# STOCKHOLM 1.0 #=GF ID Retrotrans_gag #=GF AC PF03732.18 #=GF DE Retrotransposon gag protein #=GF AU Finn RD;0000-0001-8626-2148 #=GF SE Pfam-B_3194 (release 7.0) #=GF GA 23.20 23.20; #=GF TC 23.20 23.20; #=GF NC 23.10 23.10; #=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 11600699 #=GF RT Pyret, a Ty3/Gypsy retrotransposon in Magnaporthe grisea #=GF RT contains an extra domain between the nucleocapsid and protease #=GF RT domains. #=GF RA Nakayashiki H, Matsuo H, Chuma I, Ikeda K, Betsuyaku S, Kusaba #=GF RA M, Tosa Y, Mayama S; #=GF RL Nucleic Acids Res 2001;29:4106-4113. #=GF DR INTERPRO; IPR005162; #=GF DR SO; 0100021; polypeptide_conserved_region; #=GF CC Gag or Capsid-like proteins from LTR retrotransposons. There is #=GF CC a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae #=GF CC gag-proteins, but is poorly conserved [1]. #=GF SQ 55 #=GS Q9XE67_SORBI/155-252 AC Q9XE67.1 #=GS Q9XE85_SORBI/114-212 AC Q9XE85.1 #=GS Q9AYC2_ORYSJ/729-826 AC Q9AYC2.1 #=GS Q9AYB5_ORYSJ/567-664 AC Q9AYB5.1 #=GS Q9AYB6_ORYSJ/694-791 AC Q9AYB6.1 #=GS Q9AXC5_ANTHI/295-388 AC Q9AXC5.1 #=GS Q9AUY8_ARATH/31-127 AC Q9AUY8.1 #=GS Q9SK57_ARATH/214-310 AC Q9SK57.1 #=GS Q9M252_ARATH/163-260 AC Q9M252.1 #=GS Q9LZG5_ARATH/148-244 AC Q9LZG5.1 #=GS Q9M225_ARATH/186-282 AC Q9M225.1 #=GS Q9SY43_ARATH/188-284 AC Q9SY43.1 #=GS Q9ZS84_SOLLC/150-247 AC Q9ZS84.1 #=GS Q9SLQ0_ORYSI/194-290 AC Q9SLQ0.1 #=GS Q9LQH2_ARATH/476-575 AC Q9LQH2.1 #=GS Q9ZPF9_ARATH/97-196 AC Q9ZPF9.1 #=GS Q9SYE8_ARATH/131-230 AC Q9SYE8.1 #=GS O23529_ARATH/90-186 AC O23529.2 #=GS Q9FRJ2_ORYSJ/81-182 AC Q9FRJ2.1 #=GS Q9FGL3_ARATH/131-241 AC Q9FGL3.1 #=GS Q9XII7_ARATH/126-236 AC Q9XII7.1 #=GS Q9SIM3_ARATH/131-240 AC Q9SIM3.1 #=GS Q9FWB1_ARATH/104-198 AC Q9FWB1.1 #=GS O81471_ARATH/148-242 AC O81471.1 #=GS Q9SKF2_ARATH/107-197 AC Q9SKF2.1 #=GS Q9M0T9_ARATH/89-183 AC Q9M0T9.1 #=GS Q9FZN9_ARATH/121-215 AC Q9FZN9.1 #=GS Q9ZPG6_ARATH/97-191 AC Q9ZPG6.1 #=GS Q9MA68_ARATH/89-183 AC Q9MA68.1 #=GS Q96467_HORVU/82-176 AC Q96467.1 #=GS Q9LMV1_ARATH/257-344 AC Q9LMV1.1 #=GS Q9SJP0_ARATH/291-382 AC Q9SJP0.1 #=GS Q9SUN0_ARATH/223-313 AC Q9SUN0.1 #=GS O82608_ARATH/272-360 AC O82608.1 #=GS Q9LNM2_ARATH/83-178 AC Q9LNM2.1 #=GS Q9ZQQ3_ARATH/198-290 AC Q9ZQQ3.1 #=GS Q9ZUK1_ARATH/211-302 AC Q9ZUK1.1 #=GS Q9ZNW4_SORBI/210-302 AC Q9ZNW4.1 #=GS Q9ATX2_MAIZE/179-271 AC Q9ATX2.1 #=GS Q9AV68_ORYSJ/351-443 AC Q9AV68.1 #=GS Q9ARZ4_ORYSJ/100-192 AC Q9ARZ4.1 #=GS O48967_MAIZE/245-337 AC O48967.1 #=GS Q9HFY8_COLGL/148-252 AC Q9HFY8.1 #=GS Q9UVC2_PASFU/52-153 AC Q9UVC2.1 #=GS PEG10_MOUSE/174-267 AC Q7TN75.2 #=GS O93283_TAKRU/149-242 AC O93283.1 #=GS Q98SV9_TAKRU/117-207 AC Q98SV9.1 #=GS Q9C7H8_ARATH/150-242 AC Q9C7H8.1 #=GS Q9FYC9_ARATH/102-194 AC Q9FYC9.1 #=GS Q9SX87_ARATH/132-224 AC Q9SX87.1 #=GS Q9LP90_ARATH/163-253 AC Q9LP90.1 #=GS Q9SQW9_ARATH/264-354 AC Q9SQW9.1 #=GS Q9FWC7_ORYSJ/155-249 AC Q9FWC7.1 #=GS Q9FW76_ORYSJ/181-275 AC Q9FW76.1 #=GS Q9FE41_ORYSJ/775-871 AC Q9FE41.1 Q9XE67_SORBI/155-252 GVAAHQLTGAARAWWDSYSDTHENP...........GGITWAEFTEAFREQHVPEGVMDAKVEEFRNISQ.GTQKVQEYATRF.TRTMRYAPD..ESNTE...................KKKMYFFKKGLST Q9XE85_SORBI/114-212 LYASGQLQGAAQTWWESYQAARPNNA..........SPVTWLEFCRDFRARHINEGVMELKQEEFRSLRM.GSMTVAEYHDTF.EQLARYAPN..DVRED...................ADKQRLFMKGLYY Q9AYC2_ORYSJ/729-826 AFATHQLQGPASAWWDNHMATRPPG...........TEVTWVEFCRSFRKAQVPDGVMAQKKREFRALHQ.GNRTVTEYLHEF.NRLARYAPE..DVRTD...................AEKQEKFMAGLDD Q9AYB5_ORYSJ/567-664 SFASHQLLGPASEWWDHFRLNRITA...........EPITWLEFTAAFRKTHIPSGVVSLKKKEFRSLTQ.GSRSVTEYLHEF.NRLARYAPE..DLRND...................EERQEKFLGGLND Q9AYB6_ORYSJ/694-791 IFAAHQLQGPASLWWDHFQATQPEG...........QPITWARFTAAFRRTHVPAGVVALKKREFRELKQ.GNRSVMEYLHEF.NNLARYAPE..DVRED...................EEKQEKFLAGMDP Q9AXC5_ANTHI/295-388 NFAAFRLEDAARHWWRILDQRWKNDM..........TPRTWDNFVKEFYNKYIP.....QVRERILELIQ.WSNSVCEYESKF.TRLIQYAPH..YLEDE...................GRKARKFIEGLKL Q9AUY8_ARATH/31-127 DIAIHLLEGDAHNWWLAVDKRKGER............VETFKDFEDEFNRMYFPSEAWDRLESNFLDLVQ.GRRTVREYEEEF.NKLRRYVGR..ELEDE...................AVQVRRFLRGLRV Q9SK57_ARATH/214-310 DIAVHFLEGDAHNWWLTVEKRRGDE............VRSFADFEDEFNKKYFPPEAWDRLECAYLDLVQ.GNRTVREYDEEF.NRLRRYVGR..ELEEE...................QAQLRRFIRGLRI Q9M252_ARATH/163-260 DIIVHFLREEASHWWDGVLGNTPVQ...........HVIFWEDFREEFNRKFFPQEAMDSLEDDFEELRQ.DTKKVRENEREL.SHLSRFSVR..AGRGE...................QSMIRRLMRGLRP Q9LZG5_ARATH/148-244 DLASCYLRGEAQEWWERVKQREQVG...........CVDQWSFFKEEFTRRYLPEETIDDLEMKFLRLQQ.GTKTVRKYEKEF.HSLERFERR...KRGE...................HELIHKFISGLRV Q9M225_ARATH/186-282 DLAVHFLEEDAHLWWKSVTARRRQA............DMSWADFVVEFNAKYFLQDELDRMEVRFLELTL.VERSVWEYDREF.NRVLVYAGW..GMKDG...................QAELRRFMRGLRP Q9SY43_ARATH/188-284 DLTVHFLEGDAHLWWRSVTARRRQA............DMSWADFMAEFNAKYFPREALDRMEARFLELTQ.GVRSVREYDRKF.NRLLVYAGR..GMEDD...................QAQMRRFLRGLRP Q9ZS84_SOLLC/150-247 NITTMYLSGDAKLWWRTRNADDVSAGR........PRIDTWDKLIKEMRDQFLPSNASWLARDKLKRLRQ..TGSVREYIKEF.TSVMLDIQN....MSD...................EDKLHNFISGMQG Q9SLQ0_ORYSI/194-290 RAATSEFTDFASIWWSEFVRSNPNN...........TPQTWDAMKRVMRARFVPSYHARDLLHKLQQLRQ.GNKSVEEYYQAL.QIGMLRCG...LVEND...................DAGMARFMGGLNR Q9LQH2_ARATH/476-575 KVAPTEFQNYALSWWDQLVTTRRRAGD........YPIESWTQMKTIMRKRFVPSHYYRELHNRLRNLVQ.GNKSVEEYYKEM.ETLMLRAD...IQEDN...................EAIMSRFMGGLNR Q9ZPF9_ARATH/97-196 KVAATEFYDYALSWWDQVVTTKRRLGD........DSIETWNQLKNIMKRRFVPSHYHRELHQRLRNLVQ.GNRTVEEYFKEM.ETLMLRAD...VQEEC...................EATMSRFMGGLNR Q9SYE8_ARATH/131-230 KIAATKFYNYALSWWDQLVTSRRRTRD........YPIKTWNQLKFVMRKRFVPSYYHRELHQRLRNLVQ.GSKTVEEYFLEM.ETLMLRAD...LQEDG...................EAVMSRFMGGLNR O23529_ARATH/90-186 RLIFSALIGAISPPVQPLVSRATKA............SQIWKTLTNTYAKSSYD..HIKQLRTQIKQLKK.GTKTIDEYVLSH.TTLLDQLAILGKPMEH...................EEQVERILEGLPE Q9FRJ2_ORYSJ/81-182 RRADHCV....VNWLHNSIAKNVFDVVYK...PRASAFTVWSDIEGVFRDNAVQ..RSVYLETEFRSINQ.GDMTITQYTAKL.KQLADGLRDINMPVSE...................PSQVLNLLRGLNT Q9FGL3_ARATH/131-241 SMV........KSWILNSVTKQIYKSILR....FNDAAEIWKDLDTRFHITNLP..RSYQLTQQIWSLQQ.GNMSLSDYYTTL.KTLWDDLDGASCVNTCRNCKCCS.....ATASVNEHSKIVKFLAGLND Q9XII7_ARATH/126-236 SMV........KSWLLNSVSPQIYRSILR....MNDASDIWRDLNSRFNVTNLP.RTYNLTQE.IQDFRQ.GTLSLSEYYTRL.KTLWDQLD.....STEALDEPCTCGKAMRLQQKAEQAKIVKFLAGLNE Q9SIM3_ARATH/131-240 MVKSWLLNSVSPQIYRSILRLNDAT.............DIWRDLFDRFNLTNLP.RTYNLTQE.IQDLRQ.GTMSLSEYYTLL.KTLWDQLD.....STEALDDPCTCGKAVRLYQKAEKAKIMKFLAGLNE Q9FWB1_ARATH/104-198 KLFSFSLADKTHRLFKSMNPENLR...............SWEDYKAAFLTQYFTQSRTAIMRNEISSFQQTGTKSFHEAWERF.KVYYRECPH..HGFRY...................ATLINTFYMGVDK O81471_ARATH/148-242 KLFPYSLAGEAASWLKQLKAGSLK...............IWRSIKIAFLTNFYDDAKSEELRNKLSTFTQGPAEAFKAAWVRF.KEYQRDCPH..HSFSE...................VQLLGTFFRGVDW Q9SKF2_ARATH/107-197 RLFPFSLGDRARIWEKNLPQRSIT...............SWDQCKRAFLSKFFSTTRTARLRNEISSFTQRSNESFCEAWERF.KGYKMQCPH..HGFSK...................ESILKN....LAQ Q9M0T9_ARATH/89-183 RLFPFSLGDKAHIWEKNLPHDSII...............TWDDCKKAFLSKFFSNARTARLRNEISGFSQKTGESFCEAWERF.KGYTNQCPH..HGFTK...................ASMLSTLYRGVLP Q9FZN9_ARATH/121-215 RLFPFSLGDKAHQWEKSLLQGSIT...............SWNDCKKAFLAKFFSNSRTARLRNDISGFTQTNNETFCEAWERF.KGYQTQCPH..HGFSK...................ASLLSTLYRGVLP Q9ZPG6_ARATH/97-191 RLFPFSLGDKAHHWKKTLPPDSIT...............SWDDCKKDFLAKFFSNARTARLRNEISGFTQKNNETFFEASERF.KSYTTYCPH..HGFKK...................ASLLRTLYRGALP Q9MA68_ARATH/89-183 RLFPFSLGDEAHLWEKTLLVDSVD...............TWDDCKKAFLAKFFSNSRTARLRNEISGFNQKNSESFAEAWERF.KRYSTQCPH..HGFKK...................ASLLSTLYRGALP Q96467_HORVU/82-176 KLFPFSLRDRAKTWFSSLPKSSID...............SWDKCKDAYISKYFPPAKIISLRNDIMNFKQLDHEHVAQAWERM.KLMIRNCPA..NGLSL...................WMIIQIFYAGLNF Q9LMV1_ARATH/257-344 QIFIEHLTGPAHNWFSRLKPNSID...............SFHQLTSSFLKHYAPLIENQTSNADLWSISQGAKESLRSFVDRF.KLVVTNIT.....VPD...................EAAIVA....LRN Q9SJP0_ARATH/291-382 QLFVKHLSGAALTWFSRLEANSID...............SVHALTTSFLKNYGVFMEKGASNVDLWTMAQTAKESLRSFIGRF.KEIVTSVA.....TPD...................DAAIAALRNALWH Q9SUN0_ARATH/223-313 QLFVEGLTGNALTCFSRLEANSID...............NFTQLSTAFLKQYRVFIQPGASSSDLWSMTQENGETLNDYLGRF.KEILSSYHHG.RSRGK...................QARNDR.....RR O82608_ARATH/272-360 HLFVEHLKGPALNWFTRLKGNSVD...............SFQELSTLFLKQYSVLIDPSTSDADLWSLSQQPNEPLRDFLAKF.RSTLAKVE...GINDL...................AALST.....LKK Q9LNM2_ARATH/83-178 HLFVEHLKGPALDWFSRLEGNSVD...............SFHELSTLFLKQYSVLIDPDTSDADLWSLSQQPNEPLRDFLANQ.RRGGSLCSEESTVADK...................PQGEAARGRG.RG Q9ZQQ3_ARATH/198-290 KLFSENLCGQALMWFTQLEPGSIS...............NFNELSVVFLKQYSILMDKSISDTDLWNLSQGPNETLRAFITKF.KYVLSKLSR....ISQ...................QSALSALRKGLWY Q9ZUK1_ARATH/211-302 KLFSENLFGLALTWFTQLEEGSID...............NFKQLSTAFIKQYEYFINSDITEAHLWNFSQSADEPLRTY......IYRVQGNH..VNRPET.................IQDALHRATNWINA Q9ZNW4_SORBI/210-302 KSFVIAAEGDALAWYSMLRPGSIY...............SWENLRDKILANFQGFAVESLTSTDLFQCRQNQGEALREYFQRF.VQTKARAP....GVPK...................EVAIEAAIKGLRI Q9ATX2_MAIZE/179-271 KSFVMAVRSVAQTWYSSLRPGTIT...............SWQKLKDMLLTSFQGFQTKPVTAQALFQCTQDHEEYLQAYVRRF.LRLRAQAPT....VPN...................EIVIEAMIKGLRP Q9AV68_ORYSJ/351-443 NYLPVALADSARSWLHGLPRRTIG...............SWAELRDHFIANFQGTFERPGTQFDLYNIVQKSGESLRDYIRRF.SEQRNKISD....ITD...................DVIIAAFTKGIRH Q9ARZ4_ORYSJ/100-192 KVIHLTLDGIARSWYFNLPANSIY...............SWEQLRDVFVLNFRGTYEEPKTQQHLLGIRQRPGESIREYMRRF.SQARCQVQD....ITE...................ASVINAASAGLLE O48967_MAIZE/245-337 TYFHVALSGPARTWLMNLSPGSIY...............SWEELYARFVANFASAYQQHGVEAHLHAVRQEPRETLRMFISRF.TKVQGTIPR....ISD...................ASIITAFRQGVRD Q9HFY8_COLGL/148-252 VHAATFLRGRALAWFEPLQQEWLDNPVEKYSQEVRNIFFSFDGYVKALQSLFLDPDEKRQAERDLSNLRQ..NKSATLYAAEF.RRLAARLD.....MTD...................ESKVFAFYQGLKD Q9UVC2_PASFU/52-153 IFATTFLRGRAQHWVKPFLRKYLDSNGED...NADGVFKSYNHLKHAMKSVFGVSNEIATAVRVIQHLTQ..KTSTAEYAAKF.QEYAQLTD.....WDD...................EALQVMYRRGLKE PEG10_MOUSE/174-267 CFVTSMLIGRAARWATAKLQRCTYL............MHNYTAFMMELKHVFEDPQRREAAKRKIRRLRQ.GPGPVVDYSNAF.QMIAQDLD.....WTE...................PALMDQFQEGLNP O93283_TAKRU/149-242 GFITSLLADKALSWAIAAVDLDPRL............SSDYSAFRREFKAVFEHPTYGEDAASRLLALQQ.GSRSVAEYTLEF.RILAAESR.....WGE...................TALRSAYRRGLSE Q98SV9_TAKRU/117-207 AFVVNLLSGRAAQWATAVLENQTPA............SSSFPEFTAELKRVFDHPIQSGEAASQIRSLRQ.GSSSVADY...F.RILAARSG.....WND...................TALRGVFTQGLAE Q9C7H8_ARATH/150-242 KMVAIHFDSHAATWHHSFIQSGIGLD..........VFFNWPEYVKLLKDRFED.ACDDPMAE.LKKLQE..TDGIVEYHQQF.ELIKVRLN.....LSE...................EYLVSVYLAGLRT Q9FYC9_ARATH/102-194 DIASIHFDDIDATWHQSIVQSIMWRH..........VRHDWWNYKLLLQVRYNK..HVDDSIAKLKLLQE..TEGIEVYHARF.ESICTRVK.....LDE...................DFLVSLYLTGLKT Q9SX87_ARATH/132-224 SIASTLCDGAAAKWYKSLFESDFGVK..........LLSNWNMYKLLLEEHFAE..VLDDPISELKQLKE..TNGIEEYHKKF.ELLRARVN.....LSE...................DYLVRVYLDGLHP Q9LP90_ARATH/163-253 ALVSVSVSGEALSWYNWAISRGDFV..............SWLKLKSGLMLRFGNLKLRGPSQS.LFCIKQ..TGSVAEYVQRF.EDLSSQVG....GLDD...................QKLEGIFLNGLTG Q9SQW9_ARATH/264-354 EKAVSCLTGASVTWWRCSKDREQIY..............TWREFQEKFMLRFRP.SRGSSAVDHLLNVRQ..TGTVEEYRERF.EELTVDLPH....VTS...................DILESAFLNGLRR Q9FWC7_ORYSJ/155-249 SAVVLHMSGNAAQWYHSYKLVNEVN..............SWDQFRMAVATEFEG.VVEREKMSALDTLTQ..TGTVTEYKQQF.DYLVYQIR....VFDPSV...............GGKMLVTRFMNGLTE Q9FW76_ORYSJ/181-275 KIATLNFCGNAAFWLQSVRSQLAGA..............TWFELCDRVCGRFAR.DRKQALIRQWIHITQ..TSSVADYVDRF.DSIMHQLMAYGGSNDP...................AYFVTKFVDGLKD Q9FE41_ORYSJ/775-871 APAHVTAEGDPRQHARQHAPRGENP...........SIGNWATMKEVFKKHFVA.MKKDFSIVELSQVRQWRDEAIDDYVIRFRNSFVCLARE....MHL...................EDAIEMCVHGMQQ #=GC seq_cons plhshpLputAtpWapslhssshs...............oWpchpptFhppahs.tphsphpsclhslpQ.sscolpEYhpcF.cplhppsst....hsc...................pshlptahpGLpt //