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Query: d2gk6a1 c.37.1.19 (A:295-324,A:416-702) Upf1 {Human (Homo sapiens) [TaxId: 9606]}, from SCOP207

Results of FFAS03 search in SCOP207
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 RYEDAYQYQNIFGPLVKLEADYDKKLKESQXKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYLast
1 -106.000d2gk6a1 c.37.1.19 (A:295-324,A:416-702) Upf1 {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors  100  1RYEDAYQYQNIFGPLVKLEADYDKKLKESQXKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQY 318
2 -52.700d4pj3a3 c.37.1.19 (A:416-492,A:662-1133) Pre-mRNA splicing factor Cwf11 / Aquarius {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  27  218.....................................................................................QFTHTQIEAIRAGMQPGLTMVVGPPGTGKTDVAVQIISNIYHNPEQRTLIVTHSNQALNQLFEKIMALDIHLLRLGHGEEELETEKDFSRYGRVNYVLARRIELLEEVKRLQKSTQLEEFRASELLRSGLDRSKYLLVKEAKIIAMTCTHAALKR--GFKYDNILMEEAAQILEIETFIPLLLQLKRWIMIGDHHQLPPVIKNMAFQKSNMEQSLFTRFVRVGVPTVDL.... 550
3 -48.500d3jb9x3 c.37.1.19 (X:385-460,X:619-1044) Pre-mRNA splicing factor Cwf11 / Aquarius {Schizosaccharomyces pombe 972h- [TaxId: 284812]}  ali model 3D-neighbors follow..  16  185.....................................................................................TYNDKQLESILRGSQPGLTMVNGPTRCGKHVLVCKLLEVLQDTPNDRTVVLSDSNFSMNTLFTLLEKARCHLLYLSDEGKDETLERYGTLSISKLPGLLREIGRLAASIQAPGSHDASPDTALGLLRYYEDQELYALCQQSRIIGCTWTSLSTRLGTGFCFNNLIVMNSQNISESSITSILLSNCDRLVLLGNQYLTSGNQ----DINNTSNGSLFKRLRYLKSRIIDLNT.. 503
4 -22.500d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  23  148.....................................................................................DEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGRIRLAAPTGKAAARLTESL---GKALRQLPLTDEQKKRIPEDASTLHRLLGAQPGSQRLRHHAG----------------------------------------------NPLHLDVLVVDEASMI---SRLIDALPDHARVIFLGDRDQLASV-------EAG---AVLGDICAYANAGF...... 320
5 -17.600d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}  ali model 3D-neighbors follow..  14  113.....................................................................................EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYHAMIKKIGGGASKD----------------------------------------------------DKYKNDAPVVVGTWQTVVKQPKE-SQFGMMMNDECHLATGKSISSIISGLNNCMFKFG----LSGSLRDGKANIMQYVGMF.................. 276
6 -16.900d1gkub1 c.37.1.16 (B:6-250) Helicase-like "domain" of reverse gyrase {Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors follow..  22  43..........................................................................................QKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGK-RCYVIFPTSLLVIQAAETIRKYAEKA-----------------------------------------GTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRELGHFDFIFVDDVDAILKASKNVDKL-----LHLLGFHYDLGCLMVSTATAKKGKKAELFRQLLNFDIGSSRIT... 232
7 -15.500d1yksa1 c.37.1.14 (A:187-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}  ali model 3D-neighbors follow..  15  4...................................................................................................KGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVKF--------------------------------------------------------HTQAFSAHGSGREVIDAMCHATLTYRMLEPTNWEVIIMDEA-HFLDPASIAARGWAAHATILMT---ATPP.................................. 138
8 -15.100d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}  ali model 3D-neighbors follow..  17  1.....................................................................................RLNPGQQQAVEFV-TGPCLVLAGA-GSGKTRVITNKIAHLIRGQARHIAAVTFTNKAAREMKERVHTLGLDIIK-DTDQLALLKELTEGLIEDDKVLLQQLISTISNWKNDLKTPSQAAASAIGERDRIFAHCACNVLDFDDLILLPTLLLQAN---QNKIRYLLVDE-TNTSQYELVKLLVGSRARFTVVGDDDQ---SIYSWRGARPQ-NLVLLSQ----ALKVIKLEQNY 276
9 -15.100d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors follow..  19  70.....................................................................................SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL----STPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIK---------------------------------------------------------ELKPLTVSTYDSAYVNA--GNRFMLLIFDEV-HHLPAESYVQIAQMSIAPFRLG......................................... 200
10 -14.600d3lfua1 c.37.1.0 (A:3-315) automated matches {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  17  5...................................................................................LDSLNDKQREAVAAP-RSNLLVLAGA-GSGKTRVLVHRIAWLMSVENYSIMAVTFTNKAAAEMRHRIHGLAHRLLRANLPQDFQILDSEDQLRLLKRLIKAMNLDEQKDEGLRPHHIQSYGNPVEQTWQKVYQAYQEACDRAGLVDFAELLLRAHELWLRERFTNILVDE-TNNIQYAWIRLLAGDTGKVMIVGDDDQ---SIYGWRGAQVE-NIQRFLN----GAETIRLEQNY 281
11 -13.300d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}  ali model 3D-neighbors follow..  19  11.......................................................................................RIYQEVIYAKCKETN-CLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRL----------------------------------------------FNLPPEKIVALTGEKSPEERSKAWARAKVIVAT-NDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIARE---------RQAKNPLVIGLTASPGSTPEKIMEVINNLGIEHIEYRSE. 190
12 -13.300d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors follow..  15  24....................................................................................EELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEKYFKKWEKIGLRIGISTGDY----------------------------------------------------ESRDEHLGDCDIIVTTSEKADSLIRNRKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRLSATAPNVTEIAEWLDADYYV................ 198
13 -12.700g1qhh.1 c.37.1.19 (A:,B:,C:,D:) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}  ali 3D-neighbors follow..  18  9...................................................................................LAHLNKEQQEAVRTT-EGPLLIMAGA-GSGKTRVLTHRIAYLMAEKHWNILAITFTNKAAREMRERVQSLQLSVMKTILKEKNIDPKKFEPRTILGTISAAKNELLPPEQFAKRXYYEKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHQYKFQYIHIDE-TNRAQYTLVKKLAERFQNICAVGDADQ---SIYRWRGADIQ-NILSFER----NAKVILLEQNY 284
14 -12.000d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}  ali model 3D-neighbors follow..  15  7...................................................................................................SFQVAHLHAPTGSGKSTKVPAAYAA----QGYKVLVLNPSVAATLGFGAYMSKA----IRTGVRTI---------------------------------------------------------TTGSPITYSTFLADGGCSGGA--YDIIICDEC-HSTDATSILGIGTVLDQAETAGARLVV.................................... 130
15 -11.300d2oxca_ c.37.1.0 (A:) automated matches {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  17  25.......................................................................................SPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHV----------------------------------------------IGGTPLSQDKTRLKKCHIAVGS---IELDYLNPGSIRLFILDEADKLLE-NWIYSSLPASKQMLAVS......................................... 182
16 -11.100d5y4za1 c.37.1.14 (A:178-481) automated matches {Zika virus (strain mr 766) [TaxId: 64320]}  ali model 3D-neighbors follow..  12  1.............................................................................................CFEPSMKKQLTVLDLHPGAGKTRRVLPEIVREAIKKRLRTVILAPTRVVAAEMEEALRGLPVRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPN-----------------------------------------------------YNLNIMDEA-HFTDPSSIAARGYGEAAAIFM.......................................... 138
17 -10.600d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebrafish (Danio rerio) [TaxId: 7955]}  ali model 3D-neighbors follow..  15  54....................................................................................KVLRPHQREGVKFLWD---CIMADEMGLGKTLQCITLIWTLLKQSPDKVIVVSPSSLVRNWYNEKWLGGRVQPVAIDGGSKDEIDSKLVNFIS-----------------------------------------QQGMRIPTPILIISTFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLALNSRRVLISGTPIQLGPILKGRDADASDKDRAAGEQKLQ............ 285
18 -10.400d3dkpa1 c.37.1.0 (A:139-378) automated matches {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  17  54..........................................................................................QMQAIPVMLHGRELLASAPTGSGKTLASIPILMQLKQPANKRALIISPTRELASQIHRELIKTGFRIHMIHKAA------------------------------------------------VAAKKFGPKSSKKFDILVTTLLKQDPPGIDLASVEWLVVDESDKLFEDGKT-------------GFRDQLASIFLACTSHKV--RRAMFSATFAYDVEQW...... 225
19 -10.400d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Pyrococcus furiosus [TaxId: 2261]}  ali model 3D-neighbors follow..  16  29.......................................................................................QEHIVKRLKHYVKTPHLLFAGPPGVGKTTAALALARELFGENWRHNFL-ASDERGINVIREKVKEF----------------------------------------------------------------------------------ARTKPIGGASFKIIFLDEADALTQ-DAQQALRRTMEMILSCNYSSKIIEPIQSR............................. 159
20 -10.400d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  15  34.......................................................................................SAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKQALMLAPTRELALQIQKVVMALA----------------FHMDIKVHACIGGTSFVEDAEG------------------------------LRDAQIVVGT---IQRRRFRTDKIKMFILDEADEMLQIYQIFTLLPPTTQVVLLS--ATMPNDVLE.............................. 198
21 -10.300d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}  ali model 3D-neighbors follow..  9  1..................................................................................................MTTRMIILNGGSSAGKS-GIVRCLQSVLPEPWLAF--------GVDSLIEAMPL------KMQSAEGGIEFDADGGVSIGPEFRALEGA--AEGVVAMARAGARIIIDDVFLGGAAAQERWRSFVGDLDVLWVGVRCDGAVAEGRET---VEVDTTHKESIECA---------WAIA----AHVVP.................................. 178
22 -10.100d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}  ali model 3D-neighbors follow..  15  83.....................................................................................KLTNAQKRAHQEIRND---LLQGDVGSGKTVVAQLAILDNYEAGFQTAFM-VPTSILAIRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRN---------------------------------------------GQIDVVIGT--ALIQEDVHFKNLGLVIIDEMNKGKMVDTLVMSATPIPRLAFYGD-DEMPP.................................. 264
23 -9.890d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus elongatus PCC 7942 [TaxId: 1140]}  ali model 3D-neighbors follow..  11  23.................................................................................................FFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAYEESR--AQLLRNAYSWGMDFLKIVCAYPESAGLEDHLQIIKSEINDFKPARIAIDALARGVSNNAFRQFVIGVTGYAKQEEITGLFTNTSDQFMGAHSITDSHISTITDTIILLQYVEIRGEMSRAINVFKAIREFMISDKGPDIKDSFRNFERIISGSPTRI.................. 242
24 -9.800d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  14  16.......................................................................................NEELTNFLKSLSDQPHLLLYGPNGTGKKTRCMALLESI---------------------------FGPGVYRLKIDVRQFVTASNRKLELNVVSSP------------------YHLEITPSDMGNNDRIVIQELLKEV-AQMEQVDFQDSKDGLAHRYKCVIINEANSLTK-DAQAALRRTMEKIMVCDSMSPIIAPIKSQ............................. 181
25 -9.680d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}  ali model 3D-neighbors follow..  12  25.......................................................................................TEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAQAVITAPTRELATQIYHETLKIT------------KFCPKDRMIVARCLIGGTDKQKALEKLN-----------------------------VQPHIVIGT---IREQALDVHTAHILVVDEADLMLDVDQIAARMPKDLQMLVFS--ATIPEKLKP.............................. 194
26 -9.580d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  14  25.......................................................................................SEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGSVLVMCHTRELAFQISKEYERFS------------KYMPNVKVAVFFGGLSIKKDEEVLKK-------------------------------NCPHIVVGTLALARNKSLNLKHIKHFILDECDKMLEQQEIFRMTPHEKQVMMFS--ATLSKEIRP.............................. 193
27 -9.570d4ct4b1 c.37.1.0 (B:95-301) automated matches {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  13  26.......................................................................................SPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLKKDNIQAMVIVPTRELALQVSQICIQVS---------------KHMGGAKVMATTGGTNLRDDIMRLD-----------------------------DTVHVVIAT---IKKGVAKVDHVQMIVLDEADKLLSQEDIILTLPKNRQILLYS--ATFPLSVQK.............................. 192
28 -9.560d3mwja_ c.37.1.0 (A:) automated matches {Thermus thermophilus [TaxId: 262724]}  ali model 3D-neighbors follow..  15  28..........................................................................................EAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALL-----------------------------------------------RGADAVVAT---LRQGVLDLSRVEVAVLDEADEMLEVEALLSATPPSRQTLLFS--ATLPSWAKR.............................. 191
29 -9.480d3kx2a1 c.37.1.19 (A:1-270) Pre-mRNA splicing factor DEAH RNA helicase Prp43 {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 559292]}  ali model 3D-neighbors follow..  17  95......................................................................................VHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLEMPHLENTQVACTQPRRVAAMSVAQRVAEE----VKLGE-------------EVGYSIRFENKTSNKTILKYMTDGM-----------------LLREAMEDHDL---------------SRYSCIILDEAHETLATDILMGLLKQ-----VVKRRPDLKIIIMSAT-----LDAEKFQRYF............. 259
30 -9.470g1f2t.1 c.37.1.12 (A:,B:) Rad50 {Pyrococcus furiosus [TaxId: 2261]}  ali 3D-neighbors follow..  13  10.......................................................................................NFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKFTKVGARDTYID-LIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHSEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDETIMERYLKKIPQVILVSHDEEL.................................... 270
31 -9.450d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  11  51...................................................................................................VFRAAMLYGPPGIGKTTAAHLVAQEL----GYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVII--------------------DEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFQFRRPIAIREKFKLDPNVIDRLIQTTR-----GDIRQVINLLSTISTTTKTINHENINEISKAWEKNI...... 253
32 -9.290d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus elongatus PCC 7942 [TaxId: 1140]}  ali model 3D-neighbors follow..  12  23.................................................................................................LPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVT-FEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQK----------------YRARRVSIDSVTSVFQQYDASSVVRLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVI.......................................... 193
33 -9.170d1sgwa1 c.37.1.12 (A:2-200) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}  ali model 3D-neighbors follow..  15  22................................................................................................TIEKGNVVNFHGPNGIGKT-TLLKTISTYLKPLKGEIIYNGVPITKVKGKIFFLPEEIIVPRKI--SVEDYLKAVASLYGVKVNKNEIMDALESVEVLDLKKKLGELSQGTIRRV-----QLASTLLVNAEIY--------------------VLDDPVVAIDEKSILEILKEKGIVIISSREEL..................................... 185
34 -9.110d2z0ma1 c.37.1.0 (A:1-192) automated matches {Sulfolobus tokodaii [TaxId: 111955]}  ali model 3D-neighbors follow..  18  21..........................................................................................QSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE----LGMKSLVVTPTRELTRQVASHIRDIGTKVAEV--------------------------------------------------YGGMPYKAQINRVRNADIVVAT---WSKGVIDLSSFEIVIIDEADLMFE-KIILAQTSNRKITGLFS--ATIPEEIRK.............................. 176
35 -9.000d3tqfa_ c.91.1.0 (A:) automated matches {Coxiella burnetii [TaxId: 777]}  ali model 3D-neighbors follow..  17  5............................................................................................HANFLVIDKMGVLITGEANIGKSELSLALIDRGHQLVCDDVIDLKQENNQLSVANGYILITGIGIIDVPKLFGLDAVVNQHEVHLSISLVKPEKMPLLDD.............................................................................................................................. 109
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, Godzik A. Discovering new genes with advanced homology detection. Trends Biotechnol. 2002 Aug;20(8):315-6.