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Query: 3pgg_A mol:protein length:121 U6 snRNA-associated Sm-like protein LSm5. SM, 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 SYKVNYMSETPANKSQGGSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAMLVPGGDPDSFNFSLast
1 -70.6003pgg_A mol:protein length:121 U6 snRNA-associated Sm-like protein LSm5. SM  ali model  100  1SYKVNYMSETPANKSQGGSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAMLVPGGDPDSFNFS 121
2 -51.8003jcm_f mol:protein length:93 U6 snRNA-associated Sm-like protein LSm5  ali model follow..  37  2......................SLPEILPLEVIDKTINQKVLIVLQSNREFEGTLVGFDDFVNVILEDAVEWLIDPEDESRNE-------KVMQHHGRMLLSGNNIAILVPGGKKTPTEA. 92
3 -51.7003jcr_3 mol:protein length:102 LSm3  ali model follow..  25  2.............ADDVDQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDE--ETYEEIYKSTKRNIPMLFVRGDGVVLVAP.......... 97
4 -50.3003jcm_g mol:protein length:115 U6 snRNA-associated Sm-like protein LSm7  ali model follow..  26  1...MHQQHSKSENKPQQQRKKFEGPKREAILDLAKYKDSKIRVKLMGGKLVIGVLKGYDQLMNLVLDDTVEYMSNPDDE----NNTELISKNARKLGLTVIRGTILVSLSSAEGSDVL... 111
5 -49.6004emg_A mol:protein length:93 Probable U6 snRNA-associated Sm-like protein  ali model follow..  27  2....................ESAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEE--TDKDKALKTIRKHYEMLFVRGDSVILIAPPRN....... 93
6 -49.6003jb9_G mol:protein length:115 Small nuclear ribonucleoprotein Sm D2  ali model follow..  15  2.ADLVDKPRSELSEIELARLEEYEFSAGPLSVLQQAVHDQVLINCRNNKKLLARVKAFDRHSNMVLENVKEMWTEKKRTA--SGKKGKAINKDRFISKMFLRGDGVVLVVR.......... 111
7 -49.0001b34_B mol:protein length:118 PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D  ali model follow..  15  2..SLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGK-GKKKSKPVNKDRYISKMFLRGDSVIVVLR.......... 111
8 -47.1003jcm_U mol:protein length:110 Small nuclear ribonucleoprotein Sm D2  ali model follow..  14  2SSQIIDRPKHELSRAELEELEEFEFKHGPMSLINDAMRTPVIISLRNNHKIIARVKAFDRHCNMVLENVKELWTEKKGKN--------VINRERFISKLFLRGDSVIVVLK.......... 106
9 -45.2003jcr_5 mol:protein length:91 LSm5  ali model follow..  47  2................AANATTNPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRR------------ITKLDQILLNGNNITMLVPGGEGPEV... 91
10 -45.1003swn_C mol:protein length:117 U6 snRNA-associated Sm-like protein LSm7  ali model follow..  18  6......SSLQKRPGPGNSSQPTERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLT--------GAIRKLGLVVVRGTTLVLIAPMDGSEEIPN. 111
11 -44.3003jcr_7 mol:protein length:103 LSm7  ali model follow..  25  2...................ADKEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMRDPDDQYKLT-------EDTRQLGLVVCRGTSVVLICPQDGMEAIPN. 95
12 -44.1004emk_A mol:protein length:94 U6 snRNA-associated Sm-like protein LSm5  ali model follow..  47  2...............GSSSQDPMSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTG--------------VTEKHSEMLLNGNGMCMLIPGGKPE..... 88
13 -42.4003bw1_A mol:protein length:96 U6 snRNA-associated Sm-like protein LSm3  ali model follow..  26  2.........................METPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELS--------ESERRCEMVFIRGDTVTLISTPSEDDD.... 85
14 -42.4004m75_C mol:protein length:89 U6 snRNA-associated Sm-like protein Lsm3  ali model follow..  26  1.........................METPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHSNIVLSDAVETIYQLNNEELS--------ESERRSEMVFIRGDTVTLISTPSEDDD.... 84
15 -41.6003jcm_V mol:protein length:94 Small nuclear ribonucleoprotein E  ali model follow..  19  2.................SNKVKTKAMVPPINCLQQQTPVTIWLFEQIGIRIKGKIVGFDEFMNVVIDEAVEIPVNSADGKE-------DVEKGTPLGKILLKGDNITLITSAD........ 94
16 -41.5003swn_A mol:protein length:82 U6 snRNA-associated Sm-like protein LSm5  ali model follow..  49  2.....................GMSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTG--------------VTEKHSEMLLNGNGMCMLIPGGKPE..... 82
17 -41.2003cw1_E mol:protein length:92 Small nuclear ribonucleoprotein E  ali model follow..  27  2.............AYRGQGQKVQKVMVQPINLIFRYLQNRVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTK--------------SRKQLGRIMLKGDNITLLQSVSN....... 92
18 -40.7001loj_A mol:protein length:87 small nuclear ribonucleoprotein homolog (Sm-l  ali model follow..  29  2................IDVSSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEEL---------------EDGEVTRRLGTVLIRGDNIVYISRGKLAAA.... 87
19 -39.9001i81_A mol:protein length:83 PUTATIVE SNRNP SM-LIKE PROTEIN  ali model follow..  31  2..............SVIDVSSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEEL---------------EDGEVTRRLGTVLIRGDNIVYISP.......... 83
20 -38.5003jb9_E mol:protein length:147 Small nuclear ribonucleoprotein-associated pr  ali model follow..  23  6................................MVSLLNHSLNVTTKDGRTFVGQLLAFDGFMNLVLSDCQEYRHIKKQN----VPSNSVYEEKRMLGLVILRGEFIVSLSVQGPPPMDPSM 90
21 -37.8001th7_A mol:protein length:81 Small nuclear riboprotein protein  ali model follow..  28  4......................NFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD---------------GSGKKLGTIVIRGDNVILISPLQTS...... 81
22 -37.7001i4k_A mol:protein length:77 PUTATIVE SNRNP SM-LIKE PROTEIN  ali model follow..  26  3..........................PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG---------------EVVRKVGSVVIRGDTVVFVSPAPGGE..... 77
23 -37.5003jb9_H mol:protein length:84 Small nuclear ribonucleoprotein E  ali model follow..  26  2..............SGRVQKVMIPPINFIFKLLQQHTPVSIWLFEQTDIRLQGQIRGFDEFMNIVLDDAVQV---------------DAKNNKRELGRILLKGDNITLIQA.......... 83
24 -37.1001m8v_A mol:protein length:77 PUTATIVE SNRNP SM-LIKE PROTEIN  ali model follow..  29  1......................GAMAERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMI---------------QDGEVVKRYGKIVIRGDNVLAISPTEE....... 77
25 -36.8001i8f_A mol:protein length:81 PUTATIVE SNRNP SM-LIKE PROTEIN  ali model follow..  25  1.................MASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEII----------------DGNVYKRGTMVVRGENVLFISPVPG....... 81
26 -35.9004c92_A mol:protein length:146 SM-LIKE PROTEIN LSM1  ali model follow..  21  1.............SEGEADLYLDQYNFTTTAAIVSSVDRKIFVLLRDGRMLFGVLRTFDQYANLILQDCVERIYFSEEN----------KYAEEDRGIFMIRGENVVMLGEVDIDKEDQP. 97
27 -35.2003jcm_S mol:protein length:196 Small nuclear ribonucleoprotein-associated pr  ali model follow..  18  2......................SKIQVAHSSRLANLIDYKLRVLTQDGRVYIGQLMAFDKHMNLVLNECIEERVPKTQKDSKDGTTLNIKVEKRVLGLTILRGEQILSTVVEDKPLLSKKE 107
28 -34.9003jb9_J mol:protein length:77 Small nuclear ribonucleoprotein G  ali model follow..  24  3..........................KAGAPDLKKYLDRQVFVQLNGSRKVYGVLRGYDIFLNIVLEDSIEEKVDGE---------------KVKIGSVAIRGNSVIMIETLDK....... 75
29 -34.2003jcr_8 mol:protein length:96 LSm8  ali model follow..  23  5................................LENYINRTVAVITSDGRMIVGTLKGFDQTINLILDESHERVFSSSQG-----------VEQVVLGLYIVRGDNVAVIGEIDEETDSAL. 81
30 -33.7003cw1_G mol:protein length:76 Small nuclear ribonucleoprotein G  ali model follow..  22  2.........................SKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQ---------------QNNIGMVVIRGNSIIMLEALER....... 75
31 -33.4001ljo_A mol:protein length:77 Archaeal Sm-like protein AF-Sm2  ali model follow..  33  1.......................GAMVLPNQMVKSMVGKIIRVEMKGEEQLVGKLEGVDDYMNLYLTNAMEC---------------KGEEKVRSLGEIVLRGNNVVLIQPQEE....... 77
32 -33.2004m77_A mol:protein length:109 U6 snRNA-associated Sm-like protein LSm8  ali model follow..  16  5................................LKDYLNKRVVIILVDGESLIASLNGFDKNTNLFLTNVFNRIS-----------------KEFISKAQLLRGSEIALVGLIDAENDDSL. 75
33 -33.2003jcm_b mol:protein length:109 U6 snRNA-associated Sm-like protein LSm8  ali model follow..  15  5................................LKDYLNKRVVIIKVDGECLIASLNGFDKNTNLFITNVFNRIS-----------------KEFICKAQLLRGSEIALVGLIDAENDDSL. 75
34 -32.8004xq3_A mol:protein length:91 Like-Sm ribonucleoprotein core  ali model follow..  20  1.................GAMDMQAKVENPLKSLRTAINRIVLVKLKDGSEYIGKLEQTDGTMNLVLRDCTEIR-------------EGTSEPVAKYGRVLIRGSNILFISVDYETVMNSEK 91
35 -32.1003jcm_X mol:protein length:77 Small nuclear ribonucleoprotein G  ali model follow..  25  7................................LKKYMDKKILLNINGSRKVAGILRGYDIFLNVVLDDAMEINGEDPANNHQLG-------------QTVIRGNSIISLEALDA....... 76
36 -30.1003swn_B mol:protein length:77 U6 snRNA-associated Sm-like protein LSm6  ali model follow..  25  2.......................GMDSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEY---------------VNGKKTNVYGDAFIRGNNVLYVSALDD....... 77
37 -30.0003jcm_e mol:protein length:86 U6 snRNA-associated Sm-like protein LSm6  ali model follow..  16  1.................MSGKASTEGSVTTEFLSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEHY-----------ESNNNKLLNKFNSDVFLRGTQVMYISEQK........ 85
38 -29.7003jb9_I mol:protein length:78 Small nuclear ribonucleoprotein F  ali model follow..  26  2......................SFVPVNPKPFLQGLIGKPVLVRLKWGQEYKGTLQSVDSYMNLQLLNAEEL---------------VDGVKTGDLGEILIRCNNVLWVGEST........ 77
39 -29.6003jcr_6 mol:protein length:80 LSm6  ali model follow..  23  2......................SLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEY---------------VNGQLKNKYGDAFIRGNNVLYISTQKR....... 78
40 -27.5001n9r_A mol:protein length:93 Small nuclear ribonucleoprotein F  ali model follow..  22  2..............MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKNSTEYRGTLVSTDNYFNLQLNEAEEF---------------VAGVSHGTLGEIFIRCNNVLYIRELPN....... 87
41 -27.3001n9s_A mol:protein length:93 Small nuclear ribonucleoprotein F  ali model follow..  22  2..............MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKNSTEYRGTLVSTDNYFNLQLNEAEEF---------------VAGVSHGTLGEIFIRSNNVLYIRELPN....... 87
42 -27.2004m75_G mol:protein length:122 U6 snRNA-associated Sm-like protein Lsm4  ali model follow..  21  4.......AAGTSLYKKAGENLYFQGSMLPLYLLTNAKGQQMQIELKNGEIIQGILTNVDNWMNLTLSNVTEY----SEESAINSEDNAESSKAVKLNEIYIRGTFIKFI............ 101
43 -27.1003cw1_F mol:protein length:86 Small nuclear ribonucleoprotein F  ali model follow..  22  2.......................SLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEY---------------IDGALSGHLGEVLIRCNNVLYIRGVEEEEEDGEM 84
44 -25.3001m5q_A mol:protein length:130 small nuclear ribonucleoprotein homolog  ali model follow..  16  2.............................VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASN-------------------KAGEKFNRVFIMYRYIVHIDSTER....... 67
45 -24.0004emh_A mol:protein length:105 Probable U6 snRNA-associated Sm-like protein  ali model follow..  28  1..................MGSSSQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIR--------------TMPDGDKFFRLPECYIRGNNIKYL............ 77
46 -23.0004n0a_C mol:protein length:109 U6 snRNA-associated Sm-like protein LSm2  ali model follow..  19  2...................GSSSQDPMLFFSFFKTLVDQEVVVELKNDIEIKGTLQSVDQFLNLKLDNISCT-------------DEKKYPHLGSVRNIFIRGSTVRYV............ 78
47 -22.4004c8q_B mol:protein length:105 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2  ali model follow..  20  1................SENLYFQGSGSLFFSFFKTLVDQEVVVELKNDIEIKGTLQSVDQFLNLKLDNISCTDEKKYPH---------------SVRNIFIRGSTVRYV............ 80
48 -22.3003jcm_T mol:protein length:146 Small nuclear ribonucleoprotein Sm D1  ali model follow..  14  1..........................MKLVNFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPQPRLNKLNSNQQPTASDNIASLQYINIRGNTI-IILPDS........ 100
49 -21.5004m75_B mol:protein length:95 U6 snRNA-associated Sm-like protein Lsm2  ali model follow..  21  1..........................MLFFSFFKTLVDQEVVVELKNDIEIKGTLQSVDQFLNLKLDNISST-------------DEKKYPHLGSVRNIFIRGSTVRYV............ 70
50 -21.5003jcm_R mol:protein length:101 Small nuclear ribonucleoprotein Sm D3  ali model follow..  16  2.......................TMNGIPVKLLNEAQGHIVSLELTTGATYRGKLVESEDSMNVQLRDVIATEPQGA---------------VTHMDQIFVRGSQIKFI............ 72
51 -20.1003jcm_h mol:protein length:187 U6 snRNA-associated Sm-like protein LSm4  ali model follow..  23  3............................PLYLLTNAKGQQMQIELKNGEIIQGILTNVDNWMNLTLSNVTEY----SEESAINSEDNAESSKAVKLNEIYIRGTFIKFI............ 79
52 -20.1003jb9_D mol:protein length:97 Small nuclear ribonucleoprotein Sm D3  ali model follow..  15  4............................CIKLLHETQGHIVTMELENGSTYRGKLIEAEDNMNCQMRDISVTARDGR---------------VSHLDQVYIRGSHIRFL............ 69
53 -19.9003jcr_2 mol:protein length:95 LSm2  ali model follow..  20  1..........................MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPH---------------SVKNCFIRGSVVRYV............ 70
54 -19.9003jcr_O mol:protein length:240 SmB  ali model follow..  22  7..............................SKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIK-----PKNSKQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGI 92
55 -19.9004pjo_C mol:protein length:91 Small nuclear ribonucleoprotein Sm D1  ali model follow..  20  2.....................SGSGSVKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNRE---------------PVQLETLSIRGNNIRYF............ 74
56 -19.5003jb9_F mol:protein length:117 Small nuclear ribonucleoprotein Sm D1  ali model follow..  17  1..........................MKLVRFLMKLTNETVSIELKNGTIVHGTITSVDMQMNTHLKAVKMTVKG---------------REPVPVETLSIRGNNIRYY............ 68
57 -19.4003cw1_D mol:protein length:126 Small nuclear ribonucleoprotein Sm D3  ali model follow..  15  2........................SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD---------------GRVAQLEQVYIRGCKIRFL............ 71
58 -19.3001b34_A mol:protein length:119 PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D  ali model follow..  20  1..........................MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNRE---------------PVQLETLSIRGNNIRYF............ 68
59 -18.1003jcr_4 mol:protein length:139 LSm4  ali model follow..  22  3............................PLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGD--------------KFWRMPECYIRGSTIKYL............ 69
60 -10.7001y96_A mol:protein length:86 Gem-associated protein 6  ali model follow..  18  12................................WQDYIYKEVRVTASEKNEYKGWVLTTDP--NIVLVNFLE---------------------DGSMSVTGIMGHAVQTVETMNEGDH.... 76
61 -10.5001ycy_A mol:protein length:71 Conserved hypothetical protein  ali model follow..  34  9..............................KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDV................................................. 49
62 -9.0902y90_A mol:protein length:104 PROTEIN HFQ  ali model follow..  14  24........................................VSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVY............................................... 57

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.

Ginalski K, Grishin NV, Godzik A., Rychlewski L. Practical lessons from protein structure prediction. Nucleic Acids Res. 2005 Apr 1;33(6):1874-91.