current user: public

anford Burnham Prebys Medical Discovery Institute
We are hiring bioinformatics experts and software developers. Join us!

Query: 3o7b_A mol:protein length:244 Ribosome biogenesis Nep1 RNA methyltransferas, from PDB0516

Results of FFAS03 search in HGM_OVER
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.
    .   10    .   20    .   30    .   40    .   50    .   60    .   70    .   80    .   90    .  100    .  110    .  120    .  130    .  140    .  150    .  160    .  170    .  180    .  190    .  200    .  210    .  220    .  230    .
# Score Template Links and tools%idFirst RSDITSLYKKVGENLYFQGMGSAFVFLEASLELIPQKIRGHPAVRADAIRRGKRPEKILLDDSKHHTAMKSLEFREKRGRPDIVHQCLLLLLDSPLRDFEVYVHTLNGEIIWVNRETRLPRNYNRFVGLMEKLFEERRITAGDTTLIEFKDVGLRDIVRGRDVLLFREKGGRFEFSELLDGDVAVCIGAFPHGDFFEETLRELGEFKEVSLGTESYTSLYVTSRVLCEYERVRAHKVGLast
1 -4.030HGC00915 gi|162810474|dbj|BABA01034235.1|2.0 TMP01234;  ali follow..  16  2.............................................................................................SKKKRGEERMKEEDNILKKVGKKFKVPEGY--FENLTSEVMGKLPEKEG................................................................................................ 50
2 -2.630PB078508 A6TV41_9CLOT/1-155 PB078508; Pfam-B_78508;  ali follow..  17  2.......................................................ETIKFNSEAHELFYKEMLARTN--QTDVYYKAFFYCMETTRKHIEDLFDFKEGGI-QTGTSYKVTRAYNLWNG.............................................................................................................. 84
3 -2.610PB022506 Q11RP6_CYTH3/1-298 PB022506; Pfam-B_22506;  ali follow..  10  88...................KSITVGFKNTQFSLIPEA---------------------LFEKDYLKEYLTLNTTLDREPDEEYHFYKQ-----RQTEAVNVFAQRLTSWFNKTYPLKQVRYVHHTASMIEGIMLQKDKNAAEKSVFIQVEQYFLTIIVKQGKKLIFCNSFTFNTSEDFV........................................................... 223
4 -2.590PB003645 Q65HI2_BACLD/1-230 PB003645; Pfam-B_3645;  ali follow..  12  120....................SIVVNVDATSLKIFEKNRKTQETSTNETDKQGGKRTVSEMSSDEEIVIIKNGDKEVQTKKPDIIIEAVTRVLDVPSHRVAVAPKKMKE.................................................................................................................................. 229
5 -2.320PB005684 gi|160884252|ref|ZP_02065255.1| hypothetical protein BACOVA_02230 [Bacteroides ovatus ATCC 8483]gi|156109991|gb|EDO11736.1| hypothetical protein BACOVA_02230 [Bacteroides ovatus ATCC 8483]  ali follow..  122KGILSYIRLLVEPIHDEIRKEVTIQMKAYKKEKAEYDAMGKERTKKEAPQMPPNRMFLISGNNTGTGILQNIMDSDGTG---LICEAEADTLSTAIGSSDTLRKAFDHDRLSYNSYLSVPSQVQTFIGSYSRQL........................................................................................................ 279
6 -2.320PB001934 Q6PSL5_CHLRE/821-1150 PB001934; Pfam-B_1934;  ali follow..  10  90.................RHWATVLSVRLDLDAAACEMERQRFDGVIAMMERNDGPTLVVTDSQAIDVVHPWTLDR-SSGRPLVTTFSIAMAYQQNGGRLDPFVEGLE-ALETLQDGDRV---------LISEACNHNRITSACNDIGMVQIPNKLEAALGGKKLQIEHAFPELESGGMDGLKLAIHCGGCMIDAQKMQQRMKDLHEAGVPVTNYGVFFSWA................. 295
7 -2.300PB083081 gi|160890648|ref|ZP_02071651.1| hypothetical protein BACUNI_03093 [Bacteroides uniformis ATCC 8492]gi|156859647|gb|EDO53078.1| hypothetical protein BACUNI_03093 [Bacteroides uniformis ATCC 8492]  ali follow..  12  11..................................................................................SALFMLTSCSMFEIDNYEEPSETIWGEVVDEATGKRV-LTDQGSEGIRVRLTELSWGDNVQHNPDFYCMMQNTKIFKGEYNVRIDGPFENTDGTLLHDGSVNTEISGTTKVKFEVQPFLNVEFVGNPQVSNGVIKAQVRVTR.............. 160
8 -2.300PB002794 gi|86143885|ref|ZP_01062253.1| hypothetical protein MED217_03525 [Flavobacterium sp. MED217]gi|85829592|gb|EAQ48055.1| hypothetical protein MED217_03525 [Leeuwenhoekiella blandensis MED217]  ali follow..  22  263.........................................................................................SLMTETLAR--VYVEQKNSKAKQAYRILSLPEKSGFFADQIRAI......................................................................................................... 307
9 -2.290PB128892 A6TNK2_9CLOT/1-174 PB128892; Pfam-B_128892;  ali follow..  11  1...................................................................MFFNTSEQLAENKLVLLY--IFDRVQFPLANIQLTQFIMENDIM----------NYFMLQQFIGELKESSFIMEQEK--------------DTGQLFMITDQGKKT................................................................. 80
10 -2.250HGC00816 gi|163609134|dbj|BABG01026932.1|1.0 TMP01075;  ali follow..  2.............SREKRKAKKEAEKRLSTRQFIGAKEITDYSLVTYGQGE-KPTNISVLSESSVGARIYALMTVLKGVAEEMLCLNSRESFEDNKRFLKSQMEQEENPVIR--------RLLEQDQTHLDRIQVQMATAREFLIMLRLKDEKESDIFPYLSRIEKSLKEQSFSVKRADKEDIKRILAVYYEQNVTTEKFEDFDGERWI............................. 195

FFAS is supported by the NIH grant R01-GM087218-01
1 1 7 8 9 6   jobs submitted since Jan 1, 2011
Comments and questions to: webmaster

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.

Zhang B, Jaroszewski L, Rychlewski L, Godzik A. Similarities and differences between nonhomologous proteins with similar folds: evaluation of threading strategies. Fold Des. 1997;2(5):307-17.