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Query: 3j6b_Q mol:protein length:297 54S ribosomal protein L40, mitochondrial, 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 MSGSYQHLSNVGSRVMKRLGNRPKNFLPHSEKFIKKSTPEFMKSDLKEVDEKTSFKSEKEWKFIPGDRVVVMSGASKGNIAVIKSFDKRTNSFILDENGPTKTVPVPKQFWLEGQTSHMITIPVSILGKDLRLVADIDDEKTPGKTRTVAVRDVSFNGSYYDADYKKVMPYRCVKGQPDLIIPWPKPDPIDVQTNLATDPVIAREQTFWVDSVVRNPIPKKAIPSIRNPHSKYKRGTLTAKDIAKLVAPEMPLTEVRKSHLAEKKELAEREVPKLTEEDMEAIGARVFEFLEKQKRELast
1 -105.0003j6b_Q mol:protein length:297 54S ribosomal protein L40, mitochondrial  ali model  100  1MSGSYQHLSNVGSRVMKRLGNRPKNFLPHSEKFIKKSTPEFMKSDLKEVDEKTSFKSEKEWKFIPGDRVVVMSGASKGNIAVIKSFDKRTNSFILDENGPTKTVPVPKQFWLEGQTSHMITIPVSILGKDLRLVADIDDEKTPGKTRTVAVRDVSFNGSYYDADYKKVMPYRCVKGQPDLIIPWPKPDPIDVQTNLATDPVIAREQTFWVDSVVRNPIPKKAIPSIRNPHSKYKRGTLTAKDIAKLVAPEMPLTEVRKSHLAEKKELAEREVPKLTEEDMEAIGARVFEFLEKQKRE 297
2 -52.5004ce4_Y mol:protein length:216 MRPL24  ali model follow..  15  3....LSALLALASKVTLPPNYRYGMSRPGSLSDKRKNPPGTRRR-----RVPVEPISDEDWHLFCGDKVEILEGKDAGKQGKVVQVIRQRNWVVVEGLNTHYRYVGKT----VDYRGTMIPSEAPLLHNQVKLVDPTDRKPTDVEWRFTEAGE-----------------RVRVSTRSGRIIPKPEFPPETWIDGPKDTSVEDALEKTYVPRLK--TLEEEVMEAMGIQETRRHKKVYW.......................................................... 215
3 -52.1003j7y_V mol:protein length:216 uL24  ali model follow..  13  3...............LSALLALASKVTLPPHYRYGMSPPGSVADKRKNPPWIRRRPSDEDWYLFCGDTVEILEGKDAGKQGKVVQVIRQRNWVVVGGLNTHYRYIGKT----MDYRGTMIPSEAPLLHRQVKLVDPMDRKPTEIEWRFTEAGE-----------------RVRVSTRSGRIIPKPEFPPETWIDGPKDTSVEDALERTYVPCL--KTLQEEVMEAMGIKETRKYKKVYW.......................................................... 215
4 -43.3005mmi_V mol:protein length:192 plastid ribosomal protein uL24c  ali model follow..  17  7LQSSFTSLSLSNSFLGQRLFPSPTTLQVKTEGHSPCLIVMRIKRWERKDCKPNSLPKLHKMHVKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKDLNLKTKHVKSK---EEGEQGQIIKIEAAIHSSNVMLYSKEQEVASRVGHKILEDGR-----------------KVRYLIKTGEIVDTPDRWKEIQNKKESETAVAVA............................................................................................. 191
5 -41.9005mlc_W mol:protein length:191 50S ribosomal protein L24, chloroplastic  ali model follow..  17  6LQSSFTSLSLSSSFLGQRLFPSPTTLQVKTEGHSPCLIVMRIKRWERKDCKPNSLPKLHKRHVKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKDLNFKTKHVKSKE---EGEQGQIIKIEAAIHSSNVMLILKEQEVADRVGHKILEDVR-----------------KVRYLIKTGEIVDTPDRWKEIQNKKESETAVAVA............................................................................................. 190
6 -35.5004wce_R mol:protein length:105 50S ribosomal protein L24  ali model follow..  15  1............................................................MHIKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVEGVNIMKKHQKPT---QLNPEGGILETEAAIHVSNVQLLDPKTNEPTRVGYKFVDGKKVR------------------IAKKSGEEIKSNN............................................................................................................... 105
7 -35.4004v4i_S mol:protein length:110 50S ribosomal protein L24  ali model follow..  13  3..........................................................VKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVS---PKYPQGGFIEKEAPLHASKVRPICPACGKPTRVRKKFLENGK-----------------KIRVCAKCGGALDTEE............................................................................................................... 110
8 -35.0001nkw_S mol:protein length:115 50S ribosomal protein L24  ali model follow..  14  3.................................................RPSAGSHHNDKLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEGVNVITKNVKPS---MTNPQGGQEQRELALHASKVALVDPETGKATRVRKQIVDGKKVRVAVA.......................................................................................................................................... 109
9 -33.9003j3v_U mol:protein length:103 50S ribosomal protein L24  ali model follow..  15  1............................................................MHVKKGDKVMVISGKDKGKQGTILAAFPKKDRVLVEGVNMVKKHSKPT---QANPQGGISNQEAPIHVSNVMPLDPKTGEVTRVGYKVEDGKKVRVAKK.......................................................................................................................................... 96
10 -33.4005v7q_U mol:protein length:105 50S ribosomal protein L24  ali model follow..  17  1............................................................MKVHKGDTVLVISGKDKGAKGKVLQAYPDRNRVLVEGVNRIKKHTAISTTQRGARSGGIVTQEAPIHVSNVMVVDSDGKPTR........................................................................................................................................................... 82
11 -33.1005o60_V mol:protein length:105 50S ribosomal protein L24  ali model follow..  17  1............................................................MKVHKGDTVLVISGKDKGAKGKVLVAYPDRNKVLVEGVNRIKKHTAVSANERGASSGGIVTQEAPIHVSNVMVVDSDGKPTR........................................................................................................................................................... 82
12 -32.4003j7z_U mol:protein length:104 50S ribosomal protein L24  ali model follow..  16  2...........................................................AAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVP---ALNQPGGIVEKEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKS.......................................................................................................................................... 98
13 -25.9001s72_T mol:protein length:120 50S ribosomal protein L24P  ali model follow..  11  4..........................QPDKQRKSQRRAPLHERHKQVRATLSADLREQRNVRVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVEDVTLEKTDGEE--------------VPRPLDTSNVRVTDLDLEDEKREARLESEDDS................................................................................................................................................ 119
14 -17.4005xy3_Y mol:protein length:138 Ribosomal protein L24, putative  ali model follow..  8  11..........................QARKVRKSYFNAKKDAKHVAMSAPLSKELQEIKRLPIRRDDEVMIFSGRMQNRTGKVTAVKLSEMRIYVDTFTTEKIN---------------QAVSFPVHPSNVVITKLKMDKARK.......................................................................................................................................................... 116
15 -15.8005t5h_Z mol:protein length:113 60S ribosomal protein L26  ali model follow..  14  2..........................SRRKARRAHFQAPSHVRRILMSAPLSKELRAVRAMPVRKDDEVRVKRGAYKGREGKVTACYRLRWVIHIDKVNREKAN---------------TTVPVGVHPSNVEIT................................................................................................................................................................... 98
16 -15.7003jcs_W mol:protein length:143 ribosomal protein L24  ali model follow..  13  8..........................SRRKARRAHFQAPSHVRRVLMSAPLSKELRAVRAMPVRKDDEVIVKRGTFKGREGKVTACYRLKWVILIDKVNREKAN---------------STVAVGIHPSNVEIT................................................................................................................................................................... 104
17 -15.7002ww9_L mol:protein length:127 60S RIBOSOMAL PROTEIN L26-A  ali model follow..  15  11..........................DRRKARKAYFTAPSSQRRVLLSAPLSKELRAIKALPIRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVN---------------ASVPINLHPSKLVIT................................................................................................................................................................... 107
18 -15.6005t2a_X mol:protein length:143 uL24  ali model follow..  14  8..........................SRRKARRAHFQAPSHVRRVLMSAPLSKELRAVRAMPVRKDDEVIVKRGAFKGREGKVTACYRLKWVIHIDKVNREKAN---------------STVAVGIHPSNVEIT................................................................................................................................................................... 104
19 -15.1003j79_Z mol:protein length:126 60S ribosomal protein uL24  ali model follow..  9  10..........................SRRKMRKAHFTAPAGLRRKIMSSKELRLKYKTRSLPVRKDDEVLICRGHNHGREGKVVKINRKRYKIYVERVTREKVN---------------ESTFIGIHPSNVVLTKLKVDKNRKKILDRKAAKE................................................................................................................................................ 125
20 -14.7005xxb_X mol:protein length:141 Ribosomal protein uL24  ali model follow..  10  10..........................SRRKSRKAHFSAPSSVRRKIMTAKELRKKYNVRSLPIRKDDEVMVVRGHHHDREGKVTKVYRKKWVIHIERVTRDKAN---------------ETVTIGIHPSKVVIT................................................................................................................................................................... 106
21 -13.6004ytl_A mol:protein length:99 Transcription elongation factor SPT5  ali model follow..  13  1..............................................................FQPGDRIEVLNGEQRGSKGIVTRTTKDIATIKLNGFTTPLEFPISTLRKINGEHQGDAGLVLMVEQGQVTFMSTQTSREVTITANNL.................................................................................................................................................... 97
22 -13.4003j7o_Y mol:protein length:145 Ribosomal protein uL24  ali model follow..  12  10..........................DRSKNRKRHFNAPSHIRRKIMSSPLSKELRQVRSMPIRKDDEVQVVRGHYKGQIGKVVQVYRKKYVIYIERVQREKAN---------------TTVHVGIHPSKVVIT................................................................................................................................................................... 107
23 -12.2002e6z_A mol:protein length:59 Transcription elongation factor SPT5  ali model follow..  23  7.............................................................GFQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDMLEFP.............................................................................................................................................................................................. 52
24 -11.6004zn1_A mol:protein length:147 Transcription elongation factor Spt5  ali model follow..  23  88.............................................................NIEKGDVVEIIAGPFKGERAKVIRVDKHKEEVTLE---------------------AAVPIPITLPVEGVKIVSKHKD.............................................................................................................................................................. 147
25 -11.6002do3_A mol:protein length:69 Transcription elongation factor SPT5  ali model follow..  26  18..............................................................FKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSD......................................................................................................................................................................................................... 51
26 -11.4005ohq_A mol:protein length:111 Transcription elongation factor SPT5  ali model follow..  20  60...............................................................TKNNKVKVILGEDREATGVLLSIDGEDGIVRMDL........................................................................................................................................................................................................ 93
27 -11.1003qqc_D mol:protein length:163 Transcription antitermination protein nusG  ali model follow..  28  91.............................................................GLEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQ......................................................................................................................................................................................................... 125
28 -10.9005xog_W mol:protein length:83 Spt4/5 complex component  ali model follow..  21  21.................................................................NKTVKIRQGGYKGKIGIVKEANGDRFRVELHN........................................................................................................................................................................................................ 52
29 -10.9002ckk_A mol:protein length:127 KIN17  ali model follow..  30  72...............................................................APGKRILVLNGGYRGNEGTLESINEKTFSATIV......................................................................................................................................................................................................... 104
30 -10.9002kvq_G mol:protein length:63 Transcription antitermination protein nusG  ali model follow..  24  10..............................................................FEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKV.......................................................................................................................................................................................................... 42
31 -10.5002e70_A mol:protein length:71 Transcription elongation factor SPT5  ali model follow..  23  21.................................................................GQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLTTVGSRR..................................................................................................................................................................................... 71
32 -10.4002mi6_A mol:protein length:62 Transcription termination/antitermination protein NusG  ali model follow..  20  8.............................................................DYEVGESVTVMDGPFATLPATISEVNAEQQKLKV.......................................................................................................................................................................................................... 41
33 -10.3006duq_M mol:protein length:60 Transcription termination/antitermination protein NusG  ali model follow..  23  6.............................................................LFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKV.......................................................................................................................................................................................................... 39
34 -10.2001nz9_A mol:protein length:58 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG  ali model follow..  20  4.............................................................AFREGDQVRVVSGPFADFTGTVTEINPERGKVKV.......................................................................................................................................................................................................... 37
35 -10.0004ytk_A mol:protein length:130 Transcription elongation factor SPT5  ali model follow..  20  1..............................................................LEEGSYVRIKRGIYKGDLAMVDQISENNLEVMLK......................................................................................................................................................................................................... 34
36 -9.9402lq8_A mol:protein length:177 Transcription antitermination protein nusG  ali model follow..  30  123..............................................................FKVGDMVKIISGPFEDFAGVIKEIDPERQELKV.......................................................................................................................................................................................................... 155
37 -9.6901m1g_A mol:protein length:248 Transcription antitermination protein nusG  ali model follow..  14  194.............................................................EFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVM-ISIFGR-----------------MTPVELDFDQVEKI................................................................................................................................................................... 248
38 -9.6505ms0_F mol:protein length:183 Transcription termination/antitermination protein NusG  ali model follow..  24  130..............................................................FEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKV.......................................................................................................................................................................................................... 162
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.

Veeramalai M, Ye Y, Godzik A. TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinformatics. 2008 Aug 31;9(1):35