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anford Burnham Prebys Medical Discovery Institute
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Query: 3o7b_A mol:protein length:244 Ribosome biogenesis Nep1 RNA methyltransferas, from PDB0516

Results of FFAS03 search in SCOP206
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 RSDITSLYKKVGENLYFQGMGSAFVFLEASLELIPQKIRGHPAVRADAIRRGKRPEKILLDDSKHHTAMKSLEFREKRGRPDIVHQCLLLLLDSPLRDFEVYVHTLNGEIIWVNRETRLPRNYNRFVGLMEKLFEERRITAGDTTLIEFKDVGLRDIVRGRDVLLFREKGGRFEFSELLDGDVAVCIGAFPHGDFFEETLRELGEFKEVSLGTESYTSLYVTSRVLCEYERVRAHKVGLast
1 -104.000d3o7ba_ c.116.1.0 (A:) automated matches {Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors follow..  100  1...................MGSAFVFLEASLELIPQKIRGHPAVRADAIRRGKRPEKILLDDSKHHTAMKSLEFREKRGRPDIVHQCLLLLLDSPLRDFEVYVHTLNGEIIWVNRETRLPRNYNRFVGLMEKLFEERRITAGDTTLIEFKDVGLRDIVRGRDVLLFREKGGRFEFSELLDGDVAVCIGAFPHGDFFEETLRELGEFKEVSLGTESYTSLYVTSRVLCEYERVRA.... 215
2 -86.400d3oiia_ c.116.1.6 (A:) automated matches {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  23  1........PPVLTSKDKITKRMIVVLAMASLETHKI-----------SSNGPGGDKYVLLNCDDHQGLLKKMGRDISEARPDITHQCLLTLLDSPINKLQVYIQTSRGILIEVNPTVRIPRTFKRFSGLMVQLLHKLSIRSVNSLLKVIKNPITDHLPTKCRKVTLSFDAPVIRVQDYIDESICVFVGAMARGKDNFADE---YVDEKVGLSNYPLSASVACSKFCHGAEDAWNI... 224
3 -83.700d3bbda1 c.116.1.6 (A:2-205) Ribosome biogenesis protein NEP1 {Methanococcus jannaschii [TaxId: 2190]}  ali model 3D-neighbors follow..  32  1....................TYNIILAKSALELIPEEIKNK-------IRKSRVYKYDILDSNYHYKAMEKLKDKEMRGRPDIIHISLLNILDSPINHLNIYIHTYDDKVLKINPETRLPRNYFRFLGVMEKVLKGERNH-----LIKMEEKTLEDLLNNAKKIAIMTKTGKLTHPKLLKEYDTFIIGGFPYGKLKINKEKVFGDIKEISIYNKGLMAWTVCGIICYSLS........ 203
4 -7.730d2qwva1 c.116.1.7 (A:5-205) Uncharacterized protein VCA1059 {Vibrio cholerae [TaxId: 666]}  ali model 3D-neighbors follow..  11  3.......................................................SFILRARSAPTDSQRLLDEIGGKCHTEILAHCMLVLESTRDYSRTITVEANEISDVGGFHEAALIALLVKALDASVGMGKEQTRVVQPGLTVRTIEALLGELAEHHSLYMMDKKGDSIRDIKI-GPNPCFILT--DHIPMPKKSGNSMKRVEKISLGPKMLFASQCVTLIHNEIDHQ...... 197
5 -7.270d3aiaa1 c.116.1.0 (A:2-200) automated matches {Methanocaldococcus jannaschii [TaxId: 2190]}  ali model 3D-neighbors follow..  14  24..........................SCGRLDLLCRCVSDA--FLSHDIRRDVVFYAVLYGQPNPPVCIKFVGSELKKVSPD--ERNIAIFIKKALKKFEELDEEQRKDWNQSTPGIYVRRL--GFRNLVLEKLEE-----------------------GKNIYYLHMNGE--DVENVDIENPVFIIGDHIGIGEEDERFLDEIKAKRISLSPLELHANHCITIIHNVLDKK...... 199
6 -7.070d1o6da1 c.116.1.3 (A:2-147) Hypothetical protein TM0844 {Thermotoga maritima [TaxId: 2336]}  ali model 3D-neighbors follow..  13  7...............................................................................................IGKLDGFIKEGIKHYE---------KFLRRFCKPEVLEIKRVHRGSIEEIVRKETEDLTNRILPGSFVMVMDKRGEEVSSEEFADKDITILIG----GPYGLNEEIFAKAHRVFSLSKMTFTHGMTVLIVLEQIFRAFKIIHG 145
7 -6.690d1oaca3 d.17.2.1 (A:186-300) Copper amine oxidase, domains 1 and 2 {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  12  1........................MVLLDDFASVQNIINNSEEFAAAVKKRGITDAKKVITTPLTVGYFDGKDGLKQDAR---LLKVISYLDVGPIENLVAVVDLEQKKIVKIEEGPVVP...................................................................................................................... 100
8 -6.620d3mxma_ c.55.3.5 (A:) Three prime repair exonuclease 1, TREX1 {Mouse (Mus musculus) [TaxId: 10090]}  ali model 3D-neighbors follow..  13  2.................................................PHGHMQTLIFLDLE---------ATGLPSSRPEVTELCLLAVHRRALENTSI--RVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGD..................................................................... 122
9 -6.550d1urua_ a.238.1.1 (A:) Amphiphysin {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}  ali model 3D-neighbors follow..  13  88.........................LGDQVLIPLNTYTGQFPEMKKKVEKRNRK----LIDYDGQRHSFQNLQANANKRKDD-----------VKLTKGREQLEEARRTYEILNTELHLPALYDSRILFLVTNLQT...................................................................................................... 185
10 -6.240d4a3aa_ a.238.1.0 (A:) automated matches {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  16  95.........................LVDGSLLTLDTYLGQFPDIKNRIAKRSRK----LVDYDSARHHLEALQSSKRK--------------ESRISKAEEEFQKAQKVFEEFNVDLQLPSLWSRRVGFYVNTFKN...................................................................................................... 190

FFAS is supported by the NIH grant R01-GM087218-01
1 2 0 3 2 5   jobs submitted since Jan 1, 2011
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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.

Jaroszewski L, Li W, Godzik A. In search for more accurate alignments in the twilight zone. Protein Sci. 2002 Jul;11(7):1702-13.