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Query: 1vpy_A mol:protein length:289 PROTEIN (hypothetical protein EF0366), 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 MGSDKIMIRLGLTSFSEHDYLTGKKRSTLYEYASHLPLVEMDTAYYGIPPKERVAEWVKAVPENFRFVMKVYSGISCQGEWQTYYASEEEMITAFLESMAPLIESKKLFAFLVQFSGTFGCTKENVAYLQKIRHWFKDLPIAIELRNNSWYQPNFVKQMLQFMKENQFSLVIVDEPQIPTNPVPFYPYVTNPNLVLFRFHGRNAAGWLANDAEWRKKRTLYHYNTQEIADLSEAVLKMSQEAKEVGVIFNNNSGGDAAENALQMQKVLNLSYDDLNPKQLDLFLast
1 -129.0001vpy_A mol:protein length:289 PROTEIN (hypothetical protein EF0366)  ali model  100  1MGSDKIMIRLGLTSFSEHDYLTGKKRSTLYEYASHLPLVEMDTAYYGIPPKERVAEWVKAVPENFRFVMKVYSGISCQGEWQTYYASEEEMITAFLESMAPLIESKKLFAFLVQFSGTFGCTKENVAYLQKIRHWFKDLPIAIELRNNSWYQPNFVKQMLQFMKENQFSLVIVDEPQIPTNPVPFYPYVTNPNLVLFRFHGRNAAGWLANDAEWRKKRTLYHYNTQEIADLSEAVLKMSQEAKEVGVIFNNNSGGDAAENALQMQKVLNLSYDDLNPKQLDLF 283
2 -98.2001vpq_A mol:protein length:273 hypothetical protein TM1631  ali model follow..  31  1MGSDKIMVYVGTSGFSFEDWKGVKPSQFLKYYWAGFRIVELNFTYYTQPSWRSFVQMLRKTPPDFYFTVKTPGSVTHVLWKE--GKDPKEDMENFTRQIEPLIEEQRLKMTLAQFPFSFKFSRKNVEYLEKLRESY-PYELAVEFRHYSWDRE----ETYEFLRNHGITFVVVDEPKLP--GLFPYRPITTTDYAYFRFHGRNERWF----EAEGEERYDYLYSEEELKTLFEDVVELSRRVKETYVFFNNCYKGQAAINALQFKKMLEER............ 266
3 -8.1003wqo_A mol:protein length:293 Uncharacterized protein MJ1311  ali model follow..  11.SKWVLDMKFGVSSLVFLPESLTSSMEKIAEHN--FDAWEIVCEGTHYLSPKNIKY-LMELRDRYEVEIVVHAPFSDLNPASMNERVRKLTVECIRDAIE----AFELDSEVVVVHPGYEILDNNFSTLSEIVEIAEDYGIKIGLENMPNFRGVLGITPESLLEDSKNLGITFDIGHANTAGNPAEFVEKLQNIGIIHVH--------HDNNGYDDEHLKIGEGNINFIEVLEKLKEIGYDGVISIENKNIRDAVKSKEILKEYLEIVNEKVAEKEKIE.... 292
4 -7.8902g0w_A mol:protein length:296 Lmo2234 protein  ali model follow..  31.......................SFPKRVKVAAENFDGIGL-ENYVDALAAGLTDEDMLRILDEHNMKVTEVEYITQWGTAEDRTAEQQKKEQTTFHMARLFGVKHINCGLLEKIP-----EEQIIVALGELCDRAEELIIGLEF---PYSGVADLQAAWRVAEACG-AQLICDT-ARANQTAESIKNVPADRIVSIQLCDVHETPYKELREESLHDRLAPGEGYGDTVGFAKILKEHGVNPRVMGVVISDSMVATGLEYANATKKVLDEAWPEISPR..... 290
5 -7.3001yx1_A mol:protein length:264 hypothetical protein PA2260  ali model follow..  2.HMSLHPVSISLSSYGADLVRSRGQASFLPLLAMAAQRVELREELFAGPPD-----------EALTAAIQLQGLECVFSSPLELWREDGQLNPELEPTLR---RAEACGAGWLKVSLGLLPEQPD---LAALGRRLARHGLQLLVENDQTPQGGRIEVLERFFRLAE-LAMTFDIGNWRWQEQAADEAALRLGRYVGYVHCKAVI------RNRDGKLVAVPPSAADLQYWQRLLQHFPEGV---YPLQGDDLLSLSRRHIAALARLGQ.............. 254
6 -7.2603trk_A mol:protein length:324 Nonstructural polyprotein  ali model follow..  12  20..LETAGIKLNDRQWSQKEDKAYSPEVALNEICTRMYGVDLDSGLFSKPLVSVYNHWDNRPGKMFGFNPEAASILERKYPFTKGKWNINKQICVTTRRIEDFNPTTNIIPVNRRLPHSLVAEHRPVKLVNKINGLVSGYNLALPTKRVTWVAPLGVRGA-ATLGRYDLVVINIHTP-----------QQCVDHAMKLQMLGGDSLRLLKPGGSLLIRAYGYRTSERVICVLGRKFRSSRTSNTEMFFLFSNFDNGRRNFTTHVMNNQLNAAFVG......... 324
7 -7.2203cny_A mol:protein length:301 Inositol catabolism protein IolE  ali model follow..  4.SKAEKDIKWGIAGWRNDDIPSIGKDNNLQQLLSDFQGTEVGGFF---PGPEKLNY---------ELKLRNLEIAGQWFSSYIIRDGIEKASEAFEKHCQYLKAINAPVAVVSEQTYTIQRSDTACKGLNHYGEIAAKYGLKVAYHHHMGTGIQTKEETDRLMANTDLVGLLYDTGHIAVSDGDYMALLNAHIDRVVHVHFKDVRRSKEEECRAKGLTFQFTVPGDGDLDFKPVYDKLIANNYKGWIVVEDPSKANPLEMAQIAHRYI............... 294
8 -7.1001v19_A mol:protein length:309 2-KETO-3-DEOXYGLUCONATE KINASE  ali model follow..  12  32VGGAEVNVAVALARLGVKGFVGRVGEDELGAMVEERLRAEVDLTHFRRAPGFTGLYLREYLPLG------QGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPAL----------SPEARAFSLWAMEEAKRRGVRVSLRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRVEEALRALSAPEVVLKR-GAKGAWAFVDGRRVEGSAFA-----------VEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGA............. 279
9 -7.0002wag_A mol:protein length:220 LYSOZYME, PUTATIVE  ali model follow..  11  1............................MGSSMDRYEIKGVDVASY-----QGDIDWRELEKQNMKFAIKATEGSAFVD-------------KYFSKNWTNANKTSMRVGAYHFFSFDSKGETQAEQFIRNVPKYKQALPIDVEFYANKKDNPPKREDVTKELS------VMIEMLEKHYGKKVILYATQEAYDLYIKDAYPQCDIWIRSVLTKPSLSDERKWT---FWQYTNRGKLSGYNGKEKYIDLNVFYGNEEEFENYGMKD................. 214
10 -6.8005ezq_A mol:protein length:338 Non-structural Protein 2 Cysteine Protease  ali model follow..  32..LKTAGIDMTTEQWNFETDKAHSAEIVLNQLCVRFFGLDLDSGLFSAPTVPLSNHWDNSPPNMYGLNKEVVRQLSRRYPQLPRAVATGRVYDMNTGTLRNYDPRINLVPVNRRLPHALVLHHNEVSKLKGRTVLVVGEKLSVPGKMVDWLSDRPEATFRARLDKYDIIFVNVRTP-----------QQCEDHAIKLSMLTKKACLHLNPGGTCVSIGYGYRASESIIGAIARQFKFSRLEETEVLFVFIGYDRKARTHNPYKLSSTLTNIYTGSRLHE.... 337

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. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics. 2001 Mar;17(3):282-3.