +Bacillus 4306 seqs, max length 1495, avg length 244 +00:00:45 158 MB(2%) Iter 1 100.00% K-mer dist pass 1 +00:00:45 158 MB(2%) Iter 1 100.00% K-mer dist pass 2 +00:01:53 1255 MB(15%) Iter 1 100.00% Align node +00:01:53 1255 MB(15%) Iter 1 100.00% Root alignment + + From 98791f5264e785d93924c7e22272f38aacde1e5d Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 19:10:11 -0500 Subject: [PATCH 05/27] Create Alignment 2 --- Alignment 2 | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 Alignment 2 diff --git a/Alignment 2 b/Alignment 2 new file mode 100644 index 0000000..f45d7da --- /dev/null +++ b/Alignment 2 @@ -0,0 +1,13 @@ +Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Arthrobacter.fasta -out Arthrobacter.align + +MUSCLE v3.8.31 by Robert C. Edgar + +http://www.drive5.com/muscle +This software is donated to the public domain. +Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. + +Arthrobacter 3212 seqs, max length 2033, avg length 325 +00:00:29 92 MB(1%) Iter 1 100.00% K-mer dist pass 1 +00:00:30 92 MB(1%) Iter 1 100.00% K-mer dist pass 2 +00:02:12 734 MB(9%) Iter 1 100.00% Align node +00:02:13 734 MB(9%) Iter 1 100.00% Root alignment From 8393061e57c6abd1cb77b6a54b40095043335233 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 19:14:27 -0500 Subject: [PATCH 06/27] Create Alignment 3 --- Alignment 3 | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 Alignment 3 diff --git a/Alignment 3 b/Alignment 3 new file mode 100644 index 0000000..691d104 --- /dev/null +++ b/Alignment 3 @@ -0,0 +1,13 @@ +Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Clostridium.fasta -out Clostridium.align + +MUSCLE v3.8.31 by Robert C. Edgar + +http://www.drive5.com/muscle +This software is donated to the public domain. +Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. + +Clostridium 1828 seqs, max length 1965, avg length 272 +00:00:14 32 MB(0%) Iter 1 100.00% K-mer dist pass 1 +00:00:14 32 MB(0%) Iter 1 100.00% K-mer dist pass 2 +00:01:10 512 MB(6%) Iter 1 100.00% Align node +00:01:10 512 MB(6%) Iter 1 100.00% Root alignment From 82f91943d2ade58156fccc43e8430cac42023752 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 19:37:58 -0500 Subject: [PATCH 07/27] Create Alignment 4 --- Alignment 4 | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 Alignment 4 diff --git a/Alignment 4 b/Alignment 4 new file mode 100644 index 0000000..4bc35c7 --- /dev/null +++ b/Alignment 4 @@ -0,0 +1,13 @@ +Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Flavobacterium.fasta -out Flavobacterium.align + +MUSCLE v3.8.31 by Robert C. Edgar + +http://www.drive5.com/muscle +This software is donated to the public domain. +Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. + +Flavobacterium 4309 seqs, max length 5826, avg length 355 +00:01:46 160 MB(2%) Iter 1 100.00% K-mer dist pass 1 +00:01:46 160 MB(2%) Iter 1 100.00% K-mer dist pass 2 +00:20:34 2202 MB(26%) Iter 1 100.00% Align node +00:20:37 2202 MB(26%) Iter 1 100.00% Root alignment From 7e1256d8ca2a636e1fd4f75ba186e3d5f2e4c731 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 19:39:00 -0500 Subject: [PATCH 08/27] Create Alignment 5 --- Alignment 5 | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 Alignment 5 diff --git a/Alignment 5 b/Alignment 5 new file mode 100644 index 0000000..745d71c --- /dev/null +++ b/Alignment 5 @@ -0,0 +1,13 @@ +Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Limnohabitans.fasta -out Limnohabitans.align + +MUSCLE v3.8.31 by Robert C. Edgar + +http://www.drive5.com/muscle +This software is donated to the public domain. +Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. + +Limnohabitans 3169 seqs, max length 6686, avg length 324 +00:01:10 89 MB(1%) Iter 1 100.00% K-mer dist pass 1 +00:01:10 89 MB(1%) Iter 1 100.00% K-mer dist pass 2 +00:16:00 2259 MB(26%) Iter 1 100.00% Align node +00:16:03 2259 MB(26%) Iter 1 100.00% Root alignment From f0110bf961018f07b42e0b49b9d23b7ea8315678 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 19:48:57 -0500 Subject: [PATCH 09/27] Create Alignment 6 --- Alignment 6 | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 Alignment 6 diff --git a/Alignment 6 b/Alignment 6 new file mode 100644 index 0000000..9a041e5 --- /dev/null +++ b/Alignment 6 @@ -0,0 +1,13 @@ +Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Verrucomicrobia.fasta -out Verrucomicrobia.align + +MUSCLE v3.8.31 by Robert C. Edgar + +http://www.drive5.com/muscle +This software is donated to the public domain. +Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. + +Verrucomicrobia 1793 seqs, max length 2811, avg length 326 +00:00:33 32 MB(0%) Iter 1 100.00% K-mer dist pass 1 +00:00:34 32 MB(0%) Iter 1 100.00% K-mer dist pass 2 +00:05:03 982 MB(11%) Iter 1 100.00% Align node +00:05:03 982 MB(11%) Iter 1 100.00% Root alignment From c9033910a2e02686ad64882aaedcaa5d9920d7c8 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 19:54:10 -0500 Subject: [PATCH 10/27] Create Alignment 7 --- Alignment 7 | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 Alignment 7 diff --git a/Alignment 7 b/Alignment 7 new file mode 100644 index 0000000..c5b839d --- /dev/null +++ b/Alignment 7 @@ -0,0 +1,13 @@ +Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Rhizobium.fasta -out Rhizobium.align + +MUSCLE v3.8.31 by Robert C. Edgar + +http://www.drive5.com/muscle +This software is donated to the public domain. +Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. + +Rhizobium 4696 seqs, max length 3387, avg length 320 +00:02:58 188 MB(2%) Iter 1 100.00% K-mer dist pass 1 +00:03:00 188 MB(2%) Iter 1 100.00% K-mer dist pass 2 +00:15:19 1690 MB(20%) Iter 1 100.00% Align node +00:15:21 1690 MB(20%) Iter 1 100.00% Root alignment From 26f5fbb5ae69b9e0cc31d20b765e25869e05e509 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 19:56:54 -0500 Subject: [PATCH 11/27] Create Alignment 8 --- Alignment 8 | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 Alignment 8 diff --git a/Alignment 8 b/Alignment 8 new file mode 100644 index 0000000..237292d --- /dev/null +++ b/Alignment 8 @@ -0,0 +1,13 @@ +Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Roseobacter.fasta -out Roseobacter.align + +MUSCLE v3.8.31 by Robert C. Edgar + +http://www.drive5.com/muscle +This software is donated to the public domain. +Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. + +Roseobacter 4185 seqs, max length 3284, avg length 311 +00:02:36 151 MB(2%) Iter 1 100.00% K-mer dist pass 1 +00:02:38 151 MB(2%) Iter 1 100.00% K-mer dist pass 2 +00:15:36 2320 MB(27%) Iter 1 100.00% Align node +00:15:39 2340 MB(27%) Iter 1 100.00% Root alignment From c3028acfaca97eccec92c8067db14841fb0e8274 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 20:02:06 -0500 Subject: [PATCH 12/27] Sigma.Align --- sigma.align | 681 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 681 insertions(+) create mode 100644 sigma.align diff --git a/sigma.align b/sigma.align new file mode 100644 index 0000000..c34e59a --- /dev/null +++ b/sigma.align @@ -0,0 +1,681 @@ +>SIGS_STAA8/773 +-----YNKHQKIIHYLLKKYN--------ISY----NYDEYYQLLLIKMWQLS-QIYKPS +SKQ--SLSSFLFTRLNFYLIDLFRQ-QN------ +>Q97I86_CLOAB/2395 +----FIECYGIMIHNVVTSILNK------SHE--SQSIEECVDDILMCIWRNM-DCFSKE +R-G--SLKCWIIVISKNKALDYKKK-LKKI---- +>Q98R31_MYCPU/31109 +----LYEDYYPQIKSLARKVL-S------SFYSCSLEVHDLLNIAFFNWEKLV-QDYDPT +RNI--VFEFYILKWMRLLFYQGIKN-DISKRNSF +>Q9KZF7_STRCO/2493 +----LVDGLGPLVWSVARSHG-L------SDA----DAHEVYQTAWFRFAQHL-GRIREP +--E--KTGSWLASTARHECLKLLKASKRWT---- +>Q9K7Y4_BACHD/2184 +----FYE-----MKWYCKRLT-H------NKW----ESEDLFQDSLIKIYLAM-KQQPDR +--K--MTKTFFYRIIKHTWIDRKRK-RQLQ---- +>B2HD19_MYCMM/33104 +-----LETIRPIVVRYCRARV-G------TVERSGLSADDVAQEVCLATITAL-PRYRDR +G-R--PFLAFLYGIAAHKVADAHRA-AGR----- +>Q9L1B8_STRCO/570 +----LVTSLRPLLTAEASAEAYA------SGA----EPGDLEQAVWLRLLERL-EADGPP +--P--DPHRWLRSAVRTEARRTRRR--------- +>Q9XAI9_STRCO/37103 +----TYRAHYRSLLGLAALLL-D------DTA----SCEDVVQEAFIRVHSAR-KRVRDP +--E--KTLAYLRQTVVNLSRSALRR---RI---- +>Q55192_SYNY3/2695 +----LYNRYGAVVYRLALRIL-Q------RSQ----DAEDLTQEIFLSLETTT-PYNSQR +--G--NLLNFLLTLTRSRALNRIRQGRSRG---- +>O54163_STRCO/2190 +----IFDRHGKAVYNHLFRRT-A------DWS----EAEDLTSTVFLHAWRRR-ADTVLD +R-D--SALPWLLGIANGQLSNTRRR-LRRA---- +>Q9KYF3_STRCO/138201 +----LYRRHADAVRRYARTCC-R------DAH----TADDLTAEVFARMLQAV-RGGSGP +E-H--AVRAYLLTAVRRVA-------AGWT---- +>Q9RI52_STRCO/39108 +----IYRRWGSLVHTLATRSL-G------DAH----EAEDVTQQVFVGAWRGR-HGFRPE +R-G--TLGAWLVGITRRKVVDALAA-RTRR---- +>Q9F379_STRCO/2997 +----LYDRFASLVHGLAHRVL-D------DER----AADHITRDVFAHVWEHP-DAYDPR +QGP---LRTWIATLTHRFAVQRLRA-TET----- +>Q8F7R7_LEPIN/1582 +----LYSRNYEKIYRFLLSKG-A------SKE----EAEEICQETFIKVLRHW-EKFDPS +K-G--NETSWMLTIAKNQFLDMIKK-KD------ +>RFAY_XANCP/2896 +----IVTACQNTVTAIALAIT-R------DVA----ASEDIAQEAFLRAWQRL-AQLHQP +--A--SFLPWLRQITRNLARDWLRS-HRHR---- +>Q9K7J9_BACHD/2493 +----WMEEYGTAILRVVYSYV-K------DKQ----IAEDLTQEVFVRAFQSY-HTYQTR +--S--SAKAWLYRIAINRSKDFLKSWHAKH---- +>SIGX_BACSU/875 +----LYDTYHQDLYQFLFYMV-K------DKN----QTEDLLQEVYIRVLNSY-HTFEGR +--S--SEKTWLLSIARHVAIDWFRK-QQT----- +>SIGM_BACSU/673 +----IYQMYMNDVYRFLLSMT-K------DKH----LAEDLLQETFMRAYIHI-HSYDHS +-----KVKPWLFQVARNAFIDYVRK-HKKE---- +>Q9EWE3_STRCO/55121 +----AYRLVQPGLLGYVRGLV-G------EDA------EDVAADAWLEIARDL-RRFKGD +GAG---FRGWTATIARHRALDHLRR-QKV----- +>Q9EWE1_STRCO/2694 +----VYRAVQPRLLGYVRTLV-G------DPD-----AEDVASEAWLQIARDL-ERFDGD +A-D--RFRGWAARIARNRALDHIRM-RGRR---- +>Y370_RHIME/1178 +----LVSARPQAMGALLRYFR--------NLD----LAEEAFQEACIRALKNW-PRTGPP +R----DPAAWLIFVGRNSGIDKVRR-QSRE---- +>Q9A8M4_CAUCR/133201 +----AIAAARPQAMAALLRYF-R------DMD----AAEEAFQDACLRALKAW-PKNGPP +R----DPTAWLIMVGRNAAIDAVRK-TSRN---- +>Q98HH3_RHILO/1078 +----AISAARPQAMGALLRYF-R------DLD----TAEEAFQDACLRALKNW-PQNGPP +R----DPAAWLIFVGRNSGIDAVRK-RAKQ---- +>Q98DP3_RHILO/1682 +----ARQSYGKLVAWLAARTR--------DVT----AAEDALADAFAAALERW-PKSGVP +E----KPEAWLLAVARRRRVDAVRR-RLT----- +>Q9I3Z3_PSEAE/876 +----LYREESRRVLATLIRLL-G------DFE----LAEEALHDAFIAAVEQW-PRDGIP +R----NPRAWLVSAGRFKAIDNLRR-RARF---- +>O86798_STRCO/1280 +----VFRIESPRVIAGVARLV-R------DVG----IAEELTQDALVAALEQW-PRDGVP +D----NPGAWLMTTARRRAVDLIRR-RETY---- +>Q98I35_RHILO/1077 +----VWRIEQPKLTARLARYL-R------DIG----LAEEIAGDAFLLALERW-PRDGIP +R----NPAAWLTEVARNRALDRLRR-TTM----- +>Q97E49_CLOAB/2290 +----LFHLYEKYLYNLCYGYT-Q------NTS----DAMDLVQEIYIKVFKNI-KNFDEN +--L--PFHPWVRKISVNTCLNFKRD-NRGN---- +>Q9A9J9_CAUCR/2087 +----EILPLEPDLLAYARQFCRD------GQT----DPEDLVHEAFARAIACK-TWREVG +-----NPGAFATRILRNCALDALRR-RKV----- +>Q9L0W8_STRCO/1277 +----LFAALYPRLAGWCRRLV-D------DDE----TAHEIASEAFTRLWARW-TSVE-- +-----EPRGFLYVTAANLVRDHWRK-LERE---- +>Q9A965_CAUCR/773 +----LRAQRRD-LYQFIVRRT-R------DPA----TAEDLVQETFERLL-----AYGQA +K-TIVDRAALGYGIALNLVRDHFRL-AQRR---- +>O65997_CLOAB/2291 +----IFETYSKRVYNYIYYRV-N------CQY----TAEDLMSKIFEKVMLKI-DSYSEK +K-S--SFEVWLFTIARNVLNDYFRG-LKRH---- +>Q9AD34_STRCO/65133 +----LYGHYRPQIYTYLMRRT-C------DRP----LSEDLTGDVFVRALTRI-NAFTWR +G-T--DFGAWLSTIARNLLVDHYKS-ART----- +>V6K8P9_STRNV/1986 +----LYDQYSDTVYRYIYYRV-G------GKA----TAEDLTSETFLRALRRI-STFTWQ +G-R--DFGAWLVTIARNLVADHFKS-SR------ +>SIGY_BACSU/2492 +----LFHYHYSFLYKYLLKLS-L------HPD----LSEELVQETFLKGYIHL-RSFQGR +--S--KFSTWLISIASRLYLDHQKK-RKRE---- +>RPOE_STRCO/1073 +----YVRTRQDALLRSARRLV-P------DPV----DAQDLLQTALARTYGRW-ETIEDK +R----LADAYLRRVMINTRTEWWR---------- +>Q9ADQ0_STRCO/164 +-----MKARQPVLLRTARSLT-A------NPS----DAEDLLQTALTKTYVAW-ERIEDH +R----ALDGYVRRALLNTRTSQWRK--------- +>Q9HZV1_PSEAE/3299 +----LYQRHRQGLYRFLCGLA-G------QTE----LADEIYQETWLSLIRSE-SQPQGR +--A--SFRTWLYQIARNRLIDHWRK-HGQ----- +>Q98D78_RHILO/2493 +----LYRQTSAKLFGVCLRVL-N------DRG----DAEEALQEVFVKIWTKA-DRFAVS +D-L--SPISWLVAIARNHAIDRVRA-RRKS---- +>SIGK_MYCTU/3096 +-----YDHTKSRVYGLVMRVL-R------DTG----YSEETTQEIYLEVWRNA-SEFDSA +K-G--SALAWLLTMAHRRAVDRVRC-EQ------ +>Q9RD50_STRCO/35105 +----VYDAVAGSVLGVVRAVL-R------DQA----QSEEVAQEVLVEVWRTA-PRYRPE +RGT---VINWVLTLAHRRAVDRVRS-VEAAA--- +>Q9S2A7_STRCO/2694 +----LYGLVSGPVFGLVRRVV-R------DPA----QSEEVAQEVLLELWRSA-ARFDPR +RGS---ALSWILTVAHRRAVDRVRS-ARA----- +>CNRH_CUPMC/2592 +----LVARHGVALAQAARSFG-I------PET----DVDDVVQDTFVAAWHAL-DDFDPD +R----PFRAWLFRIGLNKMRDLYRF-RRV----- +>Q9X8Z1_STRCO/2188 +----FYAESVGRLIGHLYAMT-G------DLA----EAQDVVQEAFARAWERR-TELDLN +--G--APEAWVRTVAWRLAVSRWRK-VRT----- +>Q9I2W5_PSEAE/876 +----LMRRYQRTLFNVCARYL-G------NDR----DADDVCQEVMLKVLYGL-KNFEGK +--S--KFKTWLYSITYNECITQYRK-ERRK---- +>Q9KF25_BACHD/773 +----DYEQLKPLLFSLGYRLL-G------SVT----DAEDLVQETFLRAYQAE-EREINN +KKA------YLCKMMTNRCLDVLKS-ARRK---- +>Q9RKV3_STRCO/2794 +------MAERHRLLSLAFRMM-G------TLA----DAEDVVQETYVRWYRLEPEERDSI +A----VPAAWLMRVASRISLDLLGS-ARAR---- +>Q9X8P3_STRCO/1176 +----QFELDRPRLRAVAYRIL-G------SLG----EADDALQEAWLRA-----DRANTS +EVG--NPSGWLTTVVARVCLNLLRA-RDT----- +>Q9RD74_STRCO/34100 +----RFEEHRGQLKAVAYRML-G------SLA----EAEDAVQEAWLRL-----DRSEAD +GID--NLGAWLTTVTGRICLDLLRS-RTAR---- +>Q9EWW4_STRCO/775 +----PVTGERRQLINVAYRML-G------SLT----DAEDAVQEAYARWYAMPADRREAV +G----SPGAWLTTVVSRVCLNHLRS-ARV----- +>Q9RJS2_STRCO/1179 +-----TVGERRQLINVAYRLL-G------SLA----EAEDAVQEAYAR-WYAL-PRSRQE +EIV--SPGAWLTTVTGRVCLDALGS-ARAR---- +>Q9RJ06_STRCO/1682 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+----IFNYFGPFIKSFTKNIY-I------RNF----DKSDIYEECNFSILLSI-KKCDIK +KY---NFTAYTISSIKNNIYYKIRN-QAKF---- +>Q2G0P4_STAA8/2693 +----LVMDLQPLIIRRIKTFG-F------NHY----DLEDLYQEILIRMYRSV-QTFDFS +GEQ--PFTNYVQCLITSVKYDYLRK--------Y +>Q97I83_CLOAB/2495 +----LIQEYKPFIASLLQKKT-G------KYL--QYGYDDELSIGMIAFEEAV-ESYDRN +KG---KFLSFAKRVIILRAIDYYRK-NQKF---- +>SIGI_BACSU/36107 +----LIQQYKPFIAKTVSSVCKR------YID----EKDDEFSIGLIAFNEAI-EKYSPE +KGN--SLLAFAELIIKRKVIDYIRK-EARS---- +>Q97HF9_CLOAB/2698 +----LIDSSMKYIKKIANGFCLN------NKS---LSLEDLMQEGIIAVIKAI-NSYDLD +KNV--KFSTYVYSMINFTLISEIKK-KYSY---- +>LAFS_VIBPA/28101 +----LLQRHQVMVKRVVNQLR-V---HATSHC----SIEDMQQIGLIALVEAG-RRYGDI +DDT--HFPAFAVCRVRGAILDELRR-LDWR---- +>Q97JP7_CLOAB/2091 +----VVEKYMTLVKSIARKYINR------SGT---LELEDMVQSGAISMINAV-ENFDYN +KGV--KFSTYARHCVEGGMKNYCKK-NEL----- +>O25676_HELPY/41113 +----LAIQYLPAVRAMAFRLK-E---RLPSSI----DFNDLVSIGTEELIKLA-RRYESA +LND--SFWGYAKTRVNGAMLDYLRS-LDV----- +>Q9X004_THEMA/779 +----VIRSLLPFIKRIAEDLA-Q---TLPPNV----EVDDLIQEGIVAALSSL-ERYDPS +KA---SFTTFIMKRVKGAMYDYLRK-IDWM---- +>O67268_AQUAE/1487 +----LILKYLPLVKAIATNIK-K---HLPEDV----DIRDLISYGVIGLIKAV-DNLSTE +NPK--RAEAYIKLRIKGAIYDYLRS-LDFG---- +>O84064_CHLTR/2598 +----LIESYLPLVKNVAHRLA-S---GMPSHV----KMEDLYALGVEGLIRAV-ERFDPE +KSK--RFESYALFIIKAAIIDGLRK-QDWV---- +>Q97H70_CLOAB/1385 +----LIKKYIPLVKYIASRVIIG------KSK--YIEYEDLVGYGMIGLMDAL-KKFDQS +KGM--KFSTYSSIRIKGAMIDELRK-NSP----- +>Q9KA59_BACHD/28101 +----LIRQYLPLVHYHVQRISVG----LPRSV----SKDDLISHGMLGLLDAL-EKFNPD +RDL--KFDTYASFRVRGAILDGLRK-EDWL---- +>O83707_TREPA/30103 +----FVVQYAPLVKYVASKIAVG------KPG--NVEFDDLVSYGIFGLFDAI-DKYDPE +KNI--RFNTYAVTRIRGAIFDELRS-IDWV---- +>F2R5I2_STRVP/28100 +----LILHYSPLVKYVAGRVSVG----LPSNV----EQADFVSSGVFGLIDAI-EKFDVE +RAI--KFETYAITRIRGAMIDELRA-LDW----- +>Q5NPV6_ZYMMO/2898 +----LIKTHLQLVRKIAWHVH-GRVSSAI-------EVEDLIQIGMVALIEAA-NAFENR +GFA---FATYASMRIRGAMIDYMRQ-HA------ +>FLIA_ECOLI/1689 +----LWQRYVPLVRHEALRLQ-V---RLPASV----ELDDLLQAGGIGLLNAV-ERYDAL +QGT--AFTTYAVQRIRGAMLDELRS-RDWV---- +>Q8P9F9_XANCP/2596 +-----VTQHADLVRRIAHHLA-A---RLPASV----EVDDLIQAGMIGLIEAS-RSYDSD +QGA--SFETYASIRIRGSMIDEIRR-GDW----- +>Q9KQD4_VIBCH/1992 +----FLEKYSVLVKRIAHHLI-G---RLPPSV----LIEDLIQAGMVGLLEAQ-KNYDGS +KGA--SFETYAGIRIRGAMLDDIRR-GDWV---- +>Q5ZUL1_LEGPH/42114 +----LVKTHATLVKRIAHHLL-G---RLPQSV----QLDDLIQSGMLGLLEAA-RHYDSS +KGA--SFETYAGIRIRGHMLDEVRR-NDW----- +>FLIA_PSEAE/2295 +----LIQRYAPLVKRIAYHLL-G---RLPASV----QVEDLMQAGMIGLLEAA-KKYDAG +KGA--SFETYAGIRIRGAMLDEVRK-GDWA---- +>Q9WZ04_THEMA/2998 +----IVEKYYPMVVKIASQYF-A------SWA----EHEDIVQNGLVGLIKAI-FYYDKT +KS---SFTSFAWRSVDSEIKSFLTY-LNRK---- +>D5DVR7_BACMQ/36105 +----LIHKYKNFVRAKARSYF-L------IGA----DREDIVQEGMIGLYKAI-RDFRED +KLT--SFKAFAELCITRQIITAIKT-ATR----- +>SIGE_ARATH/283356 +----LIKHNLRLVLFVMNKYF-H---EFTNGP----KFQDLCQAGMRGLITAI-DRFEPK +RKF--RLSTYGLFWIRHAIIRSMTT-SNFT---- +>SIGC_ARATH/336406 +----LVKSTRSLVLFLARNYR-G------LGI----AHEDLIQAGYVGVLQGA-ERFDHT +RGY--KFSTYVQYWIRKSMSTMVSR-HARG---- +>O83976_TREPA/64134 +----LVRANVRFVISVARHYR-T------CGL----PLADLISEGNIGLLTAA-ERFNPA +RGC--RFISYAACWIRQSILKALNE-KARI---- +>B4S455_PROA2/66135 +----LIKGNLRFVVSVAKQYQ-N------QGL----TLGDLINEGNLGLIKAA-KRFDET +RGF--KFISYAVWWIRQSILQALAE-QSR----- +>O67437_AQUAE/46116 +----LVESNLRFVVSVAKQYI-G------YGL----PFSELIAAGNLGLLEAA-KRFDPD +RGV--KFISYAVWWIRQAIMQALSQ-QTGA---- +>SIGA_ARATH/263333 +----LAMSNVRLVMSIAQRYD-N------LGA----EMSDLVQGGLIGLLRGI-EKFDSS +KGF--RISTYVYWWIRQGVSRALVD-NSRT---- +>I3VS70_THESW/2892 +----LVECNIRLVDKVAAGFL-K------SGV----EFDDLVQEGLIGLLTAI-DKFDHT +KGY--KFSTYATWYIQQSMRRYI----------- +>O51712_BORBU/45115 +----MINANLRLVLKIIKRYA-G------KGL----KIEDLIQEGNLGLIRAA-EKYDPN +KNT--KFSTYASFWIKQSLQRALNT-KTRL---- +>SIGD_ARATH/183253 +----ITRCYRRLVVSIATGYQ-G------KGL----NLQDLIQEGSIGLLRGA-ERFDPD +RGY--KLSTYVYWWIKQAILRAIAH-KSRL---- +>J3MRH6_ORYBR/343411 +-----ARSNFRLVIHVARKYE-G------YGL----DIQDLVQDGCCGLMKTF-EKFNPS +KGC--RFPTYAYWWIRQSIKKSIFK-NSR----- +>SIGF_ARATH/311381 +----LITANLRLVVHIAKQYQ-N------RGL----NFQDLLQEGSMGLMKSV-EKFKPQ +SGC--RFATYAYWWIRQSIRKSIFQ-NSRT---- +>E0WSL8_9ENTR/96166 +----MIESNLRLVVKIARRYG-N------RGL----ALLDLIEEGNLGLIRAV-EKFDPE +RGF--RFSTYATWWIRQTIERAIMN-QTRT---- +>I0HUI5_RUBGI/84153 +----MIERNLRLVVSIAKHYV-G------RGM----PMIDLIEEGNLGLMHAT-GKFEPE +RGF--RFSTYASWWIRQSIERAIMH-QAR----- +>C5WQ19_SORBI/291357 +----MVKSNVRLVISIAKEHE-G------PGM----EFSDLIQEGMQGLIRGA-EKFDAS +KGF--RFSTYSHWWIKQAIRKSVLE--------- +>SIGA4_SYNE7/78148 +----MLKANLRLVVSVAKKYQ-N------QGL----ELLDLIQEGSLGLERAV-EKFDPA +LGY--KFSTYAYWWIRQSMTRAIDN-HART---- +>P73666_SYNY3/87157 +----MVEANLRLVVSVAKKYL-K------RNL----DLLDLIQEGTIGMQRGV-EKFDPT +KGY--RFSTYAYWWIRQAITRAIAE-KSRT---- +>B2J2K2_NOSP7/98167 +----MITANLRLVVSIAKQYQ-R------RNL----ELMDLIQEGTLGLERGV-EKFNPA +LGY--RFSTYAYWWIRQGITRAIAQ-QGR----- +>A9WGX1_CHLAA/78148 +----LINSNLRLVVSIARRYQ-G------HGL----SLLDLIQEGSVGLMRAV-DKFDAS +RGL--KFSTYATYWIRQSIGRAIAD-HSRT---- +>Q98QB2_MYCPU/218288 +----LINRNLRLVINNAKKYK-N------RGL----SFIDLISEGNAGIIKAV-QKFDES +KGF--KFSTYATWWIRQSITRAVAD-QART---- +>HRDC_STRCO/106176 +----MVRANLRLVVSMAKRHA-H------RGL----PLLDVIQEGNLGLIRAV-EKFDHT +KGF--KFSTYATWWIRQAIERGLAT-HART---- +>HRDD_STRCO/100170 +----FIRSNLRLVVAVARRYP-R------SGL----PLLDLIQEGNAGLVRAV-EKFDYR +KGF--KFSTYATWWIRQAITRSIAD-QSRT---- +>A9WAH7_CHLAA/164232 +-----AAANLRLVVSIAKRYR-D------RGL----PLLDLIQEGSLGLLRAI-EKFDYT +KGY--KFSTYATWWIKQALSRALAD-QSR----- +>A9WGV1_CHLAA/148218 +----LIQANLRLVVSIAKKYT-S------YGL----TMMDLVQEGNIGLMRAV-EKFDYK +KGH--KFSTYATWWIRQAITRAIAD-QSRT---- +>HRDA_STRCO/163233 +----LIEANLRLVVSVAKRYV-G------RGL----TMLDLVQEGNLGLIRAV-EKFDYA +RGY--KFSTYATWWIRQAMSRALAD-QART---- +>SIGA_STAA8/135205 +----LAEANLRLVVSIAKRYV-G------RGM----LFLDLIQEGNMGLIKAV-EKFDFN +KGF--KFSTYATWWIRQAITRAIAD-QART---- +>RPOD_HELPY/437506 +-----AKSNLRLVVSIAKRFT-S------RGL----PFLDLIQEGNIGLMKAV-DKFEHE +KGF--KFSTYATWWIKQAISRAIAD-QART---- +>A1WW15_HALHL/368438 +----MVEANLRLVISIAKKYT-N------RGL----QFLDLIQEGNIGLMKAV-DKFEYR +RGY--KFSTYATWWIRQAITRSIAD-QART---- +>P73710_SYNY3/136206 +----MIRSNLRLVVSIAKRYL-N------RGV----PFLDLIQEGAIGLNRAA-EKFDPD +KGY--KFSTYAYWWIRQAITRTIAN-DART---- +>SIGA_SYNY3/193263 +----MVQSNLRLVVSIAKKYM-N------RGL----SFQDLIQEGSLGLIRAA-EKFDHE +KGY--KFSTYATWWIRQAITRAIAD-QSRT---- +>Q9AYR7_PHYPA/340410 +----MVNSNLRLVVSIAKNYQ-G------RGM----TLQDLIQEGSMGLVRGA-EKFDPT +KGF--KFSTYAHWWIRQAVTRSIAD-QSRT---- +>SIGB_ARATH/336406 +----MIKSNIRLVISIAKNYQ-G------AGM----NLQDLVQEGCRGLVRGA-EKFDAT +KGF--KFSTYAHWWIKQAVRKSLSD-QSRM---- +>Q9PQE2_UREPA/197267 +----LYTSNMRLVTSIAKKYL-N------RGL----DLEDLIQEGSSGLLKAI-DKFDHE +KGH--KFSTYATWWIRQSITRAIAD-QARQ---- +>SIGA_MYCPN/252322 +----LVTSNLRLVVSIAKKHL-E------RGL----DFNDLIQEGNLGLLKAI-SKFNWS +LGN--KFSTYATWWIKQAITRAIAD-QART---- +>Q98FA7_RHILO/44114 +----ITVAHMRLVISMASKFR-H------YGL----PLGDLIQEGHVGLLEAA-ARFEPE +REV--RFSTYATWWIRASMQDYILR-NWSI---- +>H8MRD8_CORCM/50117 +------SSNLAFVVAVAKKFA-N------RGA----RLDDLIQEGNVGLMKAI-EHFDPK +KNV--RFATYAVWWIRAYITRYLKD-NRS----- +>H7C6T6_BRADU/62131 +----LVTSHLRLAAKLARGYK-G------YGL----PMVDLIAEANLGLVIAA-SRFEPG +RGA--RFSTYAIWWIKAAIHEYILR--SWS---- +>Q9ZDM4_RICPR/53123 +----LVTSHLKLVAKIASSYK-T------YGL----PITELVSEGNIGLMQAV-KKFNPE +LGF--RLSTYAMWWIKASIQEYILK-SWSL---- +>D5AP35_RHOCB/53122 +----LVTSHLRLAAKIAMGYR-G------YGL----PQAEVISEANVGLMQAV-KRFDPE +RGF--RLATYAMWWIRAAIQEYILR--SWS---- +>Q1D016_MYXXD/34103 +----LVASNLRLVVKLAHEYH-R------NPL----SLLDLVQEGNIGLMQAV-KKYDPE +RGV--KLSSYAAWWIRAYILRYIMD--NWK---- +>Q09C40_STIAD/47116 +----LVTSNLRFVVKVAYEYR-S------YGL----RMSDLIQEANIGLMKAV-QKFDPD +KGI--RLISYAVWWIRAYIQGYVLK--NWS---- +>RPOH_BUCAI/53123 +----LILSHLRFVIHISRNYS-G------YGL----LQSDLIQEGNIGLMKAV-RRFNPE +IGV--RLVSFAVHWIKSEIHEYVLR-NWRI---- +>A0KF81_AERHH/54124 +----LVMSHLRFVVHVAKSYA-G------YGL----PQADLVQEGNIGLMKAV-KRFDPS +VGV--RLVSFAVHWIKAEIHEYVLR-NWRM---- +>H9L4M9_XANCP/60129 +----LVHSHLRFVVHVARGYN-G------YGL----PLGDLIQEGNIGLMKAV-KRFDPE +MGV--RLVSFAVHWIRAEMHEFILK--NWR---- +>Q9K9T9_BACHD/60130 +----LIERNLRLVVYIARKFE-N------TGI----NIEDLISIGTIGLIKAV-NTFNPE +KKI--KLATYASRCIENEILMYLRR-NNKI---- +>Q9KDC8_BACHD/54124 +----LIEHNLRLVAHIVKKFE-N------TRE----HTEDLISIGTIGLIKAI-ESFSEG +KGT--KLATYAARCIENEILMHLRA-LKKV---- +>Q7D463_CLOAB/54123 +----LIERNLRLVAHIVKKYS-Y------SGK----EVDDLISIGTIGLIKAI-DSYNVS +KGT--RLATYAARCIENEILMLIRN-NKK----- +>Q8XJI8_CLOPE/54126 +----LVERNLRLVAHIVKKYS-S---NYQNSK----EMDDLISIGTIGLIKAI-DSFDTN +KGI--RLATYAAKCIDNEILMFFRN-TKK----- +>Q9KFF0_BACHD/34104 +----LVKHYEPLVHSLARKFS-R------SRA----HDDDLIQVGMVGLLAAF-ERYDPK +YGR--SFESFAVPTIIGEIKRFIRD-KTWS---- +>Q2FWJ4_STAA8/35104 +----LVKHYQKLIESLAYKYS-K------GQS----HHEDLVQVGMVGLIGAI-NRFDMS +FER--KFEAFLVPTVIGEIKRYLRD-KTW----- +>RPSB_BACAN/34104 +----LVDHYKNLVYSIAYRYS-K------GGP----MHEDIIQVGMLGLLGAI-RRYDYS +IGN--AFEPFAIPTIVGEIKKYLRD-KTWG---- +>Q62YJ7_BACLD/34103 +----LVQTYKNLVETLAKKYS-K------GKS----FHEDLCQVGMLGLLGAI-KRYDPD +VGK--SFEAFAIPTIIGEIKRFLRD-KTW----- +>Q7AP79_LISMO/34103 +----LVVHYKNLVESIARKYS-Q------GKS----FHEDLVQVGNIGLLGAI-RRYDAT +FGK--SFEAFAVPTIVGEIKRFLRD-KTW----- +>P74595_SYNY3/32103 +----IMEVNLGLVRKEAHHWTAQ------CNE----SFEDLSQVGCLGLIRAI-ERFDVS +KGN--AFSSFAIPYVRGEIQHFLRD-KSNC---- +>Q9WWP8_SYNP2/35106 +----IVSLNIGLVRKEAHHWSRQ------CSE----NFDDLMQVGSLGLLRAI-ERFTLE +RGN--AFSSFANPYIRGEIQHYLRD-KSST---- +>Q97GR0_CLOAB/35104 +----IIENNLPLVSAISRKFL-N------RGY----EYDDIFQIGCMGLVKAV-NNFNSD +YKV--KFSTYAVPMIMGEIKRFLRD-DGI----- +>Q9K9U1_BACHD/42112 +----LVNGNLRLVLSVIQRFN-N------RGE----YVDDLFQVGCIGLMKSI-DNFDLS +QNV--KFSTYAVPMIIGEIRRYLRD-NNPI---- +>X2GJ92_9BACI/35101 +----MIEGNTRLVWSIVQRFT-T------RGV----ELEDLFQIGCIGLMKSV-DKFDLA +YDV--KFSTYAVPMIIGEIQRFLRD--------- +>E3E826_PAEPS/36103 +----LVNSNIRLVWSVVQRFM-N------RGY----EPDDLFQIGCIGLLKSV-DKFDLS +YEV--KFSTYAVPMIIGEIQRFLRD-D------- +>SIGF_MYCTU/43112 +----IVQRCLPLADHIARRFE-G------RGE----PRDDLIQVARVGLVNAA-VRFDVK +TGS--DFVSFAVPTIMGEVRRHFRD-NSW----- +>Q9K4K0_STRCO/56125 +----LVTAWLPMAHRIAGRFR-D------RGE----SIEDLRQVAALGLVKAI-DRFDPE +RGA---FESYAVPTITGEVKRHFRD-RMWA---- +>Q7AKD1_STRCO/41111 +----LIRVWLPMAERIAVRFR-G------RGE----NLEDLYQVAALGLVKAV-DHYDPE +RGH--AFEAYAVPTVTGEIKRHFRD-HMWT---- +>Q9RIT0_STRCO/141211 +----LVRMHLPLVEHLARRFR-N------RGE----PLDDLTQVATIGLIKSV-DRFDPD +RGV--EFSTYATPTVVGEIKRHFRD-KGWA---- +>B1VLU0_STRGG/65135 +----LIEMNLSLVRFAANRFRNR------GSG----DMEDIVQVGTIGLIKAI-DRFDLS +REV--EFTSFAVPYIVGEIKRFFRD-TSW----- +>Q9ADM4_STRCO/97167 +----LIELNLPLVRYAAARFR-S------RNE----PMEDIVQVGTIGLIKAI-DRFDCE +RGV--EFPTFAMPTVVGEIKRFFRD-TSWS---- From ca899ac56f71a1862122fc7a03feed9316fbfe7d Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 20:04:01 -0500 Subject: [PATCH 13/27] sporecoat.align --- sporecoat.align | 375 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 375 insertions(+) create mode 100644 sporecoat.align diff --git a/sporecoat.align b/sporecoat.align new file mode 100644 index 0000000..9ce3f66 --- /dev/null +++ b/sporecoat.align @@ -0,0 +1,375 @@ +>Q12FX3_POLSJ/50194 +TWGVLLAAGTAHATISCSVSGN---------------GFTSVYDPISTVPNDNV------ +----SSVTINCS-RASGDPTT-TTYSLASTNGLYPQGQNN--------RAYYP-----TN +KY-LKYDIYKDAAYSSRWGP----GGSAPFTGTLNFGSGTS--ASLTLP-YY-NRV--A- +AQQ--SAVAADY-------TDTMTAT +>Q4K9M8_PSEF5/21172 +--ADLQVQVRVDVLRGCQLVGQ---QREAGIEQLGTLDFG-STARLDDPAGPLSAALPGS +----RQPRLECN-PD-------TPYQMRIDGGLHGGVGEV--------RYLASNTR--AG +KP-IPYRLYQDPARRIPLPVNVPVSGRVPDSGTV------------DLP-LY-GRI-EP- +LVE--IPRAGGY-------SDVLKVT +>Q88KD3_PSEPK/43194 +--ADFLVEVRVLVQRGCMLVNQ---TRDAGAQALGRIDLG-ATARLDGPGAPLSGVLLSQ +----RPPRLECN-PD-------TPYQVRVDGGQHGGIGEL--------RYLASDD---HL +ARPIPYRLYRDAAWREPLAVGVA-QSARVPGS-----------GSVELP-LY-ARI---- +DKLAWVPDAGVY-------ADLLKVT +>A8GDM0_SERP5/177307 +--KPSTVTISLTLTKDCLFGTA------------QNVNFG-SMALVGQFNPVN------- +----QSITLTCT-KT-------EGYNTYFTDGNNPVTG-------W--RRMKSG----TS +NY-MQYQIYLPNS-TTVWNS----TNKQAGAGTG---------LAQSIP--YLARI-NP- +AQT--EVPVGTY-------QDNISFV +>A1TW02_ACIAC/189321 +--VNRLLTVRLVVTNDCTLSAP-------------NLQFG-SAPLPAAFPAVS------- +----GNISVVCT-RG-------LSVTVGLGPGAYPSGGR---------RQMAS-----GA +NR-LAYDLFRADG--SLWGTAAGTRTAGTAVTDG------T--APIVLP--YTARI--YG +DQT--PPPPGVY-------QDNVVVD +>Q4K9N4_PSEF5/184326 +--GTQSLTVNMTVSNDCVITAP-------------NISFG-SAPVISAFATVTG------ +----QTINLACT-KG-------SAYTVGLSDGQHPVSAGG-----R--RQMIS-----GS +NY-LAYDIFKSAG-STRWGSVGSARRSSTDAEVNPGNGLGT--GSQIFN--YNARI--YT +DQS--TPPAGTY-------IDNVVLD +>Q88KC7_PSEPK/182318 +----QLLNVSLTVTNDCQITTP-------------DISFA-SAPVVAGFGTVS------- +----QGINVSCT-KG-------SSYTVGLGDGQNVSGGR---------RRMKSS----AN +NY-LAYDIFKSAG-TVRWGASGAARRSSTDADINPGVGTGT--GSQVFN--YNAKV--YT +DQA--TPPAANY-------TDSVI-- +>Q87G14_VIBPA/181318 +---QSTITVELEVTPDCMITAP-------------DIDFG-SSPLVAGFDPVS------- +----QVISLTCT-KN-------SSFTIGLNDGVNASGGQ---------RRMAS-----DG +NY-LEYEIYKSSS-TERWGSAGAERREQSDVDTGDAIPDGI--TPQNYN--YRAQI--MA +SQT--TPPAGTY-------TDSIIV- +>A7MEE4_CROS8/177314 +--STFTSLVTLTVTNDCSTITA------------PNLNFA-SAPLVKDFAPVS------- +----QTIAITCT-KG-------STYTVGINNGNYAVGSV---------RNMAS-----GT +NR-LSYEIYKGST-ANRWGVSGT-ERWASDTPTQVSSD--G--LLKSYQ--YTARI--LA +TQN--TPPAGSY-------TDTLVVD +>Q6D2L8_PECAS/200332 +--TTSTLNITMTITNDCQITSA------------PNISFG-TAAFPANFAAVN------- +----NNLGVRCT-LL-------GAYTVKLVSTHPDDAN-------W--RRMTATVG--ST +PYYLQYQLYRTGN--IAWTE----TNDYSGAGTG---------ITQNIP--YTARI--NA +SQA--SKPEGTY-------KDTVTIN +>Q9HVD9_PSEAE/184311 +---SSSVNVTLTVLKDCFIDSA------------PDLSFG-SAALVSAFTAVN------- +----QNIGVRCT-LN-------ATYTIGFDNGNNFSGGW---------RRMLS-----GA +NA-IQYNLYK-PGDSTVWTT----SNTQAGTGSG---------AAQNVP--Y-RAIVNP- +AQG--NVPAGTY-------SDTVRV- +>Q0BSH4_GRABC/13154 +ILFAVLALFPKSSMAQCIVSVS-------------NLNFG-VYDPFSSTPANTS------ +----SNINVTSC-PILF-----GSYSVGLNTGQNAGGSYNN-------RSMRY-----NS +QR-LQYQIYTSNDRSNIWGNN-S-QGTVMQYGYC---YFFA--CNNSFT-MY-GVI--P- +RYQ--NVSPGFY-------SDTVVVT +>Q0C620_HYPNA/7149 +LVLSLFVLVCPALAQSCTVSST-------------PLSFT-PYHAFSGNASTGS------ +----ATVTVSCS----GLLFVGASYEVRLGGGQSGNIMA---------RKMKQAS---SG +QE-LSYQVYTQSAQ--VWGNGVQGSTINDFFLLGLL----A--RSRAHP-IT-GTI--P- +ANQ--QVNSGSY-------SDAVTMT +>Q6F7G3_ACIAD/166298 +--VQNYMKTTTKFENSCAVVGV------------NTLDFG-SIISLNQPIYGQ------- +----TSIQLKCP-TN-------TALKVGLDTGLYASGT-------Q--RRMTN-----AG +QF-IQYDLYQDSAYSIAWGTS---DNSVLKLDTY------Q--PVFTIP-VY-GRI-LP- +QNQ--NLKAGEY-------RDTITIK +>Q9HVE4_PSEAE/29179 +----GQVGVQMVIGAGCTIING---SVSGGINQWGTLDFG-SHSDLTNVVDAQTVG---- +TS--GNIQIQCS-TG-------LTPSLTVNAGLHASGG-------Q--RYMQNTTT--TS +ST-IAYNIYSDAARSALIQANTPVDISSVSTG-----------TAVNIP-LY-GRV-VPT +GQSTPTPTAGTY-------TDTLLVT +>Q6D2M2_PECAS/29179 +--INGQIPVSLTITAACTINNG-----GGAGTTWGTISFG-SHSDLTANIDSQVTSV--- +SG--NGITVSCS-VG-------TPATLSIGPGANDNTSL------R--RLAPGT----GT +YN-VPYRLYSDSTRTTEIPIGTA-TGIAIVAT--------G--NPQLVP-VY-ARI-LPA +DQTVLSPTAGTY-------TDTVTAT +>A7MEE0_CROS8/26185 +--SSGTIGATLTLTNGCLINGS----PSQNGINFGTLNFG-TSPATFSTLTTQLTG---- +AGGGNTFSIQCT-TP--------EYTVQITGSTNQAPGTVVGTPGTPGRYLVNTT---NT +AQGVAYSLYSDSAFQNVIANNASIPAASTTGGVS------------NYT-IY-GRI--QG +GGNSVTVVPGTY-------TDTINVS +>Q87G12_VIBPA/25174 +---TETFQVSATVDTGCLINGAVQEESATQAGQIGTLDFG-EHSSVYAAEVQGSVTYS-- +----SSLTLSCT-PG-------IAMNVSLNGGLNSSDGV---------RKLKHTE---EV +TT-VDYFLFQDLDYTQVLDIDTR-YSVDTTQDP----------DNIQFP-IWAKAI---- +ING--NEIAGIY-------MDTLTLT +>Q4K9M9_PSEF5/25175 +--ISGQIQARLVITAACQVSSG-GDPSASPIGDPGMLNFG-QQGPTWVAPIKASLT---- +NSAEGQLQVACNSSV-------TGFTVTINGGLNGDGTT---------RRLSN-----GR +QT-IPYRLFVDASGSDSYSIGQQ-RNFAVSSG-----------RRIPIP-VF-GSV--VA +NTR--AVPAGLY-------TDTLTIT +>Q63TD8_BURPS/27178 +---TGTMQVNLQVSRGCEVAGV------AASGDLGRLDFG-AQGPLWSDYLTADGR---- +ATSSGAVRVVCSPDV-------NGFLVSIDGGRNGDQST---------RYLVKRGANGRV +AGRIPYNVYRDAARSVPYVPLMP-QSFLVDGGR----------DDVTLP-VY-GVV--NG +MTR--AVPSGTY-------EDLLGIT +>A1TVZ8_ACIAC/43202 +--LSGVLGARMMLTSGCVINGG---PGTVSGADFGTLDFG-SRPATFVGTATATASGGEG +GA--GATQIVCSPEI-------TAFSITIDSGTHAGQGAGIGTGT---RAMSN-----GS +AF-LPYDVYRDPGHTVPYTAATAVTGIAVPSA--------G--NPFTLP-IY-GLV--N- +KTNAVALPAGLY-------TDQLQVT +>Q63TD9_BURPS/28183 +---TGTVNSQLVLTTGCAVDTG---GGSVNSANFGTLDFG-TQPSGFTGRLTSAAKGG-- +GS--TSTQVTCS--PDV-----TSIQVTIDGGQNASKGATVGTG-T--RALAN-----GA +SF-VPYEVYADAGHSQQYVSGTA-QSVAVPTP--------G--AAFELP-LY-GVV--N- +KTNASALAAGTY-------TDVLNVT +>A7MEE1_CROS8/37181 +--TTQSFQVSATVAAGCSVTTG-------TGGVMGSLNFG-THTGVESTRVSTSFVPS-- +----SSLLLACT-PG-------VALSMSINGGQNYGSSV---------RNMVRG----GG +TERVPYRLYTSSSLNAASEIGVN-QAVSIAYSNS---------NNISLP-LF-GAA--Q- +LTG--FSPAGSY-------TDTLTVT +>Q2NSS3_SODGM/17158 +--PNQSFQVAATVVAGCLINGG---------PSIGKLDFG-SQAGSDRQLFTASMVQN-- +----TAFSLACS-PG-------TTLSMRIDGGSHYTSQ----------RNLQRV----GG +TQLIGYRLYTDAGLTPANAIPVG-QDVSLSYSDA---------NHIVLP-VY-GAL--Q- +LSG--MSLSGTY-------TDTLTVT +>Q63TE0_BURPS/29171 +---TQAFTVSAQIVAGCGVAGG----GPASGLNFGTLDFG-AHPAVATGQVSAAVGG--- +----GALQIECS-PG-------STLKMTIDGGANASAGNTQ-------RNLAS-----GG +AR-VAYRLYSDPARTQAIAVG---QAVSLPVS-----------GTITLP-IY-GALTLP- +-GG--GAPAGTY-------TDTAQVT +>Q4K9N1_PSEF5/25163 +--TSQSFQVSATITAGCLVVGG--------VSNYGSLAFG-SQSALSTSTVRVALT---- +----GGVQLQCT-PG-------VTLNMTVDGGQYNSSG----------RHMQLD----SG +SARVAYQLFRDAGYSQSLGIG---QSVAVAYSDA---------NNISLP-IY-GQVQLP- +--G--NQPGGTY-------SDVLQVQ +>Q88KD0_PSEPK/24164 +--TTSTFTVTAQVVAGCLVVGG--------VTSYGTLDYG-SQSALSTGLLSTSLGG--- +----STVTFQCT-PG-------VAMSMSLDGGQNSASGT---------RNLKRTS---GT +QV-LAYQLYRDAAYSQALGIGQS-VAVSYSDPT-----------AIKLP-VY-GRV--Q- +LTG--TQPAGTY-------TDVVQVT +>Q60C08_METCA/20167 +--LLACPKISDADPYQCDIGNI-------------SVPHA-VYDPTDSNPNSSGV----- +----GTVGITCH-LKNAKQTQQVQYTIALSRGSSGSYNP---------RRMSG-----GR +GS-LGYNLYLDAARVTIWGDG-S-GGTFPLRGTLLLNPTTP--VQQVIHNIY-GLI--P- +PLQ--DVYAGTY-------TDTVTIT +>Q8XVY3_RALSO/23163 +VLVALASWAPGALAVSCSVSAN-------------ALSFG-AYNTTSNLTGT-------- +----TTVTITCGAWGGASS---INYTLSASVGSGTYAN----------RQVLN-----GS +NV-IAYNLYTTSADTSIWGDGNG-DGTVTLSGTVTKQ---V--GTVNLT-IY-GKI--N- +GGQ--NVVPGSY-------ATTIPIT +>A1VIJ0_POLNA/19170 +ALFLLLATAGPAQAGSCTVGSS-------------GLAFG-AYQPLTFAGKLTSSAVT-- +SN--ASISVVCT--GIA---SGGAYSIALGPSTTGSGDRIS----T--RYLGNSN---GG +DD-MSFNIYTSASYSTVWGNG-T-TGGLVGGSIPVG----D--SNQSQP-VY-GRI--AA +SQN--TLRAGSY-------SGSLTMT +>Q3A2W0_PELCD/10150 +--IIVLLFAVDAYAFHCEVTTT-------------PVSFG-AYDVF----SSFSLD---- +TT--GRISVSCN--NPE--KKRMPVTISISRGAA--NSFS-----P--RQMRRIG---GS +DR-MDYYLFVDASRTAVWGDG-T-GGSSTYVGMIDR----T--SPLNVP-IY-GRI--P- +ARQ--NLRAGSY-------QDILVVT +>A1VIJ3_POLNA/74223 +--DNANLAVSATVLTNCAIGPG-------TLAFPANLQLGVTKGLGTKAANPANAD---- +SDSGTSISVTCT-NG-------SSAAITAGAGANTAGVVATT------RALKS-----GS +NY-IDYELYTDTNRTTVLD---G-TNSISYTGTG------L--TEIDKTTIF-GRI--L- +GADIATAKAGAY-------ADTVAMT +>Q8XPY9_RALSO/25163 +-----------ASAQSCSVASA-------------SLNFG-SISPVQAGNTDTS------ +----TTLTVSCSGFLLQGTVARACLNLGVGSGDTGISP----------RVLSA-----GA +NQ-LQYNLYADSARSVVWGGRTTPATPAIQVDVSLGLLGFG---SATVT-VY-GRV--PG +GQT--TVPAGAY-------TQSFSGT +>A9CH19_AGRFC/11158 +--IAAAFVASPVLAQSCTFSMS-------------DMNFG-FVNLAGGAAVDTT------ +----ATLSVTCNNPLSLALSIRICPNINAGGGGQSGGI----------RRMLQ-----GS +NI-LNYQLYQTSARTTAWGSVTQ-PALGAPPPIDMALPLLI--NSTTRT-VY-GRI--NA +GQA--SAARGLY-------LSSFAGG +>Q985D8_RHILO/37183 +--SAALLLPTVAWAQSCSFGVS-------------AMNFG-LVDTLSGSSSNST------ +----ATLSVNCTGL--LLQRILVCPNLGTGSGGATASA----------RQMLS-----GA +ND-LNYQLYSDSARSVVWGSYAW-PYPPTAPGFALTLNVLG--SGSASQTIY-GAI--LG +GQA--TAVPSTY-------LSTFSGS +>Q0VRQ1_ALCBS/179310 +--TNYTLNANLAIQNQCSITAN-------------DLNFGTQSSPLPQTDSD-------- +----TFIDVRCT-NT-------SPFTVGLSDGLNPSGGS---------RRMRD-----GS +QF-VSYGLFQDAARSIPWDSTTN-RKGATGLGTS---------TSIMMS-VF-GRI--P- +AAP--STPPGNY-------TDTITVD +>Q0VRP8_ALCBS/30176 +--LTDSFDVLLNLQSSCTLDST------------TDLDFG-DQTDADVVAGNIDAA---- +----NSVTVTCS-NG-------ADFTIGLTNGANFGDGPV-----ATERAMKSA----NA +SY-VSYQIFQDSGRTTAWTD----TDDVAFNGTG---------ASQNID-IY-GRI--P- +AQTPTIDAADTFNATGLALTDTVTVT +>Q1D5L1_MYXXD/13153 +AVAGVCGLLPGLAGAVCQIRST------------IGVSFG-TYLTTDLLPRDSA------ +----GSITYRCEGQI-------TPITIDFSAGGSGTPLA---------RSMAGP----GA +QR-LEYNLYVDATRLIVWGNG-T-SGTGRYGPVV-PLF--G--VEVTVP-IF-GRI--P- +AGQ--AIPAGAY-------ADTVVMT +>Q2IFK8_ANADE/19157 +ATALSLVAPAAARAASCSLTMG------------TSIAFG-AYDPLSPVPLTTT------ +----GMLQYRCS-RG-------QPIRITFTAGSSGDVYA---------RTLRQ-----GP +WT-LAYNLYADAGFGTVWGDGTG-GTAAAPAVTTLS-------NGLTVAYVF-GRI--P- +ARQ--EPPVGPY-------SDTIVVT +>A7H7Q5_ANADF/16150 +APRAVDAAQPPSPGPSCSVSAG-------------SVAFG-AYDPL----SPTHLD---- +ST--GTIGLTCA-VR-------QLVTISLGTGQS--GTF------A--RELRGP----GG +AA-LRYDLYTDATRTQVWGDGTA-GTATWPFETE---------RGRYVP-VY-ARV--L- +AGQ--DVPAGPY-------SDTIVVT +>Q7CIW7_YERPE/27181 +---TGTLSSTLTIISGCYINDG---TGSGSLSNLGTINFG-SVVALSSVINVAFS----- +GTLSGTLSLYCS-AN-------TAYTIAIDNGLYSTSGQ---------RRLRGGAAAPTT +FEYVNYNLFKDSSYNQPWNATPT-TGVQSGTGTG-I----A--TPIPLT-IY-AQV--P- +IQT--TPSVSTY-------IDTVIVT +>Q6F7G4_ACIAD/24154 +--IANTFNVSITVKESCDIRTL----------TATDIDFG-TVTQAAQNAYNS------- +----GQLNVACT-SG-------TSYAIALQSS----------------RKMVNIA---DP +TVQVPYTLFQDSNYSKVWGSD-S-GTGLSQIGT-------G--ETQMIK-IW-GKV--DA +QDT--AVPAGQY-------LDTVTAI +>Q0AAK6_ALKEH/8153 +SLFLVAAGSGSAQAYTCSISAD-------------PLAFG-QYDPITGAQVDGA------ +----SEVSVSCSLLGLVSLL--VSYEISLDPGTGGSYHP---------RALSS-----AT +DT-LDYNLYVDTARTEIWGDG-T-DDTATVTDSY-TLGVLT--VTRYYP-VY-GRV--F- +ADQ--NVAAGVY-------DDTITAT +>Q1D5K8_MYXXD/34182 +--ATANLNVTANVGGSCAIGSG---------GGGGTLNFG-TYDPI---IVNSALGIDLF +GT--GTLSVQCT-LL-------GTAVITLGQGLHPASGSTDAAP-Q--RRMRNTA---SA +DY-LAYGLNQDVTRLIGWGNT-A-GSGLPFLGT-------G--LPVPVL-VY-GTV--P- +RGQ--NVPSGTY-------NDTVVAT +>A8GDM3_SERP5/30181 +--KTQAMTVNATVVKGCILGSG-----SSDVTTFGNLSFG-QVSSLASNISIVSSSGA-- +----GSVLFRCN-PG-------LSVTLALGIGNNVTGSISAG------RKLKNTL---TP +ET-LIYQLYQDSNYSTIWGDG-T-NGGSTEIVAA-T----G--STQEIK-VY-ARL--FS +TST--LPTSGTY-------SDTVLLT +>Q0WG87_YERPE/33182 +----SPFTVNATVLTGCVLGGG-----ATDSSNFGSINFG-NITSLATAINATSGLNA-- +----GTITIQCN-GN-------PSVTLALNSGANMTGNISAG------RHLLNSS---TG +EY-LLYQIYQNSPRTLIWGDGSN-GGATQVIATD------G--TLQQVI-LY-AQL--FA +SNT--QPTAGVY-------LDTLLVT +>Q9HVE2_PSEAE/31177 +----RAFQVQAVVANGCAFGTA----ISNNAYDLGTLSFG-TLGNLASPVNVASSSGA-- +----GSIVLTCT-PG-------MTVSVALDYGVNGGSSSQ--------RYLKRV----SG +NETLAYQLYQDAAYSQVWGNGALARTIANFPA-----------STQTYT-VY-ARL--FA +VGS--LPSAGNY-------RDTVTVT +>Q6D2M1_PECAS/27175 +--VSSTFDVEATIQKGCVFGTS----TASSQPNMGTLSFG-IRGATATNVDVASTSGS-- +----GSIIATCT-PG-------INAIIELDYGTNGGSSTQ--------RYLKNA----AG +TRLLAYQLYRDAARTLVWGTG----GLALSIVSF-P----A--TPQTYT-VY-ARY--FG +GTP--LPPAGIY-------TDNVTVS +>Q9HVE3_PSEAE/30174 +---TATIVLSATLLPACEAGSV----GSGGAITFGTLDFG-QYASLNNAISATSQQGA-- +----GSIRVRCV-SG-------QTYAITLDGGLYGSVAT---------RRMANIA---NT +ALTLTYNLYSDRPGGIVWDN----TTGVAATGNG---------NDQWYP-IY-GLV--P- +AQT--TPVAGTY-------RDTVNVT +>A8GDM4_SERP5/22164 +--KTATIGVSATLLKACEAGSS-----SGGNVSFGSLDFG-TVYFLTTSVSVAGQQ---- +NA--GAIRVKCN-NG-------TSYNVLLNGGQSGNTAA---------RYLKSA----AG +QQ-VNYNLYTNSSHSIIWDNL---TGVSQTAN--------G--QDNWLP-VY-GMI--P- +VQS--TPPIGSY-------TDTVQVT +>Q0WG86_YERPE/31173 +---TANITVTATLLPTCLARFL-----VSGSTSFGTLDFG-STVALTQPISVAGQT---- +NS--GAITVQCS-NG-------TSFNVLLSSGQSGNTNN---------RYLSGGP---SA +QQ-VSYNLYTNATYSVIWDDV---VGVSQVAT--------G--QVVTIP-VY-GLV--P- +AQS--TPAVGTY-------TDTVQVT +>Q8PAU6_XANCP/47193 +---TTTFNVKIAVTKACTITAA----------SATDVDFGSVLSTSTANADAN------- +----GSVTAQCT-AL-------TPYNIALSAGSNAGTANDVTT-----RRMKNTDALVTT +NNFVAYQLYQDLGRSTVWGS--T-SGTNTLSRTA-T----G--INQIYP-VY-GRVTNP- +SAG--NPATGTY-------QDTITAT +>Q13JY7_BURXL/27170 +--ATATLTNTATIVASCTLGAT-------------GF-TN-TYDPVTANATAPVRD---- +AT--ASVTYTCT--NGG-----TGALIALDGGNHETGTSAVP---I--RHLAGATN--TT +DL-LAYNLYQEPTYTTPWG---Y-AAAAELAAIE-D----G--VQHVLT-VY-TEI--PA +GQS--LLHVDTY-------SDTVTAT +>Q60C05_METCA/39178 +--ETASLGISATVANTCKIEST------------SNVNFT-TYDPTSTTDTATNS----- +----GQIRVKCT-KG-------STSTIYMGAGTASGATCSGTPI----RKMAN-----GA +DL-LTYNLYQNNGYTTVWGCDSS-NQYSYTASNN---------GWQNLT-VY-GVI--P- +AGQ--DVPAGSY-------TDTVTVT +>Q0AAK3_ALKEH/24160 +--DTATFDVTATVDPTCTVDAD-------------NLVFG-TYDPFSDTPLDEN------ +----SEIRVQCT-SD-------TPYDIGLDDGDNTGAEGE--------RRMALAD---ES +DF-LEYDLYHDNHGGTSWGDI-D-SGAELTGLSG-T----G--SEQSYV-VY-GRI--F- +AEQ--SVAVGNY-------VDTIEVT +>A8GDM5_SERP5/27176 +--IQGNLGVTLTIGAGCVVGGG---NSAGSANDFGSIDFG-TYSSLSNIIDASATG---- +SGGAGTLSLTCT-TG-------TAYTVALNNGLHVGAGNQ--------RQMAST----AG +SL-IKYNLYQDQARATAWSSG---ANALTGTGTG---------AAVPLI-VY-ARV--PA +AAT--TPDPDTY-------NDTVTMT +>A7H7Q6_ANADF/25150 +--ATAQFQVTATVVKKCKISAT-------------TIAFG-NYDPATILSAE-------- +----GTLTLKCT-KG-------TLYSVALDGGSTGS------------RQMTQ-----AA +EV-LDYELYSDAGHTAVWPST-A-AAPSVAAA--------G--ADEALI-IF-AQV--P- +ADQ--YPAPGAY-------ADTVTAT +>Q2IFL0_ANADE/27162 +--ATATLDVTATVVPSCTIAAT-------------PVAFG-SYDPLVTNAATALDAQ--- +----GTVTVTCT-TG-------TAYTVGLGAGNSGSGS----------RAMQHASI--AG +AQ-LPYELYQEAARTTVWDSTVMQAGTAASI------------TPVQYT-VY-GRI--P- +AAQ--NVPTGNY-------ADAVVAT +>Q0C623_HYPNA/23151 +--ANGTLDVQATVVNTCVVLTA-------------PVVFA-SVGLDEVTAN--------- +----GSITVNCT-NT-------SAFTVALDGGDSGDISA---------RSLTHA----SL +PASFNYQLYTDAGLTTVWGDG---VTGSQANGSG---------PSQTLT-VY-GRT---- +TST--PDTAGAY-------ADEVQVT +>Q985D8_RHILO/205338 +--DRPTFTINAIVPANCLLAIQ-------------NIDFG-SNGILGANVDAT------- +----GGVSITCT-PG-------TPYTVSLSNGTTGSAPTA--------RKMSK-----GV +ET-VTYGLYKDNARSQVWGDA-A-MPGSTVAGSG-S----G--AAQNLT-IY-GRV--P- +AQT--TPSAGVY-------TDTVVVT +>Q8XVY0_RALSO/26164 +--TTTTFSVSTTVNATCVINSA------------SALTFA-AFDPSQGAQAST------- +----SSISVNCT-NT-------TPFNIGLNAGTGTGATVA-----S--RVMTS-----GA +NT-LTYSLYQDSGHASVWGN--T-VGTNTVAGTG-AGMAAG--NAITKT-VY-GLI--P- +SQP--NTVPGNY-------ADTVTVT +>Q0BSH7_GRABC/37169 +--TTTTFQVTATVQASCIIQAT-------------NLSFG-NYS--GSQTDAT------- +----STIQVTCT-NS-------TPYNVGLSAGTGSGATVS-----N--RKMSLN----ST +SA-LPYALYSDASRSTNWGN--T-PNQDTVSGTG-N----G--SAQSLT-VY-GRI--Q- +TGN--YPTPGSY-------ADTITAT +>Q8XPY6_RALSO/36170 +--KTTTFTVSLTLQADCSISAN-------------ALNFG-TQGVLAANVDQT------- +----ATLSVTCS-NT-------APYNVGFDAGTTTGSTIA-----A--RLLAGS----GA +AT-VGFQLYSDSARTQIWGN--T-VGTDTVSGTG-S----G--TAQVLT-VY-GRV--P- +SQN--SPAAGTY-------STTITAT +>Q63W79_BURPS/31169 +--ATATFTVSLTIQANCTISAN-------------ALSFG-TNGVLATAVNQQ------- +----TTLSVTCS-NT-------TSYNVGLDAGNVSGSTVS-----S--RLLAGTTTGNTS +TT-VSFQLYQDSGHTTIWGN--T-VGTNTVSGTG-N----G--TAQTLS-VY-GQV--P- +AQT--TPKPDTY-------ESTVTAT +>Q7CVQ4_AGRFC/27162 +--ATTNFNVQITIQAACQINSA------------GNLDFG-TNGVIGAPIDVT------- +----SQIVVQCT-AS-------TPFSLGLSAGAGSGATVA-----N--RLMTSA----AG +AT-ISYSLYTTAAHSTVWGN--T-VGTDRQTGTG-T----G--APQNFT-VF-GRV--P- +AQT--TPAVGVY-------TDTVTAT +>Q985D5_RHILO/27162 +--ATGNMTVRITIQAECKVQTA------------TDMDFG-TNGVIDANVDQT------- +----STISVQCT-NS-------TPYNVGLSAGVGAGATVA-----V--RKMTGP----AA +AV-LNYSLYRDVARAQLWGT--T-IGTDTVAGTG-N----G--AAQPLT-VY-GRV--P- +PQT--TPGAGVY-------TDTVAIT +>A6X8A6_OCHA4/27162 +--ATGNMNVRITIQAECKIVTA------------TDLDFG-TKGVIDVNVDQT------- +----STISVQCT-NG-------TPYTVGLSAGGGAGATVA-----M--RKMTGA----AS +AT-INYTIYRDAARTQVWGV--T-AGTDVVSGTG-N----G--NAQSIT-AY-GRV--P- +AQT--TPAPGVY-------SDVVSVT +>A9CH19_AGRFC/182313 +--TQVPFTVSAAVAPTCIISAQ-------------NINFG-SHGVLNTAVDAN------- +----GAINLTCT-NG-------LNYSVALNGGLSNSPPAA--------RQMVQ-----GA +AS-IIYGLYRDVSRTNVWGSAA--GQIATGTGNG---------SLQTLT-VF-GRV--P- +AQN--TPAPGNY-------ADTVVVT +>Q63W78_BURPS/193326 +---TFAFTASATVVNDCFINAT-------------NVAFG-STGVIQGALTAT------- +----GTISAQCT-NG-------DAFRIALNGGASGNVAA---------RAMQRTG---GG +GA-VNYQLYLDAAHSTIWGDG-T-AGTSTATGTG-S----G--LSQSLT-VY-GQV--P- +AQT--TPAPGTY-------SDTITAT +>A8GDM0_SERP5/8155 +LLLALLLLIGRQALADCTTANG-------------SVTLP-GSSTFAVYNGSLSAQ---- +----GTAGLNCS-GLGLSLLTQNTVTVKINSTTH-----------N--MALANADG--SG +DT-IPYLIYPDANYQYPYSVGQT-IDYSSLNLLTL--ILIS--PNVNFP-LY-IKT--T- +AGA--NVRSGTY-------TDTVNLV +>Q6D2L8_PECAS/25179 +AFLLMALYYAPFSHAACTTPPS--------NTVLGP--YGSSVVGVNGTPQVVA------ +----SGSGFRCT-GSVLSLASTNTITATIQSDSNPSGTT---------MRMRRGT---TT +DY-VPYSLCMDSGCGTLYNINST-YTWSRTTFLDILGLFNS--TDGTMP-IY-IRT--S- +IGS--NVSAGTY-------TDTVTIK +>Q9HVD9_PSEAE/14161 +----ATLCASPLLLAACTTSSG-------------TGNFG-SLSSFTVASTAQTIT---- +----GTTGFKCT-GSLLSILSTNTIDATIASTANPLGTT---------PRLYNAA---SG +TY-LPYSICKDNGCGTVYNVGST-VRWSSTTFLGILGLFNA--TDGSLP-LY-LRT--A- +TGV--TLPAGTY-------TDTIGL- +>Q63TE3_BURPS/22161 +---------ALHAHATCSVVSA------------AAASFG-TVTSFAVARQPQSTS---- +T---TSSGLSCS-GALL-----GLFVIGDQINASITSANGG--------KLVGP----TG +DA-VPYTVFADQNYSIKLDLGVT-YNWASGQLLNLLGIFGG--PAQTLP-MY-FRT--V- +QGS--NVAAGTY-------TDTLTI- +>Q88KC7_PSEPK/8157 +LVASVLLLPSSTAWALCSSVAT------------LPAAFG-SLNSTQVRNTVQTAS---- +S---LNSGLQCT----------GSLLTLLSSGDHFYATITPA---S--GGLVGP----TG +DV-IPYTLYADNTTRYPITRGVA-YDFARNGILDLLGLLGG-TTPKAVP-IY-MRT--Q- +IGS--NVAAGLY-------QEALTVA +>Q4K9N4_PSEF5/11161 +ILGLLASVLSCTAQALCTTVPT------------APAGFGTVSSILVRTTSQPAST---- +----TNAGLSCT----------GSLLSILASNDHFYATITSTT-----SGMVGP----TG +DV-ISYTLYANNSTSYPITRGVQ-FDFARNSIIDLLGLLGSPTVAKTVP-IYLGTL---- +TGS--NVAAGVY-------TENLSIL From aa8e8fbf4dccf5921dcfcd782e8fe9596a2a948a Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 20:04:22 -0500 Subject: [PATCH 14/27] Delete Alignment 1 --- Alignment 1 | 15 --------------- 1 file changed, 15 deletions(-) delete mode 100644 Alignment 1 diff --git a/Alignment 1 b/Alignment 1 deleted file mode 100644 index ac04af2..0000000 --- a/Alignment 1 +++ /dev/null @@ -1,15 +0,0 @@ -Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Bacillus.fasta -out Bacillus.align - -MUSCLE v3.8.31 by Robert C. Edgar - -http://www.drive5.com/muscle -This software is donated to the public domain. -Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. - -Bacillus 4306 seqs, max length 1495, avg length 244 -00:00:45 158 MB(2%) Iter 1 100.00% K-mer dist pass 1 -00:00:45 158 MB(2%) Iter 1 100.00% K-mer dist pass 2 -00:01:53 1255 MB(15%) Iter 1 100.00% Align node -00:01:53 1255 MB(15%) Iter 1 100.00% Root alignment - - From a5b64e5e1465a5749a62de6c6b6c258e7b6dee34 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 20:04:32 -0500 Subject: [PATCH 15/27] Delete Alignment 2 --- Alignment 2 | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 Alignment 2 diff --git a/Alignment 2 b/Alignment 2 deleted file mode 100644 index f45d7da..0000000 --- a/Alignment 2 +++ /dev/null @@ -1,13 +0,0 @@ -Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Arthrobacter.fasta -out Arthrobacter.align - -MUSCLE v3.8.31 by Robert C. Edgar - -http://www.drive5.com/muscle -This software is donated to the public domain. -Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. - -Arthrobacter 3212 seqs, max length 2033, avg length 325 -00:00:29 92 MB(1%) Iter 1 100.00% K-mer dist pass 1 -00:00:30 92 MB(1%) Iter 1 100.00% K-mer dist pass 2 -00:02:12 734 MB(9%) Iter 1 100.00% Align node -00:02:13 734 MB(9%) Iter 1 100.00% Root alignment From 9c1cb59e66da111f73ce9474625fd90c8261af26 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 20:04:42 -0500 Subject: [PATCH 16/27] Delete Alignment 3 --- Alignment 3 | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 Alignment 3 diff --git a/Alignment 3 b/Alignment 3 deleted file mode 100644 index 691d104..0000000 --- a/Alignment 3 +++ /dev/null @@ -1,13 +0,0 @@ -Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Clostridium.fasta -out Clostridium.align - -MUSCLE v3.8.31 by Robert C. Edgar - -http://www.drive5.com/muscle -This software is donated to the public domain. -Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. - -Clostridium 1828 seqs, max length 1965, avg length 272 -00:00:14 32 MB(0%) Iter 1 100.00% K-mer dist pass 1 -00:00:14 32 MB(0%) Iter 1 100.00% K-mer dist pass 2 -00:01:10 512 MB(6%) Iter 1 100.00% Align node -00:01:10 512 MB(6%) Iter 1 100.00% Root alignment From 1c8059e142d92a63753e1c5dedcdac551f044f84 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 20:04:52 -0500 Subject: [PATCH 17/27] Delete Alignment 4 --- Alignment 4 | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 Alignment 4 diff --git a/Alignment 4 b/Alignment 4 deleted file mode 100644 index 4bc35c7..0000000 --- a/Alignment 4 +++ /dev/null @@ -1,13 +0,0 @@ -Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Flavobacterium.fasta -out Flavobacterium.align - -MUSCLE v3.8.31 by Robert C. Edgar - -http://www.drive5.com/muscle -This software is donated to the public domain. -Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. - -Flavobacterium 4309 seqs, max length 5826, avg length 355 -00:01:46 160 MB(2%) Iter 1 100.00% K-mer dist pass 1 -00:01:46 160 MB(2%) Iter 1 100.00% K-mer dist pass 2 -00:20:34 2202 MB(26%) Iter 1 100.00% Align node -00:20:37 2202 MB(26%) Iter 1 100.00% Root alignment From 6f43a82bf00702436eb934a4c1c4b5074217824c Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 20:05:02 -0500 Subject: [PATCH 18/27] Delete Alignment 5 --- Alignment 5 | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 Alignment 5 diff --git a/Alignment 5 b/Alignment 5 deleted file mode 100644 index 745d71c..0000000 --- a/Alignment 5 +++ /dev/null @@ -1,13 +0,0 @@ -Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Limnohabitans.fasta -out Limnohabitans.align - -MUSCLE v3.8.31 by Robert C. Edgar - -http://www.drive5.com/muscle -This software is donated to the public domain. -Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. - -Limnohabitans 3169 seqs, max length 6686, avg length 324 -00:01:10 89 MB(1%) Iter 1 100.00% K-mer dist pass 1 -00:01:10 89 MB(1%) Iter 1 100.00% K-mer dist pass 2 -00:16:00 2259 MB(26%) Iter 1 100.00% Align node -00:16:03 2259 MB(26%) Iter 1 100.00% Root alignment From 118636c0f2bde24f8ebf2917020d8e9003abb545 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 20:05:11 -0500 Subject: [PATCH 19/27] Delete Alignment 6 --- Alignment 6 | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 Alignment 6 diff --git a/Alignment 6 b/Alignment 6 deleted file mode 100644 index 9a041e5..0000000 --- a/Alignment 6 +++ /dev/null @@ -1,13 +0,0 @@ -Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Verrucomicrobia.fasta -out Verrucomicrobia.align - -MUSCLE v3.8.31 by Robert C. Edgar - -http://www.drive5.com/muscle -This software is donated to the public domain. -Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. - -Verrucomicrobia 1793 seqs, max length 2811, avg length 326 -00:00:33 32 MB(0%) Iter 1 100.00% K-mer dist pass 1 -00:00:34 32 MB(0%) Iter 1 100.00% K-mer dist pass 2 -00:05:03 982 MB(11%) Iter 1 100.00% Align node -00:05:03 982 MB(11%) Iter 1 100.00% Root alignment From 87f47c352dad01c9af74891bbeccf75bedc5abfb Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 20:05:21 -0500 Subject: [PATCH 20/27] Delete Alignment 7 --- Alignment 7 | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 Alignment 7 diff --git a/Alignment 7 b/Alignment 7 deleted file mode 100644 index c5b839d..0000000 --- a/Alignment 7 +++ /dev/null @@ -1,13 +0,0 @@ -Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Rhizobium.fasta -out Rhizobium.align - -MUSCLE v3.8.31 by Robert C. Edgar - -http://www.drive5.com/muscle -This software is donated to the public domain. -Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. - -Rhizobium 4696 seqs, max length 3387, avg length 320 -00:02:58 188 MB(2%) Iter 1 100.00% K-mer dist pass 1 -00:03:00 188 MB(2%) Iter 1 100.00% K-mer dist pass 2 -00:15:19 1690 MB(20%) Iter 1 100.00% Align node -00:15:21 1690 MB(20%) Iter 1 100.00% Root alignment From 18828b2899f45059da03231a8c47ff845853a0ae Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 20:05:31 -0500 Subject: [PATCH 21/27] Delete Alignment 8 --- Alignment 8 | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 Alignment 8 diff --git a/Alignment 8 b/Alignment 8 deleted file mode 100644 index 237292d..0000000 --- a/Alignment 8 +++ /dev/null @@ -1,13 +0,0 @@ -Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in Roseobacter.fasta -out Roseobacter.align - -MUSCLE v3.8.31 by Robert C. Edgar - -http://www.drive5.com/muscle -This software is donated to the public domain. -Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. - -Roseobacter 4185 seqs, max length 3284, avg length 311 -00:02:36 151 MB(2%) Iter 1 100.00% K-mer dist pass 1 -00:02:38 151 MB(2%) Iter 1 100.00% K-mer dist pass 2 -00:15:36 2320 MB(27%) Iter 1 100.00% Align node -00:15:39 2340 MB(27%) Iter 1 100.00% Root alignment From 74731f3605858b3160d3c098378bdc6b54ecfdc2 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 20:09:23 -0500 Subject: [PATCH 22/27] Add files via upload --- transporter.align | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 transporter.align diff --git a/transporter.align b/transporter.align new file mode 100644 index 0000000..2f47110 --- /dev/null +++ b/transporter.align @@ -0,0 +1,32 @@ +>A0A026RKY7_ECOLX/4411 +NIPFRNAYYRFASSYSFLFFISWSLWWSLYAIWLKGHLGLTGTELGTLYSVNQFTSILFM +MFYGIVQDKLGLKKPLIWCMSFILVLTGPFMIYVYEPLLQSNFSVGLILGALFFGLGYLA +GCGLLDSFTEKMARNFHFEYGTARAWGSFGYAIGAFFAGIFFSISPHINFWLVSLFGAVF +-MMINMRFKDKDHQCIAADAGGVKKEDF-----IAVFKDRNFWVFVIFIVGTWSFYNIFD +QQLFPVFYAGLFESHDVGTRLYGYLNSFQVVLEALCMAIIPFFVNRVGPKNALLIGVVIM +ALRILSCALFVNPWIISLVKLLHAIEVPLCVISVFKYSVANFDKRLSSTIFLIGFQIASS +LGIVLLSTPTGILFDHAGYQTVFFAISGIVCLMLLFGIFFLSKKREQIVMETPV +>RAFB_ECOLX/4415 +ASTHKNTDFWIFGLFFFLYFFIMATCFPFLPVWLSDVVGLSKTDTGIVFSCLSLFAISFQ +PLLGVISDRLGLKKNLIWSISLLLVFFAPFFLYVFAPLLHLNIWAGALTGGVFIGFVFSA +GAGAIEAYIERVSRSSGFEYGKARMFGCLGWALCATMAGILFNVDPSLVFWMGSGGALLL +LLLLYLARPSTSQTAMVMNALGANSSLISTRMVFSLFRMRQMWMFVLYTIGVACVYDVFD +QQ-FAIFFRSFFDTPQAGIKAFGFATTAGEICNAIIMFCTPWIINRIGAKNTLLVAGGIM +TIRITGSAFATTMTEVVILKMLHALEVPFLLVGAFKYITGVFDTRLSATVYLIGFQFSKQ +LAAILLSTFAGHLYDRMGFQNTYFVLGMIVLTVTVISAFTLS-SSPGIVHPSVE +>LACY_CITFR/1412 +MYYLKNTNFWMFGFFFFFYFFIMGAYFPFFPIWLHEVNHISKGDTGIIFACISLFSLLFQ +PIFGLLSDKLGLRKHLLWVITGMLVMFAPFFIYVFGPLLQVNILLGSIVGGIYLGFIYNA +GAPAIEAYIEKASRRSNFEFGRARMFGCVGWALCASIAGIMFTINNQFVFWLGSGCAVIL +ALLLLFSKTDVPSSAKVADAVGANNSAFSLKLALELFKQPKLWLISLYVVGVSCTYDVFD +QQ-FANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIVNRIGGKNALLLAGTIM +SVRIIGS-HSHTALEVVILKTLHMFEIPFLIVGCFKYITSQFEVRFSATIYLVCFCFFKQ +LAMIFMSVLAGKMYESIGFQGAYLVLGIIRVSFTLISVFTLSGPGPFSLLRRRE +>LACY_KLEOX/6416 +LAPRERHNFIYFMLFFFFYYFIMSAYFPFFPVWLAEVNHLTKTETGIVFSCISLFAIIFQ +PVFGLISDKLGLRKHLLWTITILLILFAPFFIFVFSPLLQMNIMAGALVGGVYLGIVFSS +RSGAVEAYIERVSRANRFEYGKVRVSGCVGWALCASITGILFSIDPNITFWIASGFALIL +GVLLWVSKPESSNSAEVIDALGANRQAFSMRTAAELFRMPRFWGFIIYVVGVASVYDVFD +QQ-FANFFKGFFSSPQRGTEVFGFVTTGGELLNALIMFCAPAIINRIGAKNALLIAGLIM +SVRILGSSFATSAVEVIILKMLHMFEIPFLLVGTFKYISSAFKGKLSATLFLIGFNLSKQ +LSSVVLSAWVGRMYDTVGFHQAYLILGCITLSFTVISLFTL--KGSKTLLPATA From dfaf83c831732b7fd05f640ca52768ffb1ef534b Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 20:11:06 -0500 Subject: [PATCH 23/27] Create Alignment Code --- Alignment Code | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 Alignment Code diff --git a/Alignment Code b/Alignment Code new file mode 100644 index 0000000..f75bcc7 --- /dev/null +++ b/Alignment Code @@ -0,0 +1,4 @@ +#Alignment Code +Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in transporter.ref -out transporter.align +Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in sporecoat.ref -out sporecoat.align +Madelines-MacBook:Desktop madelinebuynak$ ./muscle3.8.31_i86darwin64 -in sigma.ref -out sigma.align From 2323b2fcc3118fd7741190de302d54f295a9a1b7 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 20:56:02 -0500 Subject: [PATCH 24/27] Create hmm codes --- hmm codes | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 hmm codes diff --git a/hmm codes b/hmm codes new file mode 100644 index 0000000..3afba79 --- /dev/null +++ b/hmm codes @@ -0,0 +1,3 @@ +./hmmbuild sigma.hmm sigma.align +./hmmbuild transporter.hmm transporter.align +./hmmbuild transporter.hmm transporter.align From 456a167440993b3530b3d14f5a1f9571aeaa47ec Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 21:07:50 -0500 Subject: [PATCH 25/27] Create Search Codes --- Search Codes | 71 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 Search Codes diff --git a/Search Codes b/Search Codes new file mode 100644 index 0000000..f76df32 --- /dev/null +++ b/Search Codes @@ -0,0 +1,71 @@ +./hmmsearch --tblout sigma.hits sigma.hmm Roseobacter.fasta +cat sigma.hits | grep -v "#" | wc -l + +./hmmsearch --tblout transporter.hits transporter.hmm Roseobacter.fasta +cat transporter.hits | grep -v "#" | wc -l + +./hmmsearch --tblout sporecoat.hits sporecoat.hmm Roseobacter.fasta +cat sporecoat.hits | grep -v "#" | wc -l + +./hmmsearch --tblout sigma.hits sigma.hmm Arthrobacter.fasta +cat sigma.hits | grep -v "#" | wc -l + +./hmmsearch --tblout transporter.hits transporter.hmm Arthrobacterr.fasta +cat transporter.hits | grep -v "#" | wc -l + +./hmmsearch --tblout sporecoat.hits sporecoat.hmm Arthrobacter.fasta +cat sporecoat.hits | grep -v "#" | wc -l + +./hmmsearch --tblout sigma.hits sigma.hmm Bacilus.fasta +cat sigma.hits | grep -v "#" | wc -l + +./hmmsearch --tblout transporter.hits transporter.hmm Bacillus.fasta +cat transporter.hits | grep -v "#" | wc -l + +./hmmsearch --tblout sporecoat.hits sporecoat.hmm Bacillus.fasta +cat sporecoat.hits | grep -v "#" | wc -l + +./hmmsearch --tblout sigma.hits sigma.hmm Clostridium.fasta +cat sigma.hits | grep -v "#" | wc -l + +./hmmsearch --tblout transporter.hits transporter.hmm Clostridium.fasta +cat transporter.hits | grep -v "#" | wc -l + +./hmmsearch --tblout sporecoat.hits sporecoat.hmm Clostridium.fasta +cat sporecoat.hits | grep -v "#" | wc -l + +../hmmsearch --tblout sigma.hits sigma.hmm Flavobacterium.fasta +cat sigma.hits | grep -v "#" | wc -l + +./hmmsearch --tblout transporter.hits transporter.hmm Flavobacterium.fasta +cat transporter.hits | grep -v "#" | wc -l + +./hmmsearch --tblout sporecoat.hits sporecoat.hmm Flavobacterium.fasta +cat sporecoat.hits | grep -v "#" | wc -l + +./hmmsearch --tblout sigma.hits sigma.hmm Limnohabitans.fasta +cat sigma.hits | grep -v "#" | wc -l + +./hmmsearch --tblout transporter.hits transporter.hmm Limnohabitans.fasta +cat transporter.hits | grep -v "#" | wc -l + +./hmmsearch --tblout sporecoat.hits sporecoat.hmm Limnohabitans.fasta +cat sporecoat.hits | grep -v "#" | wc -l + +./hmmsearch --tblout sigma.hits sigma.hmm Rhizobium.fasta +cat sigma.hits | grep -v "#" | wc -l + +./hmmsearch --tblout transporter.hits transporter.hmm Rhizobium.fasta +cat transporter.hits | grep -v "#" | wc -l + +./hmmsearch --tblout sporecoat.hits sporecoat.hmm Rhizobium.fasta +cat sporecoat.hits | grep -v "#" | wc -l + +./hmmsearch --tblout sigma.hits sigma.hmm Verrucomicrobia.fasta +cat sigma.hits | grep -v "#" | wc -l + +./hmmsearch --tblout transporter.hits transporter.hmm Verrucomicrobia.fasta +cat transporter.hits | grep -v "#" | wc -l + +./hmmsearch --tblout sporecoat.hits sporecoat.hmm Verrucomicrobia.fasta +cat sporecoat.hits | grep -v "#" | wc -l From a7a0ebb9d62817e264651a64f1af317af1df1256 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 21:12:43 -0500 Subject: [PATCH 26/27] Update hmm codes --- hmm codes | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hmm codes b/hmm codes index 3afba79..fe5fe00 100644 --- a/hmm codes +++ b/hmm codes @@ -1,3 +1,3 @@ ./hmmbuild sigma.hmm sigma.align ./hmmbuild transporter.hmm transporter.align -./hmmbuild transporter.hmm transporter.align +./hmmbuild sporecoat.hmm sporecoat.align From 4fce502d71af3426ccbd2a8bd8cba7fe71706855 Mon Sep 17 00:00:00 2001 From: mbuynak <31928750+mbuynak@users.noreply.github.com> Date: Thu, 16 Nov 2017 21:41:32 -0500 Subject: [PATCH 27/27] Update hmm codes --- hmm codes | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/hmm codes b/hmm codes index fe5fe00..a509836 100644 --- a/hmm codes +++ b/hmm codes @@ -1,3 +1,3 @@ -./hmmbuild sigma.hmm sigma.align -./hmmbuild transporter.hmm transporter.align -./hmmbuild sporecoat.hmm sporecoat.align +./hmmer-3.1b2-macosx-intel/binaries/hmmbuild sigma.hmm sigma.align +./hmmer-3.1b2-macosx-intel/binaries/hmmbuild transporter.align +./hmmer-3.1b2-macosx-intel/binaries/hmmbuild sporecoat.hmm sporecoat.align