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Query: 4ytk_A mol:protein length:130 Transcription elongation factor SPT5, from PDB1018

Results of FFAS03 search in PDB1018
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
# Score Template Links and tools%idFirst LEEGSYVRIKRGIYKGDLAMVDQISENNLEVMLKIVPRLDYGKFDEIDPTTQQRKSRRPTFAHRAPPQLFNPTMALRLDQANLYKRDDRHFTYKNEDYIDGYLYKSFRIQHVETKNIQPTVEELARFGSKLast
1 -76.2004ytk_A mol:protein length:130 Transcription elongation factor SPT5  ali model  100  1LEEGSYVRIKRGIYKGDLAMVDQISENNLEVMLKIVPRLDYGKFDEIDPTTQQRKSRRPTFAHRAPPQLFNPTMALRLDQANLYKRDDRHFTYKNEDYIDGYLYKSFRIQHVETKNIQPTVEELARFGSK 130
2 -46.3005xon_W mol:protein length:612 Protein that forms a complex with Spt4p  ali model follow..  42  117LTRGSYVRVKNGKFKGDLAQVDEVLENGLEARLKLVPRLDYGKDLSHLSTSSSVDSTFYTSKFRPAQRLFSEAEARVH-EPTIRRDRDGFVTYGGEEYYEGFLYKTFRLQNLIVNSINPTLNELSLFQS. 249
3 -41.2005oik_Z mol:protein length:1087 Transcription elongation factor SPT5  ali model follow..  31  273LKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDYDRIKARMSLKDWFAKRKKFK--RPPQRLFDAEKIRSLGG-DVASDGDFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKFED. 398
4 -26.3003qqc_D mol:protein length:163 Transcription antitermination protein nusG  ali model follow..  21  92LEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQFIDAIVPIPVTIKGDYVRLISKLQKEEAAA.................................................................. 155
5 -22.7004zn1_A mol:protein length:147 Transcription elongation factor Spt5  ali model follow..  20  89IEKGDVVEIIAGPFKGERAKVIRVDKHKEEVTLELENAAVPIPITLPVEGVKIVSKHKD....................................................................... 147
6 -13.6005xog_W mol:protein length:83 Spt4/5 complex component  ali model follow..  25  21...NKTVKIRQGGYKGKIGIVKEANGDRFRVELHNPNKT........................................................................................... 56
7 -12.9002e70_A mol:protein length:71 Transcription elongation factor SPT5  ali model follow..  32  20..IGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQT........................................................................................... 56
8 -10.6002kvq_G mol:protein length:63 Transcription antitermination protein nusG  ali model follow..  17  10FEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSV............................................................................................... 44
9 -10.5001s72_T mol:protein length:120 50S ribosomal protein L24P  ali model follow..  17  43VNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVE................................................................................................ 76
10 -10.2002lq8_A mol:protein length:177 Transcription antitermination protein nusG  ali model follow..  17  123FKVGDMVKIISGPFEDFAGVIKEIDPERQELKVNV............................................................................................... 157
11 -10.1002mi6_A mol:protein length:62 Transcription termination/antitermination protein NusG  ali model follow..  14  9YEVGESVTVMDGPFATLPATISEVNAEQQKLKVLV............................................................................................... 43
12 -10.1006duq_M mol:protein length:60 Transcription termination/antitermination protein NusG  ali model follow..  17  7FEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSV............................................................................................... 41
13 -10.1005ms0_F mol:protein length:183 Transcription termination/antitermination protein NusG  ali model follow..  17  130FEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSV............................................................................................... 164
14 -10.1002ckk_A mol:protein length:127 KIN17  ali model follow..  20  72.APGKRILVLNGGYRGNEGTLESINEKTFSATIVI............................................................................................... 105
15 -10.0003j6b_Q mol:protein length:297 54S ribosomal protein L40, mitochondrial  ali model follow..  20  63FIPGDRVVVMSGASKGNIAVIKSFDKRTNSFILD................................................................................................ 96
16 -10.0005xy3_Y mol:protein length:138 Ribosomal protein L24, putative  ali model follow..  10  50IRRDDEVMIFSGRMQNRTGKVTAVKLSEMRIYVDTFTT............................................................................................ 87
17 -9.8205t2a_X mol:protein length:143 uL24  ali model follow..  13  47VRKDDEVIVKRGAFKGREGKVTACYRLKWVIHIDEITKLKLTHHRKAILERKDRSSKSDKGKGKISAADKAMQQMD...................................................... 143
18 -9.7503jcs_W mol:protein length:143 ribosomal protein L24  ali model follow..  13  47VRKDDEVIVKRGTFKGREGKVTACYRLKWVILIDEITKLKLTHHRKSILERKDRSSKSDKGKGKISAADKAMQQMD...................................................... 143
19 -9.7201nz9_A mol:protein length:58 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  22  5FREGDQVRVVSGPFADFTGTVTEINPERGKVKVMV............................................................................................... 39
20 -9.6201nkw_S mol:protein length:115 50S ribosomal protein L24  ali model follow..  20  16FKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVE................................................................................................ 49
21 -9.5205v7q_U mol:protein length:105 50S ribosomal protein L24  ali model follow..  23  3VHKGDTVLVISGKDKGAKGKVLQAYPDRNRVLVE................................................................................................ 36
22 -9.5102ww9_L mol:protein length:127 60S RIBOSOMAL PROTEIN L26-A  ali model follow..  18  50IRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTK............................................................................................ 87
23 -9.4904ytl_A mol:protein length:99 Transcription elongation factor SPT5  ali model follow..  15  1FQPGDRIEVLNGEQRGSKGIVTRTTKDIATIKL................................................................................................. 33
24 -9.4801m1g_A mol:protein length:248 Transcription antitermination protein nusG  ali model follow..  20  195FEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMI............................................................................................... 229
25 -9.4405o60_V mol:protein length:105 50S ribosomal protein L24  ali model follow..  20  3VHKGDTVLVISGKDKGAKGKVLVAYPDRNKVLVE................................................................................................ 36
26 -9.3105xxb_X mol:protein length:141 Ribosomal protein uL24  ali model follow..  8  49IRKDDEVMVVRGHHHDREGKVTKVYRKKWVIHIEVITKAKLDKDRKALLERKSRATTKGKYTEKDVAM.............................................................. 137
27 -9.2902do3_A mol:protein length:69 Transcription elongation factor SPT5  ali model follow..  22  18FKMGDHVKVIAGRFEGDTGLIVRVEENFVIL................................................................................................... 48
28 -9.2504v4i_S mol:protein length:110 50S ribosomal protein L24  ali model follow..  23  7VKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVE................................................................................................ 40
29 -9.2305t5h_Z mol:protein length:113 60S ribosomal protein L26  ali model follow..  28  41VRKDDEVRVKRGAYKGREGKVTACYRLRWVIHIDKVNR............................................................................................ 78
30 -9.2105ohq_A mol:protein length:111 Transcription elongation factor SPT5  ali model follow..  12  60.TKNNKVKVILGEDREATGVLLSIDGEDGIVRM................................................................................................. 91
31 -9.1704wce_R mol:protein length:105 50S ribosomal protein L24  ali model follow..  20  3IKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVE................................................................................................ 36
32 -9.1402xhc_A mol:protein length:352 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  17  299FKVGDMVKIISGPFEDFAGVIKEIDPERQELKVNV............................................................................................... 333
33 -9.0803j3v_U mol:protein length:103 50S ribosomal protein L24  ali model follow..  17  3VKKGDKVMVISGKDKGKQGTILAAFPKKDRVLVE................................................................................................ 36
34 -9.0303j79_Z mol:protein length:126 60S ribosomal protein uL24  ali model follow..  23  49VRKDDEVLICRGHNHGREGKVVKINRKRYKIYVERVTR............................................................................................ 86
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.

Mayya Sedova, Mallika Iyer, Zhanwen Li, Lukasz Jaroszewski, Kai W Post, Thomas Hrabe, Eduard Porta-Pardo, Adam Godzik Cancer3D 2.0:: interactive analysis of 3D patterns of cancer mutations in cancer subsets. Nucleic Acids Research, gky1098 2018; Published on November 8 2018.

Jaroszewski L, Rychlewski L, Godzik A. Improving the quality of twilight-zone alignments. Protein Sci. 2000 Aug;9(8):1487-96.