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Query: d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}, 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 PPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRTITTGSPITYSTYGKFLADGGCSGGAYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLATATPLast
1 -92.000d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}  ali model 3D-neighbors  100  1PPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRTITTGSPITYSTYGKFLADGGCSGGAYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLATATP 136
2 -48.500d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}  ali model 3D-neighbors follow..  20  2..HMLKKGMTTVLDFHPGAGKTRRFLPQILARRLRTLVLAPTRVVLSEMKEAFHGL-DVKFHTQAFSAHGSGREVIDAMCHATLTYREPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR-ANESATILMTATP 139
3 -42.800d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}  ali model 3D-neighbors follow..  18  3.DDIFRKKRLTIMDLHPGAGKTKRYLPAIVRRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHT-GREIVDLMCHATFTMRSPIRVPNYNLIIMDEAHFTDPASIAARGYI-STRVEMGEAAGIFMTATP 141
4 -24.800d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors follow..  23  84......VDKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIK--ELKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAES------YVQIAQMSIAPFRLGLTATF 205
5 -24.100d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}  ali model 3D-neighbors follow..  14  127......VNRRRILNLPTSAGRSL-ARYYLENYEGKILIIVPTTALTTQMADDFVDMIKKIGGGASKDDKYKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGKSISSI-----ISGLNNCMFKFGLSGSL 262
6 -22.500d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}  ali model 3D-neighbors follow..  21  24........TNCLIVLPTGLGKTL-AEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTKAWARAKVIVATPQTILLAGRISLEDVSLIVFDEAHRAVGNYAYVF-IAREYKRQAKNPLVIGLTASP 166
7 -20.000d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors follow..  17  57......RKESFAATAPTGVGKTS-MSLFLALKGKRCYVIFPTSLLVIQAAETIAEKAGVGTENLIGYMQNLRNFKIVITTTQFLS-KHYRELGHFDFIFVDDVDAISKNVDKLLHLLTKSWVGEARGCLMVSTAT. 213
8 -18.200d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors follow..  22  35..EKVFSGKNLLLAMPTAAGKTLLAEMAMVRKGGKSLYVVPLRALAGEKYESFKKKIGLRIGISTGDYEHLGDCDIIVTTSEKLIRNRASWIKAVSCLVVDEIHLLDSEK-TLEILVTKMRRMNKALRVIGLSAT. 181
9 -16.200d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}  ali model 3D-neighbors follow..  16  108...........LLQGDVGSGKTVVAQLAIYEAGFQTAFMVPTSILAIQHYRRTVEKFNIHVALLIGATTGLRNGQIDVVIGTHALIQEDVHFKNLGLVIIDEQHR------FGVKQREALMNKGKMVDTLVMSATP 241
10 -14.900d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}  ali model 3D-neighbors follow..  17  36.PLFLNDEYNIVAQARTGSGKTASIELVNENNGIEAIILTPTRELAIQVADEIKGNKNLKIAKIYGGKAALKNANIVVGTPGRILNRGTLNLKNVKYFILDEADEMNMGFIKDVEKILNACNKDKRILLFSATMPR 188
11 -14.300d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  15  158..AVALTRRISVISGGPGTGKTTTVAKLLAGERCRIRLAAPTGKAAARLTESLGKALR-EQKKRIPEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMIDLP---MMSRLIDALPDHARVIFL...... 294
12 -13.800d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}  ali model 3D-neighbors follow..  12  3..........IIITGEPGVGKTTLVKKIVERLGKRAIGFWTEEVRDPETKKRTGFRIFFTSKKLVGSYGVNVQYFEELAIPILERAYREAKKDRRKVIIIDEIGKMELFSKKFRDLVRQIMHDPNVNVVATIPIR. 140
13 -13.500d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}  ali model 3D-neighbors follow..  15  1......ERGIIIVFTGNGKGKTTGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEMATGFTWETQNREADTAACMAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITG.. 134
14 -13.400d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  14  2........RHVFLTGPPGVGKTTKASEVLKSSGVPVDLSGTRGPLSRVGLEPPPGKRECRVGQYVVDLTSFEQLALPVLRNADCSSGPGQ-----RVCVIDEIGKMELFSQLFIQAVRQTLSTPGTIILGTIPVP. 146
15 -13.000d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  16  80...........LVCGDVGFGKTMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWP-VRIEMISRFRSAKIDILIGTHKLLQSDVKFKDLGLLIVDEEHR------FGVRHKERIKAMRANVDILTLTATP 213
16 -12.900d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}  ali model 3D-neighbors follow..  18  53..PAILEHRDIMACAQTGSGKTAAIPIINHTAYPKCLILAPTRELAIQILSESQK---FSLNTPLRSCVVYGGADLLVATPGRLIEKNKISLEFCKYIVLDEARMLDMGFEPQIRKIIEESNSGINRQTLMFSAT. 216
17 -12.900d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  14  35..PIALSGRDILARAKNGTGKSGAYLIPLLER--QAMVIVPTRELALQVSQICIQVSKHMGGAKVDIMRLDDTVHVVIATPGRILKKGVAKVDHVQMIVLDEADKLSQDFVQIMEDIILTLPKNRQILLYSAT... 186
18 -12.900d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  18  39........MDVLCQAKSGMGKTAVFVLATLQQ--SVLVMCHTRELAFQISKEYERFSKYMPNVKV--VLKKNCPHIVVGTPGRILRNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSAT. 186
19 -12.800d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}  ali model 3D-neighbors follow..  14  33..PGALRGESMVGQSQTGTGKTHAYLLPIMEK--QAVITAPTRELATQIYHETLKTKFCPKDRMIVARCLIGGTDIVIGTPGRINREQALDVHTAHILVVDEADLMDMGFITDVDQIAARMPKDLQMLVFSATIPE 190
20 -12.700d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}  ali model 3D-neighbors follow..  10  3........WIEFITGPMFAGKTAEL-HRLEYADVKYLVFKP------KIDTRSIRNIQSRTGTSL------PSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAEN................ 105
21 -12.600d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  20  50.....GVFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTL---------------LNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICN... 162
22 -12.600d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  14  46......EGHDVLAQAQSGTGKTGTFSIAALQR--QALMLAPTRELALQIQKALAFHMDIKVHACIGGTSGLRDAQIVVGTPGRVIQRRRFRTDKIKMFILDEADEMSSGFKEQIYQIFTLLPPTTQVVLLSATMPN 194
23 -12.200d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}  ali model 3D-neighbors follow..  16  35...........CLADDMGLGKTLQTIAVFSDAKKESLVICPLSVLKEEELSKFAPHLRFAVFHEDRSKIKLEDYDIILTTYAVLLRDTRLKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKY----RIALTGTP 162
24 -12.000d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}  ali model 3D-neighbors follow..  12  3........KIILTIGCPGSGKSTWAREFIAKNGFYNINRDDYRQSIMAHEERDEYKYTKK------------KEGIVTGMQFDTAKSILYGGDSVKGVIISDTNLNPERR----LAWETFAKEYGWKVEHKVFDVP 115
25 -11.800d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}  ali model 3D-neighbors follow..  10  1.......NKVVVVTGVPGVGSTTLAMDNLRKEGVNYKMVSFGSVMFEVAKEE---------NLVSDRDQMRKMDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVSTPKGYLPGLPSWVLNELNPDLIIVVETTG 123
26 -11.700d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}  ali model 3D-neighbors follow..  16  83...........IMADEMGLGKTLQCITLIWTL-DKVIVVSPSSLVPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEVLHKKVGLVICDEGHRLKNSDNQTYLALNSMNAQR----RVLISGTP 230
27 -11.600d1yj5a2 c.37.1.1 (A:351-522) 5` polynucleotide kinase-3` phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}  ali model 3D-neighbors follow..  12  8.SLLSPNPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNRDTLGSWQRCVSS-------CQAALRQGKRVVIDNTNPDVPSRARYIQCAKDAGVPCRCFNFC................................... 100
28 -11.100d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}  ali model 3D-neighbors follow..  13  8........KTVAILGGESSGKSV-LVNKLAAVFNTTSAWEYGREFVFEKLGGDEQAM--------------QYSDYPQMALGHQRYIDYAVRHSHKIAFIDT.................................. 86
29 -10.800d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}  ali model 3D-neighbors follow..  14  2........KIGIVTGIPGVGKSTKVKEILDNQGINNKIINYGDFMLATALKLGYAKDRDEM------RKLSVEKQKKLQIDAAKGIAEEARAGGEGYLFIDTHAVIRTPSGYLPGLPSYVITEINPSVIFLLEADP 126
30 -10.800d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}  ali model 3D-neighbors follow..  17  1......AMRQCAIYGKGGIGKSTNLVAALAEMGKKVMIVDPKADSTRLILHSKAQNTIMEMAAEAGTVEDLELEDVLVITAINFLEEEGAYEDDLDFVFYD------LGDVVCGGFAMPIRENKAQEIYIVCSG.. 153
31 -10.700d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  18  35..DTVLSGRDCLVVMPTGGGKSLQIPA-LLLNGLTV-VVSPLISLMKD-AACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEH-NPVLLAVDEAHCISQPEYAALGQLRQRFPTLP-FMALTATADD 186
32 -10.700d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  17  6.....NIPPYLFFTGKGGVGKTSATAIRLAEQGKRVLLTDPASNVGQVFSQTIGNTLEIDPQAAAQQYRARIVDPIKGVLPDDVVSSINEQLTRFDHIIFDTAPTGHTIRLLQL...................... 155
33 -10.600d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}  ali model 3D-neighbors follow..  16  3..........IAIEGVDGAGKRTLLSGAFRAAGRSVATLAPRY--GQSVAADIAAEA-LHGEHGDLASSVYAMATLFALDRAGAVHTIQGLCRGYDVVILDR.................................. 95
34 -10.400d2axpa1 c.37.1.1 (A:2-165) Hypothetical protein YorR {Bacillus subtilis [TaxId: 1423]}  ali model 3D-neighbors follow..  20  1........TLIILEGPDCCFKST-------------------------VAAKLSK--------ELKYPIIKGSSFELAKSGNEKLFEHFNKLADEDNVIIDRFVYSNL............................ 67
35 -10.300d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  13  36..........LLLYGPNGTGKKTRLLESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMS. 172
36 -10.300d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}  ali model 3D-neighbors follow..  16  3......GGNILLLSGHPGSGKSTIAEALANLPGVPKVHFHSDDLWGYIKHGRIDPWLPQSHQQNRMIMQIAADVAGRYAKEGY--------------VILDGV................................. 86
37 -10.200d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  11  1.....RRGALIVLEGVDRAGKSTQLVEALCAAGHRAELLR--------------FPERSTEIGKLLSSYLQKKSDVEDHSVHLLFSANREKLSQGVTLVVDR.................................. 94
38 -10.200d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}  ali model 3D-neighbors follow..  13  48..........LLFAGPPGVGKTT---------------------AALALARELFGENWRHNFLELNASDERGINVIREKVK-EFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSS. 150
39 -10.000d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}  ali model 3D-neighbors follow..  18  11........NLWFLVGLQGSGKTTKLALYYKGKGRRPLLVDTQRPAAREQLRLLGEKVGVPV-----LEVMDGESPESIRRRVEEKARL----EARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDA.. 132
40 -9.940d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  12  5.........VTLLTGFLGAGKTTLLRHILNEQHGYKIAVIENEFGEVSVDDQLIGDRATQIKTLTNGCICCSRSNELEDALLDLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHEVLCQRYLLDGVIALV.. 129
41 -9.880d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  10  18.....NEHGLIMLMGKGGVGKTTAIAVRLADMGFDVHLTDPAAHLSMTLNGSLNNLQVSRIDPHEETERYRQHETKGKELDEAGKRLLEEDLAGKRFVVMDTAPTGHTLLLLDA...................... 153
42 -9.410d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}  ali model 3D-neighbors follow..  15  3........KLYIITGPAGVGKST---------------------TCKRLAAQLDNSAYIEGDVVGGYRPPWESDELLALTWKNITDLTVNFLLAQNDVVLD................................... 79
43 -9.380d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}  ali model 3D-neighbors follow..  15  27..KAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDKQQHPNFDELVKLYEKDVVKHVTPYSNRMTEAIISRLSD-----------QGYNLVI-----EGTGRTTDVPIQTATMLQAKGYETKMYVMAVP 146
44 -9.360d1pjza_ c.66.1.36 (A:) Thiopurine S-methyltransferase {Pseudomonas syringae [TaxId: 317]}  ali model 3D-neighbors follow..  16  27................PLCGKSQDM-SWLSGQGYHVVGAELSEAAVERYFTERGEQ---PHITSQGDFKVYAAPGIEIWC-GDFFALTARDIGHCA-AFYDRAAMIALPADM-VQHLEALMPQACSGLLITLEYDQ 143
45 -9.250d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}  ali model 3D-neighbors follow..  16  31.....EKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDL-EFMGIRDYFNTDSICLI......................................................... 112
46 -9.230d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}  ali model 3D-neighbors follow..  16  2......TTRMIILNGGSSAGKSG-IVRCLQSV........................................................................................................ 26
47 -9.200d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}  ali model 3D-neighbors follow..  11  4..AEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVMRRNGSLEQGMYNTWYKFIEESIHVQADLIIYLRTSPE 147

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.

Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A. FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W284-8.