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Query: [R] COG1341 Predicted GTPase or GTP-binding protein, from VFDB

Results of FFAS03 search in VFDB
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 MMRMASNKAMFTNDVPQDRLLAVEKIESLRKPAKVMIIGDVDTGKTTLTIYLANELLSRGFRVAIIDSDIGQKGILPPATISLAFVDSHFTSLDDLKAFSHYFIGTITPNQYFGEMVVGVMKLSELAMKFSDVVLIDTTGMIYGSGVELKRMKIEAVKPNLILALERNNELAPILKGYEDITIRLEVSEKAKDFSRSERRELRREKWRKYFENSKIVNFNLDDVLVTGTSLFQGEEIGDTEKSLLERLFKWLIIHGRKIGNKYFVVKVDASEGPRIVDKNVVKYFDFSKLSNILLGLIDKQGFCIGLGILKSINFKEKKIEVLTPVEDLSSVAEIRFGRVRVREDGEELGLLDREALLast
1 -88.200[R] COG1341 Predicted GTPase or GTP-binding protein  ali  100  1MMRMASNKAMFTNDVPQDRLLAVEKIESLRKPAKVMIIGDVDTGKTTLTIYLANELLSRGFRVAIIDSDIGQKGILPPATISLAFVDSHFTSLDDLKAFSHYFIGTITPNQYFGEMVVGVMKLSELAMKFSDVVLIDTTGMIYGSGVELKRMKIEAVKPNLILALERNNELAPILKGYEDITIRLEVSEKAKDFSRSERRELRREKWRKYFENSKIVNFNLDDVLVTGTSLFQGEEIGDTEKSLLERLFKWLIIHGRKIGNKYFVVKVDASEGPRIVDKNVVKYFDFSKLSNILLGLIDKQGFCIGLGILKSINFKEKKIEVLTPVEDLSSVAEIRFGRVRVREDGEELGLLDREAL 357
2 -62.200[A] KOG2749 mRNA cleavage and polyadenylation factor IA/II complex, subunit CLP1  ali follow..  16  102....................TSSTRDSASSQGPRVIIVGDIDSGKSTLAKMLLNWAVKDGWKPTFVDLNVGQSSITIPGTIAAAPIKMLVDPVEGFDKALIHYFGLTNPSVNLRLYRTLVEELARELKEEASGMVIDTMGFIVREGYALLLHAIRTFNASLVIVVGQEEKLVYDLKKNNLQVLNLEKSEGVFSRSSDFRKTLRNSNIQNYFYGVTNDLTVYTKTVKFSDVQVYRIG---------DFRVSGSTSAHQRGNDPLKITLVTIDEHLVNKVLAISYAIKPD---------QIISSIVAGFVCIKNVDISEERITYVSPSAAELPSKILILGTLTWHVT............ 423
3 -58.800[R] KOG2750 Uncharacterized conserved protein similar to ATP/GTP-binding protein  ali follow..  17  299....ASSISNNFEITPESWCSFSNQLLFDYVVPRLMVCGPKGSGKSSFSRYITNRLLQQYRHIAYLDLDPGQPEVVPSGHISLYYINSPLQGPVFARMLLRLHLGDISPQKDPDHYIACVTRLFAEYKDEIIPLIINCPGWIRGGGAELLSSIVDICQPTEVVYMSREDMKSSHREKKSILLESTWQYLPDPNVNKVTSADNRMLGLLSYLYFNCNLQRWDFTTSLTAATAFKGSSKGIDAVNIIGEPLNVNDVAKTINGTLMALYACDTASLDNSNTQRIVSSPEGPLIINDGLPLDPNTSHCLGLIVLRTIDLKRNEFHFVGPLNLKSLKIVLERGRLELPVQYSELPYLD.... 709
4 -56.000[A] COG5623 Pre-mRNA cleavage and polyadenylation factor IA/II complex, subunit CLP1  ali follow..  14  115.......................KIRMSNFEGPRVVIVGGSQTGKTSLSRTLCSYALKFAYQPLYINLDPQQPIFTVPGCISATPISDILDAQLPTKQPMVKNFGLERINENKDLYLECISQLGQVVGQRRSGCIVDTPSISQLDNLAELHHIIEKLNVNIMLVLCSETDPLWEKELGNNNIFFIPKLDGVSAVDDVYKRSLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWKPSNVFDNEVGRVELFPVTITPSNLQHAIIAITFAERRADQA---------------------TVIKSPILGFALITEVNEKRRKLRVLLPVPGRLPSKAMILTSYRYLE............. 445
5 -15.800[R] KOG1533 Predicted GTPase  ali follow..  12  3.MNLNEKKQLLRVRVYATSEKGENLGSTHWTMYGVLVIGAPGAGKSTFCAGLTDIFSQTKRPFLTINLDPANDTMAYAPDVNITEM------ITVNDVMDRLGLG---PNGALKYCIETLGANCNWLLQHKKYLIIDCPGQLEGELWKVIRFLEKSGVRLCALHLADSLYCSDPSKFISVALSTLAT.......................................................................................................................................................................... 189
6 -14.500[L] KOG1532 GTPase XAB1, interacts with DNA repair protein XPA  ali follow..  16  1MDPMESSSEQDIVEESQKLVDSLDKLRVSAASSSIIVVGMAGSGKTSFLHRLVCHTFDSKSHGYVVNLDPAVMSLPFGANIDIRVMKQYNLGPN----------GILTSLNLFATKFDEVVSVIEKRADQLDYVLVDTPGQIEASGAIITEAFASTFPTVVTYVVDT.............................................................................................................................................................................................. 179
7 -14.000[K] KOG1534 Putative transcription factor FET5  ali follow..  14  6..................................AFVCGVASSGKSTFCGALMSYMKSVGRSCHLVNLDPAAENFEWEPTVDIRDL------ISIDDVMEELDYG---PNGGLIYCFEFLMENLDWLNEDEDYLIFDMPGQIEPILPALIRHLQVTLNFRPCAVY................................................................................................................................................................................................ 137
8 -12.600[OK] COG0378 Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase  ali follow..  13  1............................MKRPLIIGVGGPVGAGKTMLIERLTRYLSTKGYSMAAITNDIYTKE-------ARILLNTSVLPADRIAGVETGGCPHTAIREDASMNFAAIEEMCDKH-PDLQLLFLESGGIDVAQGEKIPRKGGQGMIKSDLFIINKVDLAPYVGANVE.................................................................................................................................................................................. 162
9 -12.500[D] COG3640 CO dehydrogenase maturation factor  ali follow..  15  1..........................MEGFGMPKLIISGRGGSGKSTLVTLIAHTLKEQKKRVLVVDSDESNIGLSG--ILGIEPAEKTLMDYLGGKPRVMKKLRSMIRDGETEPMGAVTRDFLNHVREEDQWVLVDTEAGVEHFGRGIVEGA------DAVVMVVDPSSDA......................................................................................................................................................................................... 180
10 -12.500[V] COG3896 Chloramphenicol 3-O-phosphotransferase  ali follow..  12  15.......................AAMAGMPEGKLILLNGGSSAGKTSLALAFQDLA---AECWMHIGID----FALPPEQLDLARVRPEYYTWDSAVEADGLEWFTVHPGPILDLAMHSRYRAIRAYLDNGMNVIADDV-----WTREWLVDALRVFEGCRVWMVGVHVSDEEGARRELER................................................................................................................................................................................ 164
11 -12.000[D] COG0489 ATPases involved in chromosome partitioning  ali follow..  13  72.............ETLRNVKLTADVVIQERQCRVIGVISCPNEGKSVVALNLAGLIASTGKRTLVVDADIRNPGLS-AGLVEVVLDEVPWTQAVKVDTRTKMGISNQFAHSSELLSSSGMRKFIDSAREACDYIIVDLAPVVPVIDAKAFAPQVDGF----VFVTEWGKTPIQMVQNL................................................................................................................................................................................... 245
12 -11.300[C] COG3954 Phosphoribulokinase  ali follow..  11  2............................SAKHPVIAVTGSSGAGTTTTSLAFRKIFAQLNLHAAEVEGD-RHISYFGPEANDFSLLEHTFIEYGQTGKGQSRKYLHTYDEAVPWNQVPGTFTPWQPLPEPTDVLFYE--G-LHGGVVTPQHDVARHV--DLLVGVVPIVNLE-----WIQKLIRDTSERGHSREAVMDSVVRSMDDYINYITPQFSRT........................................................................................................................................... 201
13 -11.300[F] KOG3308 Uncharacterized protein of the uridine kinase family  ali follow..  14  2............................TRKTIIVGVSGASCSGKSTLCQLLHAIF----EGSSLVHED-GIADWDCQESLNLDAFLENLHYIRDHGVLPTHLRNRENKNVAPEALIEYADIIKEFKAPLEQHLVF-----VDGFMMYVNEDLINAFDIRLMLVTDFD............................................................................................................................................................................................. 148
14 -11.200[R] COG4639 Predicted kinase  ali follow..  13  3..........................ITIPELSLVVLIGASGAGKSTFARKHF-------QPFEVISSDFCRGLVS----------------------------NDENSQSASRDAFDVLHYITTKRLAAGKLTVIDATNVQPEDRKTLLQMAKQYHCFTVAIVFDLP............................................................................................................................................................................................. 109
15 -11.000[TU] KOG1954 Endocytosis/signaling protein EHD1  ali follow..  13  55.VSEGLRKIYKQKLLPLEEFHKFHDFHSPDAKPMILLVGQYSTGKTTFIRYLLES-IRIGPEPTFIAVMHGDEEGSIPGNALVVDAKKQFRALSGFGNA---FLNRFQCSTLPNQVLESVT-------------IVDTPGILSGEGYDFTGVLEWFAERVDRIILLFDAHKLDISDEFKRCIEALAGNEDKIRIVLNKSDMVDHQQLMRVY.................................................................................................................................................. 267
16 -11.000[R] COG0645 Predicted kinase  ali follow..  15  3.................................LAVTHGVSAVGKSQVAMRLVEAL-----GAVRLRSDI---------------ERKRLFGEQPEHDRGQFAAGIYSSQASEATYAH-LHQLAAKILQAGYPVVIDAAYLKQNQRQAACHIAEETGVPFLILDCQAPEAV.......................................................................................................................................................................................... 119
17 -11.000[R] KOG3062 RNA polymerase II elongator associated protein  ali follow..  18  2................................PLVVITGLPASGKSTRARQLRDHFVERGRKVHLISENEAVPKAGFGKNSH------------------------TGDSQKEKVVRSDLKSEASRHLNQEDLVILDAGNYIKGYRYELYCMSKVSRTTQCTVFTCIPQEE.......................................................................................................................................................................................... 116
18 -10.900[F] COG1618 Predicted nucleotide kinase  ali follow..  11  1......................MRIEGKEKTMLRIAVTGSPGVGKSTVVAKTAEKLAE-------------KPGFKIGGIRTAEIRKE-RDLATGKTGILSHVKGSGPRLGKYHVNLDDLERIGANAVRNALAVVIDEIGPMELISQSFVSAVEEVLESDKVLAVLHHSSRHPLAQRFRKGFEVLTVDKGNRDELPEKITNRFLRKL...................................................................................................................................................... 183
19 -10.900[R] KOG2878 Predicted kinase  ali follow..  14  13....................KFLEKQPKPEGRPFILISGPQGSGKSTLASALDTELTRKNESVVKFSLDLAKNN-GLAGTHDVTFLNNVLNAFVKGSDEEVSIPFYDKSKFGGYGDRGDESQWKKANPKTTTYVIFE--GWMVGFEPLDSCMLSVRARSTR.................................................................................................................................................................................................... 171
20 -10.800[R] COG4240 Predicted kinase  ali follow..  16  78......................IAAQHQQLKRPFIQILGSQGTGKTTMSLVIQLILQHLGYRTLSLSLD---IWRGPPGTHDIDLGLNVLEQIRQGKSPVIV------PRFDKSAHAGAGDRTKPDVITGVDILIFE--GWFVG..................................................................................................................................................................................................................... 208
21 -10.700[D] COG0455 ATPases involved in chromosome partitioning  ali follow..  14  9IQRDSRRRTGMTNKMIYDQASGLRRLTQPSVTKVISVTGKGGVGKSNVTLGMAICMAKQGKKVMVLDADLGLANVDV-GIRPKRNLGHVLAGECELKDAIV--SGTQSMTELSHAQHVGLIRAFGTLEDEMDILLIDTAAGISDMVVSFSRDVVVVVCDEPTSITDAYALIKLLSKEHQVQRFKIVANMVRSYREGRELFAKLTLVTERFLN................................................................................................................................................. 235
22 -10.600[S] COG4185 Uncharacterized protein conserved in bacteria  ali follow..  15  2.....................SIVRLKKLEQPVFLIVAGPNGSGKSSVYANADLE--LEGRSVWIVNPD-VHKTIGVETVLS-KYRRLVEAAEAVGFAIWLFYTVLDSPERSIERYARSLDQLPWFLERADRAWIWDNSG......................................................................................................................................................................................................................... 172
23 -10.600[H] COG1763 Molybdopterin-guanine dinucleotide biosynthesis protein  ali follow..  17  2................................NIFGITGWKNSGKTTLTEKLVAELVRRGWKVSTVKHAHHDFDIDKPGADSFRHRQAGATEVAIVSGNRWALMHELRGEDEPPL------ESILSRLAPCDIVLVE--GYKRESHRKIETRTPLSAGDPNIVAIAADFAVTD........................................................................................................................................................................................ 141
24 -10.300[P] KOG2825 Putative arsenite-translocating ATPase  ali follow..  15  9.....................TLENLLEQTSLKWIFVGGKGGVGKTTTSCSLAIQMSKVRSSVLLISTDPAHN-------LSDAFGTKFGKDARKVPGFDNLSAMEIDPNLSIQEMTEQADQQNPNNPLSGQDLAFTIPGIDEALAFAEILKQIKSMEFDCVIF................................................................................................................................................................................................. 146
25 -10.200[E] COG1703 Putative periplasmic protein kinase ArgK and related GTPases of G3E family  ali follow..  17  22LAQAMTLVESRHPRHQALSTQLLDAIMPYCGNTLRLVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSSP-------VTGGSILGDKTRMNDLARAEAAFIRPVPSSGHLGGASQRARELMLLCEAAGDVVIVETVGQIAGGGDDLQGIKKGLMEVADLIVINKDD............................................................................................................................................................................................ 203
26 -10.100[R] KOG2486 Predicted GTPase  ali follow..  12  136................................PEFALVGRSNVGKSSLLNSLVRR-----KRLALTSKKPGKTQVDLPG------------------------YGYASPHELKQDWNKFTKDFLNRSTLVSVFLLVDASIPVKPIDLEYASWLGQNQVPMTLIFTKCDKRKKK........................................................................................................................................................................................ 262
27 -10.100[E] COG4917 Ethanolamine utilization protein  ali follow..  16  2................................KRIAFVGSVGAGKTTLFNALQGNYTLARKDKGDIDT-PGHPRWYHALITTLQDVDMLIYVHGANDPESRLQIAVISKTDMPDADVAATRKLLLETGFEEPMFELNS---HDPQSVQQLVDYLASLTKQ..................................................................................................................................................................................................... 148
28 -10.100[G] COG3265 Gluconate kinase  ali follow..  17  2..............................SGKCIIVMGVSGTGKSCVGQALALAL-----GAKFIDGD----DLHPRANIQKMAAGQPLN------------------DQDRAPWLERLSDVAYSLQQKNEVGFLVCSA-----LKKQYRDRLREGNEGRFLWLTGDYDL.......................................................................................................................................................................................... 111
29 -9.990[F] COG2019 Archaeal adenylate kinase  ali follow..  14  2.................................RSVITGVAGVGKTTVLDIVARES--------------GIPVVNYGTLMFEVAKRRGLV------------ENRDQIRKLSRETQVDLQKLAGEEIGKMENAIVDTHMSIFGYLPGLPEWVLRSINASVFVIIEADP--AIIKRRRDNDPTRARDDEGVDSIREHQEMNRYFAAAYSIFSGATVKIVKNEE...................................................................................................................................... 166
30 -9.860[R] COG3596 Predicted GTPase  ali follow..  14  2........VMKNFEVLQPLQNSLSGLPLWHYEPVIGIMGKTGAGKSSLCNALFAGEVSPVSDVAACTRDPLRFRLQIGE-HFMTIVDLP---------------GVGESGVRDTEYAALYREQLPRLD-----WLIKADDRALATDEHFYRQVIEAYRHKMLFVISQSDKAEP........................................................................................................................................................................................ 162
31 -9.840[N] COG1419 Flagellar GTP-binding protein  ali follow..  24  141FGDLDPNSNETFKILSEQFVNLVKTNAPDFKNAKVLFVGTTGVGKTTLAKLAARFKIDEKKRVAILTLDTYR------AAAEQLKIYADIMDIP------------MKIAYTPKEAEYEMMAL-----KDYDIVLVDTAG--NDLQMSELRALSEAVKPITFLVLSMNYKLDDMKRIVE.................................................................................................................................................................................. 301
32 -9.820[L] COG1484 DNA replication protein  ali follow..  14  88.TEGKPQAIKDAFECTKEYVADYEQIKDCRKNS-IALLGQPGSGKTHLLTAAANELMRTCYVPVIYDFALLEAKLNRMKQADVLFIDD-------------LFKPVNGKPRATDWQLEQMYSVLNYRYLNHKPILLSSE--LVRVDEALGTKIYEMCSDYLVIIKGAAYELNHRLEGVR.................................................................................................................................................................................. 266
33 -9.700[E] COG0703 Shikimate kinase  ali follow..  13  59...................TNSLSSTEKMAEKRNIFLVGPMGAGKSTIGRQLAQQL-----NMEFYDSD------------------------QEIEKRTGADVGWVFDLEGEEGFRDREEKVINELTEKQ-GIVLATGG-----GSVKSRETRNRLSARGVVVYLETTIEKQLARTQRDKKRPLLHVETPPREVLEALANERNPLYEEI................................................................................................................................................... 214
34 -9.630[NU] COG2874 Predicted ATPases involved in biogenesis of archaeal flagella  ali follow..  16  24......................IDKRLGGGLGSLTLIEGENDTGKSVLCQQFVYGGLMSGHNIAYYTTENTIKSF-LRQMESLSLDVSDFYAWGYLRVFPVHLEGIDWSTEQMRSILNLVANHIKTIRENI--AIIDSLTMFTTYSLEFLTRLKNLCDNGKTILI................................................................................................................................................................................................ 170
35 -9.590[F] COG0572 Uridine kinase  ali follow..  11  1.........................MTDKAHQCVIIIAGASASGKSLIASTLYRELREQDQHIGVIPED-VKTNYDHPSAMDHNLLLEHLQALKAGKPVELPLYSYTE------------TRKKETVHLEPKKVII-----LEGILLLTDIRLRQEMNFSIFVDTPLD............................................................................................................................................................................................. 143
36 -9.530[D] COG2894 Septum formation inhibitor-activating ATPase  ali follow..  16  6..................................VVTSGKGGVGKTTSSAAIATGLAQKGKKTVVIDFDIGLRNLD----LIMGCERRVVYDFVNVRTENLYILPASQTRDKDALTREGVAKVLDDLKADFEFIVCDS-----PAGIETGALMALYFADEAIITTNPE............................................................................................................................................................................................. 146
37 -9.360[H] KOG3220 Similar to bacterial dephospho-CoA kinase  ali follow..  14  3.................................IVAVTGGIATGKSTISKVFERQ------GIPVIDADKGDEVLLPSKEINRAVLGKMIFEDKELRGK-------LNKITHPTIHRKIFWQVCKLLVTGHAWIVLDLPLLFETGVLMDFIHKIVCVTCDSDKQLERLIARNELSESEARHRVDSQMP......................................................................................................................................................................... 164
38 -9.350[G] COG2074 2-phosphoglycerate kinase  ali follow..  13  80....................MLWRKIRQCKEPLIILIGGASGVGTSSIAFEVAN-------------------RLGIRNMISTDMIREVMRKIVSRELLPSIYESSYTARDHVESVSIGVEAVIERALTEGISIVIE--------GVHIVPGFIREDKENVAMFVLTVSDENVHKGRFYSRC---RQMWARRPLKRYISYFWAIRRIHRYIENQARK............................................................................................................................................ 268
39 -9.320[C] KOG3877 NADH:ubiquinone oxidoreductase, NDUFA10/42kDa subunit  ali follow..  10  79............................DENSKVICVEGPIAAGKSKFAKELAEELDMEYYPAVDLD-DMRKLDPQLPPSCRSYDVRNFCLDPSHDLAAQFQIRMYML--------YSQYIDALQHVLSTGQGVVLERQGYLSRGARSVYNELRQNTKPHLVIYLDLPVDA-----------------KQIKARNVDYEVQSKVFS-DAYLSDLEQ............................................................................................................................................. 270
40 -9.250[F] KOG3079 Uridylate kinase/adenylate kinase  ali follow..  14  31...........................RLMKPLVVFVLGGPGAGKGTQCARIVEKY--------YTHLSAGRDERKNPDSQYGELIEKYIKE------------GKIVPVEITISLLKREMDQTMAANAQKNKFLID--GFPRNQLQGWNKTMDGKADVSFVLFFDCNNEICIERCLERGKSSGRSDDNRESLEKRIQTYLQSTKPIIDLYEEM............................................................................................................................................... 201
41 -9.240[D] KOG3022 Predicted ATPase, nucleotide-binding  ali follow..  15  33....NQEACATAPKGPDPDLVAIAERMSTVKHKILVLSGKGGVGKSTFSAQLSFALAGMDHQVGLMDIDICGPSI--PKMLGLEQSNLGWSPVYVEDNLGVMSIGFMLPNSDEAVINGLIKQFLKDVYGEIDYLVVDAPPGTSDEHISIVQYLLPTIDGAIIVTTPQEVSLIDVRKEVS.................................................................................................................................................................................. 218
42 -9.210[F] COG4088 Predicted nucleotide kinase  ali follow..  14  2................................PLIIVSGYPSSGKTTRSNELKKALEDRIHQNIDNTKD-----------YRVIIINDESLNIE----------ETYRESKNEKAARGLLYSAVQRELSKSTFVICDALNYIKGFRYQLYCESKSMYTTHCVIHVAVPQDL.......................................................................................................................................................................................... 120
43 -9.180[P] COG1348 Nitrogenase subunit NifH (ATPase)  ali follow..  16  3.................................QVAIYGKGGIGKSTTTQNLTSGLAELGKKIMVVGCDPKADTIMKTGFGNIKCVES---------------EPGVGCAGRGIITSINMLEQLGAYEDELDYVFYDVLG---DVVCGGFAMPIREGKAKEIYIVASGEMMA......................................................................................................................................................................................... 154
44 -9.140[H] COG3172 Predicted ATPase/kinase involved in NAD metabolism  ali follow..  16  10.................................TVAILGGESSGKSTLVNKLANIFVKYANKVAFIDTDFVTTQAREHPFVQALIDEYRFDLVILLENNTPWVADGLRSLGSSVDRKEFQNLLVEMLEENNIEFVRVEEEDYDSRFLRCVELVREMMG....................................................................................................................................................................................................... 184
45 -9.110[R] KOG2203 GTP-binding protein  ali follow..  13  12LIDGNGEFNVKGLD---NFVKKTKLSDCGLSYAVVAIMGPQSSGKST----LLNHLF--KTSFREMDAFAGRSQTTKGIWMARCVGIEPFTIAMDLEGTDGRERGEDD-EKQSALFAIAVADI----------VLINDIGREQAANKPLLKTVFQVMKTTLLFVIRDKTPIELLERALREDIQKI--------DSVRKPEAHKNTPLNEFFN................................................................................................................................................. 212
46 -9.050[U] KOG0090 Signal recognition particle receptor, beta subunit (small G protein superfamily)  ali follow..  15  45.....................LSIRLFRRTKSNTVLLSGLSGSGKTVLFYQLRNTKKGKVKPVHLIDV-PGHSRLISKLEEYLPRAAAVV-----------FVVDALEFLPNIRAASEYLYDILASVIKNKTPVLLNKTDKVTAHTKEFIRKQMEK......................................................................................................................................................................................................... 196

FFAS is supported by the NIH grant R01-GM087218-01
1 3 6 3 0 1   jobs submitted since Jan 1, 2011
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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