# STOCKHOLM 1.0 #=GF ID Retrotran_gag_2 #=GF AC PF14223.7 #=GF DE gag-polypeptide of LTR copia-type #=GF PI UBN2; #=GF AU Coggill P;0000-0001-5731-1588 #=GF SE Jackhmmer:A5B9L3 #=GF GA 27.00 27.00; #=GF TC 27.00 27.00; #=GF NC 26.90 26.90; #=GF BM hmmbuild HMM.ann SEED.ann #=GF SM hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq #=GF TP Family #=GF RN [1] #=GF RM 2538806 #=GF RT The nucleotide sequence of Drosophila melanogaster #=GF RT copia-specific 2.1-kb mRNA. #=GF RA Miller K, Rosenbaum J, Zbrzezna V, Pogo AO; #=GF RL Nucleic Acids Res. 1989;17:2134. #=GF DR SO; 0100021; polypeptide_conserved_region; #=GF CC This family is found in Plants and fungi, and contains #=GF CC LTR-polyproteins, or retrotransposons of the copia-type. #=GF SQ 50 #=GS K7MSY7_SOYBN/76-212 AC K7MSY7.1 #=GS K7JBR0_NASVI/56-192 AC K7JBR0.1 #=GS K7J7F1_NASVI/67-205 AC K7J7F1.1 #=GS K7JBX1_NASVI/56-194 AC K7JBX1.1 #=GS J9KKF0_ACYPI/70-208 AC J9KKF0.2 #=GS X1WMG8_ACYPI/69-207 AC X1WMG8.1 #=GS X1XSG1_ACYPI/1016-1154 AC X1XSG1.1 #=GS K7JSP6_NASVI/56-194 AC K7JSP6.1 #=GS F4WZJ7_ACREC/51-189 AC F4WZJ7.1 #=GS M5BUS0_THACB/75-214 AC M5BUS0.1 #=GS E2AMM3_CAMFO/51-188 AC E2AMM3.1 #=GS E2A5G7_CAMFO/57-194 AC E2A5G7.1 #=GS E2AJT1_CAMFO/8-145 AC E2AJT1.1 #=GS E1ZV45_CAMFO/58-195 AC E1ZV45.1 #=GS T1HSX1_RHOPR/55-192 AC T1HSX1.1 #=GS F4WEW2_ACREC/61-198 AC F4WEW2.1 #=GS K7JMW1_NASVI/53-191 AC K7JMW1.1 #=GS K7JZ52_NASVI/48-186 AC K7JZ52.1 #=GS H3GVH0_PHYRM/36-172 AC H3GVH0.1 #=GS H3GKE9_PHYRM/34-170 AC H3GKE9.1 #=GS H3H8S0_PHYRM/58-195 AC H3H8S0.1 #=GS I1R349_ORYGL/53-190 AC I1R349.1 #=GS M7ZB77_TRIUA/364-501 AC M7ZB77.1 #=GS J3N766_ORYBR/276-405 AC J3N766.1 #=GS A0A3Q7HGA5_SOLLC/50-190 AC A0A3Q7HGA5.1 #=GS H3H865_PHYRM/30-162 AC H3H865.1 #=GS H3H7I3_PHYRM/74-190 AC H3H7I3.1 #=GS H3H4T3_PHYRM/256-393 AC H3H4T3.1 #=GS A0A1X7UKX5_AMPQE/42-163 AC A0A1X7UKX5.1 #=GS A0A1X7TYL0_AMPQE/28-159 AC A0A1X7TYL0.1 #=GS A0A1X7V236_AMPQE/30-175 AC A0A1X7V236.1 #=GS A0A1X7SHM3_AMPQE/59-197 AC A0A1X7SHM3.1 #=GS A0A1X7VJZ4_AMPQE/26-163 AC A0A1X7VJZ4.1 #=GS A0A1X7U495_AMPQE/58-195 AC A0A1X7U495.1 #=GS A0A1X7SX04_AMPQE/27-156 AC A0A1X7SX04.1 #=GS M4B777_HYAAE/28-150 AC M4B777.1 #=GS H3H572_PHYRM/51-187 AC H3H572.1 #=GS H3H7F9_PHYRM/48-184 AC H3H7F9.1 #=GS K7JW30_NASVI/49-187 AC K7JW30.1 #=GS K7JWT6_NASVI/101-239 AC K7JWT6.1 #=GS H9JTX7_BOMMO/22-158 AC H9JTX7.1 #=GS X1WUQ9_ACYPI/53-190 AC X1WUQ9.1 #=GS X1XSQ9_ACYPI/36-160 AC X1XSQ9.1 #=GS J9KWH3_ACYPI/52-189 AC J9KWH3.2 #=GS M1B1W5_SOLTU/38-180 AC M1B1W5.1 #=GS W1NQ11_AMBTC/80-222 AC W1NQ11.1 #=GS M2Q9R4_CERS8/111-253 AC M2Q9R4.1 #=GS F8PLK7_SERL3/29-165 AC F8PLK7.1 #=GS D0P4M1_PHYIT/31-154 AC D0P4M1.1 #=GS F6HMS3_VITVI/69-206 AC F6HMS3.1 K7MSY7_SOYBN/76-212 WRKKDNLLRGWIIGTLFEEALRLVV.GLDTTHAIW.TALKDSYAEDSQEYEF...TLHQQITYLRKEDDQ........SIGEHIRTFQGLCDNLAAIGKPVPDKE..KVFYLLTSLGHEYETFTKTMLK.....PPRPSYSELISQLQSHDQRRNWF K7JBR0_NASVI/56-192 WIRENAKAMFLISSAMEYPQLEGLL.VYTTVKEMW.DSLKLVYEQKSASNKL...MLTQRFHAYTMDPTD........TVIQHIAKVQNMAMQLLDLGENVSQVT..IMAKILASLTSKFNHFQTASDS.....VDPDRLEYLKERLIQEENRLSRE K7J7F1_NASVI/67-205 WIKNDAKARYLITAAMEPEQMVSLL.TCETSMEMW.DRLLTIHEQKSASHKL...LVSQRFHEYRMNPKD........TVVQHVSKVQNLASQLLDLGENIPDIV..VISKIIASLPTKYRHFRSAWSSVA...PERQTIEYLQERLVEEESYRDAE K7JBX1_NASVI/56-194 WVKEDAKAMFLISSAMETEQMENLL.VCETARNMW.ERLTSVHKMKSQTHKL...LMSQRFHEYRMDPND........TIVQHISKVQNLARQLIDIGENIPDLV..IMAKILASLPAKYRHFRTSWGVME...STRQTIELLQDRLIEEEAYKTAE J9KKF0_ACYPI/70-208 WTKADNKCQKIIVTSIENGPMQYLI.NCESAYQMW.EKLLSVYEQKSEVNLY...LLQQKFFSYVKIPTD........NISAHIFKLEKLANDLKLAGENISDDM..LITKMLMTLPNSYQHFYSAWGSMQ...SVNKKVNNLTGRLLLEEARLVHL X1WMG8_ACYPI/69-207 KGQIDNKAKKCIVTSLDEQPLQYIM.NCDTENGMW.NKLLSVYEQMSDTSIT...IVQQKFYRYTMDPKD........NIASHISKLENLSRQLKQLGEPISESM..LITTILMTLPDSYRHFYSAWDSMN...SANRTLEQLTTRLMVEETRQVQG X1XSG1_ACYPI/1016-1154 WKRADNKAQKYIVTSVDEQPLLFIM.NCETAKEMW.DKLLNIYEQKSATSIS...LLQEKFYGYVMDPVE........SMAGHISKLENLSKQLAQSREPISDSM..LMTKILMTLPDTYKHFYSAWDSMS...SENKTLTNFTSRLMVEESRQPQG K7JSP6_NASVI/56-194 YNISVSRVKTIILCSINQKLRCTLI.NCTSVTKMW.EKFNELYGDTSADAKQ...AAWKKLYAFHITEDK........TVRMHLERFESIVKKLEEVDKKPPKEA..IVSKLLNSLPEKFKLFTIAWKCTP...KDDRTQKTLIARLIKEDNRLAEK F4WZJ7_ACREC/51-189 WKKKDALARSLLSKSLDDAHFNLVV.ACKSSADMW.KTLVGHYDEVSNTTKL...AALEAYNDYHWKNDM........TVTSYISGLMLIENKLKAQKLNIEKEM..IITKIVRGLPQKFDNFKQVWRICP...TKDITVEQLQAKLLDVERDVNVT M5BUS0_THACB/75-214 WKKRDREAYAQITLNMEDEAMADVM.RTRTARDAW.KKVIERWEGKGVQSLS...FLYQQLTTAKIEEDE........DIATAFNNIRSLAKKMETLGEPISDLM..LAQMMMTALPPSYSVVTSVIQTTN..QASAVNPDMVQDTVLAEEERRRKG E2AMM3_CAMFO/51-188 WTTRDEKALALIVLSVSKAELGHIR.KATTSKQAW.DELAKIHSSKGPVRKA...VLYRQLYNLKKNPSE........PMSQYINNFQEKINLLEDAGIEIPSEL..QSIMLLNSLPEDYENFCVAIES....RDQIPTVEFIKGKLIEEEARRQGS E2A5G7_CAMFO/57-194 WITGDRKAKSDLILSMNPSELKQIK.GCETSKDVW.DKLESIYASKGPARKA...TLLKSLMLRKMPDDG........DVKDHLNDLFDAVDKLQSMNVEINGDM..LAVIILYSLPESYDTFRCAIES....RDDLPDVETLKIKIFEESEARKRK E2AJT1_CAMFO/8-145 WERNDQKARSDIILSISPSELKQVK.NCATSHDMW.VRLEEIYQSKGPARKA...TLLKRLTLQKMADNG........DIRIHLNDFFDSVDKLSDMGVDINEDL..LTILLLYSLPASFENFRCAIES....RDELPKPEALRVKIVEENDARKSE E1ZV45_CAMFO/58-195 WDIQDKKAKADIILSIKSSELKQIK.GCCTSREVW.LKLKSIYQSSGPARKA...TLLKQLTLHKMNDGG........DVRDHLRRFFDTIDKLSEMDVDINADL..LTIMLLYSLPLTFDNFRCAIES....RDELPSPETLRIKIIEEYDARKND T1HSX1_RHOPR/55-192 WVRNDSKATSDIILNISPPELKQIK.NCSTSRDVW.LKLQDIYQSKGPARKA...TLLKQLILQKMQEGE........DIREHLRKFFDAVDKLNDMEVTINPDL..LAILLIYSLPISFENFRCAIES....RDQLPDPESLRIKIIEESDARNNS F4WEW2_ACREC/61-198 WDDNDNKAMSDLILSIHPSELKQIK.GCTSSREIW.LRLEGIYQSKGPARKA...TLLKRLALQKMADGE........DVREHIRTFFDAVDKLTEMEVIINPDL..LAILLLYSLPSQYENFRCAIES....RDELPTPEALRIKIIEESDARKKD K7JMW1_NASVI/53-191 WNKSNDKARVRIGLSVEDDQLIHIR.SAKTAKEAW.SALKEYHQKATLTSKV...LLLKRLCRTVLGEDG........DMEAHITNFSKTVNLLVALGTDLADDL..LAAMLLGSLPESYDTLVTALESRP...EKDITSQSWLEEIRCERRAVLTI K7JZ52_NASVI/48-186 WIKKDNQARTIIILSMEDDQLLHIK.GTSTAREIW.LKLKHHHQRSTTLSKV...HLMRRPFNIKMSSDG........DVESHITEMLTMLNKLTVMGQELDDTL..KAALVLNSMPESYDVLTSTLRCQN...EKDFTLASVKGRLLDEYHRRKDV H3GVH0_PHYRM/36-172 TSSKEQQAHAAIVLSLNDSQLMHVV.TAKSAKEAW.DKLEKFHRAQDVANRL...WLKEKFSSFKYTTS.........SVSKHVTELEQLVLEMKSAGCEPSDED..VCATLLRSLPASYESLVQAFRM....SMTELKLTDLVGKSIAEEVRQKDS H3GKE9_PHYRM/34-170 STAKEQQAHAAIVLNLNDSQLMHVV.TSTTAKEAW.DTLKKFHKTQDMANRL...WLKEKFSAFKFTAS.........SVSKHVTELEKLVMEMKNAGCEPTEED..VCATMLRSLPSSYEALAQAFRM....SVSEFKLADLVSKLIAEEVRQKDS H3H8S0_PHYRM/58-195 YVKSSNIAFGLMLLHMDADYHHVVD.DCEEAWVAW.TRLKTLYGGSQKAGRI...YLKRQLFSMEMSEGG........NVLHHCNEVLNISAKLSSIGAKMEDED..VAICLLRSLPKSYENVVLNLEM....SSAELRSQDVVKVLTNEHIKRQGE I1R349_ORYGL/53-190 EKRKDRKALSLIQLHLSNDILQEVL.QEKTAAELW.LKLESICMSKDLTSKM...HIKMKLFLHKLQESG........SVLNHISVFKEIVADLVSMEVQFDDED..LGLLLLCSLPSSYANFRDTILL....SRDELTLAEVYEALQNREKMKGMV M7ZB77_TRIUA/364-501 WEELQLKAARTIRLFLSDQVIYHVM.DENSPKKIW.EKLESQFMSKTAMTKV...YLKQKLHGMRIQEGS........DLVEYMNAFNQVVTDLARLGATVDDED..MAILLLCSLPSSYDHLITTLTH....GKETIKNEDITAALLSYDMRKKNA J3N766_ORYBR/276-405 WEDLDQKALSAMQLSLSTDVLREVI.NETSVFSLW.KKLEALYMKKSLANKL...RLKKRLSTIRMAEGT........SIRSHLNEFNSLIIDLEKLDVKIDDED..KAILLVVSLPATFKHFKEIMIY............DLFKRVILLDQSPDLN A0A3Q7HGA5_SOLLC/50-190 WKEIDEQARSLIYLYLADEILRQVI.EEKTAKQVW.DKLEALHLENIRVNKL...LKKHCLYSLRMKKGTT.....TASVTSHINDFESIVTDLENLDEKIDDET..KALLLLRTLPCSYEDFVDEIVD....GKDAISFDEVKSSLLKISSTESSS H3H865_PHYRM/30-162 FREHE.......LLEIAEGKLTRAELTSQESEAAFDKKLEGHFKKKSLANKL...FLRRRFFTTMMDEGD........DVLEHINKLKTLAEQLDAVGAPVSEDD..LVITLLGSLSESYQFLITALES....RADSLSWELVTSRLLHEDMKRKEQ H3H7I3_PHYRM/74-190 FKRKSRKALAIICLAMEDSQLPLVR.SAKDAHDAW.SRLEGHFEKKSLANKL...FLRRRFFTTMMDEGD........DVLEHINKLKTLAEQLDAVGA..PSER.......VVPVPDH....GVGVES..............RLAVVGTRDVSAAA H3H4T3_PHYRM/256-393 FKRKSRKALAIICLAMEDSQLPLVR.SAKDAHDAW.SRLEGHFEKKSLANKL...FLRRRFFTTMMDEGD........DVLEHINKLKTLAEQLDAVGAPVSEDD..LVITLLGSLSESYQFLITALES....RADSLSWELVTSRLLHEDMKRKEQ A0A1X7UKX5_AMPQE/42-163 FKKWQEKTFSIVALAISPAQLNLIT.SYDKPKPAW.YALCEHFEKDTFANKL...LFKKQY....LKDGT........SIENHMNELKEIADRLAVLGVAVSEED..QVVTLLGSLPPSFHMPVTTFELVMNCYLTTFS................SH A0A1X7TYL0_AMPQE/28-159 FESRRDKAIAIIILSIEPSLLYLLGENPDDPVKVW.KALQDQFQRESWANKL...SLRRKLYSLKLREQD........SVQDHIKSMIEIFNELSIVGDAISEED..QVVHLLASLPDYFGVLVTAPES....NSEVPKMQLVTERLL.......GN A0A1X7V236_AMPQE/30-175 FMVRYNRALATIVLTVDPALLYLLG.EPDSPVTVW.EKLASEFQKMTWANKL...TLWKKLYSFRLKEGDSFRLKEGDSIHDHIKAMTEIFNELSVIGAEMTEED..RVVHLLASLPDSYSTLVTALEA....RPDVPKIDTVIEKLVYEEQKSNDR A0A1X7SHM3_AMPQE/59-197 YAARKDKALATIVLSVDPSLLYLVGADPDDPVIVW.NKLKEQFQKKSWVNRL...NLRRKLHSLKLNDSE........SVQEHIKTMMETFHELSVVGDAVEDDD..KVVFLLASLPHSYTTLVTALEA....SATVPEMDVVIEKLLHEERKHKER A0A1X7VJZ4_AMPQE/26-163 LAVCRDRALATIVLSLDPSLLYLIG.DPTDPAVAW.DKLYFYICRKTWANRL...TLRRRLHSLKLKEGQ........SAHNHVTNIIKTFNELPIVEDEFSNED..RVVYLLASLLDSFDELVTALEA....SSTVPEMETVIEHLLREEQKLKEK A0A1X7U495_AMPQE/58-195 YKSKKDKALATIVLSIEPSLLYIIG.EPDDPVVVW.QKLADQFQKKTWANKL...VLRRKLQSLKLKDGG........SVQQHIREMTETFNELSVMGVAMDDED..RVVQLLASLPESYSTIVTALEA....NEKVPSLEVVTERLLHEERKLNER A0A1X7SX04_AMPQE/27-156 FQTRKDRALATIILSIDPSLLYLVG.EPDDPVEVW.RLLSNHFQKKTWANRL...ALRCKLHSLRLEKGQ........SVQEHIKSMTEVFSELSVIGDNISDEDHVHVVYLLASLPESFDMLVTAFEA....NSDVPNLETVIKKL.......... M4B777_HYAAE/28-150 WKVNDMKAFANVCTMINPSLQSMVR.IAATTAESW.GILKSFFLRRSIHNRV...QRRRQLHKFKMQKGA........SVMDHFLKFDELGMSIQAIGDKVAHDE..RLVILLESLSDEYYQIIKIIENMR...................DIDLFQE H3H572_PHYRM/51-187 WLLNDMKALGLIAQGVAVEHHTKIR.SATSAIMAW.NTLRDFYNRTTMHNRV...TMTRRLHEFKMEGGV........TMAKHLDDFDELIVGLQTLGEPLDEAR..QLVILLSSLPTEYELICSIVEN.....AKDFTLIEVKEKLLKEYERLDKK H3H7F9_PHYRM/48-184 WLVNDAKALGIIAQGVELQHQTKIR.SATRAIQAW.GTLREFYNRTTLHNRV...TMTRRLHDFKMDDGT........SMAKHLDDFDELVVGLQTMGEPVDEAR..QLVVLLSSLPAEYEMITSIIEN.....AKDITLIEVKEKLLKEHERLEKK K7JW30_NASVI/49-187 WDDNDLKAINIIYCAIPNKQLKFVC.EETTAFEII.KNFDSMYMKESTALQI...VCRNKLEKLKLEKYS........DTATFFSDFEKAVNELKGAGAKINEKE..KLNYMLNTLPNQYSYIGDLIDTFS...EIEQTAKHVKNKIQIAEMKNGNE K7JWT6_NASVI/101-239 WKKKEIRAKNYIVNSMTNTQLELII.SEEIAKKMI.DKLDENYLIKSSAVKL...LCKRKLLDLKMEESE........NPTDFYNNFEKLVNELKNAGENVTKED..RLNYFLLALPESLSHIVDIVDALP...EKDKTVEFVKSKLELEFMKRNGD H9JTX7_BOMMO/22-158 .KTADAAAKALIVKCVPDKYLDIIK.DATTSYTML.ASLDKVFERKGIFTKL...HLRRKLLSLKLRDD.........KLEDYFMRFESLIREIENIDKKMDEED..KICYLLTGMSEKYNTVITAIETMS...ADKIDMEFVKARLLDEELKLNNK X1WUQ9_ACYPI/53-190 WNINDKKCMSLLVQCIADTHLEYV..RGKASKEAW.DCLAATFERKGIAGQL...YLRKRLLTLRLAEGD........PLEEHFVIFDSRVRQLKTSGAKLDELD..VVCNLLLTLPSSFDNVVTAIETLS...PDKLKIDFIKSRLLDDEEKCKNK X1XSQ9_ACYPI/36-160 LE..............SNSHLEYVR.EGTTAKQKW.DKLIATFERKGVSSRL...YLLKRLLTIKYNEEE........PIENYLIRFDDLVRQLKSAGGKIEEDF..LACLLLLSLPESYGIVVTAIETLS...NNSITVDFVKCRLMDEYLKRINS J9KWH3_ACYPI/52-189 FDKTDAKATNLIIQCTADTHVEYV..RGESAKEIW.NKLKTTFERKGTSSRL...YLLKKLITMKFDDNE........SMETHLSQFDDLLRQVRLSGGKLDDDL..IACMLLLTLPDSFNMVITAIETLS...SDKITLEFVKSRLLDEEIKRNSR M1B1W5_SOLTU/38-180 RKTRKSKAKACLFSAISSSIFTRIM.SLKSAKAIW.DYLKVEYEGDEMIRGMQVLNLIRDFEIQKMKETE........TIKDYSERLLNIANRVRLLGSVLNDSR..IVEKILVTVPERFEATINTLENTK..DLSKITFAELLNALQAHEQRRVMR W1NQ11_AMBTC/80-222 MLSKNAKAKYALICGLDRDIFKNIE.QASTAYDMW.KMLEVTHQGTSAMKETKIQIYSTQYENFKMKSDE........TIANMYTRFTTITNGLNSLGKVLTQKD..MVTKILRSLTKAYQGKVVAIQEAK..DLSTLPLEELIGSLMNHEIFMSAQ M2Q9R4_CERS8/111-253 WRKKEAKARDLLARLVPDSVLRRMKRNGDSVADMW.IWICSEFEDKTPLVQS...NMLERFQTTRCSEHG........DVSKHLDTLGEMVEELSAIGVEVSDQD..YCAQILKSVPSQYADFLSGMMNAGRLLGTFITPDQAIQYLKQEYERKRLP F8PLK7_SERL3/29-165 WSKKEYCAKNILGCMVSDLTLQQIL.HKDTVVEMW.DLIHQENKNKTKLIQA...ELQDKLAALHCPKKG........NMHTHIDKIRDMWEQLSAAGVYLTDKE..KALNMLRSLSSTCAIFVSQLSVSAHMNGKSINPETLIVNLLQEY.....D D0P4M1_PHYIT/31-154 ........TVFFMTTLSDEMVVAVN.NKRYAYEIF.EHLEKTYEPRSWGCLC...ALREQFVALKYQDGA........DMLTHINGLKTLAGRLSNQGKPVDDTE..KVDQLLSSLPRSGDSFKSHYYI..........QETLIAWISMETNVMAEA F6HMS3_VITVI/69-206 REEDELICRGHILNALSDKLYDPYT.NTYSAREIW.EALENKYKAEEEGTKK...FLISQYIDFKFFDEK........PLLPQIHELQVIVNKLKVLKIELLEAF..QVGAIVAKLPSSWKVYRKRILH....KSEDYSLEEIQKHLHIEEESRLRD #=GC seq_cons appp-pKAhuhIhhulsss.Lphlh.sspoutchW.p+Lcshapp+ohss+l...hLp++Lhsh+hp-ss........slppHlschpplsscLpshGspls--p..hsshLLtSLPpoYcphhsul-s.....spp.sh-plpp+LlpE-pcpppp //