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Query: 3sb2_A mol:protein length:79 Protein hfq, 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.
    .   10    .   20    .   30    .   40    .   50    .   60    .   70    .
# Score Template Links and tools%idFirst MSNKGQLLQDPFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLLRNTVTQMVYKHAISTVVPARAVNLSLESSSDELast
1 -66.6003sb2_A mol:protein length:79 Protein hfq  ali model  100  1MSNKGQLLQDPFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLLRNTVTQMVYKHAISTVVPARAVNLSLESSSDE 79
2 -63.7003inz_A mol:protein length:82 Protein hfq  ali model follow..  70  2..SKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKTAISTVVPSRPVRLPSGDQPAE 78
3 -63.6001u1s_A mol:protein length:82 Hfq protein  ali model follow..  71  2..SKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLPSGDQPAE 78
4 -63.5004mmk_A mol:protein length:82 Protein hfq  ali model follow..  70  2..SKGHSLADPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLPSGDQPAE 78
5 -63.5004mml_A mol:protein length:82 Protein hfq  ali model follow..  70  2..SKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFAQFVILLKNTVSQMVYKHAISTVVPSRPVRLPSGDQPAE 78
6 -63.5003m4g_A mol:protein length:82 Protein hfq  ali model follow..  70  2..SKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKAAISTVVPSRPVRLPSGDQPAE 78
7 -63.3005i21_A mol:protein length:82 RNA-binding protein Hfq  ali model follow..  70  2..SKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVWKHAISTVVPSRPVRLPSGDQPAE 78
8 -59.6004jrk_A mol:protein length:68 Protein hfq  ali model follow..  79  1..AKGQSLQDPWLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVS......... 68
9 -59.5004jri_A mol:protein length:68 Protein hfq  ali model follow..  79  1..AKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESWDQFVILLKNTVSQMVYKHAISTVVPSRPVS......... 68
10 -59.5004jli_A mol:protein length:68 Protein hfq  ali model follow..  80  1..AKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQWVILLKNTVSQMVYKHAISTVVPSRPVS......... 68
11 -59.5004juv_A mol:protein length:68 Protein hfq  ali model follow..  79  1..AKGQSLQDPFLNALRRERVPVSIWLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVS......... 68
12 -58.8004nl2_D mol:protein length:77 Protein hfq  ali model follow..  46  1MKQGGQGLQDYYLNQLRKEKILATVFLTNGFQLRGRVVSFDNFTVLLDEGKQQLVFKHAISTFSPQKNVALNPDAE... 77
13 -58.7002y90_A mol:protein length:104 PROTEIN HFQ  ali model follow..  71  4..AKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSNNAGGG 80
14 -58.7004noy_D mol:protein length:77 Protein Hfq  ali model follow..  46  1MKQGGQGLQDYYLNQLRKEKILATVFLTNGFQLRGRVVSFDNWTVLLDEGKQQLVFKHAISTFSPQKNVALNPDAE... 77
15 -55.2003ahu_A mol:protein length:78 Protein hfq  ali model follow..  47  5.SMKPINIQDQFLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLLEEGKQQLIYKHAISTFAPQKNVQLELE..... 78
16 -55.2001kq1_A mol:protein length:77 Host Factor for Q beta  ali model follow..  30  2..IANENIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNQGKQHLIYKHAISTYTVETEGQASTESEE.. 77
17 -55.0004y91_A mol:protein length:95 RNA-binding protein Hfq  ali model follow..  40  5ALAEKFNLQDRFLNHLRVNKIEVKVYLVNGFQTKGFIRSFDSYTVLLEGNQQSLIYKHAISTIIPSSYVMLMPKKQETA 84
18 -51.0002qtx_A mol:protein length:71 Uncharacterized protein MJ1435  ali model follow..  25  6KKQQPKKVIPNFEYARRLNGKKVKIFLRNGEVLDAEVTGVSNYEIMVKGDRNLLVFKHAIDYI................ 69
19 -37.4003hfo_A mol:protein length:70 Ssr3341 protein  ali model follow..  28  1MSRFDSGLSVRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDGLGLVDERSTIVRLAAIAYITPRR............ 70
20 -37.2003hfn_A mol:protein length:72 Asl2047 protein  ali model follow..  29  2....AITEFDTSLPSIRKQAAPVEIKLVTGDAITGRVLWQDPTCVCIADSRQTTIWKQAIAYLQPK............. 71
21 -11.6003jcr_7 mol:protein length:103 LSm7  ali model follow..  14  1MADKEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMR....................... 56
22 -11.0003jcm_U mol:protein length:110 Small nuclear ribonucleoprotein Sm D2  ali model follow..  25  33...........LINDAMVTRTPVIISLRNNHKIIARVKAFDRHCNMVLENVKELW........................ 76
23 -10.5003jb9_G mol:protein length:115 Small nuclear ribonucleoprotein Sm D2  ali model follow..  30  32...........VLQQAVKNHDQVLINCRNNKKLLARVKAFDRHSNMVLENVKEM......................... 74
24 -10.3003bw1_A mol:protein length:96 U6 snRNA-associated Sm-like protein LSm3  ali model follow..  21  1MMETPLDLLKLNLDE------RVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQ...................... 51
25 -10.0001b34_B mol:protein length:118 PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D  ali model follow..  30  31...........VLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEM......................... 73
26 -9.9601i8f_A mol:protein length:81 PUTATIVE SNRNP SM-LIKE PROTEIN  ali model follow..  29  23.....................QVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEII........................ 56
27 -9.7503jcm_V mol:protein length:94 Small nuclear ribonucleoprotein E  ali model follow..  14  14.......INCIFNFLQQQTPVTIWLFEQIGIRIKGKIVGFDEFMNVVIDEAVEIPVN...................... 63
28 -9.6203cw1_E mol:protein length:92 Small nuclear ribonucleoprotein E  ali model follow..  19  27................NRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSK...................... 67
29 -9.4504m75_C mol:protein length:89 U6 snRNA-associated Sm-like protein Lsm3  ali model follow..  22  16......................VYIKLRGARTLVGTLQAFDSHSNIVLSDAVETIYQ...................... 50
30 -9.4203swn_A mol:protein length:82 U6 snRNA-associated Sm-like protein LSm5  ali model follow..  16  1MGMSMTILPLELIDKCIGSN--LWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYD........................ 53
31 -9.4103jcm_X mol:protein length:77 Small nuclear ribonucleoprotein G  ali model follow..  15......................ILLNINGSRKVAGILRGYDIFLNVVLDDAMEINGEDPANNH................ 55
32 -9.1603cw1_G mol:protein length:76 Small nuclear ribonucleoprotein G  ali model follow..  26  16.....................KLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMA........................ 49
33 -9.1003jb9_H mol:protein length:84 Small nuclear ribonucleoprotein E  ali model follow..  19  22................QHTPVSIWLFEQTDIRLQGQIRGFDEFMNIVLDDAVQVDAKNNKREL................ 68
34 -9.0503swn_C mol:protein length:117 U6 snRNA-associated Sm-like protein LSm7  ali model follow..  16  18SQPTERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLR....................... 73

FFAS is supported by the NIH grant R01-GM087218-01
8 3 0 3 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.

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