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1d3bA
Query: 1d3b_A mol:protein length:75 PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D, 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.
    .   10    .   20    .   30    .   40    .   50    .   60    .   70    .
# Score Template Links and tools%idFirst MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPDLast
1 -53.2001d3b_A mol:protein length:75 PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D  ali model  100  1MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPD 75
2 -47.5002y9a_D mol:protein length:126 SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3  ali model follow..  98  1MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPD 75
3 -46.1002y9a_F mol:protein length:86 SMALL NUCLEAR RIBONUCLEOPROTEIN F  ali model follow..  24  1MSLPLPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVE 76
4 -44.5003swn_B mol:protein length:77 U6 snRNA-associated Sm-like protein LSm6  ali model follow..  18  3.MDSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGNNVLYVSALD 76
5 -43.6001b34_A mol:protein length:119 PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D  ali model follow..  29  2....KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPD 72
6 -42.8001n9s_A mol:protein length:93 Small nuclear ribonucleoprotein F  ali model follow..  17  12.QPVNPKPFLKGLVNHRVGVKLKNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRSNNVLYIRELP 86
7 -42.4001n9r_A mol:protein length:93 Small nuclear ribonucleoprotein F  ali model follow..  18  15....NPKPFLKGLVNHRVGVKLKNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELP 86
8 -40.8001m8v_A mol:protein length:77 PUTATIVE SNRNP SM-LIKE PROTEIN  ali model follow..  20  7.....PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISPTE 76
9 -39.9001ljo_A mol:protein length:77 Archaeal Sm-like protein AF-Sm2  ali model follow..  21  2.AMVLPNQMVKSMVGKIIRVEMKGEEQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQPQE 76
10 -39.8001loj_A mol:protein length:87 small nuclear ribonucleoprotein homolog (Sm-l  ali model follow..  18  9VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISRGK 83
11 -38.8001i4k_A mol:protein length:77 PUTATIVE SNRNP SM-LIKE PROTEIN  ali model follow..  22  5.....PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSPAP 74
12 -38.0001i81_A mol:protein length:83 PUTATIVE SNRNP SM-LIKE PROTEIN  ali model follow..  19  11VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYIS... 82
13 -37.7001m5q_A mol:protein length:130 small nuclear ribonucleoprotein homolog  ali model follow..  21  2......VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGE----KFNRVFIMYRYIVHIDSTE 66
14 -36.6003swn_A mol:protein length:82 U6 snRNA-associated Sm-like protein LSm5  ali model follow..  13  5.MTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGTEKHSEMLLNGNGMCMLIPGG 79
15 -35.0001th7_A mol:protein length:81 Small nuclear riboprotein protein  ali model follow..  24  10.....AHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISPLQ 79
16 -33.0002y9a_G mol:protein length:76 SMALL NUCLEAR RIBONUCLEOPROTEIN G  ali model follow..  20  5.....HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALE 74
17 -32.6001i8f_A mol:protein length:81 PUTATIVE SNRNP SM-LIKE PROTEIN  ali model follow..  14  12.....LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNV-YKRGTMVVRGENVLFISPVP 80
18 -30.6002y9a_E mol:protein length:92 SMALL NUCLEAR RIBONUCLEOPROTEIN E  ali model follow..  16  16QPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKRKQLGRIMLKGDNITLLQSVS 91
19 -30.6003bw1_A mol:protein length:96 U6 snRNA-associated Sm-like protein LSm3  ali model follow..  20  5.....PLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETELSESERRCEMVFIRGDTVTLISTPS 81
20 -28.0003pgg_A mol:protein length:121 U6 snRNA-associated Sm-like protein LSm5. SM  ali model follow..  14  25.NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYLKRVMVNRLETILLSGNNVAMLVPGG 113
21 -27.9003swn_C mol:protein length:117 U6 snRNA-associated Sm-like protein LSm7  ali model follow..  18  32.........LSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQKLTGAIRKLGLVVVRGTTLVLIAPMD 104
22 -24.5001b34_B mol:protein length:118 PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D  ali model follow..  13  28.....PLSVLTQSVNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMKPVNKDRYISKMFLRGDSVIVVL... 110
23 -13.6001y96_A mol:protein length:86 Gem-associated protein 6  ali model follow..  11  12.........WQDYIYKEVRVTASEKNEYKGWVLTTDP-----VSANIVLVNFLEDGSMSVTGIMGHAVQTVET.. 70
24 -11.9003pgw_B mol:protein length:231 Sm B  ali model follow..  16  1MTVGKSSK-MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFAEREEKRVLGLVLLRGENLVSMTVEG 84
25 -11.3002fb7_A mol:protein length:95 Sm-like protein, LSm-14_N (RAP55)  ali model follow..  16  9..........TPYIGSKISLISKAEIRYEGILYTIDENSTVALAKVRSFGTEDRPTDFEYIIFRGSDIKDLTVCE 83
26 -10.9002vxe_A mol:protein length:88 CG10686-PA  ali model follow..  15  9..........LPELGSKISLISKADIRYEGRLYTVDQECTIALSSVRSFGTEDRDTQYDYILFRGSDIKDIRVVN 83
27 -9.8101y96_B mol:protein length:85 Gem-associated protein 7  ali model follow..  15  21......LRSLLAMVGHQVSFTLHEGVRVAAHFGATDDVANFYVSQLQ-----TPIGVQAEALLRCSDIISYTF.. 83

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.

Jaroszewski L, Slabinski L, Wooley J, Deacon AM, Lesley SA, Wilson IA, Godzik A. Genome pool strategy for structural coverage of protein families. Structure. 2008 Nov 12;16(11):1659-67.