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Query: 2lq8_A mol:protein length:177 Transcription 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.
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# Score Template Links and tools%idFirst GAMKKKWYIVLTMSGYEEKVKENIEKKVEATGIKNLVGRIVIPIRGGQRRKSEKLFPGYVFVEMIMNDEAYNFVRSVPYVMGFVSSGGQPVPVKDREMRPILRLAGLEEYEEKKKPVKVELGFKVGDMVKIISGPFEDFAGVIKEIDPERQELKVNVTIFGRETPVVLHVSEVEKIELast
1 -89.5002lq8_A mol:protein length:177 Transcription antitermination protein nusG  ali model  100  1GAMKKKWYIVLTMSGYEEKVKENIEKKVEATGIKNLVGRIVIPIRGGQRRKSEKLFPGYVFVEMIMNDEAYNFVRSVPYVMGFVSSGGQPVPVKDREMRPILRLAGLEEYEEKKKPVKVELGFKVGDMVKIISGPFEDFAGVIKEIDPERQELKVNVTIFGRETPVVLHVSEVEKIE 177
2 -74.0005ms0_F mol:protein length:183 Transcription termination/antitermination protein NusG  ali model follow..  39  5EAPKKRWYVVQAFSGFEGRVATSLREHIKLHNMEDLTEEVVEIRGGQRRKSERKFFPGYVLVQMVMNDASWHLVRSVPRVMGFIGTSDRPAPISDKEVDAIMNRLQQVG-----DKPRPKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKA. 183
3 -72.0002oug_A mol:protein length:162 Transcriptional activator rfaH  ali model follow..  21  1...MQSWYLLYCKRGQLQRAQEHLERQAVNCLAPMI--TLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYKPKDIVDPAT--------PYPGDKVIITEGAFEGFQAIFTEPD-GEARSMLLLNLINKEIKHSVKNTEFRKL. 162
4 -70.2001m1g_A mol:protein length:248 Transcription antitermination protein nusG  ali model follow..  31  76SVLGKKGVTTFRIENGEVKVVESVEGDTCVNAPPISKPTCKENKTEAKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRPVMVGGKPVPLKEEEVQNILNQIKRG-------VKPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTPVELDFDQVEKI. 248
5 -62.8002xhc_A mol:protein length:352 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  73  165PDGEQDVYYIPLDVFDRDRIKKGKEVKQGEMLAEAVVDYSTRKEIRIYKTKRRKLFPGYVFVEMIMNDEAYNFVRSVPYVMGFVSSGGQPVPVKDREMRPILRLAGLEEYEEKKKPVKVELGFKVGDMVKIISGPFEDFAGVIKEIDPERQELKVNVTIFGRETPVVLHVSEVEKI. 352
6 -48.6001nz8_A mol:protein length:119 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  39  1...SIEWYAVHTLVGQEEKAKANLEKRIKAFGLQDKIFQVLLREGGKKEVVRKKLFPGYLFIQMDLGDEAWEVVRGTPGITGFVGAGMRPVPLSPDEVRHILEVSGLLG.................................................................... 119
7 -42.4004zn1_A mol:protein length:147 Transcription elongation factor Spt5  ali model follow..  24  2......IFAVRTMVGQEKNIAGLMASRAEKEQLDV------------YSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIV-----PGTIAIEEIEPLLT------------PKKIIENIEKGDVVEIIAGPFKGERAKVIRVDKHKEEVTLELENAAVPIPITLPVEGVKIVS 143
8 -40.2003qqc_D mol:protein length:163 Transcription antitermination protein nusG  ali model follow..  23  1..MAGKIFAVRVTHGQEETTAKLIYSKVRTYNLPI------------YAILAPSRVKGYIFVEAPNKGVVDEAIRGIRHARGVLP-----GEVPFKEIEHFLE------------EKPAVSGLEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQFIDAIVPIPVTIKGDYVRLIS 146
9 -33.0002kvq_G mol:protein length:63 Transcription antitermination protein nusG  ali model follow..  47  1.................................................................................................................GAMGRPKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKA. 63
10 -32.6002mi6_A mol:protein length:62 Transcription termination/antitermination protein NusG  ali model follow..  45  2...................................................................................................................RPVVEVDYEVGESVTVMDGPFATLPATISEVNAEQQKLKVLVSIFGRETPVELTFGQVSKI. 62
11 -32.1006duq_M mol:protein length:60 Transcription termination/antitermination protein NusG  ali model follow..  50  1....................................................................................................................SNAKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKA. 60
12 -30.6001nz9_A mol:protein length:58 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  56  1......................................................................................................................AQVAFREGDQVRVVSGPFADFTGTVTEINPERGKVKVMVTIFGRETPVELDFSQVVK.. 57
13 -28.6002lcl_A mol:protein length:66 Transcriptional activator rfaH  ali model follow..  21  1.............................................................................................................GAMGPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPD-GEARSMLLLNLINKEIKHSVKNTEFRKL. 66
14 -17.7002e6z_A mol:protein length:59 Transcription elongation factor SPT5  ali model follow..  19  8..........................................................................................................................FQPGDNVEVCEGELINLQGKILSVDGN--KITIMPKHEDLKDMLEFPAQELRK.. 58
15 -16.9005xon_W mol:protein length:612 Protein that forms a complex with Spt4p  ali model follow..  17  17TVDDPGIWGVKVRLGKEKDVVRQILKKKLAR-------EGTKNPLEIYSAFQRDSFKGHVYIEARKAEAINDALKGNVNVF----SNNSKFLVGIVEYKDLLRPVKSS-----------DVKLTRGSYVRVKNGKFKGDLAQVDEVLENGLEARLKL.................... 151
16 -15.8005oik_Z mol:protein length:1087 Transcription elongation factor SPT5  ali model follow..  15  173GVKDPNLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQI-------KSVVAPEHVKGYIYVEAYKQTHVKQAIE---GVGNLRLGYWNQQMVPIKEMTDVLKVVKE------------VANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKM.................... 307
17 -15.7005xog_W mol:protein length:83 Spt4/5 complex component  ali model follow..  20  20............................................................................................................................LNKTVKIRQGGYKGKIGIVKEANGDR----FRVELHNPNKTIPIPCSFLLIES 68
18 -15.1002e70_A mol:protein length:71 Transcription elongation factor SPT5  ali model follow..  18  20............................................................................................................................IGQTVRISQGPYKGYIGVVKDATEST----ARVELHSTCQTISVDRQRLTTVG 68
19 -13.8004ytl_A mol:protein length:99 Transcription elongation factor SPT5  ali model follow..  22  1..........................................................................................................................FQPGDRIEVLNGEQRGSKGIVTRTTKD----IATIKLNGFTTPLEFPISTLRKI. 50
20 -12.4001s72_T mol:protein length:120 50S ribosomal protein L24P  ali model follow..  24  40.......................................................................................................................NVRVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVLEKTDGEEVPRPLDTSNVRVTD 101
21 -12.2003lpe_A mol:protein length:92 Putative transcription antitermination protein nusG  ali model follow..  20  6SVGAHMIFAVRTMVGQEKNIAGLMASRAEKEQLDV------------YSILASESLKGYVLVEAETKGDVEELIKGMPRV-----RGIVPGTIAIEEIEPLLT.......................................................................... 91
22 -11.8003h7h_B mol:protein length:106 Transcription elongation factor SPT5  ali model follow..  16  2SHMDPNLWTVKCKIGEERATAISLMRKFIAY-------QFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIE---GVGNLRLGYWNQQMVPIKEMTDVLK.......................................................................... 94
23 -11.4002do3_A mol:protein length:69 Transcription elongation factor SPT5  ali model follow..  33  18..........................................................................................................................FKMGDHVKVIAGRFEGDTGLIVRVEENF--VILFSDLTMHELKV........... 59
24 -11.1003ewg_A mol:protein length:91 Putative transcription antitermination protein nusG  ali model follow..  21  3.......FAVRTMVGQEKNIAGLMASRAEKEQLDV------------YSILASESLKGYVLVEAETKGDVEELIKGMPRV-----RGIVPGTIAIEEIEPLLTPKLE...................................................................... 85
25 -11.0002exu_A mol:protein length:200 Transcription initiation protein SPT4/SPT5  ali model follow..  15  98GSGSATIWGVRCRPGKEKELIRKLLKKKFNLDRAMGKKKLKI-----LSIFQRDNYTGRIYIEAPKQSVIEKFCNGVPDI-----YISQKLLIPVQELPLLLKPNLE...................................................................... 194
26 -10.7002ckk_A mol:protein length:127 KIN17  ali model follow..  8  19...........................................................IIVKIITKKLGEKYHKKKAIVKEVIDDSGDKLKLDQTHLETVI---------------------APGKRILVLNGGYRGNEGTLESINEKTFSATIVIE-LKGRRVEGIQYEDISKL. 126
27 -10.4005v7q_U mol:protein length:105 50S ribosomal protein L24  ali model follow..  27  3..........................................................................................................................VHKGDTVLVISGKDKGAKGKVLQAYPDRNRVLVEVNRIKKHTA............ 46
28 -10.3005ohq_A mol:protein length:111 Transcription elongation factor SPT5  ali model follow..  26  60...........................................................................................................................TKNNKVKVILGEDREATGVLLSIDGED----GIVRMDLDEQLKILNLRFLGKL. 108
29 -10.2004v4i_S mol:protein length:110 50S ribosomal protein L24  ali model follow..  30  1....................................................................................................................MRVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIV...................... 39
30 -10.2005o60_V mol:protein length:105 50S ribosomal protein L24  ali model follow..  27  3..........................................................................................................................VHKGDTVLVISGKDKGAKGKVLVAYPDRNKVLVEVNRIKKHTA............ 46
31 -10.2004ytk_A mol:protein length:130 Transcription elongation factor SPT5  ali model follow..  17  1..........................................................................................................................LEEGSYVRIKRGIYKGDLAMVDQISENNLEVMLKI.................... 35
32 -10.1001nkw_S mol:protein length:115 50S ribosomal protein L24  ali model follow..  33  16..........................................................................................................................FKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVV...................... 48
33 -10.1005xy3_Y mol:protein length:138 Ribosomal protein L24, putative  ali model follow..  22  47.......................................................................................................................RLPIRRDDEVMIFSGRMQNRTGKVTAVKLSEMRIYV--KINGQAVSFPVHPSNVVITK 108
34 -10.0005mmi_V mol:protein length:192 plastid ribosomal protein uL24c  ali model follow..  27  70..........................................................................................................................VKVGDTVKVISGGEKGKIGEISKIHKHNSTVII-LNLKTKKIEAAIHSSNVMLYS 139
35 -9.9503j6b_Q mol:protein length:297 54S ribosomal protein L40, mitochondrial  ali model follow..  30  63..........................................................................................................................FIPGDRVVVMSGASKGNIAVIKSFDKRTNSFIL...................... 95
36 -9.9104wce_R mol:protein length:105 50S ribosomal protein L24  ali model follow..  30  3..........................................................................................................................IKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVV...................... 35
37 -9.8903j3v_U mol:protein length:103 50S ribosomal protein L24  ali model follow..  33  3..........................................................................................................................VKKGDKVMVISGKDKGKQGTILAAFPKKDRVLV...................... 35
38 -9.5903jcs_W mol:protein length:143 ribosomal protein L24  ali model follow..  18  44.......................................................................................................................AMPVRKDDEVIVKRGTFKGREGKVTACYRLKWVILI--KANGSTVAVGIHPSNV.... 101
39 -9.5704ce4_Y mol:protein length:216 MRPL24  ali model follow..  20  56..........................................................................................................................LFCGDKVEILEGKDAGKQGKVVQVIRQRNWVVVELNTHYRPSEAPLLHNQVKLVD 124
40 -9.5705t2a_X mol:protein length:143 uL24  ali model follow..  18  44.......................................................................................................................AMPVRKDDEVIVKRGAFKGREGKVTACYRLKWVIHI--KANGSTVAVGIHPSNV.... 101
41 -9.5605mlc_W mol:protein length:191 50S ribosomal protein L24, chloroplastic  ali model follow..  29  69..........................................................................................................................VKVGDTVKVISGGEKGKIGEISKIHKHNSTVII-LNFKTKKIEAAIHSSNVMLIL 138
42 -9.5502ww9_L mol:protein length:127 60S RIBOSOMAL PROTEIN L26-A  ali model follow..  22  47.......................................................................................................................ALPIRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQV--KVNGASVPINLHPSKL.... 104
43 -9.5103j7z_U mol:protein length:104 50S ribosomal protein L24  ali model follow..  13  1......................................................................................................................MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVE...................... 37
44 -9.4603j7y_V mol:protein length:216 uL24  ali model follow..  20  56..........................................................................................................................LFCGDTVEILEGKDAGKQGKVVQVIRQRNWVVVGLNTHYRPSEAPLLHRQVKLVD 124
45 -9.3705t5h_Z mol:protein length:113 60S ribosomal protein L26  ali model follow..  20  38.......................................................................................................................AMPVRKDDEVRVKRGAYKGREGKVTACYRLRWVIHI--KANGTTVPVGVHPSNV.... 95
46 -9.0503j79_Z mol:protein length:126 60S ribosomal protein uL24  ali model follow..  25  46.......................................................................................................................SLPVRKDDEVLICRGHNHGREGKVVKINRKRYKIYV--KVNGESTFIGIHPSNV.... 103
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.