Hello, I'm trying to add some missing domains to a big homodimeric protein, pdb 8em4. I predicted the missing structures with Alphafold and now I want to create an entire model of 8em4 using multiple templates. I am using the following directives: # Comparative modeling by the AutoModel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the AutoModel class
log.verbose() # request verbose output
class MyModel(AutoModel): def special_restraints(self,aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = Selection(self.chains['A']).only_atom_types('CA') s2 = Selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(Symmetry(s1, s2, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0)
env = Environ() # create a new MODELLER environment to build this model in
# directories for input atom files env.io.atom_files_directory = ['.']
a = MyModel(env, alnfile = 'ali_lrp2.ali', # alignment filename knowns = ("8em4","domain1","domain2","domain3"), # codes of the templates sequence = 'A0A6P5R9N9') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual comparative modeling
In ali_lrp2.ali I have aligned the entire lrp2 sequence with the known 8em4 sequence for the two monomers. Headers are the following: >P1;A0A6P5R9N9 sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00
>P1;8em4 structureX:8em4:28:A:4414:B::: 2.83:-1.00
I don't report the sequences, but for each of the headers I am separating the two monomers with a /, for example
>P1;A0A6P5R9N9 sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00 AAAAAAAAAAAAAAAAAAAA/ BBBBBBBBBBBBBBBBBBBB*
>P1;8em4 structureX:8em4:28:A:4414:B::: 2.83:-1.00 AAAAAA-----AAA-AAAAA/ BBBBBB-----BBB-BBBBB*
Then I add the missing domain template sequence in the following way: >P1;domain1 structureX:domain1::A::B:::: ------AAAAA---------/ ------BBBBB---------*
>P1;domain2 structureX:domain2::A::B:::: --------------A-----/ --------------B-----*
I keep obtaining knots, especially in the long domain. I made sure that the alignment is correct, but maybe the request of symmetry or the use of multiple templates are badly implemented. I attach the long alignment file
>P1;A0A6P5R9N9 sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00 MERGAAAAAAWMLLLAIAACLAPVSGQECGSGNFRCDNGYCIPASWRCDG TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE QQNCPGTTCSSQQLTCSNGQCVPIEYRCDHVSDCPDGSDERNCYYPTCDQ LTCANGACYNTSQKCDHKVDCRDSSDEANCTTLCSQKEFQCGSGECILRA YVCDHDNDCEDNSDEHNCNYDTCGGHQFTCSNGQCINQNWVCDGDDDCQD SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDENN ATSGRYCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD DCQIWGICDQKCENRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQSKVFS TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDTD EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA QHSTVFYSDLSKDIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW TDGGLKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSASRLYWVDAFFDKIEHSNLD GLDRKRLGHVDQMTHPFGLTVFEDNVFLTDWRLGAIIRVRKSDGGDMTVV RSGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC PYGMKLQRDQMTCEGDPAREPPTQQCGSFSFPCNNGKCVPSIFRCDGVDD CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ NCPTHSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW ECDGHPDCIQGSDEHNGCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC NQDSCSHFNGGCTHQCMQGPFGATCVCPIGYQLANDTKTCEDVNECDTPG FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLAVASRDKIVV DNITAHMHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLQGKTWSAFQNGT DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRKQVIASDLVLHHPHAL TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVHQPLGIIAIHPSRQP SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL MSVRENVIFGISLDPEVKSNDAMVPISGIHHGYDVEFDDSEQFIYWVENP GEIHRVKTDGSNRTVFAPLSLLGSSLGLALDWISKNIYYTTPASRSIEVL TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA KIASANMDGTSLKILFTGNMDHLEVVTLDIQEQKLYWAVTSRGVIERGNV DGTERMILVHHLAHPWGLAVHGSYLYYSDEQYEVIERVDKSSGSNKVVFR DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG FKLSPDGRSCSPYNSFMVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR KVFQASKQPGNTDPPTVIRDNINLLRDVTIFDEHVQPLSPAELNNNPCLQ SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL RSLHFDPQDHNLPFQAISVEGTAIALDYDRRNNRIFFTQKLNPIRGQISY VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVIVSTAFHSFGL TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA RCNQFQFTCLNGRCITQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC ANGRCVPYHYRCDFYNDCGDNSDEAGCLFRSCNSTTEFTCSNGRCIPLSY VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQFTCQNGQCITK LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK RTCVDIDECKESPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI EPYLIFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEKRLYWIDAE KQIIERMFLNKTNRETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS DLEGRQRRMLAQHCVDANNTFCFENPRGIVLHPQRGHVYWADWGDKAYIA RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFRCNNGRC IPQSWKCDVDNDCGDYSDEPTHECMTAAYNCDNHTEFSCKTNYRCIPQWA VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF ECKNHVCIQSFWICDGENDCVDGSDEEIHLCFNVPCESPQRFRCDNSRCI YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFKP STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQTIDYDWDPEGIG LSVVYYTVLAQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNDDRIYWS DSKEDVIESIKYDGTDRRLIINEAMKPFSLDIFEDQLFWVAKEKGEVWRQ NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP KCKCSSGYSGEYCEIGLSRGIPPGTTMAVLLTFVIVIIVGALVLVGFFHY RKTGSLLPSLPKLPSLSSLAKPSENGNGVTFRSGADVNMDIGVSPFGPET IIDRSMAMNEHFVMEVGKQPVIFENPMYAAKDSTSKVGLAVQGPSVSSQV TVSENVENQNYGRSVDPSEIVPEPKPASPGADETQGTKWNIFKRKPKQTT NFENPIYAEMDTEQKEAVAVAPPPSPSLPAKASKRSSTPGYTATEDTFKD TANLVKEDSDV/ MERGAAAAAAWMLLLAIAACLAPVSGQECGSGNFRCDNGYCIPASWRCDG TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE QQNCPGTTCSSQQLTCSNGQCVPIEYRCDHVSDCPDGSDERNCYYPTCDQ LTCANGACYNTSQKCDHKVDCRDSSDEANCTTLCSQKEFQCGSGECILRA YVCDHDNDCEDNSDEHNCNYDTCGGHQFTCSNGQCINQNWVCDGDDDCQD SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDENN ATSGRYCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD DCQIWGICDQKCENRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQSKVFS TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDTD EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA QHSTVFYSDLSKDIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW TDGGLKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSASRLYWVDAFFDKIEHSNLD GLDRKRLGHVDQMTHPFGLTVFEDNVFLTDWRLGAIIRVRKSDGGDMTVV RSGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC PYGMKLQRDQMTCEGDPAREPPTQQCGSFSFPCNNGKCVPSIFRCDGVDD CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ NCPTHSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW ECDGHPDCIQGSDEHNGCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC NQDSCSHFNGGCTHQCMQGPFGATCVCPIGYQLANDTKTCEDVNECDTPG FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLAVASRDKIVV DNITAHMHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLQGKTWSAFQNGT DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRKQVIASDLVLHHPHAL TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVHQPLGIIAIHPSRQP SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL MSVRENVIFGISLDPEVKSNDAMVPISGIHHGYDVEFDDSEQFIYWVENP GEIHRVKTDGSNRTVFAPLSLLGSSLGLALDWISKNIYYTTPASRSIEVL TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA KIASANMDGTSLKILFTGNMDHLEVVTLDIQEQKLYWAVTSRGVIERGNV DGTERMILVHHLAHPWGLAVHGSYLYYSDEQYEVIERVDKSSGSNKVVFR DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG FKLSPDGRSCSPYNSFMVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR KVFQASKQPGNTDPPTVIRDNINLLRDVTIFDEHVQPLSPAELNNNPCLQ SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL RSLHFDPQDHNLPFQAISVEGTAIALDYDRRNNRIFFTQKLNPIRGQISY VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVIVSTAFHSFGL TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA RCNQFQFTCLNGRCITQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC ANGRCVPYHYRCDFYNDCGDNSDEAGCLFRSCNSTTEFTCSNGRCIPLSY VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQFTCQNGQCITK LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK RTCVDIDECKESPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI EPYLIFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEKRLYWIDAE KQIIERMFLNKTNRETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS DLEGRQRRMLAQHCVDANNTFCFENPRGIVLHPQRGHVYWADWGDKAYIA RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFRCNNGRC IPQSWKCDVDNDCGDYSDEPTHECMTAAYNCDNHTEFSCKTNYRCIPQWA VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF ECKNHVCIQSFWICDGENDCVDGSDEEIHLCFNVPCESPQRFRCDNSRCI YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFKP STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQTIDYDWDPEGIG LSVVYYTVLAQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNDDRIYWS DSKEDVIESIKYDGTDRRLIINEAMKPFSLDIFEDQLFWVAKEKGEVWRQ NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP KCKCSSGYSGEYCEIGLSRGIPPGTTMAVLLTFVIVIIVGALVLVGFFHY RKTGSLLPSLPKLPSLSSLAKPSENGNGVTFRSGADVNMDIGVSPFGPET IIDRSMAMNEHFVMEVGKQPVIFENPMYAAKDSTSKVGLAVQGPSVSSQV TVSENVENQNYGRSVDPSEIVPEPKPASPGADETQGTKWNIFKRKPKQTT NFENPIYAEMDTEQKEAVAVAPPPSPSLPAKASKRSSTPGYTATEDTFKD TANLVKEDSDV*
>P1;8em4 structureX:8em4:28:A:4414:B:MOL_ID 1; MOLECULE LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN CHAIN A, B; SYNONYM LRP-2,GLYCOPROTEIN 330,GP330,MEGALIN:MOL_ID 1; ORGANISM_SCIENTIFIC MUS MUSCULUS; ORGANISM_COMMON HOUSE MOUSE; ORGANISM_TAXID 10090: 2.83:-1.00 ----------------------------CGSGNFRCDNGYCIPASWRCDG TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE QQNC---------------------------------------------- -------------------------------------------------- --------------------DTCGGHQFTCSNGQCINQNWVCDGDDDCQD SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDE-- -----YCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD DCQIWGICDQKCESRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQAKVFS TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDAD EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA QHSTIFYSDLSKNIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW TDGGSKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSTSRLYWVDAFFDKIEHSNLD GLDRKRLGHVDQMTHPFGLTVFKDNVFLTDWRLGAIIRVRKSDGGDMTVV RRGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC PYGMKLQRDQMTCEGDPAREPPTQQCGSSSFPCNNGKCVPSIFRCDGVDD CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ NCPTRSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW ECDGHPDCIQGSDEHNGCVPKT---------------------------- -------------------------------------------------- NQDSCLHFNGGCTHRCIQGPFGATCVCPIGYQLANDTKTCEDVNECDIPG FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLVVASRDKIIM DNITAHTHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLEGKTWSAFQNGT DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRRQVIASDLVLHHPHAL TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVPQPLGIIAIHPSRQP SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL ISVRENVIFGISLDPEVKSNDAMVPISGIQHGYDVEFDDSEQFIYWVENP GEIHRVKTDGSNRTAFAPLSLLGSSLGLALDWVSRNIYYTTPASRSIEVL TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA KIASANMDGTSLKILFTGNMEHLEVVTLDIQEQKLYWAVTSRGVIERGNV DGTERMILVHHLAHPWGLVVHGSFLYYSDEQYEVIERVDKSSGSNKVVFR DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG FKLSPDGRSCSPYNSFIVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR KVFQASKQPGNTDPPTVIRDSINLLRDVTIFDEHVQPLSPAELNNNPCLQ SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL RSLHFDPQDHNLPFQAISVEGMAIALDYDRRNNRIFFTQKLNPIRGQISY VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVVISTAFHSFGL TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA RCNQFQFTCLNGRCISQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC ANGRCVPYHYRCDFYNDCGDNSDEAGCLF--------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----------------------------------CRDDQFTCQNGQCITK LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK RTCVDIDECKETPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI EPYLVFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEERLYWIDAE KQIIERMFLNKTNQETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS DLEGRQRKMLAQHCVDANNTFCFENPRGIVLHPQRGYVYWADWGDHAYIA RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFKCNNGRC IPQSWKCDVDNDCGDYSDEPIHECMTAAYNCDNHTEFSCKTNYRCIPQWA VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF ECKNHVCIQSFWICDGENDCVDGSDEEIHLC------------------- -------------------------------------------------- -------------------------------------------CRPGFKP STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQAIDYDWDPEGIG LSVVYYTVLSQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNGDRIYWS DSKEDVIESIKYDGTDRRLIINDAMKPFSLDIFEDQLYWVAKEKGEVWRQ NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP KCKCSSGYSGEYCE------------------------------------ -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------/ ----------------------------CGSGNFRCDNGYCIPASWRCDG TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE QQNC---------------------------------------------- -------------------------------------------------- --------------------DTCGGHQFTCSNGQCINQNWVCDGDDDCQD SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDE-- -----YCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD DCQIWGICDQKCESRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQAKVFS TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDAD EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA QHSTIFYSDLSKNIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW TDGGSKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSTSRLYWVDAFFDKIEHSNLD GLDRKRLGHVDQMTHPFGLTVFKDNVFLTDWRLGAIIRVRKSDGGDMTVV RRGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC PYGMKLQRDQMTCEGDPAREPPTQQCGSSSFPCNNGKCVPSIFRCDGVDD CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ NCPTRSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW ECDGHPDCIQGSDEHNGCVPKT---------------------------- -------------------------------------------------- NQDSCLHFNGGCTHRCIQGPFGATCVCPIGYQLANDTKTCEDVNECDIPG FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLVVASRDKIIM DNITAHTHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLEGKTWSAFQNGT DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRRQVIASDLVLHHPHAL TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVPQPLGIIAIHPSRQP SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL ISVRENVIFGISLDPEVKSNDAMVPISGIQHGYDVEFDDSEQFIYWVENP GEIHRVKTDGSNRTAFAPLSLLGSSLGLALDWVSRNIYYTTPASRSIEVL TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA KIASANMDGTSLKILFTGNMEHLEVVTLDIQEQKLYWAVTSRGVIERGNV DGTERMILVHHLAHPWGLVVHGSFLYYSDEQYEVIERVDKSSGSNKVVFR DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG FKLSPDGRSCSPYNSFIVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR KVFQASKQPGNTDPPTVIRDSINLLRDVTIFDEHVQPLSPAELNNNPCLQ SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL RSLHFDPQDHNLPFQAISVEGMAIALDYDRRNNRIFFTQKLNPIRGQISY VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVVISTAFHSFGL TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA RCNQFQFTCLNGRCISQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC ANGRCVPYHYRCDFYNDCGDNSDEAGCLF--------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----------------------------------CRDDQFTCQNGQCITK LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK RTCVDIDECKETPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI EPYLVFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEERLYWIDAE KQIIERMFLNKTNQETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS DLEGRQRKMLAQHCVDANNTFCFENPRGIVLHPQRGYVYWADWGDHAYIA RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFKCNNGRC IPQSWKCDVDNDCGDYSDEPIHECMTAAYNCDNHTEFSCKTNYRCIPQWA VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF ECKNHVCIQSFWICDGENDCVDGSDEEIHLC------------------- -------------------------------------------------- -------------------------------------------CRPGFKP STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQAIDYDWDPEGIG LSVVYYTVLSQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNGDRIYWS DSKEDVIESIKYDGTDRRLIINDAMKPFSLDIFEDQLYWVAKEKGEVWRQ NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP KCKCSSGYSGEYCE------------------------------------ -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------*
>P1;cluster4_2c_now_3875-3998 structureX:cluster4_2c_now_3875-3998::A::B:::: -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- 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-------------------------------------------------- -------------------------------------------------- -------------------------EEIHLCFNVPCESPQRFRCDNSRCI YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFK- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------/ -------------------------------------------------- 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-------------------------EEIHLCFNVPCESPQRFRCDNSRCI YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFK- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------*
>P1;cluster3_2c_now_2773-3039 structureX:cluster3_2c_now_2773-3039::A::B:::: -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- 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-------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------------------EAGCLFRSCNSTTEFTCSNGRCIPLSY VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQF---------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- 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TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQF---------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- 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>P1;cluster2_2c_now_1266-1355 structureX:cluster2_2c_now_1266-1355::A::B:::: -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----------------GCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC NQDSCS-------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- 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-------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----------------GCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC NQDSCS-------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- 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Hi Alphafold Multimer may be able to predict the entire oligomer depending on the residues, thanks:)
On Tuesday, July 25, 2023, g.m.tuveri--- via modeller_usage < modeller_usage@salilab.org> wrote:
> Hello, I'm trying to add some missing domains to a big homodimeric > protein, pdb 8em4. I predicted the missing structures with Alphafold and > now I want to create an entire model of 8em4 using multiple templates. I am > using the following directives: > # Comparative modeling by the AutoModel class > from modeller import * # Load standard Modeller classes > from modeller.automodel import * # Load the AutoModel class > > log.verbose() # request verbose output > > class MyModel(AutoModel): > def special_restraints(self,aln): > # Constrain the A and B chains to be identical (but only restrain > # the C-alpha atoms, to reduce the number of interatomic distances > # that need to be calculated): > s1 = Selection(self.chains['A']).only_atom_types('CA') > s2 = Selection(self.chains['B']).only_atom_types('CA') > self.restraints.symmetry.append(Symmetry(s1, s2, 1.0)) > def user_after_single_model(self): > # Report on symmetry violations greater than 1A after building > # each model: > self.restraints.symmetry.report(1.0) > > env = Environ() # create a new MODELLER environment to build this model in > > # directories for input atom files > env.io.atom_files_directory = ['.'] > > a = MyModel(env, > alnfile = 'ali_lrp2.ali', # alignment filename > knowns = ("8em4","domain1","domain2","domain3"), # codes > of the templates > sequence = 'A0A6P5R9N9') # code of the target > a.starting_model= 1 # index of the first model > a.ending_model = 1 # index of the last model > # (determines how many models to > calculate) > a.make() # do the actual comparative modeling > > In ali_lrp2.ali I have aligned the entire lrp2 sequence with the known > 8em4 sequence for the two monomers. Headers are the following: > >P1;A0A6P5R9N9 > sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00 > > >P1;8em4 > structureX:8em4:28:A:4414:B::: 2.83:-1.00 > > I don't report the sequences, but for each of the headers I am separating > the two monomers with a /, for example > > >P1;A0A6P5R9N9 > sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00 > AAAAAAAAAAAAAAAAAAAA/ > BBBBBBBBBBBBBBBBBBBB* > > >P1;8em4 > structureX:8em4:28:A:4414:B::: 2.83:-1.00 > AAAAAA-----AAA-AAAAA/ > BBBBBB-----BBB-BBBBB* > > Then I add the missing domain template sequence in the following way: > >P1;domain1 > structureX:domain1::A::B:::: > ------AAAAA---------/ > ------BBBBB---------* > > >P1;domain2 > structureX:domain2::A::B:::: > --------------A-----/ > --------------B-----* > > I keep obtaining knots, especially in the long domain. I made sure that > the alignment is correct, but maybe the request of symmetry or the use of > multiple templates are badly implemented. > I attach the long alignment file > > >P1;A0A6P5R9N9 > sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00 > MERGAAAAAAWMLLLAIAACLAPVSGQECGSGNFRCDNGYCIPASWRCDG > TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE > QQNCPGTTCSSQQLTCSNGQCVPIEYRCDHVSDCPDGSDERNCYYPTCDQ > LTCANGACYNTSQKCDHKVDCRDSSDEANCTTLCSQKEFQCGSGECILRA > YVCDHDNDCEDNSDEHNCNYDTCGGHQFTCSNGQCINQNWVCDGDDDCQD > SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDENN > ATSGRYCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD > DCQIWGICDQKCENRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN > GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQSKVFS > TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ > RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD > LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL > VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV > YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDTD > EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA > QHSTVFYSDLSKDIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW > TDGGLKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK > IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSASRLYWVDAFFDKIEHSNLD > GLDRKRLGHVDQMTHPFGLTVFEDNVFLTDWRLGAIIRVRKSDGGDMTVV > RSGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC > PYGMKLQRDQMTCEGDPAREPPTQQCGSFSFPCNNGKCVPSIFRCDGVDD > CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ > NCPTHSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT > CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS > SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW > ECDGHPDCIQGSDEHNGCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD > MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC > NQDSCSHFNGGCTHQCMQGPFGATCVCPIGYQLANDTKTCEDVNECDTPG > FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLAVASRDKIVV > DNITAHMHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLQGKTWSAFQNGT > DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS > KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY > WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRKQVIASDLVLHHPHAL > TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVHQPLGIIAIHPSRQP > SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL > MSVRENVIFGISLDPEVKSNDAMVPISGIHHGYDVEFDDSEQFIYWVENP > GEIHRVKTDGSNRTVFAPLSLLGSSLGLALDWISKNIYYTTPASRSIEVL > TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA > KIASANMDGTSLKILFTGNMDHLEVVTLDIQEQKLYWAVTSRGVIERGNV > DGTERMILVHHLAHPWGLAVHGSYLYYSDEQYEVIERVDKSSGSNKVVFR > DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG > FKLSPDGRSCSPYNSFMVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL > HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR > GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD > PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI > YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR > KVFQASKQPGNTDPPTVIRDNINLLRDVTIFDEHVQPLSPAELNNNPCLQ > SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL > RSLHFDPQDHNLPFQAISVEGTAIALDYDRRNNRIFFTQKLNPIRGQISY > VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS > NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT > SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVIVSTAFHSFGL > TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ > QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA > RCNQFQFTCLNGRCITQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC > ANGRCVPYHYRCDFYNDCGDNSDEAGCLFRSCNSTTEFTCSNGRCIPLSY > VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC > GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD > TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN > CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE > FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQFTCQNGQCITK > LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV > DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK > RTCVDIDECKESPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI > EPYLIFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEKRLYWIDAE > KQIIERMFLNKTNRETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS > DLEGRQRRMLAQHCVDANNTFCFENPRGIVLHPQRGHVYWADWGDKAYIA > RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH > HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT > THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF > QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL > CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN > EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFRCNNGRC > IPQSWKCDVDNDCGDYSDEPTHECMTAAYNCDNHTEFSCKTNYRCIPQWA > VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD > NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT > CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF > ECKNHVCIQSFWICDGENDCVDGSDEEIHLCFNVPCESPQRFRCDNSRCI > YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC > DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFKP > STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC > AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQTIDYDWDPEGIG > LSVVYYTVLAQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL > AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG > LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNDDRIYWS > DSKEDVIESIKYDGTDRRLIINEAMKPFSLDIFEDQLFWVAKEKGEVWRQ > NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG > GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP > KCKCSSGYSGEYCEIGLSRGIPPGTTMAVLLTFVIVIIVGALVLVGFFHY > RKTGSLLPSLPKLPSLSSLAKPSENGNGVTFRSGADVNMDIGVSPFGPET > IIDRSMAMNEHFVMEVGKQPVIFENPMYAAKDSTSKVGLAVQGPSVSSQV > TVSENVENQNYGRSVDPSEIVPEPKPASPGADETQGTKWNIFKRKPKQTT > NFENPIYAEMDTEQKEAVAVAPPPSPSLPAKASKRSSTPGYTATEDTFKD > TANLVKEDSDV/ > MERGAAAAAAWMLLLAIAACLAPVSGQECGSGNFRCDNGYCIPASWRCDG > TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE > QQNCPGTTCSSQQLTCSNGQCVPIEYRCDHVSDCPDGSDERNCYYPTCDQ > LTCANGACYNTSQKCDHKVDCRDSSDEANCTTLCSQKEFQCGSGECILRA > YVCDHDNDCEDNSDEHNCNYDTCGGHQFTCSNGQCINQNWVCDGDDDCQD > SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDENN > ATSGRYCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD > DCQIWGICDQKCENRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN > GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQSKVFS > TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ > RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD > LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL > VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV > YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDTD > EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA > QHSTVFYSDLSKDIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW > TDGGLKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK > IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSASRLYWVDAFFDKIEHSNLD > GLDRKRLGHVDQMTHPFGLTVFEDNVFLTDWRLGAIIRVRKSDGGDMTVV > RSGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC > PYGMKLQRDQMTCEGDPAREPPTQQCGSFSFPCNNGKCVPSIFRCDGVDD > CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ > NCPTHSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT > CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS > SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW > ECDGHPDCIQGSDEHNGCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD > MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC > NQDSCSHFNGGCTHQCMQGPFGATCVCPIGYQLANDTKTCEDVNECDTPG > FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLAVASRDKIVV > DNITAHMHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLQGKTWSAFQNGT > DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS > KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY > WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRKQVIASDLVLHHPHAL > TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVHQPLGIIAIHPSRQP > SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL > MSVRENVIFGISLDPEVKSNDAMVPISGIHHGYDVEFDDSEQFIYWVENP > GEIHRVKTDGSNRTVFAPLSLLGSSLGLALDWISKNIYYTTPASRSIEVL > TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA > KIASANMDGTSLKILFTGNMDHLEVVTLDIQEQKLYWAVTSRGVIERGNV > DGTERMILVHHLAHPWGLAVHGSYLYYSDEQYEVIERVDKSSGSNKVVFR > DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG > FKLSPDGRSCSPYNSFMVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL > HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR > GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD > PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI > YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR > KVFQASKQPGNTDPPTVIRDNINLLRDVTIFDEHVQPLSPAELNNNPCLQ > SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL > RSLHFDPQDHNLPFQAISVEGTAIALDYDRRNNRIFFTQKLNPIRGQISY > VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS > NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT > SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVIVSTAFHSFGL > TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ > QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA > RCNQFQFTCLNGRCITQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC > ANGRCVPYHYRCDFYNDCGDNSDEAGCLFRSCNSTTEFTCSNGRCIPLSY > VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC > GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD > TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN > CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE > FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQFTCQNGQCITK > LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV > DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK > RTCVDIDECKESPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI > EPYLIFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEKRLYWIDAE > KQIIERMFLNKTNRETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS > DLEGRQRRMLAQHCVDANNTFCFENPRGIVLHPQRGHVYWADWGDKAYIA > RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH > HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT > THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF > QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL > CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN > EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFRCNNGRC > IPQSWKCDVDNDCGDYSDEPTHECMTAAYNCDNHTEFSCKTNYRCIPQWA > VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD > NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT > CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF > ECKNHVCIQSFWICDGENDCVDGSDEEIHLCFNVPCESPQRFRCDNSRCI > YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC > DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFKP > STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC > AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQTIDYDWDPEGIG > LSVVYYTVLAQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL > AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG > LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNDDRIYWS > DSKEDVIESIKYDGTDRRLIINEAMKPFSLDIFEDQLFWVAKEKGEVWRQ > NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG > GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP > KCKCSSGYSGEYCEIGLSRGIPPGTTMAVLLTFVIVIIVGALVLVGFFHY > RKTGSLLPSLPKLPSLSSLAKPSENGNGVTFRSGADVNMDIGVSPFGPET > IIDRSMAMNEHFVMEVGKQPVIFENPMYAAKDSTSKVGLAVQGPSVSSQV > TVSENVENQNYGRSVDPSEIVPEPKPASPGADETQGTKWNIFKRKPKQTT > NFENPIYAEMDTEQKEAVAVAPPPSPSLPAKASKRSSTPGYTATEDTFKD > TANLVKEDSDV* > > >P1;8em4 > structureX:8em4:28:A:4414:B:MOL_ID 1; MOLECULE LOW-DENSITY LIPOPROTEIN > RECEPTOR-RELATED PROTEIN CHAIN A, B; SYNONYM LRP-2,GLYCOPROTEIN > 330,GP330,MEGALIN:MOL_ID 1; ORGANISM_SCIENTIFIC MUS MUSCULUS; > ORGANISM_COMMON HOUSE MOUSE; ORGANISM_TAXID 10090: 2.83:-1.00 > ----------------------------CGSGNFRCDNGYCIPASWRCDG > TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE > QQNC---------------------------------------------- > -------------------------------------------------- > --------------------DTCGGHQFTCSNGQCINQNWVCDGDDDCQD > SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDE-- > -----YCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD > DCQIWGICDQKCESRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN > GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQAKVFS > TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ > RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD > LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL > VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV > YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDAD > EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA > QHSTIFYSDLSKNIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW > TDGGSKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK > IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSTSRLYWVDAFFDKIEHSNLD > GLDRKRLGHVDQMTHPFGLTVFKDNVFLTDWRLGAIIRVRKSDGGDMTVV > RRGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC > PYGMKLQRDQMTCEGDPAREPPTQQCGSSSFPCNNGKCVPSIFRCDGVDD > CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ > NCPTRSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT > CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS > SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW > ECDGHPDCIQGSDEHNGCVPKT---------------------------- > -------------------------------------------------- > NQDSCLHFNGGCTHRCIQGPFGATCVCPIGYQLANDTKTCEDVNECDIPG > FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLVVASRDKIIM > DNITAHTHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLEGKTWSAFQNGT > DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS > KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY > WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRRQVIASDLVLHHPHAL > TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVPQPLGIIAIHPSRQP > SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL > ISVRENVIFGISLDPEVKSNDAMVPISGIQHGYDVEFDDSEQFIYWVENP > GEIHRVKTDGSNRTAFAPLSLLGSSLGLALDWVSRNIYYTTPASRSIEVL > TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA > KIASANMDGTSLKILFTGNMEHLEVVTLDIQEQKLYWAVTSRGVIERGNV > DGTERMILVHHLAHPWGLVVHGSFLYYSDEQYEVIERVDKSSGSNKVVFR > DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG > FKLSPDGRSCSPYNSFIVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL > HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR > GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD > PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI > YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR > KVFQASKQPGNTDPPTVIRDSINLLRDVTIFDEHVQPLSPAELNNNPCLQ > SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL > RSLHFDPQDHNLPFQAISVEGMAIALDYDRRNNRIFFTQKLNPIRGQISY > VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS > NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT > SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVVISTAFHSFGL > TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ > QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA > RCNQFQFTCLNGRCISQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC > ANGRCVPYHYRCDFYNDCGDNSDEAGCLF--------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > ----------------------------------CRDDQFTCQNGQCITK > LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV > DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK > RTCVDIDECKETPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI > EPYLVFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEERLYWIDAE > KQIIERMFLNKTNQETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS > DLEGRQRKMLAQHCVDANNTFCFENPRGIVLHPQRGYVYWADWGDHAYIA > RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH > HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT > THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF > QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL > CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN > EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFKCNNGRC > IPQSWKCDVDNDCGDYSDEPIHECMTAAYNCDNHTEFSCKTNYRCIPQWA > VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD > NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT > CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF > ECKNHVCIQSFWICDGENDCVDGSDEEIHLC------------------- > -------------------------------------------------- > -------------------------------------------CRPGFKP > STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC > AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQAIDYDWDPEGIG > LSVVYYTVLSQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL > AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG > LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNGDRIYWS > DSKEDVIESIKYDGTDRRLIINDAMKPFSLDIFEDQLYWVAKEKGEVWRQ > NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG > GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP > KCKCSSGYSGEYCE------------------------------------ > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -----------/ > ----------------------------CGSGNFRCDNGYCIPASWRCDG > TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE > QQNC---------------------------------------------- > -------------------------------------------------- > --------------------DTCGGHQFTCSNGQCINQNWVCDGDDDCQD > SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDE-- > -----YCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD > DCQIWGICDQKCESRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN > GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQAKVFS > TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ > RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD > LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL > VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV > YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDAD > EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA > QHSTIFYSDLSKNIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW > TDGGSKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK > IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSTSRLYWVDAFFDKIEHSNLD > GLDRKRLGHVDQMTHPFGLTVFKDNVFLTDWRLGAIIRVRKSDGGDMTVV > RRGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC > PYGMKLQRDQMTCEGDPAREPPTQQCGSSSFPCNNGKCVPSIFRCDGVDD > CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ > NCPTRSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT > CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS > SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW > ECDGHPDCIQGSDEHNGCVPKT---------------------------- > -------------------------------------------------- > NQDSCLHFNGGCTHRCIQGPFGATCVCPIGYQLANDTKTCEDVNECDIPG > FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLVVASRDKIIM > DNITAHTHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLEGKTWSAFQNGT > DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS > KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY > WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRRQVIASDLVLHHPHAL > TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVPQPLGIIAIHPSRQP > SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL > ISVRENVIFGISLDPEVKSNDAMVPISGIQHGYDVEFDDSEQFIYWVENP > GEIHRVKTDGSNRTAFAPLSLLGSSLGLALDWVSRNIYYTTPASRSIEVL > TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA > KIASANMDGTSLKILFTGNMEHLEVVTLDIQEQKLYWAVTSRGVIERGNV > DGTERMILVHHLAHPWGLVVHGSFLYYSDEQYEVIERVDKSSGSNKVVFR > DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG > FKLSPDGRSCSPYNSFIVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL > HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR > GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD > PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI > YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR > KVFQASKQPGNTDPPTVIRDSINLLRDVTIFDEHVQPLSPAELNNNPCLQ > SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL > RSLHFDPQDHNLPFQAISVEGMAIALDYDRRNNRIFFTQKLNPIRGQISY > VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS > NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT > SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVVISTAFHSFGL > TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ > QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA > RCNQFQFTCLNGRCISQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC > ANGRCVPYHYRCDFYNDCGDNSDEAGCLF--------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > ----------------------------------CRDDQFTCQNGQCITK > LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV > DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK > RTCVDIDECKETPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI > EPYLVFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEERLYWIDAE > KQIIERMFLNKTNQETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS > DLEGRQRKMLAQHCVDANNTFCFENPRGIVLHPQRGYVYWADWGDHAYIA > RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH > HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT > THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF > QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL > CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN > EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFKCNNGRC > IPQSWKCDVDNDCGDYSDEPIHECMTAAYNCDNHTEFSCKTNYRCIPQWA > VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD > NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT > CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF > ECKNHVCIQSFWICDGENDCVDGSDEEIHLC------------------- > -------------------------------------------------- > -------------------------------------------CRPGFKP > STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC > AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQAIDYDWDPEGIG > LSVVYYTVLSQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL > AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG > LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNGDRIYWS > DSKEDVIESIKYDGTDRRLIINDAMKPFSLDIFEDQLYWVAKEKGEVWRQ > NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG > GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP > KCKCSSGYSGEYCE------------------------------------ > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -----------* > > >P1;cluster4_2c_now_3875-3998 > structureX:cluster4_2c_now_3875-3998::A::B:::: > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > 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-------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------EEIHLCFNVPCESPQRFRCDNSRCI > YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC > DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFK- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > 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-------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------EEIHLCFNVPCESPQRFRCDNSRCI > YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC > DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFK- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -----------* > > >P1;cluster3_2c_now_2773-3039 > structureX:cluster3_2c_now_2773-3039::A::B:::: > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > 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-------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -----------------------EAGCLFRSCNSTTEFTCSNGRCIPLSY > VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC > GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD > TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN > CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE > FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQF---------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > 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-------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -----------------------EAGCLFRSCNSTTEFTCSNGRCIPLSY > VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC > GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD > TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN > CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE > FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQF---------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -----------* > > >P1;cluster2_2c_now_1266-1355 > structureX:cluster2_2c_now_1266-1355::A::B:::: > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > ----------------GCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD > MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC > NQDSCS-------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > 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-------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > ----------------GCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD > MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC > NQDSCS-------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > 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-------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -------------------------------------------------- > -----------* > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/ >
* on the number of residues
On Tuesday, July 25, 2023, Joel Subach mjsubach@alumni.ncsu.edu wrote:
> Hi Alphafold Multimer may be able to predict the entire oligomer depending > on the residues, thanks:) > > On Tuesday, July 25, 2023* , g.m.tuveri--- via modeller_usage < > modeller_usage@salilab.org> wrote: > >> Hello, I'm trying to add some missing domains to a big homodimeric >> protein, pdb 8em4. I predicted the missing structures with Alphafold and >> now I want to create an entire model of 8em4 using multiple templates. I am >> using the following directives: >> # Comparative modeling by the AutoModel class >> from modeller import * # Load standard Modeller classes >> from modeller.automodel import * # Load the AutoModel class >> >> log.verbose() # request verbose output >> >> class MyModel(AutoModel): >> def special_restraints(self,aln): >> # Constrain the A and B chains to be identical (but only restrain >> # the C-alpha atoms, to reduce the number of interatomic distances >> # that need to be calculated): >> s1 = Selection(self.chains['A']).only_atom_types('CA') >> s2 = Selection(self.chains['B']).only_atom_types('CA') >> self.restraints.symmetry.append(Symmetry(s1, s2, 1.0)) >> def user_after_single_model(self): >> # Report on symmetry violations greater than 1A after building >> # each model: >> self.restraints.symmetry.report(1.0) >> >> env = Environ() # create a new MODELLER environment to build this model >> in >> >> # directories for input atom files >> env.io.atom_files_directory = ['.'] >> >> a = MyModel(env, >> alnfile = 'ali_lrp2.ali', # alignment filename >> knowns = ("8em4","domain1","domain2","domain3"), # codes >> of the templates >> sequence = 'A0A6P5R9N9') # code of the target >> a.starting_model= 1 # index of the first model >> a.ending_model = 1 # index of the last model >> # (determines how many models to >> calculate) >> a.make() # do the actual comparative modeling >> >> In ali_lrp2.ali I have aligned the entire lrp2 sequence with the known >> 8em4 sequence for the two monomers. Headers are the following: >> >P1;A0A6P5R9N9 >> sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00 >> >> >P1;8em4 >> structureX:8em4:28:A:4414:B::: 2.83:-1.00 >> >> I don't report the sequences, but for each of the headers I am separating >> the two monomers with a /, for example >> >> >P1;A0A6P5R9N9 >> sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00 >> AAAAAAAAAAAAAAAAAAAA/ >> BBBBBBBBBBBBBBBBBBBB* >> >> >P1;8em4 >> structureX:8em4:28:A:4414:B::: 2.83:-1.00 >> AAAAAA-----AAA-AAAAA/ >> BBBBBB-----BBB-BBBBB* >> >> Then I add the missing domain template sequence in the following way: >> >P1;domain1 >> structureX:domain1::A::B:::: >> ------AAAAA---------/ >> ------BBBBB---------* >> >> >P1;domain2 >> structureX:domain2::A::B:::: >> --------------A-----/ >> --------------B-----* >> >> I keep obtaining knots, especially in the long domain. I made sure that >> the alignment is correct, but maybe the request of symmetry or the use of >> multiple templates are badly implemented. >> I attach the long alignment file >> >> >P1;A0A6P5R9N9 >> sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00 >> MERGAAAAAAWMLLLAIAACLAPVSGQECGSGNFRCDNGYCIPASWRCDG >> TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE >> QQNCPGTTCSSQQLTCSNGQCVPIEYRCDHVSDCPDGSDERNCYYPTCDQ >> LTCANGACYNTSQKCDHKVDCRDSSDEANCTTLCSQKEFQCGSGECILRA >> YVCDHDNDCEDNSDEHNCNYDTCGGHQFTCSNGQCINQNWVCDGDDDCQD >> SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDENN >> ATSGRYCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD >> DCQIWGICDQKCENRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN >> GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQSKVFS >> TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ >> RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD >> LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL >> VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV >> YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDTD >> EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA >> QHSTVFYSDLSKDIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW >> TDGGLKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK >> IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSASRLYWVDAFFDKIEHSNLD >> GLDRKRLGHVDQMTHPFGLTVFEDNVFLTDWRLGAIIRVRKSDGGDMTVV >> RSGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC >> PYGMKLQRDQMTCEGDPAREPPTQQCGSFSFPCNNGKCVPSIFRCDGVDD >> CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ >> NCPTHSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT >> CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS >> SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW >> ECDGHPDCIQGSDEHNGCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD >> MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC >> NQDSCSHFNGGCTHQCMQGPFGATCVCPIGYQLANDTKTCEDVNECDTPG >> FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLAVASRDKIVV >> DNITAHMHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLQGKTWSAFQNGT >> DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS >> KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY >> WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRKQVIASDLVLHHPHAL >> TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVHQPLGIIAIHPSRQP >> SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL >> MSVRENVIFGISLDPEVKSNDAMVPISGIHHGYDVEFDDSEQFIYWVENP >> GEIHRVKTDGSNRTVFAPLSLLGSSLGLALDWISKNIYYTTPASRSIEVL >> TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA >> KIASANMDGTSLKILFTGNMDHLEVVTLDIQEQKLYWAVTSRGVIERGNV >> DGTERMILVHHLAHPWGLAVHGSYLYYSDEQYEVIERVDKSSGSNKVVFR >> DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG >> FKLSPDGRSCSPYNSFMVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL >> HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR >> GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD >> PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI >> YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR >> KVFQASKQPGNTDPPTVIRDNINLLRDVTIFDEHVQPLSPAELNNNPCLQ >> SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL >> RSLHFDPQDHNLPFQAISVEGTAIALDYDRRNNRIFFTQKLNPIRGQISY >> VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS >> NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT >> SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVIVSTAFHSFGL >> TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ >> QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA >> RCNQFQFTCLNGRCITQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC >> ANGRCVPYHYRCDFYNDCGDNSDEAGCLFRSCNSTTEFTCSNGRCIPLSY >> VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC >> GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD >> TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN >> CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE >> FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQFTCQNGQCITK >> LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV >> DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK >> RTCVDIDECKESPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI >> EPYLIFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEKRLYWIDAE >> KQIIERMFLNKTNRETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS >> DLEGRQRRMLAQHCVDANNTFCFENPRGIVLHPQRGHVYWADWGDKAYIA >> RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH >> HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT >> THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF >> QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL >> CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN >> EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFRCNNGRC >> IPQSWKCDVDNDCGDYSDEPTHECMTAAYNCDNHTEFSCKTNYRCIPQWA >> VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD >> NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT >> CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF >> ECKNHVCIQSFWICDGENDCVDGSDEEIHLCFNVPCESPQRFRCDNSRCI >> YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC >> DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFKP >> STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC >> AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQTIDYDWDPEGIG >> LSVVYYTVLAQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL >> AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG >> LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNDDRIYWS >> DSKEDVIESIKYDGTDRRLIINEAMKPFSLDIFEDQLFWVAKEKGEVWRQ >> NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG >> GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP >> KCKCSSGYSGEYCEIGLSRGIPPGTTMAVLLTFVIVIIVGALVLVGFFHY >> RKTGSLLPSLPKLPSLSSLAKPSENGNGVTFRSGADVNMDIGVSPFGPET >> IIDRSMAMNEHFVMEVGKQPVIFENPMYAAKDSTSKVGLAVQGPSVSSQV >> TVSENVENQNYGRSVDPSEIVPEPKPASPGADETQGTKWNIFKRKPKQTT >> NFENPIYAEMDTEQKEAVAVAPPPSPSLPAKASKRSSTPGYTATEDTFKD >> TANLVKEDSDV/ >> MERGAAAAAAWMLLLAIAACLAPVSGQECGSGNFRCDNGYCIPASWRCDG >> TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE >> QQNCPGTTCSSQQLTCSNGQCVPIEYRCDHVSDCPDGSDERNCYYPTCDQ >> LTCANGACYNTSQKCDHKVDCRDSSDEANCTTLCSQKEFQCGSGECILRA >> YVCDHDNDCEDNSDEHNCNYDTCGGHQFTCSNGQCINQNWVCDGDDDCQD >> SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDENN >> ATSGRYCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD >> DCQIWGICDQKCENRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN >> GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQSKVFS >> TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ >> RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD >> LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL >> VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV >> YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDTD >> EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA >> QHSTVFYSDLSKDIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW >> TDGGLKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK >> IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSASRLYWVDAFFDKIEHSNLD >> GLDRKRLGHVDQMTHPFGLTVFEDNVFLTDWRLGAIIRVRKSDGGDMTVV >> RSGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC >> PYGMKLQRDQMTCEGDPAREPPTQQCGSFSFPCNNGKCVPSIFRCDGVDD >> CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ >> NCPTHSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT >> CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS >> SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW >> ECDGHPDCIQGSDEHNGCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD >> MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC >> NQDSCSHFNGGCTHQCMQGPFGATCVCPIGYQLANDTKTCEDVNECDTPG >> FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLAVASRDKIVV >> DNITAHMHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLQGKTWSAFQNGT >> DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS >> KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY >> WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRKQVIASDLVLHHPHAL >> TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVHQPLGIIAIHPSRQP >> SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL >> MSVRENVIFGISLDPEVKSNDAMVPISGIHHGYDVEFDDSEQFIYWVENP >> GEIHRVKTDGSNRTVFAPLSLLGSSLGLALDWISKNIYYTTPASRSIEVL >> TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA >> KIASANMDGTSLKILFTGNMDHLEVVTLDIQEQKLYWAVTSRGVIERGNV >> DGTERMILVHHLAHPWGLAVHGSYLYYSDEQYEVIERVDKSSGSNKVVFR >> DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG >> FKLSPDGRSCSPYNSFMVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL >> HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR >> GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD >> PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI >> YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR >> KVFQASKQPGNTDPPTVIRDNINLLRDVTIFDEHVQPLSPAELNNNPCLQ >> SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL >> RSLHFDPQDHNLPFQAISVEGTAIALDYDRRNNRIFFTQKLNPIRGQISY >> VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS >> NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT >> SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVIVSTAFHSFGL >> TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ >> QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA >> RCNQFQFTCLNGRCITQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC >> ANGRCVPYHYRCDFYNDCGDNSDEAGCLFRSCNSTTEFTCSNGRCIPLSY >> VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC >> GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD >> TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN >> CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE >> FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQFTCQNGQCITK >> LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV >> DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK >> RTCVDIDECKESPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI >> EPYLIFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEKRLYWIDAE >> KQIIERMFLNKTNRETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS >> DLEGRQRRMLAQHCVDANNTFCFENPRGIVLHPQRGHVYWADWGDKAYIA >> RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH >> HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT >> THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF >> QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL >> CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN >> EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFRCNNGRC >> IPQSWKCDVDNDCGDYSDEPTHECMTAAYNCDNHTEFSCKTNYRCIPQWA >> VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD >> NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT >> CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF >> ECKNHVCIQSFWICDGENDCVDGSDEEIHLCFNVPCESPQRFRCDNSRCI >> YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC >> DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFKP >> STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC >> AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQTIDYDWDPEGIG >> LSVVYYTVLAQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL >> AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG >> LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNDDRIYWS >> DSKEDVIESIKYDGTDRRLIINEAMKPFSLDIFEDQLFWVAKEKGEVWRQ >> NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG >> GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP >> KCKCSSGYSGEYCEIGLSRGIPPGTTMAVLLTFVIVIIVGALVLVGFFHY >> RKTGSLLPSLPKLPSLSSLAKPSENGNGVTFRSGADVNMDIGVSPFGPET >> IIDRSMAMNEHFVMEVGKQPVIFENPMYAAKDSTSKVGLAVQGPSVSSQV >> TVSENVENQNYGRSVDPSEIVPEPKPASPGADETQGTKWNIFKRKPKQTT >> NFENPIYAEMDTEQKEAVAVAPPPSPSLPAKASKRSSTPGYTATEDTFKD >> TANLVKEDSDV* >> >> >P1;8em4 >> structureX:8em4:28:A:4414:B:MOL_ID 1; MOLECULE LOW-DENSITY LIPOPROTEIN >> RECEPTOR-RELATED PROTEIN CHAIN A, B; SYNONYM LRP-2,GLYCOPROTEIN >> 330,GP330,MEGALIN:MOL_ID 1; ORGANISM_SCIENTIFIC MUS MUSCULUS; >> ORGANISM_COMMON HOUSE MOUSE; ORGANISM_TAXID 10090: 2.83:-1.00 >> ----------------------------CGSGNFRCDNGYCIPASWRCDG >> TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE >> QQNC---------------------------------------------- >> -------------------------------------------------- >> --------------------DTCGGHQFTCSNGQCINQNWVCDGDDDCQD >> SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDE-- >> -----YCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD >> DCQIWGICDQKCESRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN >> GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQAKVFS >> TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ >> RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD >> LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL >> VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV >> YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDAD >> EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA >> QHSTIFYSDLSKNIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW >> TDGGSKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK >> IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSTSRLYWVDAFFDKIEHSNLD >> GLDRKRLGHVDQMTHPFGLTVFKDNVFLTDWRLGAIIRVRKSDGGDMTVV >> RRGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC >> PYGMKLQRDQMTCEGDPAREPPTQQCGSSSFPCNNGKCVPSIFRCDGVDD >> CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ >> NCPTRSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT >> CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS >> SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW >> ECDGHPDCIQGSDEHNGCVPKT---------------------------- >> -------------------------------------------------- >> NQDSCLHFNGGCTHRCIQGPFGATCVCPIGYQLANDTKTCEDVNECDIPG >> FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLVVASRDKIIM >> DNITAHTHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLEGKTWSAFQNGT >> DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS >> KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY >> WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRRQVIASDLVLHHPHAL >> TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVPQPLGIIAIHPSRQP >> SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL >> ISVRENVIFGISLDPEVKSNDAMVPISGIQHGYDVEFDDSEQFIYWVENP >> GEIHRVKTDGSNRTAFAPLSLLGSSLGLALDWVSRNIYYTTPASRSIEVL >> TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA >> KIASANMDGTSLKILFTGNMEHLEVVTLDIQEQKLYWAVTSRGVIERGNV >> DGTERMILVHHLAHPWGLVVHGSFLYYSDEQYEVIERVDKSSGSNKVVFR >> DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG >> FKLSPDGRSCSPYNSFIVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL >> HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR >> GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD >> PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI >> YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR >> KVFQASKQPGNTDPPTVIRDSINLLRDVTIFDEHVQPLSPAELNNNPCLQ >> SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL >> RSLHFDPQDHNLPFQAISVEGMAIALDYDRRNNRIFFTQKLNPIRGQISY >> VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS >> NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT >> SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVVISTAFHSFGL >> TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ >> QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA >> RCNQFQFTCLNGRCISQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC >> ANGRCVPYHYRCDFYNDCGDNSDEAGCLF--------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> ----------------------------------CRDDQFTCQNGQCITK >> LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV >> DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK >> RTCVDIDECKETPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI >> EPYLVFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEERLYWIDAE >> KQIIERMFLNKTNQETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS >> DLEGRQRKMLAQHCVDANNTFCFENPRGIVLHPQRGYVYWADWGDHAYIA >> RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH >> HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT >> THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF >> QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL >> CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN >> EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFKCNNGRC >> IPQSWKCDVDNDCGDYSDEPIHECMTAAYNCDNHTEFSCKTNYRCIPQWA >> VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD >> NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT >> CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF >> ECKNHVCIQSFWICDGENDCVDGSDEEIHLC------------------- >> -------------------------------------------------- >> -------------------------------------------CRPGFKP >> STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC >> AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQAIDYDWDPEGIG >> LSVVYYTVLSQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL >> AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG >> LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNGDRIYWS >> DSKEDVIESIKYDGTDRRLIINDAMKPFSLDIFEDQLYWVAKEKGEVWRQ >> NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG >> GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP >> KCKCSSGYSGEYCE------------------------------------ >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -----------/ >> ----------------------------CGSGNFRCDNGYCIPASWRCDG >> TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE >> QQNC---------------------------------------------- >> -------------------------------------------------- >> --------------------DTCGGHQFTCSNGQCINQNWVCDGDDDCQD >> SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDE-- >> -----YCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD >> DCQIWGICDQKCESRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN >> GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQAKVFS >> TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ >> RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD >> LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL >> VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV >> YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDAD >> EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA >> QHSTIFYSDLSKNIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW >> TDGGSKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK >> IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSTSRLYWVDAFFDKIEHSNLD >> GLDRKRLGHVDQMTHPFGLTVFKDNVFLTDWRLGAIIRVRKSDGGDMTVV >> RRGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC >> PYGMKLQRDQMTCEGDPAREPPTQQCGSSSFPCNNGKCVPSIFRCDGVDD >> CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ >> NCPTRSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT >> CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS >> SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW >> ECDGHPDCIQGSDEHNGCVPKT---------------------------- >> -------------------------------------------------- >> NQDSCLHFNGGCTHRCIQGPFGATCVCPIGYQLANDTKTCEDVNECDIPG >> FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLVVASRDKIIM >> DNITAHTHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLEGKTWSAFQNGT >> DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS >> KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY >> WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRRQVIASDLVLHHPHAL >> TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVPQPLGIIAIHPSRQP >> SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL >> ISVRENVIFGISLDPEVKSNDAMVPISGIQHGYDVEFDDSEQFIYWVENP >> GEIHRVKTDGSNRTAFAPLSLLGSSLGLALDWVSRNIYYTTPASRSIEVL >> TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA >> KIASANMDGTSLKILFTGNMEHLEVVTLDIQEQKLYWAVTSRGVIERGNV >> DGTERMILVHHLAHPWGLVVHGSFLYYSDEQYEVIERVDKSSGSNKVVFR >> DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG >> FKLSPDGRSCSPYNSFIVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL >> HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR >> GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD >> PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI >> YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR >> KVFQASKQPGNTDPPTVIRDSINLLRDVTIFDEHVQPLSPAELNNNPCLQ >> SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL >> RSLHFDPQDHNLPFQAISVEGMAIALDYDRRNNRIFFTQKLNPIRGQISY >> VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS >> NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT >> SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVVISTAFHSFGL >> TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ >> QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA >> RCNQFQFTCLNGRCISQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC >> ANGRCVPYHYRCDFYNDCGDNSDEAGCLF--------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> ----------------------------------CRDDQFTCQNGQCITK >> LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV >> DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK >> RTCVDIDECKETPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI >> EPYLVFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEERLYWIDAE >> KQIIERMFLNKTNQETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS >> DLEGRQRKMLAQHCVDANNTFCFENPRGIVLHPQRGYVYWADWGDHAYIA >> RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH >> HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT >> THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF >> QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL >> CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN >> EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFKCNNGRC >> IPQSWKCDVDNDCGDYSDEPIHECMTAAYNCDNHTEFSCKTNYRCIPQWA >> VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD >> NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT >> CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF >> ECKNHVCIQSFWICDGENDCVDGSDEEIHLC------------------- >> -------------------------------------------------- >> -------------------------------------------CRPGFKP >> STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC >> AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQAIDYDWDPEGIG >> LSVVYYTVLSQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL >> AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG >> LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNGDRIYWS >> DSKEDVIESIKYDGTDRRLIINDAMKPFSLDIFEDQLYWVAKEKGEVWRQ >> NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG >> GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP >> KCKCSSGYSGEYCE------------------------------------ >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -----------* >> >> >P1;cluster4_2c_now_3875-3998 >> structureX:cluster4_2c_now_3875-3998::A::B:::: >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> 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-------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -----------* >> >> >P1;cluster3_2c_now_2773-3039 >> structureX:cluster3_2c_now_2773-3039::A::B:::: >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> 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CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE >> FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQF---------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> 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VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC >> GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD >> TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN >> CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE >> FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQF---------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> 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-------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> ----------------GCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD >> MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC >> NQDSCS-------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> 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-------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -------------------------------------------------- >> -----------* >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage@salilab.org >> https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/ >> >
On 7/25/23 6:52 AM, g.m.tuveri--- via modeller_usage wrote: > Hello, I'm trying to add some missing domains to a big homodimeric > protein, pdb 8em4. I predicted the missing structures with Alphafold > and now I want to create an entire model of 8em4 using multiple > templates. ... > I keep obtaining knots, especially in the long domain.
I suggest you look at the initial model (file with a .ini extension, which by default is a regular PDB file). This is filled in by copying coordinates from the templates, so if your templates are in different orientations (or you have large insertions, which will be constructed in extended chain conformation) you may have atoms on top of each other, and the optimizer will likely be unable to recover. If this is the case, try structurally aligning your templates beforehand or providing your own initial model (https://salilab.org/modeller/10.4/manual/node27.html)
Ben Webb, Modeller Caretaker
participants (3)
-
g.m.tuveri＠gmail.com -
Joel Subach -
Modeller Caretaker