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d2fz4a1
Query: d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}, from SCOP175

Results of FFAS03 search in SCOP175
Master-slave alignment 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 IAEIYYERGTIVVKGDAHVPHAKFDSRSGTYRALAFRYRDIIEYFESNGIEFVDNAADPIPTPYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFELast
1 -97.400d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors  100  1IAEIYYERGTIVVKGDAHVPHAKFDSRSGTYRALAFRYRDIIEYFESNGIEFVDNAADPIPTPYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFE 206
2 -51.300d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}  ali model 3D-neighbors follow..  21  65.....................................VGQIKKFCDNFGYKAWDPQINEKEELSRKKRIEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLLENYEGKILIIVPTTALTTQMADDFVDYRHAMIKKIGGGYKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGKSISSIIGLNNCMFKFGLSGSLR 263
3 -28.400d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}  ali model 3D-neighbors follow..  24  9.....................................................................QPRIYQEVIYAKCKETNC-LIVLPTGLGKTLIAMMIAEYRGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVAARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVVFIAREYKRQAKNPLVIGLTASP. 166
4 -25.300d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors follow..  27  25.....................................................................ELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREGGKSLYVVPLRALAGEKYESFKKWIGLRIGISTGDYEGDCDIIVTTADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRIGLSATA. 182
5 -24.500d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}  ali model 3D-neighbors follow..  20  8.................................................................NIKANLRPYQIKGFSWMRFMNKICLADDMGLGKTLQTIAVFSDAKKPSLVICPL-SVLKNWEEELSKFAHLRFAVFHEDRSKIKDIILTTYAVLLRDTRLKEVEWKYIVIDEAQNIPQTKIFKAVKELKSKYRIALTGTP. 162
6 -23.900d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}  ali model 3D-neighbors follow..  19  2...............................................................................HMLKKGMTTVLDFHPGAGKTRRFLPQILRRRLRTLVLAPTRVVLSEMKEAFHGLVKFHTQAFSAHGSGREVIDAMCHATLTYREPTRVVNWEVIIMDEAHFLDPASIAHRARANESATIL-MTATP. 139
7 -23.000d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}  ali model 3D-neighbors follow..  19  38....................................................DKEKLPVHVVVDPVLSKVLRPHQREGVKFLWDSYGCIMADEMGLGKTLQCITLIWTLEIDKVIVVSPSSLVRNWYNEVGKWLGGRVQPVQQGMRIPTPILIISYETFRLHAEVLHKKVGLVICDEGHRLSDNQTYLALNSMNAQRRVLISGTP. 230
8 -22.600d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}  ali model 3D-neighbors follow..  24  12........................................................................................HLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRTITSPITYSTYGKFLADGGCSGGAYDIIICDECHSTDATSVLDQAETAGARLVVLATATP. 136
9 -19.800d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors follow..  21  43.....................................................................EPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMLALKGKRCYVIFPTSLLVIQAAETIRKYAENLIGYYHGRIPKREKIVITTTQFLSKHYREL-GHFDFIFVDDVDAI----LKASKNVDKLLHLLGFH.... 191
10 -16.800d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}  ali model 3D-neighbors follow..  24  79.................................................................SLPFKLTNAQKRAHQEIRND-NRLLQGDVGSGKTVVAQLAIYEAGFQTAFMVPTSILAIQHYRRTVESFNIHVALLIGATTPSEQIDVVIGTHALIQEDVHFKNLGLVIIDEQHRFGVKQREALMNKGKMVDTLVMSATP. 241
11 -15.900d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}  ali model 3D-neighbors follow..  20  4...............................................................................DIFRKKRLTIMDLHPGAGKTKRYLPAIVRRGLRTLILAPTRVVAAEMEEALRGLPIRYQTAIRAEHTGREIVDLMCHATFTMRSPIRVPNYNLIIMDEAHFTDPASIAARGYISTRVEMIFMTATPP 142
12 -15.200d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  23  25.....................................................................QFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLISLMKDQVDQLQA-NGVAAACLNSTQTREQQLEVGQIRLLYIAPERLMLNPVLLAVDEAHCISQAALGQLRQRFPTLPFMALTATAD 185
13 -13.800d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  23  51.................................................................SFPFETTPDQAQAINAVLSDMCQLVCGDVGFGKTEVAMRAAVDNHKQVAVLVPTTLLAQQHYDNFRD-AKEQTQILAEVAEGKIDILIGTHKLLQSDVK---KDLGLLIVDEEHRFGVRHKERIKAMRANVDILTLTATP. 213
14 -11.600d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  20  28........................................................................PIQEESIPIALSGRDILARAKNGTGKSGALIPLLERLNIQAMVIVPTRELALQVSQICIQVSGAKVMATTGGTDDTVHVVIATPGRILDLIKK--DHVQMIVLDEADKLLSQDFVQIMEDIILRQILLYSAT.. 186
15 -11.400d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  20  26........................................................................EVQHECIPQAILGMDVLCQAKSGMGKTAVVLATLQQLQVSVLVMCHTRELAFQISKEYERFSNVKVAVFFGGKKNCPHIVVGTILALARNKSLNLKHIKHFILDECDKM-RRDVQEIFRMTPHEKQVMMSATLS 188
16 -11.300d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  19  35........................................................................AIQQRAIMPIIEGHDVLAQAQSGTGKTGTSIAALQRIAPQALMLAPTRELALQIQKALAFHMDIKVHACIGGTSRDAQIVVGTVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEIFTLLPPTTQVVLSATM. 192
17 -11.200d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}  ali model 3D-neighbors follow..  16  23.....................................................................KPTEIQERIIPGALRGESMVGQSQTGTGKTIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKIVARCLIGGTNVQPHIVIGTINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARQMLVFSATI. 188
18 -10.800d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  17  151........................................................................NWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALRCRIRLAAPTGKAAARLTESLGKALRQ---PLTDEQKKRIPEDASTLHRLLRHHAGNPLHLDVLVVDEASMIDLPMMSRLIDALPDHARVIFLGDRD 298
19 -10.600d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}  ali model 3D-neighbors follow..  20  26.....................................................................KPTDIQMKVIPLFLNDEYNIVQARTGSGKTASAIPLIELVGIEAIILTPTRELAIQVADEIESLKGNKAKIYGGKAIYPQNIVVGTPGRILDHINRGTKNVKYFILDEADEMLNMGFIKDVEKILNKRILLFSATM. 186
20 -10.200d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}  ali model 3D-neighbors follow..  21  46........................................................................PIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIKTAYPKCLILAPTRELAIQILSESQKFSLNTCVVYGGADTHSQHLLVATLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIERQTLMFSAT.. 216

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.

Alexey M. Eroshkin, Andrew LeBlanc, Dana Weekes, Kai Post, Zhanwen Li, Akhil Rajput, Sal T. Butera, Dennis R. Burton, Adam Godzik. bNAber: database of broadly neutralizing HIV antibodies. Nucl. Acids Res. 2013; published on November 7, 2013.

Ginalski K, Grishin NV, Godzik A., Rychlewski L. Practical lessons from protein structure prediction. Nucleic Acids Res. 2005 Apr 1;33(6):1874-91.