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Query: 4zn1_A mol:protein length:147 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 MIFAVRTMVGQEKNIAGLMASRAEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPLLTPKKIIENIEKGDVVEIIAGPFKGERAKVIRVDKHKEEVTLELENAAVPIPITLPVEGVKIVSKHKDLast
1 -75.6004zn1_A mol:protein length:147 Transcription elongation factor Spt5  ali model  100  1MIFAVRTMVGQEKNIAGLMASRAEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPLLTPKKIIENIEKGDVVEIIAGPFKGERAKVIRVDKHKEEVTLELENAAVPIPITLPVEGVKIVSKHKD 147
2 -71.1003qqc_D mol:protein length:163 Transcription antitermination protein nusG  ali model follow..  44  5.IFAVRVTHGQEETTAKLIYSKVRTYNLPIYAILAPSRVKGYIFVEAPNKGVVDEAIRGIRHARGVLPGEVPFKEIEHFLEEKPAVSGLEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQFIDAIVPIPVTIKGDYVRLISKLQK 150
3 -42.4002lq8_A mol:protein length:177 Transcription antitermination protein nusG  ali model follow..  24  7.WYIVLTMSGYEEKVKENIEKKVEATGIKNQRRKSEKLFPGYVFVEMIMNDEAYNFVRSVPYVMGFVPVPVKDREMRPILRPVKVELGFKVGDMVKIISGPFEDFAGVIKEIDPERQELKVNVTIFGRETPVVLHVSEVEKIE.... 177
4 -42.1005oik_Z mol:protein length:1087 Transcription elongation factor SPT5  ali model follow..  22  179.LWTVKCKIGEERATAISLMRKFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRYWNQQMVPIKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDYDRIKARMSLKDWFAKRKK 331
5 -41.5003ewg_A mol:protein length:91 Putative transcription antitermination protein nusG  ali model follow..  97  1MIFAVRTMVGQEKNIAGLMASRAEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPLLTPKLE.............................................................. 85
6 -41.1005ms0_F mol:protein length:183 Transcription termination/antitermination protein NusG  ali model follow..  21  11.WYVVQAFSGFEGRVATSLREHIKLHNME-RRKSERKFFPGYVLVQMVMNDASWHLVRSVPRVMGFIPAPISDKEVDAIMNKPRPKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKA..... 183
7 -40.7005xon_W mol:protein length:612 Protein that forms a complex with Spt4p  ali model follow..  25  23.IWGVKVRLGKEKDVVRQILKKKTKNPLEIYSAFQRDSFKGHVYIEARKAEAINDALKGNVNVFSNSKFLVGIVEYKDLLRVKSSDVKLTRGSYVRVKNGKFKGDLAQVDEVLENGLEARLKLVPRLDYGKDLSHLSTSSSVDSTKN 175
8 -40.6003lpe_A mol:protein length:92 Putative transcription antitermination protein nusG  ali model follow..  100  12.IFAVRTMVGQEKNIAGLMASRAEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPLLTP................................................................. 92
9 -38.2003h7h_B mol:protein length:106 Transcription elongation factor SPT5  ali model follow..  26  8.LWTVKCKIGEERATAISLMRKFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLGYQQMVPIKEMTDVLKVVKEVANLGSGC...................................................... 106
10 -36.5001m1g_A mol:protein length:248 Transcription antitermination protein nusG  ali model follow..  21  82.GVTTFRIENGEVKVVESVEGDTCVNAPPIKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRPVPVPLKEEEVQNILNQIKRKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTPVELDFDQVEKI..... 248
11 -35.1002exu_A mol:protein length:200 Transcription initiation protein SPT4/SPT5  ali model follow..  25  104.IWGVRCRPGKEKELIRKLLKKKGKKKLKILSIFQRDNYTGRIYIEAPKQSVIEKFCNGVPDIYISQKLLIPVQELPLLLKPNLE.............................................................. 194
12 -35.0002xhc_A mol:protein length:352 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  22  171.VYYIPLDVFDRDRIKKGKEVKQGEKEIRIYKTKRRKLFPGYVFVEMIMNDEAYNFVRSVPYVMGFVPVPVKDREMRPILRPVKVELGFKVGDMVKIISGPFEDFAGVIKEIDPERQELKVNVTIFGRETPVVLHVSEVEKI..... 352
13 -33.5002oug_A mol:protein length:162 Transcriptional activator rfaH  ali model follow..  17  4.WYLLYCKRGQLQRAQEHLERQAVNCLAPMITLVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVPAIVPSAVIHQLSVYKPKPATPYPGDKVIITEGAFEGFQAIFTEPD-GEARSMLLLNLINKEIKHSVKNTEFRKL..... 162
14 -23.9002kvq_G mol:protein length:63 Transcription antitermination protein nusG  ali model follow..  20  2................................................................................AMGRPKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKA..... 63
15 -23.5002mi6_A mol:protein length:62 Transcription termination/antitermination protein NusG  ali model follow..  18  2.................................................................................RPVVEVDYEVGESVTVMDGPFATLPATISEVNAEQQKLKVLVSIFGRETPVELTFGQVSKI..... 62
16 -23.4006duq_M mol:protein length:60 Transcription termination/antitermination protein NusG  ali model follow..  21  1..................................................................................SNAKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKA..... 60
17 -22.7004ytk_A mol:protein length:130 Transcription elongation factor SPT5  ali model follow..  20  1........................................................................................LEEGSYVRIKRGIYKGDLAMVDQISENNLEVMLKIVPRLDYGKFDEIDPTTQQRKSRRP 59
18 -22.4001nz9_A mol:protein length:58 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  19  1....................................................................................AQVAFREGDQVRVVSGPFADFTGTVTEINPERGKVKVMVTIFGRETPVELDFSQVVK...... 57
19 -19.7001nz8_A mol:protein length:119 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  22  4.WYAVHTLVGQEEKAKANLEKRIKAFGLQ-KEVVRKKLFPGYLFIQMDLGDEAWEVVRGTPGITGFVPVPLSPDEVRHILEVSGLL............................................................. 118
20 -18.3002lcl_A mol:protein length:66 Transcriptional activator rfaH  ali model follow..  19  6................................................................................KDIVDPATPYPGDKVIITEGAFEGFQAIFTEPD-GEARSMLLLNLINKEIKHSVKNTEFRKL..... 66
21 -15.4002e70_A mol:protein length:71 Transcription elongation factor SPT5  ali model follow..  23  20..........................................................................................IGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQT----ISVDRQRLTTVGSRR. 71
22 -14.3002e6z_A mol:protein length:59 Transcription elongation factor SPT5  ali model follow..  17  2..................................................................................SSGSSGFQPGDNVEVCEGELINLQGKILSVD--GNKITIMPKHEDLKDMLEFPAQELRK...... 58
23 -14.2005xog_W mol:protein length:83 Spt4/5 complex component  ali model follow..  27  20..........................................................................................LNKTVKIRQGGYKGKIGIVKEANGDRFRVELHNPNKT----IPIPCSFLLIESTH.. 70
24 -12.3001s72_T mol:protein length:120 50S ribosomal protein L24P  ali model follow..  26  39....................................................................................RNVRVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVEEKTDGEEVPRPLDTSNVRVTDLDLE 105
25 -12.1002do3_A mol:protein length:69 Transcription elongation factor SPT5  ali model follow..  19  9...............................................................................FPAQELRKYFKMGDHVKVIAGRFEGDTGLIVRVEEN----FVILFSDLTMHELKVLPRDLQLCSE... 69
26 -11.6003j6b_Q mol:protein length:297 54S ribosomal protein L40, mitochondrial  ali model follow..  23  62.......................................................................................KFIPGDRVVVMSGASKGNIAVIKSFDKRTNSFILD-TSHMITIPVSILGKDLRLVADIDD 139
27 -11.6002ckk_A mol:protein length:127 KIN17  ali model follow..  11  38.......................................................IVKEVIDKYTAVVKMIDSGDKLKLDQTHLETVIPAPGKRILVLNGGYRGNEGTLESINEKTFSATIVI........................ 105
28 -11.4005xy3_Y mol:protein length:138 Ribosomal protein L24, putative  ali model follow..  17  46....................................................................................KRLPIRRDDEVMIFSGRMQNRTGKVTAVKLSEMRIYVDTFTTGQAVSFPVHPSNVVITKLKMD 112
29 -11.3004ytl_A mol:protein length:99 Transcription elongation factor SPT5  ali model follow..  20  1........................................................................................FQPGDRIEVLNGEQRGSKGIVTRTTKD----IATIKLNGFTTPLEFPISTLRKIFEPGD 55
30 -11.3002ww9_L mol:protein length:127 60S RIBOSOMAL PROTEIN L26-A  ali model follow..  25  46....................................................................................KALPIRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKGASVPINLHPSKLVITKLHLD 112
31 -11.2005t5h_Z mol:protein length:113 60S ribosomal protein L26  ali model follow..  19  37....................................................................................RAMPVRKDDEVRVKRGAYKGREGKVTACYRLRWVIHIDKVNRGTTVPVGVHPSNVEITKLKLN 103
32 -11.1005v7q_U mol:protein length:105 50S ribosomal protein L24  ali model follow..  34  2.......................................................................................KVHKGDTVLVISGKDKGAKGKVLQAYPDRNRVLVE......................... 36
33 -11.1003jcs_W mol:protein length:143 ribosomal protein L24  ali model follow..  20  43....................................................................................RAMPVRKDDEVIVKRGTFKGREGKVTACYRLKWVILIDKVNRGSTVAVGIHPSNVEITKLKLT 109
34 -11.1005t2a_X mol:protein length:143 uL24  ali model follow..  20  43....................................................................................RAMPVRKDDEVIVKRGAFKGREGKVTACYRLKWVIHIDKVNRGSTVAVGIHPSNVEITKLKLT 109
35 -11.1005o60_V mol:protein length:105 50S ribosomal protein L24  ali model follow..  34  2.......................................................................................KVHKGDTVLVISGKDKGAKGKVLVAYPDRNKVLVE......................... 36
36 -11.0003j79_Z mol:protein length:126 60S ribosomal protein uL24  ali model follow..  19  45....................................................................................RSLPVRKDDEVLICRGHNHGREGKVVKINRKRYKIYVERVTRGESTFIGIHPSNVVLTKLKVD 111
37 -10.9004wce_R mol:protein length:105 50S ribosomal protein L24  ali model follow..  45  2.......................................................................................HIKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVE......................... 36
38 -10.9003j3v_U mol:protein length:103 50S ribosomal protein L24  ali model follow..  31  2.......................................................................................HVKKGDKVMVISGKDKGKQGTILAAFPKKDRVLVE......................... 36
39 -10.9004v4i_S mol:protein length:110 50S ribosomal protein L24  ali model follow..  33  2...................................................................................RVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVE......................... 40
40 -10.8005xxb_X mol:protein length:141 Ribosomal protein uL24  ali model follow..  22  45....................................................................................RSLPIRKDDEVMVVRGHHHDREGKVTKVYRKKWVIHIERVTRGETVTIGIHPSKVVITKAKLD 111
41 -10.6001nkw_S mol:protein length:115 50S ribosomal protein L24  ali model follow..  31  15.......................................................................................HFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVE......................... 49
42 -10.3003j7z_U mol:protein length:104 50S ribosomal protein L24  ali model follow..  28  4.......................................................................................KIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEG......................... 38
43 -9.9004ce4_Y mol:protein length:216 MRPL24  ali model follow..  27  50..................................................................................SDEDWHLFCGDKVEILEGKDAGKQGKVVQVIRQRNWVVVEGLNTHYPSEAPLLHNQVKLVDPTDR 128
44 -9.7605ohq_A mol:protein length:111 Transcription elongation factor SPT5  ali model follow..  13  44.........................................................................EKVVSISSEHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLR.............. 103
45 -9.7001wi5_A mol:protein length:119 RRP5 protein homolog  ali model follow..  14  2...............SSGSSGKNVNRVLSAEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAF-------LPLLKAQEYIRQKNKGAKLKVGQYLNCI----------VEKVKGNGGVVSLSV........................ 92
46 -9.6903j7y_V mol:protein length:216 uL24  ali model follow..  28  55.......................................................................................YLFCGDTVEILEGKDAGKQGKVVQVIRQRNWVVVGGLNTHYPSEAPLLHRQVKLVDPMDR 128
47 -9.6705mlc_W mol:protein length:191 50S ribosomal protein L24, chloroplastic  ali model follow..  23  68.......................................................................................HVKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKDLNFKTKIEAAIHSSNVMLILKEQE 142
48 -9.6005mmi_V mol:protein length:192 plastid ribosomal protein uL24c  ali model follow..  25  69.......................................................................................HVKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKDLNLKTKIEAAIHSSNVMLYSKEQE 143
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.