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Query: 1m1g_A mol:protein length:248 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 MSEQQVQELEKKWYALQVEPGKENEAKENLLKVLELEGLKDLVDEVIVPAEEKVVIRAQGKEKYRLSLKGNARDISVLGKKGVTTFRIENGEVKVVESVEGDTCVNAPPISKPGQKITCKENKTEAKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRPVMVGGKPVPLKEEEVQNILNQIKRGVKPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTPVELDFDQVEKILast
1 -103.0001m1g_A mol:protein length:248 Transcription antitermination protein nusG  ali model  100  1MSEQQVQELEKKWYALQVEPGKENEAKENLLKVLELEGLKDLVDEVIVPAEEKVVIRAQGKEKYRLSLKGNARDISVLGKKGVTTFRIENGEVKVVESVEGDTCVNAPPISKPGQKITCKENKTEAKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRPVMVGGKPVPLKEEEVQNILNQIKRGVKPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTPVELDFDQVEKI 248
2 -74.4002xhc_A mol:protein length:352 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  28  1........MKKKWYIVLTMSGYEEKVKENIEKKVEATGIKNLVGRIVIPEEVVLDATSPSERLILSPKAKLHVNNGKDEQDVYYIPLDVFDRDRIKKGKEVKQGEMLAEARKFFAKVYSTRKEIRIYKTKRRKLFPGYVFVEMIMNDEAYNFVRSVPYVMGFVSSGGQPVPVKDREMRPILRLAKKKPVKVELGFKVGDMVKIISGPFEDFAGVIKEIDPERQELKVNVTIFGRETPVVLHVSEVEKI 352
3 -70.2002lq8_A mol:protein length:177 Transcription antitermination protein nusG  ali model follow..  31  1...........................................................................GAMKKKWYIVLTMSGYEEKVKENIEKKVEATGIKNLVG----RIVIPIRGGQRRKSEKLFPGYVFVEMIMNDEAYNFVRSVPYVMGFVSSGGQPVPVKDREMRPILRLAGLEPVKVELGFKVGDMVKIISGPFEDFAGVIKEIDPERQELKVNVTIFGRETPVVLHVSEVEKI 176
4 -68.8005ms0_F mol:protein length:183 Transcription termination/antitermination protein NusG  ali model follow..  38  1..GAMSEAPKKRWYVVQAFSGFEGRVATSLREHIKLHNMEDLFGEVMVPTEEVV------------------------------------------------------------------EIRGGQRRKSERKFFPGYVLVQMVMNDASWHLVRSVPRVMGFIGTSDRPAPISDKEVDAIMNRLQQVKPRPKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKA 183
5 -65.6002oug_A mol:protein length:162 Transcriptional activator rfaH  ali model follow..  14  2...............................................................................QSWYLLYCKRGQLQRAQEHLERQAVNCLAPM------ITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYKPKDI-VDPATPYPGDKVIITEGAFEGFQAIFTEPD-GEARSMLLLNLINKEIKHSVKNTEFRKL 162
6 -43.0001nz8_A mol:protein length:119 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  33  1.........SIEWYAVHTLVGQEEKAKANLEKRIKAFGLQDKIFQVLIPTEEVVELR-----------------------------------------------------------------EGGKKEVVRKKLFPGYLFIQMDLGDEAWEVVRGTPGITGFVGAGMRPVPLSPDEVRHILEVSGLL............................................................. 118
7 -36.5004zn1_A mol:protein length:147 Transcription elongation factor Spt5  ali model follow..  21  2.................................................................................IFAVRTMVGQEKNIAGLMASRAEKEQLDV----------------YSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIV-----PGTIAIEEIEPLLTPKKI-----IENIEKGDVVEIIAGPFKGERAKVIRVDKHKEEVTLELENAAVPIPITLPVEGVKIV 142
8 -34.2003qqc_D mol:protein length:163 Transcription antitermination protein nusG  ali model follow..  21  2..............................................................................AGKIFAVRVTHGQEETTAKLIYSKVRTYNLPI----------------YAILAPSRVKGYIFVEAPNKGVVDEAIRGIRHARGVLPG-----EVPFKEIEHFLEEKPA-----VSGLEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQFIDAIVPIPVTIKGDYVRLI 145
9 -29.6002mi6_A mol:protein length:62 Transcription termination/antitermination protein NusG  ali model follow..  50  1..........................................................................................................................................................................................GRPVVEVDYEVGESVTVMDGPFATLPATISEVNAEQQKLKVLVSIFGRETPVELTFGQVSKI 62
10 -29.5002kvq_G mol:protein length:63 Transcription antitermination protein nusG  ali model follow..  59  3...........................................................................................................................................................................................MGRPKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKA 63
11 -28.7006duq_M mol:protein length:60 Transcription termination/antitermination protein NusG  ali model follow..  60  1............................................................................................................................................................................................SNAKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKA 60
12 -27.8001nz9_A mol:protein length:58 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  63  1..............................................................................................................................................................................................AQVAFREGDQVRVVSGPFADFTGTVTEINPERGKVKVMVTIFGRETPVELDFSQVVK. 57
13 -26.8002lcl_A mol:protein length:66 Transcriptional activator rfaH  ali model follow..  13  1.....................................................................................................................................................................................GAMGPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPD-GEARSMLLLNLINKEIKHSVKNTEFRKL 66
14 -16.5002e6z_A mol:protein length:59 Transcription elongation factor SPT5  ali model follow..  29  8..................................................................................................................................................................................................FQPGDNVEVCEGELINLQGKILSVDGN--KITIMPKHEDLKDMLEFPAQELRK. 58
15 -15.4005oik_Z mol:protein length:1087 Transcription elongation factor SPT5  ali model follow..  14  99ILEKEEIEASNIDNVVLDEDRSGARRLQNLWRDQREEELGEYYMK-KYAKSSVGETVYGGSDELSDDITQQQLLPGVKDPNLWTVKCKIGEERATAISLMRKFIA-----------YQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIE---GVGNLRLGYWNQQMVPIKEMTDVLKVVKE-----VANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKM................... 307
16 -15.0005xon_W mol:protein length:612 Protein that forms a complex with Spt4p  ali model follow..  19  17...........................................................................TVDDPGIWGVKVRLGKEKDVVRQILKKKLA-----------REGTKNPLEIYSAFQRDSFKGHVYIEARKAEAINDALKGNVNVFS----NNSKFLVGIVEYKDLLRPVKSS----DVKLTRGSYVRVKNGKFKGDLAQVDEVLENGLEARLKL................... 151
17 -14.4005xog_W mol:protein length:83 Spt4/5 complex component  ali model follow..  10  20....................................................................................................................................................................................................LNKTVKIRQGGYKGKIGIVKEANGDR----FRVELHNPNKTIPIPCSFLLIE 67
18 -13.7002e70_A mol:protein length:71 Transcription elongation factor SPT5  ali model follow..  16  20....................................................................................................................................................................................................IGQTVRISQGPYKGYIGVVKDATEST----ARVELHSTCQTISVDRQRLTTV 67
19 -13.5004ytl_A mol:protein length:99 Transcription elongation factor SPT5  ali model follow..  28  1..................................................................................................................................................................................................FQPGDRIEVLNGEQRGSKGIVTRTTKD----IATIKLNGFTTPLEFPISTLRKI 50
20 -13.1001s72_T mol:protein length:120 50S ribosomal protein L24P  ali model follow..  23  14......................................................................................................................................................................RAPLHERHKQVRALSADLREEYGQRNVRVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVLEKTDGEEVPRPLDTSNVRVT 100
21 -11.4002do3_A mol:protein length:69 Transcription elongation factor SPT5  ali model follow..  23  1...................................................................................................................................................................GSSGSSGEFPAQELRKY--------------FKMGDHVKVIAGRFEGDTGLIVRVEEN--FVILFSDLTMHELKV.......... 59
22 -11.3005xy3_Y mol:protein length:138 Ribosomal protein L24, putative  ali model follow..  16  21......................................................................................................................................................................NAKKDAKHVAMSALSKELQEANGIKRLPIRRDDEVMIFSGRMQNRTGKVTAVKLSEMRIYV--KINGQAVSFPVHPSNV... 104
23 -11.1002ckk_A mol:protein length:127 KIN17  ali model follow..  13  19..........................................................................................................................................IIVKIITKKLGEKYHKKKAIVKEVMIDSGDKLKLDQTHLETVI--------------APGKRILVLNGGYRGNEGTLESINEKTFSATIVIE-LKGRRVEGIQYEDISKL 126
24 -10.8002ww9_L mol:protein length:127 60S RIBOSOMAL PROTEIN L26-A  ali model follow..  15  21......................................................................................................................................................................TAPSSQRRVLLSALSKELRAQYGIKALPIRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQV--KVNGASVPINLHPSKL... 104
25 -10.8003jcs_W mol:protein length:143 ribosomal protein L24  ali model follow..  16  18......................................................................................................................................................................QAPSHVRRVLMSALSKELRAKYNVRAMPVRKDDEVIVKRGTFKGREGKVTACYRLKWVILI--KANGSTVAVGIHPSNV... 101
26 -10.7005t2a_X mol:protein length:143 uL24  ali model follow..  16  18......................................................................................................................................................................QAPSHVRRVLMSALSKELRAKYNVRAMPVRKDDEVIVKRGAFKGREGKVTACYRLKWVIHI--KANGSTVAVGIHPSNV... 101
27 -10.6005t5h_Z mol:protein length:113 60S ribosomal protein L26  ali model follow..  16  12......................................................................................................................................................................QAPSHVRRILMSALSKELRAKYNVRAMPVRKDDEVRVKRGAYKGREGKVTACYRLRWVIHI--KANGTTVPVGVHPSNV... 95
28 -10.5005ohq_A mol:protein length:111 Transcription elongation factor SPT5  ali model follow..  20  8..........................................................................................................................................IQVKV-RDTYLDTQVVGQTGVIRSVTGGMCSVYLKDSEKVVSISSEHLEPITP----TKNNKVKVILGEDREATGVLLSIDGED----GIVRMDLDEQLKILNLRFLGKL 108
29 -10.5001nkw_S mol:protein length:115 50S ribosomal protein L24  ali model follow..  29  1...................................................................................................................................................................................MPRPSAGSHHNDKLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVV..................... 48
30 -10.4003j79_Z mol:protein length:126 60S ribosomal protein uL24  ali model follow..  17  20......................................................................................................................................................................TAPAGLRRKIMSSLSKELRLKYKTRSLPVRKDDEVLICRGHNHGREGKVVKINRKRYKIYV--KVNGESTFIGIHPSNV... 103
31 -10.1005xxb_X mol:protein length:141 Ribosomal protein uL24  ali model follow..  15  20......................................................................................................................................................................SAPSSVRRKIMTALCKELRKKYNVRSLPIRKDDEVMVVRGHHHDREGKVTKVYRKKWVIHI--KANGETVTIGIHPSKV... 103
32 -9.9402exu_A mol:protein length:200 Transcription initiation protein SPT4/SPT5  ali model follow..  9  42...................TSPSFEGLVGMCKPTKSWVAKWLSVDHSIAGMYAIKVDGRLPAEVVELLPHYKPRDGSGSATIWGVRCRPGKEKELIRKLLKKKFNL---------DRAMGKKKLKILSIFQRDNYTGRIYIEAPKQSVIEKFCNGVPDI-----YISQKLLIPVQELPLLLKPNLE.............................................................. 194
33 -9.8405v7q_U mol:protein length:105 50S ribosomal protein L24  ali model follow..  27  2.................................................................................................................................................................................................KVHKGDTVLVISGKDKGAKGKVLQAYPDRNRVLVEVNRIKKHTA........... 46
34 -9.7405mmi_V mol:protein length:192 plastid ribosomal protein uL24c  ali model follow..  16  69.................................................................................................................................................................................................HVKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKLNLKTKKIEAAIHSSNVMLY 138
35 -9.6903j6b_Q mol:protein length:297 54S ribosomal protein L40, mitochondrial  ali model follow..  14  62.................................................................................................................................................................................................KFIPGDRVVVMSGASKGNIAVIKSFDKRTNSFILDNGPTKTTIPVSILGKDLRLV 134
36 -9.6705o60_V mol:protein length:105 50S ribosomal protein L24  ali model follow..  29  2.................................................................................................................................................................................................KVHKGDTVLVISGKDKGAKGKVLVAYPDRNKVLVEVNRIKKHTA........... 46
37 -9.4804ytk_A mol:protein length:130 Transcription elongation factor SPT5  ali model follow..  20  1..................................................................................................................................................................................................LEEGSYVRIKRGIYKGDLAMVDQISENNLEVMLKI................... 35
38 -9.4604v4i_S mol:protein length:110 50S ribosomal protein L24  ali model follow..  32  4...............................................................................................................................................................................................KMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEVNIVKKAVR........... 50
39 -9.3603lpe_A mol:protein length:92 Putative transcription antitermination protein nusG  ali model follow..  18  6...........................................................................SVGAHMIFAVRTMVGQEKNIAGLMASRAEKEQLDV----------------YSILASESLKGYVLVEAETKGDVEELIKGMPRV-----RGIVPGTIAIEEIEPLLT.................................................................. 91
40 -9.3005mlc_W mol:protein length:191 50S ribosomal protein L24, chloroplastic  ali model follow..  16  49..............................................................................................................................................................................KRWERKDCKPNSLPKLHKRHVKVGDTVKVISGGEKGKIGEISKIHKHNSTVII-LNFKTKKIEAAIHSSNVMLI 137
41 -9.2304wce_R mol:protein length:105 50S ribosomal protein L24  ali model follow..  30  3..................................................................................................................................................................................................IKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVEVNIMKKHQK........... 46
42 -9.1703h7h_B mol:protein length:106 Transcription elongation factor SPT5  ali model follow..  17  2...........................................................................SHMDPNLWTVKCKIGEERATAISLMRKFIA-----------YQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIE---GVGNLRLGYWNQQMVPIKEMTDVLKVVKE-----VANLGSG.................................................. 105
43 -9.1704ce4_Y mol:protein length:216 MRPL24  ali model follow..  24  56..................................................................................................................................................................................................LFCGDKVEILEGKDAGKQGKVVQVIRQRNWVVVELNTHYRPSEAPLLHNQVKLV 123
44 -9.1603j7y_V mol:protein length:216 uL24  ali model follow..  19  42....................................................................................................................................................................................RPVVVEPISDEDWYLFCGDTVEILEGKDAGKQGKVVQVIRQRNWVVVGLNTHYRPSEAPLLHRQVKLV 123
45 -9.1603j3v_U mol:protein length:103 50S ribosomal protein L24  ali model follow..  36  3..................................................................................................................................................................................................VKKGDKVMVISGKDKGKQGTILAAFPKKDRVLV..................... 35
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.