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Query: [K] COG0195 Transcription elongation factor, from COG1018

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 MNSEFMDALTTLEKEKGISKEVIIEAIEAALISGYKRNFNQAQNVRVDVNRENGSIRVFARKEVVEEVFDARLEISLDEAKGINPNYEVDDVVEIEVTPKDFGRIAAQTAKQVVTQRVREAERGIIYADFIDREEDIMTGIVQRQDNRFIYVDLGKVEALLPLSEQMPNESYRHNDRIKAYITKVEKTTKGPQIMISRTHPGLLKRLFELEVPEIYDGTVELKSVAREAGDRSKISVHAENPEVDPVGACVGPKGSRVQTIVNELKGEKIDIVRWSEDPVEYVANALSPSKVVKVNVNEEEKTTQVIVPDYQLSLAIGKRGQNARLAAKLTGWKIDIKSESEAQELGLLEDEAASHETLALDQETADQPEATVETSKNHEEELast
1 -121.0001l2f_A mol:protein length:369 N utilization substance protein A  ali model follow..  49  20MNIGLLEALDQLEEEKGISKEEVIPILEKALVSAYRKNFGNSKNVEVVIDRNTGNIKVYQLLEVVEEVEDPATQISLEEAKKIDPLAEVGSIVKKELNVKNFGRIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEWIPGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRVPEFVIGLMKLEIPEVENGIVEIKAIAREPGVRTKVAVASNDPNVDPIGACIGEGGSRIAAILKELKGEKLDVLKWSDDPKQLIANALAPATVIEVEIDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPIMN........................................ 362
2 -112.0005ms0_M mol:protein length:497 Transcription termination/antitermination protein NusA  ali model follow..  36  3MNKEILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVQIDRKSGDFDTFRRWLVVDEVTQPTKEITLEAARYEDESLNLGDYVEDQIESVTFDRITTQTAKQVIVQKVREAERAMVVDQFREHEGEIITGVVKKVNRDNISLDLGNAEAVILREDMLPRENFRPGDRVRGVLYSVRPEARGAQLFVTRSKPEMLIELFRIEVPEIGEEVIEIKAAARDPGSRAKIAVKTNDKRIDPVGACVGMRGARVQAVSTELGGERIDIVLWDDNPAQFVINAMAPADVASIVVDEDKHTMDIAVEAGNLAQAIGRNGQNVRLASQLSGWELNVMTVDDLQAKHQAEAHAAIDTFTKYLDIDEDFATVLVEEGFSTLEE 385
3 -103.0001k0r_A mol:protein length:366 NusA  ali model follow..  41  13HMNIDMAALHAIEVDRGISVNELLETIKSALLTAYRHTQGHQTDARIEIDRKTGVVRVIARETDEAGNLISEWDD----------------------TPEGFGRIAATTARQVMLQRFRDAENERTYGEFSTREGEIVAGVIQRDSRANIGTETKASEGVIPAAEQVPGESYEHGNRLRCYVVGVTRGAREPLITLSRTHPNLVRKLFSLEVPEIADGSVEIVAVAREAGHRSKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDDPARFVANALSPAKVVSVSIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAPPPPPGQPEPGVSRGMAHDR..................... 360
4 -102.0004mtn_A mol:protein length:407 Transcription termination factor NusA  ali model follow..  37  4NGNEVLRIVDSIHRDKSIDKEIVFEGVEQAILSAARKHFGEEEVIEVHIDRTSGQPMVKTNGREIDR----------------------------DELGDILGRISAQTAKQVMIQKIREAERDTLFDEYAQLRGQIVSGTVTRNEGSAITVNIGKAEAILPRSEMIPGESHRPNERIRAVVLEVKKMGPRVRVVLSRAHPDFVRRLLELEIPEVNERIIEIRSLAREAGYRTKVAVSCADSNIDPVGACVGVRGARIRNVGEELGGERIEVVRWNDSLQVLVPNAMQPSEVEDVILCPMLGRVLVLVRDDQLSLAIGKRGQNVRLASKLVGWDIDVMTREELDQQLDQAVVAYSQI----PGVSEELAEGLVSQGFLSFED 353
5 -94.6005lm9_A mol:protein length:329 Transcription termination/antitermination protein NusA  ali model follow..  37  1.................................................................................................GAMTFDRITTQTAKQVIVQKVREAERAMVVDQFREHEGEIITGVVKKVNRDNISLDLGNAEAVILREDMLPRENFRPGDRVRGVLYSVRPEARGAQLFVTRSKPEMLIELFRIEVPEIGEEVIEIKAAARDPGSRAKIAVKTNDKRIDPVGACVGMRGARVQAVSTELGGERIDIVLWDDNPAQFVINAMAPADVASIVVDEDKHTMDIAVEAGNLAQAIGRNGQNVRLASQLSGWELNVMTVDDLQAKHQAEAHAAIDTFTKYLDIDEDFATVLVEEGFSTLEE 286
6 -86.4002asb_A mol:protein length:251 Transcription elongation protein nusA  ali model follow..  46  1...............................................................................................................................GEFSTREGEIVAGVIQRDSRANIGTETKASEGVIPAAEQVPGESYEHGNRLRCYVVGVTRGAREPLITLSRTHPNLVRKLFSLEVPEIADGSVEIVAVAREAGHRSKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDDPARFVANALSPAKVVSVSVDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAPPPPPGQPEPGVSRGMAHDRLE................... 245
7 -47.3002kwp_A mol:protein length:129 Transcription elongation protein nusA  ali model follow..  37  1MNKEILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVQIDRKSGDFDTFRRWLVVDEVTQPTKEITLEAARYEDESLNLGDYVEDQIESVTFDRITTQTAKQVIVQKVREAERAMLVPR............................................................................................................................................................................................................................................................. 129
8 -45.9002mt4_A mol:protein length:124 Transcription termination/antitermination protein NusA  ali model follow..  84  1MSSELLDALTILEKEKGISKEIIIEAIEAALISAYKRNFNQAQNVRVDLNRETGSIRVFARKDVVDEVYDQRLEISIEEAQGIHPEYMVGDVVEIEVTPKDFGRIAAQTAKQVVTQRVREAERG.................................................................................................................................................................................................................................................................. 124
9 -39.4002cxc_A mol:protein length:144 NusA  ali model follow..  22  1...................................................................................................................................................................................................MSGDYRITLEELRYISVFHSITGVTAYRCIVDEENNRLIFLVSE-----GEAGRAIGRGGRLIKLL-REALGKNIEVVEYSSDLERIVKNLFPGVKIESINVRERNKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVEKVV......................................... 142
10 -13.7005hm5_A mol:protein length:854 Topoisomerase V  ali model follow..  12  279...........VEHKRDIMRRYLEQRIVECALKL-QDRYGIREDVALCLARAFDGSISMIATTPYRTLKDVCPDLTLEEAKSVNRTLTLIDEHGLSPDAADELIEHFESIAGILATDLEEIERMYEEGRLSEEAYRAAVEIQL---------------AELTKKEGVGRKTAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSLVPGY-ASLISIRGIDRERAERLLKKYGGYS-KVREAGVEELREDGLTDAQIRELKGEKADELKRKYGSASAVRRLPVEESDDEIAEIKGIPKKLREAFDLETAAELYERYGSLKEIGRRLSYD-DLLELGATPKAAAEIKGPEFKFLLNIEGVGPKLAERILEAVDYDLER 648
11 -11.2005aj3_f mol:protein length:188 MITORIBOSOMAL PROTEIN MS28, MRPS28  ali model follow..  16  79...................................................................................................................ESFASMLRHSPLTQMGPAKNKLVIGQIFHIVEDDLYIDFGKFHCVCKRPE-VDGEKYQKGTRVRLRLLDLELTSR---LGATT-------DTTILEADAVLLGLQESKDSKSKEERHEK.................................................................................................................................................... 188
12 -11.0002jvz_A mol:protein length:164 Far upstream element-binding protein 2  ali model follow..  16  1.....................................................................................................................................................................................................................................GTVQEIMIPA-----GKAGLVIGKGGETIKQL-QERAGVKMILIQ-NVDKPLRIIGDPYKVQQACEMVMDIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEK................................... 136
13 -10.6002n8l_A mol:protein length:191 Insulin-like growth factor 2 mRNA-binding protein 1  ali model follow..  17  32....................................................................................................................................................................................................................................................QAVGAIIGKKGQHIKQL-SRFASASIKIAP-SKVRMVVITGPPEAQFKAQGRIYGVKLETHIRVPASAAGRVIGDDGKTVNELQNLTAAEVVVPRDQTPDENEQV................................. 152
14 -10.5002n8m_A mol:protein length:191 Insulin-like growth factor 2 mRNA-binding protein 1  ali model follow..  17  32....................................................................................................................................................................................................................................................QAVGAIIGDDGQHIKQL-SRFASASIKIAP-SKVRMVVITGPPEAQFKAQGRIYGVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENEQV................................. 152
15 -10.5003krm_A mol:protein length:163 Insulin-like growth factor 2 mRNA-binding protein 1  ali model follow..  19  12....................................................................................................................................................................................................................................................QAVGAIIGKKGQHIKQL-SRFASASIKIAP-SKVRMVIITGPPEAQFKAQGRIEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQ......................................... 124
16 -10.4002jzx_A mol:protein length:160 Poly(rC)-binding protein 2  ali model follow..  21  14....................................................................................................................................................................................................................................................KEVGSIIGKKGESVKKM-REESGARINISE-CPERIITLAGPTNAIFKAFAMIIDPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDM......................................... 128
17 -10.3003jd5_f mol:protein length:189 28S ribosomal protein S28, mitochondrial  ali model follow..  16  79...................................................................................................................ESFASMLRHSPLTQMGPAKDKIVIGRIFHIVENDLYIDFGKFHCVCKRPE-VDGEKYQKGTRVRLRLLDLELTSRTTDTTILEAEAVLLGLQESKDSKS........................................................................................................................................................................ 181
18 -10.1002qnd_A mol:protein length:144 FMR1 protein  ali model follow..  16  15......................................................................................................................................................................................................................................................MGLAIGTHGANIQQARKVPG---VTAIDLDEDTCTFHIYGEDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKN..................................... 110
19 -10.1002ann_A mol:protein length:178 neuro-oncological ventral antigen 1  ali model follow..  16  9.........................................................................................................................................................................................................................................KVLIPS-----YAAGSIIGKGGQTIVQL-QKETGATIKLSK-TTERVCLIQGTIEALNAVHGFIAERANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD........................................ 144
20 -9.9401j4w_A mol:protein length:174 FUSE binding protein  ali model follow..  17  12....................................................................................................................................................................................................................................................FAVGIVIGRNGEMIKKI-QNDAGVRIQFKP-TPERIAQITGPPDRAQHAAEIITDGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPP........................................ 144
21 -9.0802k4k_A mol:protein length:130 General stress protein 13  ali model follow..  20  6....................................................................................................................................EVGSVYTGKVTGLQAYGAFVALDETQGLVHISEKDINEHLSVGDEVQVKVLAVDEEKG--KISLSIR....................................................................................................................................................................................... 77
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.

Li W, Jaroszewski L, Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics. 2002 Jan;18(1):77-82.