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Query: 3s7x_A mol:protein length:267 Major capsid protein VP1, from PDB0312

Results of FFAS03 search in PDB0312
Master-slave alignment 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 -146.0003s7x_A mol:protein length:267 Major capsid protein VP1  ali model  100  1GSHMGGVDVLAAVPLSEETEFKVELFVKPVIGNAEGTTPHYWSISSPLKTAEAANVTPDADTTVCYSLSQVAPPDIPNQVSECDMLIWELYRMETEVLVLPVLNAGILTTGGVGGIAGPQLYFWAVGGQPLDVLGLAPTEKYKGPAQYTVNPKTNGTVPHVYSSSETPKARVTNEKYSIESWVADPSRNDNCRYFGRMVGGAATPPVVSFSNNSTIPLLDENGIGILCLQGRLYITCADLLGVNKNRVHTGLSRFFRLHFRQRRVRN 267
2 -129.0003s7v_A mol:protein length:277 Major capsid protein VP1  ali model follow..  71  1GSHMGGVEVLAAVPLSEETEFKVELFVKPVIGNTTAATPHYWSISSAIHDKESVEETPDADTTVCYSLAEIAPPDIPNQVSECDMKVWELYRMETELLVVPLVNALGNTNGVVHGLAGTQLYFWAVGGQPLDVVGVTPTDKYKGPTTYTINPP--GDPRTLHVYNSNTPKAKVTSEYSVESWAPDPSRNDNCRYFGRVVGGAATPPVVSYGNNSTIPLLDENGIGILCLQGRLYITCADMLGTANSRIHTPMARFFRLHFRQRRVKN 277
3 -126.0003nxd_C mol:protein length:272 Major capsid protein VP1  ali model follow..  31  1GSHMGGVEVLE-VKTGVDSITEVECFLTPEMGDPDE---HLRGFSKSISISDTESDSPNRDMLPCYSVARIPLPNLNEDLTCGNILMWEAVTLKTEVIGVTSLGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPK---NATVQSQVMNTEHKAYLDKNKYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMSGSQQWRGLSRYFKVQLRKRRVKN 272
4 -126.0003bwq_A mol:protein length:272 Capsid protein VP1  ali model follow..  32  1GSHMGGIEVLG-VKTGVDSFTEVECFLNPQMGNPDE--HQKGLSKSLAAEKQFTDDSPDKEQLPCYSVARIPLPNINEDLTCGNILMWEAVTVKTEVIGVTAMTQKTHENGAGKPIQGSNFHFFAVGGEPLELQGVLANYRTKYPAQTVTPK---NATVDSQQMNTDHKAVLDKDNYPVECWVPDPSKNENTRYFGTYTGGENVPPVLHITNTATTVLLDEQGVGPLCKADSLYVSAVDICGLSGTQQWKGLPRYFKITLRKRSVKN 272
5 -108.0003iys_A mol:protein length:343 Major capsid protein VP1  ali model follow..  31  22....GGIEVLD-VKSGPDSITTIEAYLQPRPGQK------NGYSTVITVQAEGYQDAPHSTEVPCYSCARIPLPTINDDITCPTLLMWEAVSVKTEVVGVSSIFRAFNGYGGGFTICGPRIHFFSVGGEPLDLQACMQNSKTVYPAP-LIGPGEGERRETAQVLDTGYKARLDKDGYPIECWCPDPAKNENTRYYGNLTGGPETPPVLAFTNTTTTILLDENGVGPLCKGDGLFLSAADVAGTRGRQYWRGLPRYFSIQLRKRNVRN 288
6 -106.0001sva_1 mol:protein length:361 SIMIAN VIRUS 40  ali model follow..  31  30....GGIEVLG-VKTGVDSFTEVECFLNPQMGNPDE--HQKGLSKSLAAEKQFTDDSPDKEQLPCYSVARIPLPNINEDLTCGNILMWEAVTVKTEVIGVTAMTQKTHENGAGKPIQGSNFHFFAVGGEPLELQGVLANYRTKYPAQTVTPK---NATVDSQQMNTDHKAVLDKDNYPVECWVPDPSKNENTRYFGTYTGGENVPPVLHITNTATTVLLDEQGVGPLCKADSLYVSAVDICGLSGTQQWKGLPRYFKITLRKRSVKN 297
7 -105.0001sid_A mol:protein length:383 POLYOMAVIRUS COAT PROTEIN VP1  ali model follow..  31  32....GGMEVLD-LVTGPDSVTEIEAFLNPRMGQPPTPEGQYYGWSRGINLATSTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTKDMVNKDQVLNPISKAKLDKDGYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWYDVHHWRGLPRYFKITLRKRWVKN 317
8 -8.0203h8h_A mol:protein length:112 E3 ubiquitin-protein ligase RING2  ali model follow..  11  1...............GMDGASEIELVFRPHMEKDDSAQTRYIKTSGNATV----------DHLSKYLAVRLALEELRSKGESNQMNL-DTASEKQYTIYIATASGQFTVLNGSFSLELVSEKYWKVN-KPMEL...................................................................................................................................... 109
9 -6.7602l5t_A mol:protein length:77 Lipoamide acyltransferase  ali model follow..  13  1...................................................................MYEFKLPDIGEGVTEGEIVRWDMVEKDQDLVEVMTDKVTVK---IPSPVRGKIVKILYREGQVVPVGSTLLQIDT............................................................................................................................. 77
10 -6.6101pmr_A mol:protein length:80 DIHYDROLIPOYL SUCCINYLTRANSFERASE  ali model follow..  19  1..................................................................SSVDILVPDLPESVADATVATWVLVEIETDKVVLEVPA----------SADGILDAVLEDEGTTVTSRQIL.................................................................................................................................. 73
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, Godzik A. cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006 May 26;