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3pggA
Query: 3pgg_A mol:protein length:121 U6 snRNA-associated Sm-like protein LSm5. SM, 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    .   80    .   90    .  100    .  110    .  120
# Score Template Links and tools%idFirst SYKVNYMSETPANKSQGGSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAMLVPGGDPDSFNFSLast
1 -69.5003pgg_A mol:protein length:121 U6 snRNA-associated Sm-like protein LSm5. SM  ali model  100  1SYKVNYMSETPANKSQGGSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAMLVPGGDPDSFNFS 121
2 -49.7001b34_B mol:protein length:118 PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D  ali model follow..  14  2..SLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGK-GKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAG.... 117
3 -48.2003swn_C mol:protein length:117 U6 snRNA-associated Sm-like protein LSm7  ali model follow..  19  7.......SLQKRPGPGNSSQPTERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLT--------GAIRKLGLVVVRGTTLVLIAPMDGSEEIP.. 110
4 -44.9003bw1_A mol:protein length:96 U6 snRNA-associated Sm-like protein LSm3  ali model follow..  24  1........................MMETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEEL--------SESERRCEMVFIRGDTVTLISTPSEDDDGA.. 87
5 -43.6001loj_A mol:protein length:87 small nuclear ribonucleoprotein homolog (Sm-l  ali model follow..  29  2................IDVSSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEEL---------------EDGEVTRRLGTVLIRGDNIVYISRGKLAAA.... 87
6 -42.7003swn_A mol:protein length:82 U6 snRNA-associated Sm-like protein LSm5  ali model follow..  49  2.....................GMSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTG--------------VTEKHSEMLLNGNGMCMLIPGGKPE..... 82
7 -42.4001i81_A mol:protein length:83 PUTATIVE SNRNP SM-LIKE PROTEIN  ali model follow..  31  1.............GSVIDVSSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEEL---------------EDGEVTRRLGTVLIRGDNIVYISP.......... 83
8 -41.4002y9a_E mol:protein length:92 SMALL NUCLEAR RIBONUCLEOPROTEIN E  ali model follow..  26  2.............AYRGQGQKVQKVMVQPINLIFRYLQNQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT--------------KSRKQLGRIMLKGDNITLLQSVSN....... 92
9 -40.7001i8f_A mol:protein length:81 PUTATIVE SNRNP SM-LIKE PROTEIN  ali model follow..  25  1.................MASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDG----------------NVYKRGTMVVRGENVLFISPVPG....... 81
10 -40.5001th7_A mol:protein length:81 Small nuclear riboprotein protein  ali model follow..  27  2....................AMNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD---------------GSGKKLGTIVIRGDNVILISPLQTS...... 81
11 -39.8001i4k_A mol:protein length:77 PUTATIVE SNRNP SM-LIKE PROTEIN  ali model follow..  25  1........................MPPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG---------------EVVRKVGSVVIRGDTVVFVSPAPGGE..... 77
12 -39.1001m8v_A mol:protein length:77 PUTATIVE SNRNP SM-LIKE PROTEIN  ali model follow..  29  1......................GAMAERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMI---------------QDGEVVKRYGKIVIRGDNVLAISPTEE....... 77
13 -37.1002y9a_G mol:protein length:76 SMALL NUCLEAR RIBONUCLEOPROTEIN G  ali model follow..  22  1........................MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATS---------------GQQNNIGMVVIRGNSIIMLEALER....... 75
14 -36.0003swn_B mol:protein length:77 U6 snRNA-associated Sm-like protein LSm6  ali model follow..  25  2.......................GMDSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNG---------------KKTNVYGDAFIRGNNVLYVSALDD....... 77
15 -34.9002y9a_F mol:protein length:86 SMALL NUCLEAR RIBONUCLEOPROTEIN F  ali model follow..  23  2.......................SLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDG---------------ALSGHLGEVLIRCNNVLYIRGVEEEEEDG.. 82
16 -34.4001ljo_A mol:protein length:77 Archaeal Sm-like protein AF-Sm2  ali model follow..  33  1.......................GAMVLPNQMVKSMVGKIIRVEMKGEEQLVGKLEGVDDYMNLYLTNAMEC---------------KGEEKVRSLGEIVLRGNNVVLIQPQEE....... 77
17 -33.8001n9s_A mol:protein length:93 Small nuclear ribonucleoprotein F  ali model follow..  22  3...............SESSDISAMQPVNPKPFLKGLVNHRVGVKLKNSTEYRGTLVSTDNYFNLQLNEAEEFVAG---------------VSHGTLGEIFIRSNNVLYIRELPN....... 87
18 -33.6001n9r_A mol:protein length:93 Small nuclear ribonucleoprotein F  ali model follow..  22  3...............SESSDISAMQPVNPKPFLKGLVNHRVGVKLKNSTEYRGTLVSTDNYFNLQLNEAEEFVAG---------------VSHGTLGEIFIRCNNVLYIRELPN....... 87
19 -32.6001m5q_A mol:protein length:130 small nuclear ribonucleoprotein homolog  ali model follow..  15  2.............................VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNK-------------------AGEKFNRVFIMYRYIVHIDSTERRIDMR.. 72
20 -28.0001d3b_A mol:protein length:75 PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D  ali model follow..  14  2........................SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVT---------------YRDGRVAQLEQVYIRGCKIRFLILPD........ 75
21 -27.6002y9a_D mol:protein length:126 SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3  ali model follow..  14  6............................PIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVT---------------YRDGRVAQLEQVYIRGSKIRFLILPDM....... 76
22 -26.7001b34_A mol:protein length:119 PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D  ali model follow..  21  1..........................MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMT---------------LKNREPVQLETLSIRGNNIRYFILPDS....... 73
23 -23.1003pgw_B mol:protein length:231 Sm B  ali model follow..  20  1........................MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKN-----SKQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGI 92
24 -15.5001y96_A mol:protein length:86 Gem-associated protein 6  ali model follow..  18  12................................WQDYIYKEVRVTASEKNEYKGWVLTTDPVANIVLVNFLE---------------------DGSMSVTGIMGHAVQTVETMNEGDH.... 76
25 -10.0002y90_A mol:protein length:104 PROTEIN HFQ  ali model follow..  13  21.....................................RVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMV................................................ 56
26 -9.7603hfn_A mol:protein length:72 Asl2047 protein  ali model follow..  11  1.................MAITEFDTSLPSIRQLQNLIKQAVEIKLVTGDAITGRVLWQDPTC-VCIADENS-------------------------RQTTIWKQAIAYLQPKG........ 72
27 -9.4603hfo_A mol:protein length:70 Ssr3341 protein  ali model follow..  11  2....................SRFDSGLPSVRQVQLLIKDQVEIKLLTGDSLFGTIRWQDTDGLGLVDDSER--------------------------STIVRLAAIAYITPR......... 69
28 -9.3602vxe_A mol:protein length:88 CG10686-PA  ali model follow..  15  9.................................LPELGSKISLISKADIRYEGRLYTVDQECTIALSSVRSF------GTEDRDTQFQIAPQSQIYDYILFRGSDIKDIRVVNNHT..... 86
29 -9.3502fb7_A mol:protein length:95 Sm-like protein, LSm-14_N (RAP55)  ali model follow..  18  9.................................TPYIGSKISLISKAEIRYEGILYTIDENSTVALAKVRSF------GTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCEPPKPI... 88
30 -9.1401u1s_A mol:protein length:82 Hfq protein  ali model follow..  13  19.....................................RVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMV................................................ 54
31 -9.1303sb2_A mol:protein length:79 Protein hfq  ali model follow..  16  20.....................................HVPVSIYLVNGIKLQGHVESFDQYVVLLRNTVTQMV................................................ 55
32 -9.0803inz_A mol:protein length:82 Protein hfq  ali model follow..  13  19.....................................RVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMV................................................ 54
33 -9.0803m4g_A mol:protein length:82 Protein hfq  ali model follow..  13  19.....................................RVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMV................................................ 54

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.

Damiano JS, Stehlik C, Pio F, Godzik A., Reed JC. CLAN, a novel human CED-4-like gene. Genomics. 2001 Jul;75(1-3):77-83.