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Query: 4ytl_A mol:protein length:99 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.
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# Score Template Links and tools%idFirst FQPGDRIEVLNGEQRGSKGIVTRTTKDIATIKLNGFTTPLEFPISTLRKIFEPGDHVTVINGEHQGDAGLVLMVEQGQVTFMSTQTSREVTITANNLSKLast
1 -46.1004ytl_A mol:protein length:99 Transcription elongation factor SPT5  ali model  100  1FQPGDRIEVLNGEQRGSKGIVTRTTKDIATIKLNGFTTPLEFPISTLRKIFEPGDHVTVINGEHQGDAGLVLMVEQGQVTFMSTQTSREVTITANNLSK 99
2 -37.0005xon_W mol:protein length:612 Protein that forms a complex with Spt4p  ali model follow..  41  275FQPGDNVEIINGELNHLTGTVSSVNQSTIVSVRTINSETVEIPTSDLRKIFNVGDHVRVIHGKHTDDTGLIVEVNGDKVEFISNQTKRTVIVFSNYLIK 379
3 -34.7005oik_Z mol:protein length:1087 Transcription elongation factor SPT5  ali model follow..  38  420FQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDDMLEFPAQELRKYFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQL 520
4 -26.7005ohq_A mol:protein length:111 Transcription elongation factor SPT5  ali model follow..  16  4VTTDIQVKVRDTQVVGQTGVIRSVTGGMCSVYLKDSEKVVSISSEHLEPITTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRFLGK 107
5 -26.6002do3_A mol:protein length:69 Transcription elongation factor SPT5  ali model follow..  39  3...................................SGSSGEFPAQELRKYFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQL 66
6 -18.6002e6z_A mol:protein length:59 Transcription elongation factor SPT5  ali model follow..  38  8FQPGDNVEVCEGELINLQGKILSVDGNKITIMPKDLKDMLEFPAQELRKY................................................. 59
7 -16.3002ckk_A mol:protein length:127 KIN17  ali model follow..  18  15LQPEIIVKIITEKYHKKKAIVKEVDKYTAVVKMIDSGDKLKLDQTHLETVIAPGKRILVLNGGYRGNEGTLESINEKTFSATIVIETGPLK........ 111
8 -15.9005xog_W mol:protein length:83 Spt4/5 complex component  ali model follow..  21  20..LNKTVKIRQGGYKGKIGIVKEANGDRFRVELHNPNKTIPIPCSFLL................................................... 65
9 -15.0002e70_A mol:protein length:71 Transcription elongation factor SPT5  ali model follow..  19  20..IGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT................................................... 65
10 -13.9003h8z_A mol:protein length:128 Fragile X mental retardation syndrome-related protein 2  ali model follow..  20  2YFQGLPVEVRGSNGAFYKGFVKDVHEDSVTIFFENNWQSERIPFGDVRKEITEGDEVEVYSRANEQELARVRMMKGDFYVIEYAACDATYNVTLERLR. 115
11 -13.9002lq8_A mol:protein length:177 Transcription antitermination protein nusG  ali model follow..  22  123FKVGDMVKIISGPFEDFAGVIKEIDPEKVNVTIFGRETPVVLHVSEVEKI................................................. 176
12 -13.6003j6b_Q mol:protein length:297 54S ribosomal protein L40, mitochondrial  ali model follow..  13  63FIPGDRVVVMSGASKGNIAVIKSFDKRTNSFILDENGPTKTVPVPKQFW----------LEGQTSHMITIPVSILGKDLRLVADIDDEKTPGKTRTV.. 149
13 -13.5005ms0_F mol:protein length:183 Transcription termination/antitermination protein NusG  ali model follow..  26  130FEPGEMVRVNDGPFADFNGVVEEVDYEKVSVSIFGRATPVELDFSQVEKA................................................. 183
14 -13.5001m1g_A mol:protein length:248 Transcription antitermination protein nusG  ali model follow..  28  195FEKGDQVRVIEGPFMNFTGTVEEVHPETVMISIFGRMTPVELDFDQVEKI................................................. 248
15 -13.2005oho_A mol:protein length:113 Transcription elongation factor SPT5  ali model follow..  14  2.PWGELVQLDPQT----VGVIVRLERETFQV-LNMYGKVVTVRHQAVTNNIHVKDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVEN.......... 99
16 -13.0002kvq_G mol:protein length:63 Transcription antitermination protein nusG  ali model follow..  26  10FEPGEMVRVNDGPFADFNGVVEEVDYEKVSVSIFGRATPVELDFSQVEKA................................................. 63
17 -12.9002mam_A mol:protein length:118 AT-rich interactive domain-containing protein 4A  ali model follow..  9  7LTVGTDVSA-RGAF--CEAKIKTVKRLKVKVLLKQDNTTQLVQDDQVKGPLRVGAIVETRTSDGSFQEAIISKLTDASWYTVVFDDGDERTLRRTSL.. 103
18 -12.9002lcl_A mol:protein length:66 Transcriptional activator rfaH  ali model follow..  20  14PYPGDKVIITEGAFEGFQAIFTEPDGEMLLLNLINKEIKHSVKNTEFRKL................................................. 66
19 -12.9004qvz_A mol:protein length:214 Fragile X mental retardation protein 1  ali model follow..  17  2.MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPDRIPFHDVRKDINESDEVEVYSRANEKELAKVRMIKGEFYVIEYAACDATYNVTIERLR. 114
20 -12.6004ce4_Y mol:protein length:216 MRPL24  ali model follow..  15  56LFCGDKVEILEGKDAGKQGKVVQVIRQRNWVVVEGLNTHYR--------------YVGKTVDYRGTMIPSEAPLLHNQVKLVDPTDRKPTDVEWRFTEA 140
21 -12.6006duq_M mol:protein length:60 Transcription termination/antitermination protein NusG  ali model follow..  26  7FEPGEMVRVNDGPFADFNGVVEEVDYEKVSVSIFGRATPVELDFSQVEKA................................................. 60
22 -12.5002mi6_A mol:protein length:62 Transcription termination/antitermination protein NusG  ali model follow..  16  9YEVGESVTVMDGPFATLPATISEVNAEKVLVSIFGRETPVELTFGQVSK.................................................. 61
23 -12.5003j7y_V mol:protein length:216 uL24  ali model follow..  15  56LFCGDTVEILEGKDAGKQGKVVQVIRQRNWVVVGGLNTHYR--------------YIGKTMDYRGTMIPSEAPLLHRQVKLVDPMDRKPTEIEWRFTEA 140
24 -12.5001s72_T mol:protein length:120 50S ribosomal protein L24P  ali model follow..  34  43VNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVED................................................................ 77
25 -12.3005mmi_V mol:protein length:192 plastid ribosomal protein uL24c  ali model follow..  16  70VKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKD-----------------LNLKTKHVKSKEEGEQGQIIKIEASNVMLYSKEQEVASRVGHKILED 155
26 -12.2001nz9_A mol:protein length:58 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  28  5FREGDQVRVVSGPFADFTGTVTEINPERVMVTIFGRETPVELDFSQVVK.................................................. 57
27 -12.0002gf7_A mol:protein length:119 Jumonji domain-containing protein 2A  ali model follow..  10  7ITAGQKVISKHKNGRFYQCEVVRLTTEFYEVNFDDGSFSDNLYPEDIFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDV.. 111
28 -11.9002oug_A mol:protein length:162 Transcriptional activator rfaH  ali model follow..  20  110PYPGDKVIITEGAFEGFQAIFTEPDGEMLLLNLINKEIKHSVKNTEFRKL................................................. 162
29 -11.9002xhc_A mol:protein length:352 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  22  299FKVGDMVKIISGPFEDFAGVIKEIDPERVNVTIFGRETPVVLHVSEVEKI................................................. 352
30 -11.9005mlc_W mol:protein length:191 50S ribosomal protein L24, chloroplastic  ali model follow..  16  69VKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKD----LNFKTKHVKSK---------EEGEQGQIIKIEAAIHSSNVMLILKEQEVADRVGHKILED 154
31 -11.8005d6w_A mol:protein length:121 Lysine-specific demethylase 4A  ali model follow..  10  9ITAGQKVISKHKNGRFYQCEVVRLTTEFYEVNFDDGSFSDNLYPEDIFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDV.. 113
32 -11.7004tse_A mol:protein length:174 E3 ubiquitin-protein ligase MIB1  ali model follow..  21  11LQIGDLVNIDLDETLTTTGTVCGIDEDHDIVVQYPSGNRWTFNPAVLTKAFQVGDLVQVCYDLERGKVGRVQQIYSD--DLKVEVCGTSWTYNPAAVSK 164
33 -11.5001nkw_S mol:protein length:115 50S ribosomal protein L24  ali model follow..  28  16FKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEG................................................................ 50
34 -11.5004uc4_A mol:protein length:119 Lysine-specific demethylase 4B  ali model follow..  6  7VSLGQVVITKNRNGLYYRCRVIGAASQCYEVNFDDGSYSDNLYPESITSRPSEGELVELRWTDGNLYKAKFISSVTSHIYQVEFEDGSQLTVKRGDI.. 111
35 -11.5005o60_V mol:protein length:105 50S ribosomal protein L24  ali model follow..  24  3VHKGDTVLVISGKDKGAKGKVLVAYPDRNKVLVEGVNRIKK--------------HTAVSANERGASSGGIVTQE........................ 63
36 -11.4002xdp_A mol:protein length:123 LYSINE-SPECIFIC DEMETHYLASE 4C  ali model follow..  7  7ISVGQTVITKHRNTRYYSCRVMAVTSQFYEVMFDDGSFSRDTFPEDIVSRPAEGEVVQVKWPDGKLYGAKYFGSNIAHMYQVEFEDGSQIAMKREDI.. 111
37 -11.4005v7q_U mol:protein length:105 50S ribosomal protein L24  ali model follow..  21  3VHKGDTVLVISGKDKGAKGKVLQAYPDRNRVLVEGVNRIKK--------------HTAISTTQRGARSGGIVTQE........................ 63
38 -11.4005xy3_Y mol:protein length:138 Ribosomal protein L24, putative  ali model follow..  17  50IRRDDEVMIFSGRMQNRTGKVTAVKLSEMRIYVD................................................................. 83
39 -11.3004zn1_A mol:protein length:147 Transcription elongation factor Spt5  ali model follow..  20  89IEKGDVVEIIAGPFKGERAKVIRVDKHTLELENAAVPIPITLPVEGVKIVSKHKD............................................ 147
40 -11.2003j7z_U mol:protein length:104 50S ribosomal protein L24  ali model follow..  21  1..............................................MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEG............... 38
41 -11.1004v4i_S mol:protein length:110 50S ribosomal protein L24  ali model follow..  13  7VKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEG-----------------VNIVKKAVRVSPKYPQGGFIEKEASKVRPICPACGKPTRVRKKFLEN 92
42 -11.0004wce_R mol:protein length:105 50S ribosomal protein L24  ali model follow..  25  3IKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVEG................................................................ 37
43 -11.0003j3v_U mol:protein length:103 50S ribosomal protein L24  ali model follow..  20  3VKKGDKVMVISGKDKGKQGTILAAFPKKDRVLVEG................................................................ 37
44 -10.9003qqc_D mol:protein length:163 Transcription antitermination protein nusG  ali model follow..  22  92LEPGDLVEVIAGPFKGQKAKVVKIDESVVQFIDAIVPIPVTIKGDYVRL.................................................. 144
45 -10.9003jcs_W mol:protein length:143 ribosomal protein L24  ali model follow..  23  47VRKDDEVIVKRGTFKGREGKVTACYRLKWVILID................................................................. 80
46 -10.9002ww9_L mol:protein length:127 60S RIBOSOMAL PROTEIN L26-A  ali model follow..  14  50IRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQVD................................................................. 83
47 -10.9005t2a_X mol:protein length:143 uL24  ali model follow..  23  47VRKDDEVIVKRGAFKGREGKVTACYRLKWVIHID................................................................. 80
48 -10.6003kuf_A mol:protein length:131 Fragile X mental retardation syndrome-related protein 1  ali model follow..  18  1...AETVEVRGSNGAFYKGFIKDVHEDSLTVVFENNWQPERVPFNEVRKEISEGDEVEVYSRANDQELAKVRMMKGEFYVIEYAACDATYNVTFERLR. 112
49 -10.5005t5h_Z mol:protein length:113 60S ribosomal protein L26  ali model follow..  23  41VRKDDEVRVKRGAYKGREGKVTACYRLRWVIHID................................................................. 74
50 -10.5003j79_Z mol:protein length:126 60S ribosomal protein uL24  ali model follow..  17  49VRKDDEVLICRGHNHGREGKVVKINRKRYKIYVE................................................................. 82
51 -10.4005xxb_X mol:protein length:141 Ribosomal protein uL24  ali model follow..  20  49IRKDDEVMVVRGHHHDREGKVTKVYRKKWVIHIE................................................................. 82
52 -9.9201s72_Q mol:protein length:96 50S ribosomal protein L21e  ali model follow..  18  24........................................TSPPQRAVEEFDDGEKVHLKIDPFDGQTGTVEGKQGDAVDIVDGGKEKTIIVTAAHLRR 94
53 -9.6705xxb_Y mol:protein length:146 Ribosomal protein eL27  ali model follow..  20  5LKSGRVVVVLNGRHAGKKGVVVNTWEGSAGIEKAPLKVHKKMPAKKIEKRMRVKPFLKYINVNHLMPTRYTVSSDMDVKTMVPEDAMRTVDDRKAAKKG 113
54 -9.5504mdw_A mol:protein length:166 Uncharacterized protein YdhK  ali model follow..  16  43YKVGSQVIINTSHMKGMKGAEATVTGAVVSYTPTNGGQRVDVIQEEIKKTLQPGDQVILEASHMKGMKGEIDSAEKTTVYMVD................ 142
55 -9.4904ytk_A mol:protein length:130 Transcription elongation factor SPT5  ali model follow..  15  1LEEGSYVRIKRGIYKGDLAMVDQISENNLEVML.................................................................. 33
56 -9.3805xy3_T mol:protein length:159 Ribosomal protein L21e, putative  ali model follow..  16  24........................................APAPSITLRTFRIGDIVDIKVNGYHGATGIVWNVSPHAVGILVKRRPKRIYVRTEHVFP 98
57 -9.3403jcs_S mol:protein length:159 ribosomal protein L21e  ali model follow..  20  24........................................APSVSTILTNIKVGDYVDVVADSYHGRTGIVWNVTPRGVGVIINKPRKRICVRFEHVRK 98
58 -9.1903j79_V mol:protein length:161 60S ribosomal protein eL21  ali model follow..  15  25........................................ECTANKYLEKLNYGDYVDIVCDSYHGKTGKIFHITKRGVGVLVNKRQKKVCVRIEHVRK 99
59 -9.0104fib_A mol:protein length:129 Uncharacterized protein ydhK  ali model follow..  14  1MKVGSQVIINTSHMKGMKGAEATVTGAVVSYTPTNGGQRVDVIQEEIKDALQPGDQVILEASHMKGMKGATAEIDS....................... 90
60 -9.0005xxb_S mol:protein length:157 Ribosomal protein eL21  ali model follow..  22  24........................................MPAVSRLLVIHKKGDYVDIVCDPYHGRTGIVFNVTQRAVGVEVNKVKKRIHVRLEHVRK 98
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.

Plewczynski D, Tkacz A, Godzik A., Rychlewski L. A support vector machine approach to the identification of phosphorylation sites. Cell Mol Biol Lett. 2005;10(1):73-89.