# 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
//