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Query: d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}, from SCOP206

Results of FFAS03 search in SCOP206
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 IAEIYYERGTIVVKGDAHVPHAKFDSRSGTYRALAFRYRDIIEYFESNGIEFVDNAADPIPTPYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFELast
1 -99.500d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors  100  1IAEIYYERGTIVVKGDAHVPHAKFDSRSGTYRALAFRYRDIIEYFESNGIEFVDNAADPIPTPYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFE 206
2 -52.900d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}  ali model 3D-neighbors follow..  21  65.....................................VGQIKKFCDNFGYKAWDEWLSKLEIYSGNKRIEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLLENYEGKILIIVPTTALTTQMADDFVDYRHAMIKKIGGGYKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGKSISSIIGLNNCMFKFGLSGSLR 263
3 -25.700d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors follow..  27  25.....................................................................ELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREGGKSLYVVPLRALAGEKYESFKKWIGLRIGISTGDYEGDCDIIVTTADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRIGLSATA. 182
4 -24.300d1z63a1 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
5 -23.100d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}  ali model 3D-neighbors follow..  27  7...................................................................LIQPRIYQEVIYAKCKETNC-LIVLPTGLGKTLIAMMIAEYRGGKVLMLAPTKPLVLQHAERLFNLPPEKIVALTGEKSARAKVIVATPQTIENDLLA-LEDVSLIVFDEAHRAVGNIAREYKRQAKNPLVIGLTASP. 166
6 -22.300d1yksa1 c.37.1.14 (A:187-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}  ali model 3D-neighbors follow..  19  2.................................................................................LKKGMTTVLDFHPGAGKTRRFLPQILRRRLRTLVLAPTRVVLSEMKEAFHGLVKFHTQAFSAHGSGREVIDAMCHATLTYRMPTRVVNWEVIIMDEAHFLDPASIAHRARANESATIL-MTATP. 137
7 -22.100d3kqna1 c.37.1.14 (A:189-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}  ali model 3D-neighbors follow..  23  13........................................................................................HLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRTITAPITYSTYGKFLADGGCSGGAYDIIICDECHSTDSTTVLDQAETAGARLVVLATATP. 137
8 -20.800d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebrafish (Danio rerio) [TaxId: 7955]}  ali model 3D-neighbors follow..  21  35.................................................IKADKEKLPVHVVVDPVLSKVLRPHQREGVKFLWDNSYGCIMADMGLGKTLQCITLICKPEIDKVIVVSPSSLVRNWYNEVGKWLGGRVQPVQQGMRIPTPILIISYETFRLHAEVLHKKVGLVICDEGHRLKNSDNQLALNSMNAQRRVLISGTP. 230
9 -20.600d1gkub1 c.37.1.16 (B:6-250) Helicase-like "domain" of reverse gyrase {Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors follow..  20  38.....................................................................EPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMLALKGKRCYVIFPTSLLVIQAAETIRKYAENLIGYYHGRIPKREKIVITTTQFLSKHYREL-GHFDFIFVDDVDAI----LKASKNVDKLLHLLGFHYDLK 190
10 -16.900d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}  ali model 3D-neighbors follow..  24  82....................................................................FKLTNAQKRAHQEIRND-NRLLQGDVGSGKTVVAQLAIYEAGFQTAFMVPTSILAIQHYRRTVESFNIHVALLIGATTPSEQIDVVIGTHALIQEDVHFKNLGLVIIDEQHRFGVKQREALMNKGKMVDTLVMSATP. 241
11 -16.100d2jlqa1 c.37.1.14 (A:172-482) automated matches {Dengue virus 4 [TaxId: 408688]}  ali model 3D-neighbors follow..  18  10...............................................................................DIFRKKRLTIMDLHPGAGKTKRILPSIVRRRLRTLILAPTRVVAAEMEEALRG-IRYQTPAVKSDHTGREIVDLMCHATFTTRSSTRVPNYNLIVMDEAHFTDPCSVAARGYISTRVEMIFMTATPP 148
12 -15.100d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  23  25.....................................................................QFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLISLMKDQVDQLQA-NGVAAACLNSTQTREQQLEVGQIRLLYIAPERLMLNPVLLAVDEAHCISGHDFRQLRQRFPTLPFMALTATAD 185
13 -13.600d2eyqa3 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 -13.300d2z0ma1 c.37.1.0 (A:1-192) automated matches {Sulfolobus tokodaii [TaxId: 111955]}  ali model 3D-neighbors follow..  25  16.....................................................................NFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELGMKSLVVTPTRELTRQVASHIRDIMDTKVAEVYGGMPRNADIVVATPGRLLDLWSK--SSFEIVIIDEADLMFEMGFIILAQTSNRKITGLFSAT.. 169
15 -12.600d2pl3a1 c.37.1.0 (A:47-278) automated matches {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  20  45.....................................................................LVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEAGLGVLIISPTRELAYQ-LRKVGKNHDFSAGLIIGGKDLKHEILVCTPGRLLQHMDETVTDLQMLVLDEADRILDMGFADTMNAVKKRQTLLFSAT.. 209
16 -12.400d3dkpa1 c.37.1.0 (A:139-378) automated matches {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  22  52........................................................................PIQMQAIPVMLHGRELLASAPTGSGKTLMQLKQPANKGFRALIISPTRELASQIHRELIKISEVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLLVVDESDKL-RDQLASIFLACTSHKVRRASAT.. 217
17 -11.500d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  19  25.....................................................................KPSPIQEESIPIALSGRDILARAKNGTGKSLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSGAKVMATTGGTDDTVHVVIATPGRILDLIKK--DHVQMIVLDEADKLLSQDFVQIMEDIILRQILLYSATF. 187
18 -11.300d1t6na_ 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
19 -11.200d3iuya1 c.37.1.0 (A:213-439) automated matches {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  17  44........................................................................PIQSQAWPIILQGIDLIVVAQTGTGKTLSYLSREQRNGPGMLVLTPTRELALHVEAECSKYSYKGL-IYGGRNRNGQDIIIATLNDLQMNNSVNLRSITYLVIDEADKMLDMEFKILLDVRPDRQTVMTSAT.. 206
20 -11.100d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  19  32.....................................................................EPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTSIAALQRIAPQALMLAPTRELALQIQKALAFHMDIKVHACIGGTSRDAQIVVGTPGRVFDNIQR-TDKIKMFILDEADEMLSSGFKEIFTLLPPTTQVVLSATM. 192
21 -11.000d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}  ali model 3D-neighbors follow..  16  23.....................................................................KPTEIQERIIPGALRGESMVGQSQTGTGKTIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKIVARCLIGGTNVQPHIVIGTINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARQMLVFSATI. 188
22 -10.800d2oxca_ c.37.1.0 (A:) automated matches {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  22  26........................................................................PVQLKAIPLGRCGLDLIVQAKSGTGKTCVSTIALDSLSTQILILAPTREIAVQIHSVITAIEGLECHVFIGGTPKKCHIAVGSIKQLIELDYLNPGSIRLFILDEAKLLEEGSFQEQINWIASKQMLAVSAT.. 184
23 -10.700d2gxqa_ c.37.1.0 (A:) automated matches {Thermus thermophilus [TaxId: 262724]}  ali model 3D-neighbors follow..  22  23.....................................................................TPTPIQAAALPLALEGKDLIGQARTGTGKTLAALPIAERLAPSALVLTPTRELALQVASELTAVAP--VAVYGGTGLRGADAVVATPGRALDYLRQ--SRVEVAVLDEADEMLSMGFEEEVEALLSRQTLLFSATL. 185
24 -9.840d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}  ali model 3D-neighbors follow..  20  43.....................................................................RPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIKTAYPKCLILAPTRELAIQILSESQKFSGADTHSQIREVQMGCHLLVATLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIERQTLMFSAT.. 216
25 -9.520d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}  ali model 3D-neighbors follow..  15  8........................................................................................LLSGHPGSGKSTIAEALANLPGVPKVHF--HSDDLWGYIKH---------GRIDPWLPQSHQQNRMIMQIAADVAGRYAKEGYFVILDGV--VRPDWLPAFTALARPLHYIVLRTTAA 112
26 -9.350d4lcba_ c.37.1.0 (A:) automated matches {Acidianus hospitalis [TaxId: 933801]}  ali model 3D-neighbors follow..  18  37......................................................................................RGILLYPPGNGKTMLA-AAVANEIDSYFIHVDAASIMSKW--------------LGEAEKNVAKI------NTAREYSKKDNKPAIIFVDEIDALLGTEMDGIMDKNENYMVYVIGAT.. 152
27 -9.290d1w36d1 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
28 -9.120d3peya1 c.37.1.0 (A:91-286) automated matches {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  18  29..........................................................................QERALPLLLHNPPRNMISQSGTGKTAASLTMLTRVNPEAICLAPSRELARQTLEVVQEMGK---DSFEKNKQINAQVIVGTPGTVLDLMRR-LQKIKIFVLDEADNM-GDQCIRVKRFLPKDTQLVLSATFA 185

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.

Zmasek CM, Zhang Q, Ye Y, Godzik A. Surprising complexity of the ancestral apoptosis network. Genome Biol. 2007 Oct 24;8(10):R226 [Epub ahead of print]