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Query: 3s7x_A mol:protein length:267 Major capsid protein VP1, from PDB0516

Results of FFAS03 search in PDB0516
Master-slave alignment(slide right to see more) does not show gaps in the query sequence, use ali links to display alignment between query and templates.
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# Score Template Links and tools%idFirst GSHMGGVDVLAAVPLSEETEFKVELFVKPVIGNAEGTTPHYWSISSPLKTAEAANVTPDADTTVCYSLSQVAPPDIPNQVSECDMLIWELYRMETEVLVLPVLNAGILTTGGVGGIAGPQLYFWAVGGQPLDVLGLAPTEKYKGPAQYTVNPKTNGTVPHVYSSSETPKARVTNEKYSIESWVADPSRNDNCRYFGRMVGGAATPPVVSFSNNSTIPLLDENGIGILCLQGRLYITCADLLGVNKNRVHTGLSRFFRLHFRQRRVRNLast
1 -143.0003s7x_A mol:protein length:267 Major capsid protein VP1  ali model  100  1GSHMGGVDVLAAVPLSEETEFKVELFVKPVIGNAEGTTPHYWSISSPLKTAEAANVTPDADTTVCYSLSQVAPPDIPNQVSECDMLIWELYRMETEVLVLPVLNAGILTTGGVGGIAGPQLYFWAVGGQPLDVLGLAPTEKYKGPAQYTVNPKTNGTVPHVYSSSETPKARVTNEKYSIESWVADPSRNDNCRYFGRMVGGAATPPVVSFSNNSTIPLLDENGIGILCLQGRLYITCADLLGVNKNRVHTGLSRFFRLHFRQRRVRN 267
2 -130.0003s7v_A mol:protein length:277 Major capsid protein VP1  ali model follow..  71  1GSHMGGVEVLAAVPLSEETEFKVELFVKPVIGNTTAATPHYWSISSAIHDKESVEETPDADTTVCYSLAEIAPPDIPNQVSECDMKVWELYRMETELLVVPLVNALGNTNGVVHGLAGTQLYFWAVGGQPLDVVGVTPTDKYKGPTTYTINPP--GDPRTLHVYNSNTPKAKVTSEYSVESWAPDPSRNDNCRYFGRVVGGAATPPVVSYGNNSTIPLLDENGIGILCLQGRLYITCADMLGTANSRIHTPMARFFRLHFRQRRVKN 277
3 -124.0004x0y_A mol:protein length:272 Major capsid protein  ali model follow..  31  1GSHMGGVEVLE-VKTGVDSITEVECFLTPEMGDPD---EHLRGFSKSISISDTESDSPNKDMLPCYSVARIPLPNLNEDLTCGNILMWEAVTLKTEVIGVTTLMNATHDNGAAKPVQGTSFHFFSVGGEALELQGVVFNYRTTYPDGTIF---PKNATVQSQVMNTEHKAYLDKNKYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMSGSQQWRGLSRYFKVQLRKRRVKN 272
4 -124.0004poq_A mol:protein length:278 VP1  ali model follow..  32  1GSHMGGVEVLE-VRTGPDAITQIEAYLNPRMGNNNPT-DELYGYSADINVASSASDNPNATTLPTYSVAVIKLPMLNEDMTCDTLLMWEAVSVKTEVMGISSLVYIYGSSSGTIPVQGTTLHMFSVGGEPLELQGLVASSTTTYPTDMVTIK---NMKPVNQALDPNAKALLDKDGYPVEVWSPDPSKNENTRYYGSFTGGATTPPVMQFTNSVTTVLLDENGVGPLCKGDKLFLSAVDIVGISESQNWRGLPRYFNVTLRKRVVKN 275
5 -123.0003nxd_C mol:protein length:272 Major capsid protein VP1  ali model follow..  31  1GSHMGGVEVLE-VKTGVDSITEVECFLTPEMGDPD---EHLRGFSKSISISDTESDSPNRDMLPCYSVARIPLPNLNEDLTCGNILMWEAVTLKTEVIGVTSLGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTI---FPKNATVQSQVMNTEHKAYLDKNKYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMSGSQQWRGLSRYFKVQLRKRRVKN 272
6 -123.0004mbx_A mol:protein length:278 Major Capsid Protein VP1  ali model follow..  34  1GSHMGGVEVLE-VRTGPDAITQIEAYLNPRMGNNIPS-EDLYGYSNSINTAFSASDTPNKDTLPCYSVAVIKLPLLNEDMTCDTILMWEAVSVKTEVVGISSLVNIYGSSSGCVPVQGTTYHMFAVGGEPLELQGLVASSTATYPDDVVAIK---NMKPGNQGLDPKAKALLDKDGYPVEVWCPDPSKNENTRYYGSFTGGATTPPVMQFTNSVTTVLLDENGVGPLCKGDKLFLSCADIAGVSETQVWRGLPRYFNVTLRKRIVKN 275
7 -123.0004mj0_A mol:protein length:275 VP1 capsid protein  ali model follow..  32  1GSHMGGVEVLE-VKTGVDAITEVECFLNPEMGDPD---ENLRGFSLKLSAENDSSDSPERKMLPCYSTARIPLPNLNEDLTCGNLLMWEAVTVQTEVIGITSMSQKVHEHGGGKPIQGSNFHFFAVGGDPLEMQGVLMNYRTKYPDGTI---TPKNPTAQSQVMNTDHKAYLDKNNYPVECWVPDPSRNENTRYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSAADICGLSGTQQWRGLARYFKIRLRKRSVKN 272
8 -123.0003bwq_A mol:protein length:272 Capsid protein VP1  ali model follow..  32  1GSHMGGIEVLG-VKTGVDSFTEVECFLNPQMGNPD---EHQKGLSKSLAAEKQTDDSPDKEQLPCYSVARIPLPNINEDLTCGNILMWEAVTVKTEVIGVTAMLNKTHENGAGKPIQGSNFHFFAVGGEPLELQGVLANYRTKYPAQTVT---PKNATVDSQQMNTDHKAVLDKDNYPVECWVPDPSKNENTRYFGTYTGGENVPPVLHITNTATTVLLDEQGVGPLCKADSLYVSAVDICGLSGTQQWKGLPRYFKITLRKRSVKN 272
9 -123.0004pch_A mol:protein length:273 VP1  ali model follow..  43  1GSHMGGVEVLDTVPLTEDTQYKVEAVLLPNFGKAATT-GNFQSRGLPYTMS----DTLGPGAALCYSVAVINLPEIPDAMCEDTMIVWEAYRLETELLFAPQMASSQRANGTLAGIEGTQLYFWACGGGPLDVIGINPDPERLKVNEALEGP------GNSDVASLQALRKQVNAAFPVELWVADPTKNDNTRYFGRVVGGGVTPPVVSYGNQSTTPLIDENGVGILCTFGSVYLTSADMVGMNQRTVQAGYGRFFRVHCRQRRIKQ 273
10 -121.0004fmg_A mol:protein length:289 VP1  ali model follow..  32  1GSHMGGVEVLSVV-TGEDSITQIELYLNPRMGVNSPDTSNWYTYTYDLQPKGSSPDQPIKENLPAYSVARVSLPMLNEDITCDTLQMWEAISVKTEVVGISSLMKRVHDYGAGIPVSGVNYHMFAIGGEPLDLQGLVLDYQTQYPKTTNGGPLGRKMTPKNQGLDPQAKAKLDKDGYPIEVWCPDPSKNENSRYYGSIQTGSQTPTVLQFSNTLTTVLLDENGVGPLCKGDGLFISCADIVGFSGKMALHGLPRYFNVTLRKRWVKN 289
11 -119.0004pcg_A mol:protein length:276 VP1  ali model follow..  44  1GSHMGGVEVMETVPLSEDTIYKVEAILLPNFASGSNT-AVYQSRGAPYTF----TDTLDAGSSLCYTLAVVNLPEIPEALCDDTLLVWEAFRVETELIFTPQLGSYIRAQGTPAGVEGSQMYFWACGGSPLDVIGINPDPERMNVAAGLEGPSKEN---QPSVAGIKATRKQVTAAFPIEIWSADPTRNENCRYFGRIVGGSVTPPVVSFGNQSTTPLVDENGVGILCLFGAIYLTSADMLGMQQRSVQAAFGRFFRVHFRQRRVKH 276
12 -118.0004u5z_A mol:protein length:280 Structural protein VP1  ali model follow..  28  1GSHMGNIEVLNLV-TGPDSITTIELYLNTRMGQND-ESKDNYGYSEKVTVANSDQDKPTSGEIPTYSTARINLPMLNEDLTCNTLTMWEAVSVKTEVVGVSSLVNMYDDKGIGFPVEGMNFHMFAVGGEPLELQFLTGNYRTDYSANDKLV-VPPIKHQSTQGLNPHYKQKLTKDGFPVECWCPDPSKNENTRYYGSYTGGQSTPPVLQFTNTVTTVLLDENGVGPLCKGDGLYVSCCDIVGFDGDMQYRGLPRYFNILLRKRTVRN 280
13 -104.0003iys_A mol:protein length:343 Major capsid protein VP1  ali model follow..  31  22....GGIEVLD-VKSGPDSITTIEAYLQPRPGQK-------NGYSTVITVQEGYQDAPHSTEVPCYSCARIPLPTINDDITCPTLLMWEAVSVKTEVVGVSSILRAFNGYGGGFTICGPRIHFFSVGGEPLDLQACMQNSKTVYPAP-LIGPGEGERRETAQVLDTGYKARLDKDGYPIECWCPDPAKNENTRYYGNLTGGPETPPVLAFTNTTTTILLDENGVGPLCKGDGLFLSAADVAGTRGRQYWRGLPRYFSIQLRKRNVRN 288
14 -101.0001sva_1 mol:protein length:361 SIMIAN VIRUS 40  ali model follow..  31  30....GGIEVLG-VKTGVDSFTEVECFLNPQMGNPD---EHQKGLSKSLAAEKQTDDSPDKEQLPCYSVARIPLPNINEDLTCGNILMWEAVTVKTEVIGVTAMLNKTHENGAGKPIQGSNFHFFAVGGEPLELQGVLANYRTKYPAQTVT---PKNATVDSQQMNTDHKAVLDKDNYPVECWVPDPSKNENTRYFGTYTGGENVPPVLHITNTATTVLLDEQGVGPLCKADSLYVSAVDICGLSGTQQWKGLPRYFKITLRKRSVKN 297
15 -100.0005fua_1 mol:protein length:362 MAJOR CAPSID PROTEIN VP1  ali model follow..  31  31....GGVEVLE-VKTGVDAITEVECFLNPEMGDPD---ENLRGFSLKLSAENDSSDSPERKMLPCYSTARIPLPNLNEDLTCGNLLMWEAVTVQTEVIGITSMSQKVHEHGGGKPIQGSNFHFFAVGGEPLEMQGVLMNYRSKYPDGTI---TPKNPTAQSQVMNTDHKAYLDKNNYPVECWVPDPSRNENARYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSAADICGLSGTQQWRGLARYFKIRLRKRSVKN 298
16 -100.0001sid_A mol:protein length:383 POLYOMAVIRUS COAT PROTEIN VP1  ali model follow..  31  32....GGMEVLDLV-TGPDSVTEIEAFLNPRMGQPPTEGGQYYGWSRGINLATSTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKKKDMVNKDQVLNPISKAKLDKDGYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWYDVHHWRGLPRYFKITLRKRWVKN 317
FFAS is supported by the NIH grant R01-GM087218-01
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Selected papers from Godzik Lab
Ying Zhang, Ines Thiele, Dana Weekes, Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley Deacon, John Wooley, Scott Lesley, Ian Wilson, Bernhard Palsson, Andrei Osterman, Adam Godzik. Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima. Science. 2009 Sep 18;325(5947):1544-9.

Alexey M. Eroshkin, Andrew LeBlanc, Dana Weekes, Kai Post, Zhanwen Li, Akhil Rajput, Sal T. Butera, Dennis R. Burton, Adam Godzik. bNAber: database of broadly neutralizing HIV antibodies. Nucl. Acids Res. 2013; published on November 7, 2013.

Li W, Jaroszewski L, Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics. 2002 Jan;18(1):77-82.