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3thoA
Query: 3tho_A mol:protein length:382 Probable DNA double-strand break repair Rad50, from PDB0312

Results of FFAS03 search in PDB0312
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 SSGENLYFQGHMRPERLTVRNFLGLKNVDIEFQSGITVVEGPNGAGKSSLFEAISFALFGNGIRYPNSYDYVNRNAVDGTARLVFQFERGGKRYEIIREINALQRKHNAKLSEILENGKKAAIAAKPTSVKQEVEKILGIEHRTFIRTVFLPQGEIDKLLISPPSEITEIISDVFQSKETLEKLEKLLKEKMKKLENEISSGGAGGAGGSLEKKLKEMSDEYNNLDLLRKYLFDKSNFSRYFTGRVLEAVLKRTKAYLDILTNGRFDIDFDDEKGGFIIKDWGIERPARGLSGGERALISISLAMSLAEVASGRLDAFFIDEGFSSLCTENKEKIASVLKELERLNKVIVFITCDREFSEAFDRKLRITGGVVVNELast
1 -113.0003tho_A mol:protein length:382 Probable DNA double-strand break repair Rad50  ali model  100  1SSGENLYFQGHMRPERLTVRNFLGLKNVDIEFQSGITVVEGPNGAGKSSLFEAISFALFGNGIRYPNSYDYVNRNAVDGTARLVFQFERGGKRYEIIREINALQRKHNAKLSEILENGKKAAIAAKPTSVKQEVEKILGIEHRTFIRTVFLPQGEIDKLLISPPSEITEIISDVFQSKETLEKLEKLLKEKMKKLENEISSGGAGGAGGSLEKKLKEMSDEYNNLDLLRKYLFDKSNFSRYFTGRVLEAVLKRTKAYLDILTNGRFDIDFDDEKGGFIIKDWGIERPARGLSGGERALISISLAMSLAEVASGRLDAFFIDEGFSSLCTENKEKIASVLKELERLNKVIVFITCDREFSEAFDRKLRITGGVVVNE 376
2 -70.8003aux_A mol:protein length:371 DNA double-strand break repair rad50 ATPase  ali model follow..  23  2..........SMILKEIRMNNFKSHVNSRIKFEKGIVAIIGENGSGKSSIFEAVFFALFGAGSNF-NYDTIITKGKKS--VYVELDFEVNGNNYKIIREYDSGRGGAK---------KNGKPYATTISAVNKAVNEILGVDRNMFLNSIYIKQGEIAKFLSLKPSEKLETVAKLLGIDEFVKEYEKRLERIEGELNYKEESLKARLKEMSNLEKEKEKLTKFVEYLDKVRRIFGRNGFQAYLREKYVPLIQKYLNEAFSEFDLPYSFVELTKDF-EVRVHAPNGVLTIDNLSGGEQIAVALSLRLAIANALINRVECIILDEPTVYLDENRRAKLAEIFRKVKSIPQMI-IITHHRELEDVADVIINVKKDGNVSK 366
3 -64.0003qku_A mol:protein length:359 DNA double-strand break repair rad50 ATPase  ali model follow..  20  1...........MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRKDIKKDEFTKVGARD--TYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKL-IPYNIFLNAIYIRQGQIDAILESD-EAREKVVREVLNL--------DKFETAYKKLSELKKTINNRIKEYGGSGGIKDLEKAKDFTEELIEKVKKYKALAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSK 354
4 -62.2003qkt_A mol:protein length:339 DNA double-strand break repair rad50 ATPase  ali model follow..  21  1...........MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRKDIKKDEFTKVGARD--TYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKL-IPYNIFLNAIYIRQGQIDAILESDEAR-----------------------------EKVVREVLNLDKFETAYKKLSELKGGSGGTEELIEKVKKYKALAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSK 334
5 -51.1003qkr_A mol:protein length:203 DNA double-strand break repair rad50 ATPase  ali model follow..  22  1...........MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGAR-DTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAKRLVGNEWKHVTEPSSKAISAFMEKLIP--YNIFLNAIYIRQGQIDAILES-DEAREKVVREVLNLDKFETAYKKLSELKKTINNRIKEYRDILAR......................................................................................................................................................................... 193
6 -32.5001w1w_A mol:protein length:430 STRUCTURAL MAINTENANCE OF CHROMOSOME 1  ali model follow..  16  2...........GRLVGLELSNFKSYRGVTK-GESNFTSIIGPNGSGKSNMMDAISFVL-SNHLRSNILKDLIYRGVLNDENSDDYD-SSNPQSAYVKAFYQKGNKLVELMRIISRNGDTSYKIDGKTVSYKDYSIFLENENILIKAKNFLVFQGDVEQIAAQSPVELSRMFEEVSGSIQYKKEYEELKEKIEKLSKSATESIKNRRRIHGELKETEQLKAEEKKILNQFLKIKKKRKELFEKTFDYVSDHLDAIYRELTKNPNSNVELAGGNASLTIEDEDEKRFKDMEYLSGGEKTVAALALLFAINSYQPSPF--FVLDEVDAALDITNVQRIAAYIRRHRNPDLQFIVISLKNTMFEKSDALVGVYRQENSSK 419
7 -30.4003euj_A mol:protein length:483 Chromosome partition protein mukB, Linker  ali model follow..  11  1.........GHMKFRSLTLINWNGFFARTFDFDELVTTLSGGNGAGKSTTMAGFVTALIPDLTTSSSRDKGLYGKLKAGVCYAVLETVNSRAQRIIDLGILPKRLRSSSDRNKFYKLIEASLYGGISSVITKSLRDYLLPENSGVRQAFQDMEAALRENSGGAESVANILRKTIQREQNRILQLNQGLQNIAFGQVKGVRLVVNIRDTHSILLNADQHEQHKDLFESQKLSFSEALAMLYKRINPHIELGQRMPQTIGEELLDYRNYLDLEVETLRGAYGWMRASSALSTGEAIGTGMSILLMVVQSWEEEILPCRLLFLDQA-ARLDAMSINTLFELCERLDMQ-----LIAAPENISPERGTTYKLVRKILANQ 471
8 -29.1001e69_A mol:protein length:322 CHROMOSOME SEGREGATION SMC PROTEIN  ali model follow..  21  1...........MRLKKLYLKGFKSFGRSLIGFSDRVTAIVGPNGSGKSNIIDAIKWVF--KELRASEKFDMIFAGSENLPAYVELVFEENGEEITVARELKRTGENTYYLNGSPVRLKD--------------IRDRFAGTGLGVDFYSIVGQGQIDRIVNASPEELRLESSKHPTSLVPRGSYQRVNES----------------------------------------------------FNRFISLLFFGGEGRLNIVSEAKSILDAGFEISI--RKPGRRDQKLSLLSGGEKALVGLALLFALMEI--KPSPFYVLDEVDSPLDDYNAERFKRLLKENSKHTQFI-VITHNKIVMEAADLLHGVTMVNGVSA 302
9 -28.3001qhl_A mol:protein length:227 PROTEIN (CELL DIVISION PROTEIN MUKB)  ali model follow..  26  1.......MIERGKFRSLTLINWNGFFARTFDLDELVTTLSGGNGAGKSTTMAAFVTALIPDLTL........................................................................................................................................................................................................................................................................................................................ 57
10 -24.7001xew_X mol:protein length:182 SMC protein  ali model follow..  24  2...........PYIEKLELKGFKSYGNVVIPFSKGFTAIVGANGSGKSNIGDAILFVL-AKAMRASRISDLIFAGSKNEPAEVAIYFNNEDRGFPIDEDEVVIRRR-------VYPDGRSSYWLNGRRATRSEILDILTAAMISPDGYNIVLQGDITKFIKMSPLERRLLIDDISGIAEYDSKKEKALEE.......................................................................................................................................................................................... 182
11 -23.4003qkr_B mol:protein length:179 DNA double-strand break repair rad50 ATPase  ali model follow..  16  1..........................................................................................................................................................................................................AEKENRERVKKEIKDLEKAKDFTEELIEKVKKYKALAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSK 174
12 -20.6002o5v_A mol:protein length:359 DNA replication and repair protein recF  ali model follow..  13  2.........GDVRLSALSTLNYRNLAPGTLNFPEGVTGIYGENGAGKTNLLEAAYLALTGQ-TDAPRIEQLIQAGETEAYVRADLQQGGSLSIQEVGLGRGRRQLKVDGVRARTGDLPRGGAVWIRPEDSESGRRAYLDSLLSRLSARYGEQLSRYERTVSQRNAALRGGEEWAMHVDVLLKLGTEIMLFRRRALTRLDELAREANAQLGSRKTLALTLTESTSPETYAADLRGRRAEELARGSTVTGPHRDDLLLTLGDFPASDYA------------------------SRGEGRTVALALRRAELELLREKFPVLLLDDFTAELDPHRRQYLLDLAASVPQAIVTGTELAPGAALTLRAQRFTPVADEEMQAE 356
13 -11.4001g6h_A mol:protein length:257 HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANS  ali model follow..  13  2RDTMEIL---RTENIVKYFGEFKALDGVSISVNKGVTLIIGPNGSGKSTLINVITVYFENKDITNKEPAELYHYGIVRTFQTPQP------KEMTVLENLLIGEICPGESPLNSLFYKKWIPKEEEMVEKAFKILEFLKLSHLYDRKAGELSGGQ--------------------------------------------------------------------------------------------------------------------------------------------------MKLVEIGRALMTNPKMIVMDEPIAGVAPGLAHDIFNHVLELKAKGITFLIIEHRLDIVLNYIDHLYV........ 225
14 -11.3002ihy_A mol:protein length:279 ABC transporter, ATP-binding protein  ali model follow..  16  9PRGSHMLIQ--LDQIGRMKQGKTILKKISWQIAKGKWILYGLNGAGKTTLLNILN---------------------------------------------------------------AYEPATSGTVNLFGKMPGKVGYSAETVRQHIGFVSHSLLEKFQEGERVIDVVISGAFKSIGVYQDIDDEIRNEAHQLLKLVGMSAKAQ-------------------------------------------------------------------------------QYIGYLSTGEKQ------RVMIARALMGQPQVLILDEPAAGLDFIARESLLSILDSLSDSYPAMIYVTHIEEITANFSKILLLKDGQ.... 234
15 -10.7001l7v_C mol:protein length:249 Vitamin B12 transport ATP-binding protein btu  ali model follow..  20  5................MQLQDVAELGPLSGEVRAGILHLVGPNGAGKSTLLARMAGMTSGKGSIQFAGQPLEAWSATKLALHRAYLSQQQTPPFATP------------------------------------VWHYLTLH--------------------QHDKTRTELLNDVAGALALDDKLG----------------------------------------------------------------------------------------------------RSTNQLSGGEWQRVRLAAVVLITPQANPAGQLLLLDEPMNSLDVAQQSALDKILSALCQQGLAIVMSSHDLNHTLRHAHRAWLLKGG.... 209
16 -10.3002pcj_A mol:protein length:224 Lipoprotein-releasing system ATP-binding prot  ali model follow..  22  5................LRAENIKKLKGISLSVKKGEFVIIGASGSGKSTLLYIL------------------------------LDAPTEGKVFLEGKEVDYTNEKELSLL-------------------------------------------------------RNRKLGFVFQFHYLIPELTALENVIVPMLKMGKPKKEAKERGEYLLSEL-----------------------------------------------------------------GDKLSRKPYELSGGEQ------QRVAIARALANEPILLFADEPTGNLDSANTKRVMDIFLKINEGGTSIVMVTHERELAELTHRTLEMKDGK.... 216
17 -10.2002zu0_C mol:protein length:267 Probable ATP-dependent transporter sufC  ali model follow..  16  10..........PRGSHMLSIKDLHVLRGLSLDVHPGVHAIMGPNGSGKSTLSATLA----------------------------------GREDYEVTGG-------------TVEFKGKDLLALSPEDRAGEGIQYPVEIPGVSNQFFLQTALNAVRSYRGQETLDRFDFQDLMEEKIALLKMPEDLLTRSVN-----------------------------------------------------------------------------------------------VGFSGGEKKRNDILQMAVL------EPELCILDESDSGLDIDALKVVADGVNSLRDGKRSFIIVTHYQRILDYI.............. 225
18 -10.0002iw3_A mol:protein length:986 ELONGATION FACTOR 3A  ali model follow..  14  438AYGAKILLN-----------------KTQLRLKRA-YGICGPNGCGKSTLMRAIATVYVEHDIDGTHSDDFVFESGVGTKEAIEFGFT-DEMIAMPISALSGGWKMKLALARAVLRNADILLLDEPTNHLDTVNVAWLVNYLNTCGITSITISHDCEYIINYEGLKLRKYKGNFTEFVKKCPAAKAYEELSNTDLEFKFPEPGYLEGVKTKQKAIVKVTNMEFQYPGTSKPQITDINFQCSLSSRIRGELVESHSKMVAEVDMKEALASGQFRPLTRLDPEIVSHSRIRGLSGGQK------VKLVLAAGTWQRPHLIVLDEPTNYLDRDSLGALSKALKEFEGG---VIIITHSAEFTKNLTEEV.......... 962
19 -9.9702nq2_C mol:protein length:253 Hypothetical ABC transporter ATP-binding prot  ali model follow..  19  1.......MNKALSVENLGFY----FQQLNFDLNKGILAVLGQNGCGKSTLLDLLLGIH----------------RPIQGKIEVYQSIGFVPQFFSSPFAY-------------------------------------------SVLDIVLMGRSTHINTFAKPKSHDYQVAMQALDYLNLTHLAK----------------------------------------------------------------------------------------------------REFTSLSGGQRQLILIARAIA------SECKLILLDEPTSALDLANQDIVLSLLIDLQSQNMTVVFTTHQPNQVVAIANKTLLLNKQ.... 205
20 -9.9303kta_B mol:protein length:173 Chromosome segregation protein smc  ali model follow..  19  57..........................................................................................................................................................................................................................................................................................KDVKRIEAMSGGEKALTALAFVFAIQKF--KPAPFYLFDEIDAHLDDANVKRVADLIKESSKESQFI-VITLRDVMMANADKIIGVSMRDGVSK 147
21 -9.9002grg_A mol:protein length:120 hypothetical protein; Ynr034w-ap  ali model follow..  33  5SSGENLYFQGHMK-SSIPITEVLPRAVGSLTFDENYNLL--TSGVAKSPIAEIIRKS............................................................................................................................................................................................................................................................................................................................... 64
22 -9.9003bk7_A mol:protein length:607 ABC transporter ATP-binding protein  ali model follow..  14  84................ISIVNLPEQLDEDCVHRYGVVGIVGPNGTGKTTAVKILAGQLIPNLCEDNDSWDNVIRAFRGNELQNYFERLKNGEIRPVVKP-----QYVDLLPKAVKGKVRELLKKVDEVGKFEEVVKELELENVLDRELHQLSGGELQRVAIAAA-RQRLKVARVIRRLANEGKAVLVVEHDLAVLDYLSDVIHVVYGEPGVYGIFSKPKGTRNGINEFLQGYLKDENVRFRPYEIRFTKLSERVDVERETLSSKLNSNFYKTELLKPLGIIDLYDRNVEDLSGGEL------QRVAIAATLLRDADIYLLDEPSAYLDVEQRLAVSRAIRHLMEKEKTALVVEHDVLMIDYVSDRLIVFEGEPGRH 552
23 -9.7501yqt_A mol:protein length:538 RNase l inhibitor  ali model follow..  16  12...........SHMEQLEEDCVHRYGVNAFVVKEGVVGIVGPNGTGKSTAVKILAGQLIPNLCGDNDSWDGVIRAFRGNELQNYFEKLKNGEIRPVVKP-----QYVDLIPKAVKGKVIELLKKADETGKLEEVVKALELENVLEREIQHLSGGELQRVAIAAALNAARAIRRLSEEGKSVLVVEHDLPKGTRNGINEFLRGYLKDENVRFRPYEIKFTKTGERVEIERETLVTYPRLVKDYGSFRLEVEPGEIKK-SKIDASKLNSNFYKTELLKPLGIIDLYDREVNELSGGELQRVAIAATLL------RDADIYLLDEPSAYLDVEQRLAVSRAIRHLEKNEKTALVVEHDVLMIDYVSDRLMVFEGEPGKY 476
24 -9.6001grq_A mol:protein length:178 CHLORAMPHENICOL 3-O PHOSPHOTRANSFERASE  ali model follow..  22  1...............................MTTRMIILNGGSSAGKSGIVRCLQSVL.............................................................................................................................................................................................................................................................................................................................. 27
25 -9.4702pjz_A mol:protein length:263 Hypothetical protein ST1066  ali model follow..  13  2................IQLKNVGSLENINLEVNGEKVIILGPNGSGKTTLLRAI-------------------SGLLPYSGNIFIN--------------------------------------MEVRKIRNYIRYSTNLPEAYEIGVTVNDIVYLYEELKGLDRDLFLEMLKALKLGEEI------------------------------------------------------------------------------------------------------LRRKLYKLSAGQS------VLVRTSLALASQPEIVGLDEPFENVDAARRHVISRYIKEY---GKEGILVTHELDMLNLYKEYKAYFLVGN... 202
26 -9.3903j16_B mol:protein length:608 Rli1p  ali model follow..  12  81...AHVTHR---------YSANSFKLHRLPTPRPGVLGLVGTNGIGKSTALKILA-AIKGPVQKVGELLKLRMEKSPEDVKRYIKILQLENVLKRDIEKLSGGELQRFAIGMSCVQEADVYMFDEPSSKQRLNAAQIIRSLLAPTKYVICVEHDDFVCIIYGVPSVYGVVTLPASVREGINIFLDGHIPAENLRFRTEALQFRIADATEDLQNDSASRAFSYPSLKKTQGDFQDIPKLNVSMKPQKIAPKFPGTVRQLKKIRGQFLNPQFQTDVVKPLRIDDIIDQEVQHLSGGELQRVAIVLALGI------PADIYLIDEPSAYLDSEQRIICSKVIRRFLHNKKTAFIVEHDFIMATYLADKVIVFEGIPSKN 548
27 -9.2901sgw_A mol:protein length:214 putative ABC transporter  ali model follow..  16  5................LEIRDLSVLERITMTIEKGVVNFHGPNGIGKTTLLKTISTYL----------------KPLKGEIIYN------------------------------------------------------GVPITKVKGKIFFLPEEIIVPRKISVEDYLKAVASLYGVKVNKNEIMDALES----------------------------------------------------------------------------------------VEVLDLKKKLGELSQGTIR------RVQLASTLLVNAEIYVLDDPVVAIDEDSKHKVLKSILEILKEKGIVIISSR--EELSYCDVNENLHKYS.... 201
28 -9.2203ozx_A mol:protein length:538 RNase L inhibitor  ali model follow..  15  3...GEVIHRNGFKLFGLPTPK-----------NNTILGVLGKNGVGKTTVLKILAGEIFGDPNSKVGKDEVLKRFRGKEIYNY-------KELYSNELKIVHKIQYVEYASKFLKGTVNEILTKIDERGKKDEVKELLNMTNLWNKDANILSGGGLQRLLVADVRERMNMAKAIRELLKRVSKSYAARVGINNFLKGYLPAENMKIRPDEIKFMLKEVSDLDLSKDLKTKMKWTKIIKKLGDFQLVVDNGEAKEGEIIGILGPNSTSSWFFEEVTKRLNLHRLLESNVNDLSGGELQKLYIAATLA------KEADLYVLDQPSSYLDVEERYIVAKAIKRVTRERKATFIIDHDLSIHDYIADRIIVFKGE.... 462
29 -9.1701vpl_A mol:protein length:256 ABC transporter, ATP-binding protein  ali model follow..  18  2.GSDKIMGAVVVKDLRKRIGKKEILKGISFEIEEGIFGLIGPNGAGKTTTLRIISTLIKPSSGIVTVFGKNVVEEPHEVRKLISY-----------------------------------------LPEEAGAYRNMQGIEYLRF----------VAGFYASSSSEIEEMVERATEIAGLGEKIKDRVSTYSKGMVR----------------------------------------------------------------------------------------------------------KLLIARALMVNPRLAILDEPTSGLDVLNAREVRKILKQASQEGLTILVSSHNMLEVEFLCDRIAL........ 212

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, Godzik A. Improving the quality of twilight-zone alignments. Protein Sci. 2000 Aug;9(8):1487-96.