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Query: 6duq_M mol:protein length:60 Transcription termination/antitermination protein NusG, 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
# Score Template Links and tools%idFirst SNAKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKALast
1 -37.0006duq_M mol:protein length:60 Transcription termination/antitermination protein NusG  ali model  100  1SNAKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKA 60
2 -35.4002kvq_G mol:protein length:63 Transcription antitermination protein nusG  ali model follow..  95  4GRPKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKA 63
3 -34.9001nz9_A mol:protein length:58 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  60  1..AQVAFREGDQVRVVSGPFADFTGTVTEINPERGKVKVMVTIFGRETPVELDFSQVVKA 58
4 -34.6002mi6_A mol:protein length:62 Transcription termination/antitermination protein NusG  ali model follow..  51  3PVVEVDYEVGESVTVMDGPFATLPATISEVNAEQQKLKVLVSIFGRETPVELTFGQVSKI 62
5 -32.4005ms0_F mol:protein length:183 Transcription termination/antitermination protein NusG  ali model follow..  95  124PRPKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKA 183
6 -32.1002lq8_A mol:protein length:177 Transcription antitermination protein nusG  ali model follow..  50  117VKVELGFKVGDMVKIISGPFEDFAGVIKEIDPERQELKVNVTIFGRETPVVLHVSEVEKI 176
7 -29.5002lcl_A mol:protein length:66 Transcriptional activator rfaH  ali model follow..  17  9.VDPATPYPGDKVIITEGAFEGFQAIFTEPD-GEARSMLLLNLINKEIKHSVKNTEFRKL 66
8 -29.3002xhc_A mol:protein length:352 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  50  294.KVELGFKVGDMVKIISGPFEDFAGVIKEIDPERQELKVNVTIFGRETPVVLHVSEVEKI 352
9 -28.8001m1g_A mol:protein length:248 Transcription antitermination protein nusG  ali model follow..  60  189KPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTPVELDFDQVEKI 248
10 -24.4002oug_A mol:protein length:162 Transcriptional activator rfaH  ali model follow..  17  106..DPATPYPGDKVIITEGAFEGFQAIFTEPD-GEARSMLLLNLINKEIKHSVKNTEFRKL 162
11 -23.5004zn1_A mol:protein length:147 Transcription elongation factor Spt5  ali model follow..  21  83KKIIENIEKGDVVEIIAGPFKGERAKVIRVDKHKEEVTLELENAAVPIPITLPVEGVKIV 142
12 -20.8003qqc_D mol:protein length:163 Transcription antitermination protein nusG  ali model follow..  26  86KPAVSGLEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQFIDAIVPIPVTIKGDYVRLI 145
13 -17.8002e6z_A mol:protein length:59 Transcription elongation factor SPT5  ali model follow..  21  2SSGSSGFQPGDNVEVCEGELINLQGKILSVDGN--KITIMPKHEDLKDMLEFPAQELRK. 58
14 -13.1002e70_A mol:protein length:71 Transcription elongation factor SPT5  ali model follow..  20  20........IGQTVRISQGPYKGYIGVVKDATEST----ARVELHSTCQTISVDRQRLTTV 67
15 -12.7005xog_W mol:protein length:83 Spt4/5 complex component  ali model follow..  14  20........LNKTVKIRQGGYKGKIGIVKEANGDR----FRVELHNPNKTIPIPCSFLLIE 67
16 -12.6004ytl_A mol:protein length:99 Transcription elongation factor SPT5  ali model follow..  26  1......FQPGDRIEVLNGEQRGSKGIVTRTTKD----IATIKLNGFTTPLEFPISTLRKI 50
17 -11.4001s72_T mol:protein length:120 50S ribosomal protein L24P  ali model follow..  33  40...NVRVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVLEKTDGEEVPRPLDTSNV... 97
18 -11.0005xon_W mol:protein length:612 Protein that forms a complex with Spt4p  ali model follow..  14  549........LNKTVKIRQGGYKGKIGIVKEANGDR----FRVELHNPNKTIPIPCSFLLIE 596
19 -10.7005t5h_Z mol:protein length:113 60S ribosomal protein L26  ali model follow..  20  38...AMPVRKDDEVRVKRGAYKGREGKVTACYRLRWVIHIREKANGTTVPVGVHPSNV... 95
20 -10.6005t2a_X mol:protein length:143 uL24  ali model follow..  20  44...AMPVRKDDEVIVKRGAFKGREGKVTACYRLKWVIHI--KANGSTVAVGIHPSNV... 101
21 -10.5002ww9_L mol:protein length:127 60S RIBOSOMAL PROTEIN L26-A  ali model follow..  20  47...ALPIRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQV--KVNGASVPINLHPSKL... 104
22 -10.5005xy3_Y mol:protein length:138 Ribosomal protein L24, putative  ali model follow..  22  47...RLPIRRDDEVMIFSGRMQNRTGKVTAVKLSEMRIYVTEKINGQAVSFPVHPSNV... 104
23 -10.5003j79_Z mol:protein length:126 60S ribosomal protein uL24  ali model follow..  16  46...SLPVRKDDEVLICRGHNHGREGKVVKINRKRYKIYV--KVNGESTFIGIHPSNV... 103
24 -10.5003jcs_W mol:protein length:143 ribosomal protein L24  ali model follow..  20  44...AMPVRKDDEVIVKRGTFKGREGKVTACYRLKWVILI--KANGSTVAVGIHPSNV... 101
25 -10.4002do3_A mol:protein length:69 Transcription elongation factor SPT5  ali model follow..  27  12QELRKYFKMGDHVKVIAGRFEGDTGLIVRVEEN------FVILFSDLTMHELKV...... 59
26 -10.3003j6b_Q mol:protein length:297 54S ribosomal protein L40, mitochondrial  ali model follow..  23  62.....KFIPGDRVVVMSGASKGNIAVIKSFDKRTNSFIL..................... 95
27 -10.2005v7q_U mol:protein length:105 50S ribosomal protein L24  ali model follow..  24  3......VHKGDTVLVISGKDKGAKGKVLQAYPDRNRVLV..................... 35
28 -10.1004ytk_A mol:protein length:130 Transcription elongation factor SPT5  ali model follow..  17  1......LEEGSYVRIKRGIYKGDLAMVDQISENNLEVMLKI................... 35
29 -10.1004v4i_S mol:protein length:110 50S ribosomal protein L24  ali model follow..  28  2.RVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIV..................... 39
30 -10.1005o60_V mol:protein length:105 50S ribosomal protein L24  ali model follow..  21  3......VHKGDTVLVISGKDKGAKGKVLVAYPDRNKVLV..................... 35
31 -10.0005xxb_X mol:protein length:141 Ribosomal protein uL24  ali model follow..  20  46...SLPIRKDDEVMVVRGHHHDREGKVTKVYRKKWVIHI--KANGETVTIGIHPSKV... 103
32 -9.8404wce_R mol:protein length:105 50S ribosomal protein L24  ali model follow..  27  3......IKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVV..................... 35
33 -9.8203j3v_U mol:protein length:103 50S ribosomal protein L24  ali model follow..  24  3......VKKGDKVMVISGKDKGKQGTILAAFPKKDRVLV..................... 35
34 -9.7401nkw_S mol:protein length:115 50S ribosomal protein L24  ali model follow..  25  13...KLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVV..................... 48
35 -9.6802ckk_A mol:protein length:127 KIN17  ali model follow..  13  72.......APGKRILVLNGGYRGNEGTLESINEKTFSATIVIE-LKGRRVEGIQYEDISKL 126
36 -9.4403j7z_U mol:protein length:104 50S ribosomal protein L24  ali model follow..  16  2...AAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVE..................... 37
37 -9.2004ce4_Y mol:protein length:216 MRPL24  ali model follow..  24  56......LFCGDKVEILEGKDAGKQGKVVQVIRQRNWVVV..................... 88
38 -9.1106bph_A mol:protein length:69 AT-rich interactive domain-containing protein 4A  ali model follow..  11  1GEDMEPCLTGTKVKVKYGRGKTYEASIKSTEIDDGEVLYLVHYYGWNVRYD......... 54
39 -9.0203j7y_V mol:protein length:216 uL24  ali model follow..  24  56......LFCGDTVEILEGKDAGKQGKVVQVIRQRNWVVV..................... 88
FFAS is supported by the NIH grant R01-GM087218-01
1 4 7 3 0 1   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.

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.

Rychlewski L, Godzik A. Secondary structure prediction using segment similarity. Protein Eng. 1997 Oct;10(10):1143-53.