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Query: 2o4g_A mol:protein length:247 Three prime repair exonuclease 1, from PDB0516

Results of FFAS03 search in PDB0516
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 MKPMGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYGTPATTGTTNLRLast
1 -120.0002o4g_A mol:protein length:247 Three prime repair exonuclease 1  ali model  100  1MKPMGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYGTPATTGTTNLR 241
2 -106.0003u3y_B mol:protein length:314 Three prime repair exonuclease 1  ali model follow..  98  6.LPHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGHVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYGTPATTGTTNLR 245
3 -94.3001y97_A mol:protein length:238 Three prime repair exonuclease 2  ali model follow..  45  4.SEAPRAETFVFLDLEATGLPSVEPEIAELSLFAVHRSSLENPEHDESGAL---VLPRVLDKLTLCMCPERPFTAKASEITGLSSEGLARCRKAGFDGAVVRTLQAFLSRQAGPICLVAHNGFDYDFPLLCAELRRLGARLPRD-TVCLDTLPALRGLDRAHSHGTRRGRQGYSLGSLFHRYFRAEPSAAHSAEGDVHTLLLIFLHRAAELLAWADEQARGWAHIEPMYLPPDDPSLEA.. 238
4 -58.0002p1j_A mol:protein length:186 DNA polymerase III polC-type  ali model follow..  25  11......DATFVVLDFETTGLDPQVDEIIEIGAVKI-------------------QGGQIVDEYHTLIKPSREISRKSSEITGITQEMLENK--RSIEEVLPEFL-----GFLEDSIIVAHNA-NFDYRFLRLWIKKVMGLDWERPY--IDTLALAKSLLK---------LRSYSLDSVVEKL-GLGPFRHHRALDDARVTAQVFLRFVEMMKK............................ 178
5 -50.1004fzx_C mol:protein length:175 Exodeoxyribonuclease 10  ali model follow..  19  2.........LRIIDTETCGLQ---GGIVEIASVDV-------------------IDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADK--PWIEDVIPHYY--------GSEWYVAHNA-SFDRRVLPEMPGEW-----------ICTMKLARRLWPGIKYSNMALYKTRKLN-----VQTPPGLHHHRALYDCYITAALLIDIMNT............................... 153
6 -45.1002f96_A mol:protein length:224 Ribonuclease T  ali model follow..  16  22MARRFRGYLPVVVDVETGGFNSATDALLEIAATTVGMDEKGFLFPEH--------------TYFFRIEPGANIEPAALEFTGIKLDHPAVQEEAALTEIFRGIRKALKANGCKRAILVGHNS-SFDLGFLNAAVARTGIK-PFHPFSSFDTATLAGLAYG-----------QTVLAKACQAAMEFDNREAHSARYDTEKTAELFCGIVNRWKE............................ 215
7 -41.8003ngy_A mol:protein length:235 Ribonuclease T  ali model follow..  13  24LCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDE------------------MPDTTLHFHVEPGANLQPEALAFNGIDPNDPDR-GAVSGYEALHEIFKVVRKGIKNRAIMVAHNA-NFDHSFMMAAAERASLK-PFHPFATFDTAALAG-----------LALGQTVLSKACQTAMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAAEEV................ 229
8 -37.5002gui_A mol:protein length:194 DNA polymerase III epsilon subunit  ali model follow..  20  2IEFSTAITRQIVLDTETTGMNQEGHKIIEIGAVEVVNRRLTG------------------NNFHVYLKPDRLVDPEAFGVHGIADEFLLD--KPTFAEVADEFM-----DYIRGAELVIHNA-AFDIGFMDYEFSLLKRDIPKTNTFCTDSLAVARKMFPG---------KRNSLDALCARYIDNSKRTLHGALLDAQILAEVYLAMT................................. 182
9 -36.1005fku_D mol:protein length:243 DNA POLYMERASE III SUBUNIT EPSILON  ali model follow..  22  9..........IVLDTETTGMNQEGHKIIEIGAVEVVNRRLTG------------------NNFHVYLKPDRLVDPEAFGVHGIADEFLLD--KPTFAEVADEFM-----DYIRGAELVIHNA-AFDIGFMDYEFSLLKRDIPKTNTFCTDSLAVARKMFPG---------KRNSLDALCARYIDNSKRTLHGALLDAQILAEVYLAMT................................. 179
10 -35.2004wbq_A mol:protein length:240 QDE-2-interacting protein  ali model follow..  15  4...PEKSVVFVAIDLEAYELD--QSIITEVGLAILDTAEITNVAPGEGSKNWFDFIKARVKEFSWAQNSRHVQGRAEYFDFGESEFIEVAKIASVLKETIEGESSIGGEGAKRPVVLVFHDQ-SQDLKYIRM--LGYDVASADNILEVVDTREMYQYLSR--------SNNASKLSNVCGYL-DIPWKNMHNAGNDAVYTLQAMMGLAID............................... 199
11 -27.9003cg7_A mol:protein length:308 Cell death-related nuclease 4  ali model follow..  13  21.........LLILDFETTANQDYPCEVIQFAIVAYDVPNDK----------------REDISFNKYVKPVLTLTKNCVDFTGIPQRSIDTA--DTFDVVYEQFQQWLITLGLEEGKFAFVCDSRQDLWIAQYQMKLSNIQMPAFFRQYINLYKIFTNEMDRMGP--KELSATTNIGKMNEYYDLPTIGRAHDAMDDCLNIATILQRMINM............................... 208
12 -26.3001w0h_A mol:protein length:204 3`-5` EXONUCLEASE ERI1  ali model follow..  13  12.........ICIIDFEATNPPEFVHEIIEFPVVLLNTHTL-----------------EIEDTFQQYVRPEINLSDFCISLTGITQDQVDRA--DTFPQVLKKVIDWMKLKELGTKYKYSLTDGSWDMSFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKV-------PRSQTKLTIMLEKLGMDYDGRPHCGLDDSKNIARIAVRMLQD............................... 194
13 -25.7002xri_A mol:protein length:224 ERI1 EXORIBONUCLEASE 3  ali model follow..  16  27.........FLVLDFEAT--QIHPQEIIEFPILKLNGRTM-----------------EIESTFHMYVQPVVHLTPFCTELTGIIQAMVDGQ--PSLQQVLERVDEWMAKELDPNVKSIFVTCGDWDLKMLPGQCQYLGLPVADYFKQWINLKKAYSFAM--------GCWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTLAYR............................... 207
14 -25.0004l8r_B mol:protein length:303 3`-5` exoribonuclease 1  ali model follow..  14  76.........ICIIDFEATNPPEFVHEIIEFPVVLLNTHTL-----------------EIEDTFQQYVRPEINLSDFCISLTGITQDQVDRA--DTFPQVLKKVIDWMKLKELYKYSLLTDG--SWDMSFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKV-------PRSQTKLTIMLEKLGMDYDGRPHCGLDDSKNIARIAVRMLQD............................... 258
15 -24.7001zbu_A mol:protein length:349 3`-5` exonuclease ERI1  ali model follow..  14  130.........ICIIDFEATNPPEFVHEIIEFPVVLLNTHTL-----------------EIEDTFQQYVRPEINLSDFCISLTGITQDQVDRA--DTFPQVLKKVIDLMKLKELYKYSLLTDG--SWDMSFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKV-------PRSQTKLTIMLEKLGMDYDGRPHCGLDDSKNIARIAVRMLQD............................... 312
16 -20.7001fxx_A mol:protein length:482 EXONUCLEASE I  ali model follow..  16  2MNDGKQQSTFLFHDYETFGTHPALDRPAQFAAIRTDSE------------------NVIGEPEVFYCKPADDYQPGAVLITGITPQEARAKGENE-AAFAARIHSLFTV---PKTCILGYNNVRFDDEVTRNIFYRNFYD-DNSRWDLLDVMRACYALRPENWPENDDGLPSFRLEHLTKA--GIEHSNAHDAMADVYATIAMAKLVKTR............................... 200
17 -20.4001wlj_A mol:protein length:189 interferon stimulated gene 20kDa  ali model follow..  17  5.......REVVAMDCEMVGLPHRESGLARCSLVNVHGA--------------------LYDKF---IRPEGEITDYRTRVSGVTPQHMVGA--TPFAVARLEIL-----QLLKGKLVVGH-DLKHDFQALK---------EDMSGYTIYDT----STDRLLWREAKLDHCRRVSLRVLSERLLHKSIQNSHSSVEDARATMELYQISQRIRARRGLPR....................... 176
18 -19.6004rg8_A mol:protein length:523 Exonuclease I  ali model follow..  15  42FQGMSSCCSLYWYDYETFGTDPRRDRPAQFAGIRTDLE------------------NPIGEPVTLFCKPARDVVPEACLITGITPQMAAERGLKE-AEFITRIHEQFSV---PGTCVAGYNNIRFDDEVTRHCLYRNLFD-GNSRWDIIDMLRLTRALRPEEWPVDGSGKPSLRLEALTVA--GIQHENAHDALADVRATIAVARLVRER............................... 240
19 -19.1004hec_A mol:protein length:190 Putative uncharacterized protein  ali model follow..  13  19..........YFYDTEFIEDG-HTIELISIGVVAEDGREYYAVSTEFDPERAGSWVRTHV----------------LPKLPPPASQLWRSRQQ------IRLDLEEFLRIDGTDSIELWAWVGAYDHVALCQLWGPMTALPPTVPRFTRELRQLWEDRGCPRMPPRPRDV--------------------HDALVDARDQLRRFRLITST............................... 175
20 -18.3004czw_A mol:protein length:653 PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE S  ali model follow..  14  433.TEIPGPDTVIAIDTEFIRLKEREIHIDEDGKSKIRPISHAIARASVVRGQGSREGVAFIDDY---IHIKETIVDYLTEWSGITPTDLDPINSQRNLVSPKTAYKKLWVLVNLGCKFLGHG--------LSQDFRVINIQVPRNQV--IDTSIIFMK---------PPSQRKISLAFLAWYLLKEDIQNTHDSIEDAQTALKLYRKYEE................................ 620
21 -17.3004xr7_G mol:protein length:776 PAB-dependent poly(A)-specific ribonuclease s  ali model follow..  13  559.DEAPKSGTLVAIDAEFVSLQSEL-ALARISIIRGEEGELYGV---------------FVDDY---VVNTNHIEDYLTRYSGILPGDLDPEKSTKRLVRRNVVYRKVWLLMQLGCVFVGHG--------LNNDFKHININVPRNQI--RDTAIYFLQ-----------GKRYLSLRYLAYVLLGMNIQGNHDSIEDAHTALILYKKYLH................................ 745
22 -17.0001yta_A mol:protein length:180 Oligoribonuclease  ali model follow..  14  4......ENNLIWIDLEMTGLDPERDRIIEIATLVTDANLNILAEGPTIAVHQSDEQLALMDDWNVRTHTA----------SGLVERV--KASTMGDREAELATLEFLKQWVPAGKSPICGNSIGQDRRFLFKYMPELEAYFHYRYLDVSTLKELARRWKP-------------------EILDGFTKQGTHQAMDDIRESVAELAYYREHFIK............................ 179
23 -16.8002gbz_A mol:protein length:194 Oligoribonuclease  ali model follow..  14  9.......DRLIWIDLEMTGLDTDRDSIIEIATIVTDAQLNVLAEGPELAIAHSLETLEAMDEWNRNQHRR----------SGLWQRV--LDSQVTHAQAEAQTVAFLGEWIRAGASPMCGNSICQDRRFLHRQMSRLERYFHYRNLDVSTIKELARRWAP-------------------AVASGFAKSSAHTALSDVRDSIDELRHYRQFMGT............................ 183
24 -16.8001j9a_A mol:protein length:184 OLIGORIBONUCLEASE  ali model follow..  12  8.......QNLIWIDLEMTGLDPEKERIIEIATIVTDKNLNILAEGPVLAVHQSDELLNKMNDWCQKTHSE----------NGLIERI--KASKLTERAAELQTLDFLKKWVPKGASPICGNSIAQDKRFLVKYMPDLADYFHYRHLDVSTLKELAARWKP-------------------EILEGFKKENTHLALDDIRESIKELAYYREHFMK............................ 182
25 -16.8005cy4_A mol:protein length:196 Oligoribonuclease  ali model follow..  14  9.......TRLIWIDLEMTGLDTDNDQIIEIATIITDDHLNVLAEGPVLAIHQPDRILNAMDEWNTRQHGQ----------SGLIERV--RRSKLTARDAELQTLEFLKKWVNPKVSPMCGNSICQDRRFLHRLMPELEQYFHYRNLDVSTVKELSKRWRP-------------------EIMSGLKKNASHLAMDDIRDSISELKYYREYFFI............................ 183
26 -16.6003tr8_A mol:protein length:186 Oligoribonuclease  ali model follow..  14  8......DDNLIWLDLEMTGLDPERDRIIEIATIVTNSHLDILAEGPAFAIHQPDKLLTAMDNWNTSHHTA----------SGLLERV--KNSSVDEVEAETLTLAFLEKYVSAGKSPLCGNSVCQDRRFLSRYMPRLNQFFHYRHLDVTTLKILAQRWAP-------------------QIAAAHIKESQHLALQDIRDSIEELRYYRAHLLN............................ 183
27 -14.4001noy_A mol:protein length:388 PROTEIN (DNA POLYMERASE (E.C.2.7.7.7))  ali model follow..  11  108.........VANCDIEVTGDKFPDPMKAEYEIDAITHYDSIDDRFYVFDLLNSMYGS------VSKWDAKLAAKLDCEGGDEVPQEILDRVIYMPFDN--RDMLMEYINEQKRPAIFTGWNIEGFDVPYIMNRVKMILGEYSIDGVSILDYLDLYKKF-------AFTNLPSFSLESVAQHETKKGKLPYDGPINK------LRETNHQRYISYNIIDVESVQAIDKI............. 334
28 -11.9003cfo_A mol:protein length:909 DNA polymerase  ali model follow..  15  110.........VANFDIEVTGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNE---------KELLMEYLNQQKTPVILTGWNVESFDIPYVYNRIKNIFGEITLFGISVLDYIDLYKKF-------SFTNQPSYSLDYISEFELNVGKLKYDGPISDVYRVLQIDAKR.................................. 338
29 -11.9004m8o_A mol:protein length:1228 DNA polymerase epsilon catalytic subunit A  ali model follow..  10  286.........VMAFAIATTPLKFPDSAVDQIMMISYMIDG------EGFLITNREIISEDIEDFEYTPKPEYPGFFTIFN-----------------ENDEVALLQRFFEHIRDPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPDAEGEYKSCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIESEYSVSDAVATYYLYMKYVHPFI............................. 493
30 -11.7004b8a_B mol:protein length:286 POLY(A) RIBONUCLEASE POP2  ali model follow..  12  28IRQLVSQYNHVSISTEFVGTNVDFLNPIQLGLSLSDANGNKPDNGPSTWQ-----------NFEFDPKKEIMSTESLELLSGINFEKHENLGIDVFE--FSQLLMDSGLMMDDSVTWITYHA-AYDLGFLINILMNDSMPNNKEDFEFYDLNLVYKIIQELQQSSQQQQQQQYSLTTLADELGLPRFSIFTTTGGQSLLMLLSFCQLSKLSMHKFPNG....................... 269
31 -11.6001uoc_A mol:protein length:289 POP2  ali model follow..  12  31IRQLVSQYNHVSISTEFVGTNVDFLNPIQLGLSLSDANGNKPDNGPSTWQ-----------NFEFDPKKEIMSTESLELLSGINFEKHENLGIDVFE--FSQLLMDSGLMMDDSVTWITYHA-AYDLGFLINILMNDSMPNNKEDFEFYDLNLVYKIIQELQQSSQQQQQQQYSLTTLADELGLPRFSIFTTTGGQSLLMLLSFCQLSKLSMHKFPNG....................... 272
32 -11.4003kd1_E mol:protein length:913 DNA polymerase  ali model follow..  14  110.........VANFDIEVTGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNE---------KELLMEYLNQQKTPVILTGWNVESFAIPYVYNRIKNIFGEITLFGISVLDYIDLYKKF-------SFTNQPSYSLDYISEFELNVGKLKYDGPISDVYRVLQIDAKR.................................. 338
33 -11.4004gmj_B mol:protein length:285 CCR4-NOT transcription complex subunit 7  ali model follow..  11  27IRQVIRKYNYVAMDTEFPGVNVDLLKIIQLGLTFMNEQGEYPPGTSTWQ------------NFKFNLTEDMYAQDSIELLSGIQFKKHEEEGIETQY--FAELLMTSGVVLCEGVKWLSFHS-GYDFGYLIKIL--TNSNLPEEELDFFEILRFFPVIYDVKYLMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFE............................ 247
34 -9.9602p51_A mol:protein length:333 SPCC18.06c protein  ali model follow..  11  38IMSLIERYPVVSMDTEFPGVNVDSLKIIQIGLALSDEEGNAPVEACTWQ------------NFTFNLQDDMYAPESIELLSGIDFKKHQEVGIEPAD--FAELLIGSGLVLQEEVTWITFHS-GYDFAYLLKAM--TQIPLPAEYEEFYKILCIFPKNYDIKYIMKSVLNNSKGLQDIADDLQIHRIGPQHQAGSDALLTARIFFEIRSRYFD............................ 258
35 -9.2701d5a_A mol:protein length:733 PROTEIN (DNA POLYMERASE)  ali model follow..  11  137.........MLAFDIETLAHAGAAAGAGPILMISYADEEGARVITWK--------------------------NIDLPYVESVSTE--------------KEMIKRFLKQEKDPDVLITYNGDNFDFAYLKKRSEMLGVKFEVKGRIHFDLYPVIRRTI---------NLPTYTLETVYEPVFGQPAEKVYAEEEDAKATYELGKEFFPMEAQLSRLVGQSLWDVSR.............. 346
36 -9.1002jgu_A mol:protein length:775 DNA POLYMERASE  ali model follow..  12  137.........ILAFDIETLGEEFGKGPIIMISYADENEARVITWK-----------------------------NIDLPYVESVSTE--------------KEMIKRFLRREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLEVKGRIHFDLYHVIRTTI---------NLPTYTLEAVYEAIFGKPKEKVYADEEDAKATYELGKEFLPMEIQLSRLVGQPLWDVSR.............. 346

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.

Slabinski L, Jaroszewski L, Rychlewski L, Wilson IA, Lesley SA, Godzik A. XtalPred: a web server for prediction of protein crystallizability. Bioinformatics. 2007 Dec 15;23(24):3403-5. Epub 2007 Oct 5.