modeller_usage

modeller_usage@salilab.org

1 participants
3147 discussions

[modeller] sequence mismatch error
by Yang, Li-Yen 29 Nov '23

29 Nov '23

Hello, I am trying to use the modeler comparative tool in Chimera to model the structure of a protein (in fasta format) by another similar protein’s structure (in pdb format). I first associated this sequence (in fasta) with the corresponding chain in the pdb, and I used the modeller comparative tool to model the structure. However, I’m getting this error: _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb : From the log window, I didn’t get any other details beyond the above error. Does anyone know how I can figure out what is going wrong? Thank you! I really appreciate it! Best, Zoey

2 2

DNA atoms changed by modeller
by Pedro Guillem 06 Nov '23

06 Nov '23

Hello all, I have a PDB with a small protein-DNA complex... I induce a point mutation in the protein and then save the mutated PDB. The DNA molecule remains untouched. I noticed my original pdb defines the first base (adenine) with 18 atoms - but the output modeller builds 21 atoms. The first 3 atoms are added. I believe the original input is missing the phosphate group. But I want modeller to leave the DNA alone the way it is. Is there a way to set modeller to leave some chains untouched in the output? Thanks in advance Pedro *MODIFIED BY MODELLER* *A* *TOM 1 P DA B 1 11.378 26.105 39.925 1.00 0.00 PATOM 2 OP1 DA B 1 11.702 25.899 40.057 1.00 0.00 OATOM 3 OP2 DA B 1 12.983 26.076 41.112 1.00 0.00 O* ATOM 4 O5' DA B 1 12.613 25.783 40.890 1.00 27.98 O ATOM 5 C5' DA B 1 13.939 25.889 40.375 1.00 25.91 C *ORIGINAL* CRYST1 45.400 56.200 130.800 90.00 90.00 90.00 C 2 2 21 ATOM 1 O5' DA B 1 12.613 25.783 40.890 1.00 27.98 O ATOM 2 C5' DA B 1 13.939 25.889 40.375 1.00 25.91 C ATOM 3 C4' DA B 1 14.898 24.947 41.083 1.00 26.90 C ATOM 4 O4' DA B 1 14.923 25.240 42.497 1.00 26.42 O ATOM 5 C3' DA B 1 14.466 23.490 40.907 1.00 27.31 C ATOM 6 O3' DA B 1 15.624 22.725 40.560 1.00 29.53 O ATOM 7 C2' DA B 1 13.955 23.125 42.294 1.00 25.13 C ATOM 8 C1' DA B 1 14.747 24.029 43.236 1.00 24.42 C ATOM 9 N9 DA B 1 14.020 24.367 44.474 1.00 21.51 N ATOM 10 C8 DA B 1 14.404 24.071 45.742 1.00 20.32 C ATOM 11 N7 DA B 1 13.590 24.502 46.649 1.00 21.20 N ATOM 12 C5 DA B 1 12.581 25.132 45.948 1.00 20.03 C ATOM 13 C6 DA B 1 11.424 25.786 46.361 1.00 20.34 C ATOM 14 N6 DA B 1 11.075 25.916 47.640 1.00 20.30 N ATOM 15 N1 DA B 1 10.641 26.293 45.396 1.00 21.27 N ATOM 16 C2 DA B 1 10.993 26.155 44.127 1.00 20.67 C ATOM 17 N3 DA B 1 12.054 25.563 43.615 1.00 21.50 N ATOM 18 C4 DA B 1 12.825 25.060 44.609 1.00 21.31 C

2 1

Making a heterotetramer model, while one of the chain is built by using two template
by rpw641＠sund.ku.dk 03 Nov '23

03 Nov '23

Dear Modeller users As the Subject said, I want to make a heterotetramer model, and make one of the chains by using two template. I know how to make heterotetramer model or build a single chain with multitemplate. The problem is that I don't know how to combine these two in my case. Thank you in advance Best Zhucheng

2 1

Missing residues - restrain crystal coordinates
by Isabel Elliott 18 Oct '23

18 Oct '23

Good afternoon, I am trying to model missing residues into my crystal structure following the method on the website: https://salilab.org/modeller/wiki/Missing_residues. I am also trying to restrain the crystal coordinates so that only missing residues move (and the rest of the original crystal coordinates remain the same) during refinement using the select_atoms method. However when I compare my final models produced by my script to my original crystal structure, I find that the side chains of several amino acids three of four amino acids away from the missing residues have been flipped. How can I ensure that only the missing residues are refined and the crystal coordinates remain the same? I am wondering if I’ve missed something important out of my script. See my script below. Many thanks. from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the AutoModel class log.verbose() # Create log file env = Environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] env.io.water = True # Only refine/move missing residues - restrain crystal coordinates class MyModel(LoopModel): #picks residues to be refined by loop modelling def select_loop_atoms(self): #refines residue ranges defined simultaneously return Selection(self.residue_range('5:A', '13:A'), self.residue_range('99:B', '105:B'), self.residue_range('251:D', '256:D')) # redefine the special_patches routine to include additional disulfides def special_patches(self,aln): self.patch(residue_type='DISU',residues=(self.residues['26:A'],self.residues['199:C'])) self.patch(residue_type='DISU',residues=(self.residues['29:A'],self.residues['201:C'])) a = MyModel(env, alnfile = 'alignment.ali', # alignment file knowns = 'xxx', # aa sequence of original template - crystal coordinates sequence = 'xxx_fill', # aa sequence of original template with missing residues filled in loop_assess_methods = (assess.DOPE, assess.DOPEHR, assess.GA341)) a.starting_model= 1 # Index of the first model a.ending_model = 1 # Index of the last model a.loop.starting_model = 1 # First loop refined model a.loop.ending_model = 10 # Last loop refined model a.loop.md_level = refine.fast # Loop model refinement level a.make() # Do modelling

3 7

Add Modeller to Spack
by Gabriel CRETIN 11 Oct '23

11 Oct '23

Hi, I am a French System. administrator and I just wanted to know it you would consider adding Modeller to the Spack package manager ? It is a very useful and flexible package managers that is used mostly in HPC Supercomputer environments. There are already 7000+ package recipes available and many worldwide HPC supercomputers use Spack. I believe it would be really useful for the scientific (and bioinformatics) community to have Modeller available too. Here are some useful links: Main homepage: https://spack.io/ Documentation: https://spack.readthedocs.io/en/latest/index.html Github: https://github.com/spack/spack Adding a recipe to build/compile a program such as Modeller would not be too complicated, it is just that one must adapt the actual Install script. As is, the installation of modeler via your Install script does not really fit into the “usual” ways of building softwares such as make, cmake, or for python packages pypi, setuptools, etc. Thank you in advance for considering the effort, Best regards, Gabriel Cretin -------------------- Gabriel Cretin Ingénieur d'études - Administrateur des systèmes d'information Inserm | Université Paris Cité | DSIMB UMR_S U1134 Site Broussais, Bâtiment Ady Steg 8 rue Maria Helena Vieira Da Silva | 75014 Paris Tél. 01 81 72 43 31 | Mob. 07 81 70 35 15 [signature_2765755402]

2 1

CONECT records writing mutated PDB
by Pedro Guillem 13 Sep '23

13 Sep '23

Hello there, I use Modeller to induce point mutations on a PDB. This part works very well (see code below). My problem is the protein has several disulfides defined by CONECT records in the template PDB. The output pdb is missing these records and they are required later. Since the atom count changes after several point mutations, it can not be done as easily, and doing it by hand is not an option. Is there a way to force Modeller to do so? or it lacks the code to recompute the sulfurs?. I read it does if the output file is a PSF, but not with PDB. Thanks in advance. Pedro mdl = model(env, file=pdb_file) aln = alignment(env) aln.append_model(mdl, atom_files=pdb_file, align_codes=pdb_file) for mutation in mutations: for pos, new_residue in mutation.items(): chain_id, res_id = pos.split(":") pointmut = f'{res_id}:{chain_id}' sel = selection(mdl.residues[pointmut]) sel.mutate(residue_type=self.res1to3[new_residue]) #mutate position aln.append_model(mdl, align_codes='mut') mdl.clear_topology() mdl.generate_topology(aln['mut']) mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl2 = model(env, file=pdb_file) mdl.res_num_from(mdl2,aln) mdl.write(file=output_file, model_format='PDB')

2 1

Re: to model heterodimer protein of mossing residue
by Arun Dhanasekaran 01 Sep '23

01 Sep '23

3 3

to model heterodimer protein of mossing residue
by Arun Dhanasekaran 31 Aug '23

31 Aug '23

i tried a build a homology model of a heterodimer protein,since it contains missing residue i have to model that. But i am only familiar with single chain homology modelling and fro multi chain i am getting many errors like in greeting ali flie. and from tutorial also i am not getting everything clearly. can i get a detailed explantiojn on multi chain modelling

3 4

generate a psf file
by sedmo.info＠gmail.com 08 Aug '23

08 Aug '23

Dear all, I have used modeller to generate a pdb file. unfortunately, the pdb file is not regular as the columns 10 and 11 interfere. What can I do? I can not use the pdb file to generate a psf file.

2 1

Homodimer modelling
by g.m.tuveri＠gmail.com 26 Jul '23

26 Jul '23

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:::: -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- 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-------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----------------GCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC NQDSCS-------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- 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