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Query: 2do3_A mol:protein length:69 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    .
# Score Template Links and tools%idFirst GSSGSSGEFPAQELRKYFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLCSELast
1 -37.5002do3_A mol:protein length:69 Transcription elongation factor SPT5  ali model  100  1GSSGSSGEFPAQELRKYFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLCSE 69
2 -26.7004ytl_A mol:protein length:99 Transcription elongation factor SPT5  ali model follow..  39  36..FTTPLEFPISTLRKIFEPGDHVTVINGEHQGDAGLVLMVEQGQVTFMSTQTSREVTITANNLSK... 99
3 -26.3005xon_W mol:protein length:612 Protein that forms a complex with Spt4p  ali model follow..  37  317...SETVEIPTSDLRKIFNVGDHVRVIHGKHTDDTGLIVEVNGDKVEFISNQTKRTVIVFSNYLIKSTD 382
4 -23.7005oik_Z mol:protein length:1087 Transcription elongation factor SPT5  ali model follow..  93  458...KDMLEFPAQELRKYFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLCSE 523
5 -15.3005ohq_A mol:protein length:111 Transcription elongation factor SPT5  ali model follow..  22  43..SEKVVSISSEHLEPITTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRFLGKLLE 110
6 -15.1005xog_W mol:protein length:83 Spt4/5 complex component  ali model follow..  14  20...................LNKTVKIRQGGYKGKIGIVKEANGDRFRVELHNPNKTIPIPCSFLLIEST 69
7 -15.0002e6z_A mol:protein length:59 Transcription elongation factor SPT5  ali model follow..  21  2...........SSGSSGFQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEKDMLEFPAQELRK... 58
8 -14.8002e70_A mol:protein length:71 Transcription elongation factor SPT5  ali model follow..  18  20...................IGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLTTVGS 69
9 -12.6003j7z_U mol:protein length:104 50S ribosomal protein L24  ali model follow..  18  1.............MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEG.................. 38
10 -12.1004zn1_A mol:protein length:147 Transcription elongation factor Spt5  ali model follow..  19  80........LTPKKIIENIEKGDVVEIIAGPFKGERAKVIRVDKHTLELENAAVPIPITLPVEGVKIVSK 144
11 -12.0001s72_T mol:protein length:120 50S ribosomal protein L24P  ali model follow..  26  43.................VNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVE.................. 76
12 -11.9003qqc_D mol:protein length:163 Transcription antitermination protein nusG  ali model follow..  22  83........LEEKPAVSGLEPGDLVEVIAGPFKGQKAKVVKIDESVVQFIDAIVPIPVTIKGDYVRLISK 147
13 -11.9001nkw_S mol:protein length:115 50S ribosomal protein L24  ali model follow..  29  16.................FKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVE.................. 49
14 -11.8004v4i_S mol:protein length:110 50S ribosomal protein L24  ali model follow..  23  2............RVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVE.................. 40
15 -11.7004wce_R mol:protein length:105 50S ribosomal protein L24  ali model follow..  32  3.................IKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVE.................. 36
16 -11.7005v7q_U mol:protein length:105 50S ribosomal protein L24  ali model follow..  23  3.................VHKGDTVLVISGKDKGAKGKVLQAYPDRNRVLVE.................. 36
17 -11.6005o60_V mol:protein length:105 50S ribosomal protein L24  ali model follow..  23  3.................VHKGDTVLVISGKDKGAKGKVLVAYPDRNKVLVE.................. 36
18 -11.6003j3v_U mol:protein length:103 50S ribosomal protein L24  ali model follow..  29  3.................VKKGDKVMVISGKDKGKQGTILAAFPKKDRVLVE.................. 36
19 -11.6003j6b_Q mol:protein length:297 54S ribosomal protein L40, mitochondrial  ali model follow..  26  63.................FIPGDRVVVMSGASKGNIAVIKSFDKRTNSFILD.................. 96
20 -11.5001m1g_A mol:protein length:248 Transcription antitermination protein nusG  ali model follow..  23  164MVGGKPVPLKEEEVQNIFEKGDQVRVIEGPFMNFTGTVEEVHPEKLTVMISIFGRMTPV.......... 238
21 -11.4005xy3_Y mol:protein length:138 Ribosomal protein L24, putative  ali model follow..  24  37...........KELQEANRRDDEVMIFSGRMQNRTGKVTAVKLSEMRIYVDTFTTE............. 88
22 -11.4002lq8_A mol:protein length:177 Transcription antitermination protein nusG  ali model follow..  33  123.................FKVGDMVKIISGPFEDFAGVIKEIDPERLKVNVTIFGRETPV.......... 166
23 -11.3005ms0_F mol:protein length:183 Transcription termination/antitermination protein NusG  ali model follow..  18  130.................FEPGEMVRVNDGPFADFNGVVEEVDYEKVSVSIFGRATPVELDFSQVEKA.. 183
24 -11.3003jcs_W mol:protein length:143 ribosomal protein L24  ali model follow..  26  34...........KELRAKYRKDDEVIVKRGTFKGREGKVTACYRLKWVILIDKVNRE............. 85
25 -11.2003jcs_S mol:protein length:159 ribosomal protein L21e  ali model follow..  19  24.......APSVSTILTNIKVGDYVDVVADYYHGRTGIVWNVTPRGVGVIINKPRKRICVRFEHVRKSR. 100
26 -11.2001s72_Q mol:protein length:96 50S ribosomal protein L21e  ali model follow..  21  24.......TSPPQRAVEEFDDGEKVHLKIDRFDGQTGTVEGKQGDAVDIVDGGKEKTIIVTAAHLRRQE. 96
27 -11.2005t2a_X mol:protein length:143 uL24  ali model follow..  26  34...........KELRAKYRKDDEVIVKRGAFKGREGKVTACYRLKWVIHIDKVNRE............. 85
28 -11.0003j79_V mol:protein length:161 60S ribosomal protein eL21  ali model follow..  18  25.......ECTANKYLEKLNYGDYVDIVCDYYHGKTGKIFHITKRGVGVLVNKRQKKVCVRIEHVRKSR. 101
29 -10.9002ww9_L mol:protein length:127 60S RIBOSOMAL PROTEIN L26-A  ali model follow..  28  37...........KELRAQYRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKE............. 88
30 -10.8005xxb_S mol:protein length:157 Ribosomal protein eL21  ali model follow..  18  24.......MPAVSRLLVIHKKGDYVDIVCDYYHGRTGIVFNVTQRAVGVENRVIKKRIHVRLEHVRKSR. 100
31 -10.8005xy3_T mol:protein length:159 Ribosomal protein L21e, putative  ali model follow..  16  24.......APAPSITLRTFRIGDIVDIKVNVYHGATGIVWNVSPHAVGILNHIAPKRIYVRTEHVFPSK. 100
32 -10.8005xxb_X mol:protein length:141 Ribosomal protein uL24  ali model follow..  22  36...........KELRKKYRKDDEVMVVRGHHHDREGKVTKVYRKKWVIHIERVTRD............. 87
33 -10.7004ce4_Y mol:protein length:216 MRPL24  ali model follow..  23  56.................LFCGDKVEILEGKDAGKQGKVVQVIRQRNWVVVE.................. 89
34 -10.7005mlc_W mol:protein length:191 50S ribosomal protein L24, chloroplastic  ali model follow..  32  69.................VKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIK.................. 102
35 -10.6003j7o_T mol:protein length:160 Ribosomal protein eL21  ali model follow..  18  24.......VVPLATYMRIYKKGDIVDIKGMCYHGKTGRVYNVTQHAVGIVGKILAKRINVRIEHIKHSK. 100
36 -10.6003jct_T mol:protein length:160 60S ribosomal protein L21-A  ali model follow..  19  24.......AVHLSTYLKVYKVGDIVDIKANFYQGKTGVVYNVTKSSVGVINRYLEKRLNLRVEHIKHSK. 100
37 -10.6003j7y_V mol:protein length:216 uL24  ali model follow..  23  56.................LFCGDTVEILEGKDAGKQGKVVQVIRQRNWVVVG.................. 89
38 -10.5005mmi_V mol:protein length:192 plastid ribosomal protein uL24c  ali model follow..  27  70.................VKVGDTVKVISGGEKGKIGEISKIHKHNSTVI-----KDLNLKTKHVKSKEE 117
39 -10.5002kvq_G mol:protein length:63 Transcription antitermination protein nusG  ali model follow..  30  10.................FEPGEMVRVNDGPFADFNGVVEEVDYESVSIFGRATPVELDF.......... 57
40 -10.5003j79_Z mol:protein length:126 60S ribosomal protein uL24  ali model follow..  22  36...........KELRLKYRKDDEVLICRGHNHGREGKVVKINRKRYKIYVERVTRE............. 87
41 -10.4002ckk_A mol:protein length:127 KIN17  ali model follow..  19  55..SGDKLKLDQTHLETVIAPGKRILVLNGGYRGNEGTLESINEKTFSATIVIETGPLK........... 111
42 -10.4006duq_M mol:protein length:60 Transcription termination/antitermination protein NusG  ali model follow..  27  1...........SNAKTLFEPGEMVRVNDGPFADFNGVVEEVDYESVSIFGRATPVELDF.......... 54
43 -10.3005t5h_Z mol:protein length:113 60S ribosomal protein L26  ali model follow..  24  28...........KELRAKYRKDDEVRVKRGAYKGREGKVTACYRLRWVIHIDKVNRE............. 79
44 -10.3002oug_A mol:protein length:162 Transcriptional activator rfaH  ali model follow..  26  110.................PYPGDKVIITEGAFEGFQAIFTEPDGERSMLLLNLINKEIKH.......... 152
45 -10.3005xxb_Y mol:protein length:146 Ribosomal protein eL27  ali model follow..  34  1.............MVKLLKSGRVVVVLNGRHAGKKGVVVNTWEGS........................ 32
46 -10.3002lcl_A mol:protein length:66 Transcriptional activator rfaH  ali model follow..  26  14.................PYPGDKVIITEGAFEGFQAIFTEPDGERSMLLLNLINKEIKH.......... 56
47 -10.2005t5h_U mol:protein length:146 Ribosomal protein L21E (60S)  ali model follow..  21  23........PSVSTILTNFKVGDYVDVVADYYHGRTGIVWNVTPRGVGVIVNKPRKRICVRFEHVRKSR. 98
48 -10.2002xhc_A mol:protein length:352 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  35  261SSGGQPVPVKDREMRPIFKVGDMVKIISGPFEDFAGVIKEIDPENVTIFGRETPVVLHV.......... 346
49 -10.1002mi6_A mol:protein length:62 Transcription termination/antitermination protein NusG  ali model follow..  28  9.................YEVGESVTVMDGPFATLPATISEVNAELVSIFGRETPVELTF.......... 56
50 -9.7905oho_A mol:protein length:113 Transcription elongation factor SPT5  ali model follow..  26  58..............QNNIHVKDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVEN............. 99
51 -9.7203jct_Z mol:protein length:136 60S ribosomal protein L27-A  ali model follow..  29  1.............MAKFLKAGKVAVVVRGRYAGKKVVIVKPHDE......................... 31
52 -9.6603j7o_Z mol:protein length:136 Ribosomal protein eL27  ali model follow..  35  1.............MGKFMKPGKVVLVLAGRYSGRKAVIVKNIDD......................... 31
53 -9.6601nz9_A mol:protein length:58 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  20  5.................FREGDQVRVVSGPFADFTGTVTEINPEKVMVTIFGRETPVELDFSQVVKA.. 58
54 -9.5603jcs_Y mol:protein length:134 ribosomal protein L27e  ali model follow..  35  1.............MTKFLKPGKVVIVTAGRYAGHKAVIVQNSDI......................... 31
55 -9.5403j79_N mol:protein length:165 60S ribosomal protein eL14  ali model follow..  11  21.............FKRFVEPGRLCLIEYGPYAGKLCFIVDIVTITRVIVDGAFITGVP........... 65
56 -9.3703j79_1 mol:protein length:146 60S ribosomal protein eL27  ali model follow..  29  1.............MGKLLKPGKVIIILNGRRAGKKAVIVNTYEG......................... 31
57 -9.3605t5h_a mol:protein length:132 Ribosomal protein L27  ali model follow..  34  1...............KFLKPGKVVIVTSGRYAGKKAVIVQNTDS......................... 29
58 -9.3605xxb_L mol:protein length:134 Ribosomal protein eL14  ali model follow..  16  1..........MGLFTRYYQPGRLCVVQYGPDAGKLCFVVDIINQTRVLVDGAGVTGVK........... 48
59 -9.2904ytk_A mol:protein length:130 Transcription elongation factor SPT5  ali model follow..  22  1.................LEEGSYVRIKRGIYKGDLAMVDQISENNLEV..................... 31
60 -9.1204adx_7 mol:protein length:126 RPL14E  ali model follow..  20  3.............FNKFVQVGRVVYINYGADKGKLAVIVNIINQNRILIDGEHIVRQVIPIRRVHLTK. 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.

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.