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3auxA
Query: 3aux_A mol:protein length:371 DNA double-strand break repair rad50 ATPase, 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 MSMILKEIRMNNFKSHVNSRIKFEKGIVAIIGENGSGKSSIFEAVFFALFGAGSNFNYDTIITKGKKSVYVELDFEVNGNNYKIIREYDSGRGGAKLYKNGKPYATTISAVNKAVNEILGVDRNMFLNSIYIKQGEIAKFLSLKPSEKLETVAKLLGIDEFEKCYQKMGEIVKEYEKRLERIEGELNYKEESLKARLKEMSNLEKEKEKLTKFVEYLDKVRRIFGRNGFQAYLREKYVPLIQKYLNEAFSEFDLPYSFVELTKDFEVRVHAPNGVLTIDNLSGGEQIAVALSLRLAIANALIGNRVECIILDEPTVYLDENRRAKLAEIFRKVKSIPQMIIITHHRELEDVADVIINVKKDGNVSKVKINGLast
1 -118.0003aux_A mol:protein length:371 DNA double-strand break repair rad50 ATPase  ali model  100  1MSMILKEIRMNNFKSHVNSRIKFEKGIVAIIGENGSGKSSIFEAVFFALFGAGSNFNYDTIITKGKKSVYVELDFEVNGNNYKIIREYDSGRGGAKLYKNGKPYATTISAVNKAVNEILGVDRNMFLNSIYIKQGEIAKFLSLKPSEKLETVAKLLGIDEFEKCYQKMGEIVKEYEKRLERIEGELNYKEESLKARLKEMSNLEKEKEKLTKFVEYLDKVRRIFGRNGFQAYLREKYVPLIQKYLNEAFSEFDLPYSFVELTKDFEVRVHAPNGVLTIDNLSGGEQIAVALSLRLAIANALIGNRVECIILDEPTVYLDENRRAKLAEIFRKVKSIPQMIIITHHRELEDVADVIINVKKDGNVSKVKING 371
2 -75.1003qku_A mol:protein length:359 DNA double-strand break repair rad50 ATPase  ali model follow..  29  1..MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISIPYNIFLNAIYIRQGQIDAILESD-EAREKVVREVLNLDKFETAYKKLSELKKTINNRIKEYGGS------------GGIKDLEKAKDFTEELIEKVKKYKAL-----AREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLA-GEISLLILDEPTPYLDEERRRKLITIMERYKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEV.. 357
3 -73.1003qkt_A mol:protein length:339 DNA double-strand break repair rad50 ATPase  ali model follow..  32  1..MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISIPYNIFLNAIYIRQGQIDAILESD-EAREKVVREVLNLDKFETAYKKLSELKGGSGGTEELIEKVKKYKALAREAALSKIGELASEIFAEFTEGKYSEVVVR-------------------------------------AEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGE-ISLLILDEPTPYLDEERRRKLITIMERYKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEV.. 337
4 -70.8003tho_A mol:protein length:382 Probable DNA double-strand break repair Rad50  ali model follow..  23  11.HMRPERLTVRNFLGLKNVDIEFQSGITVVEGPNGAGKSSLFEAISFALFGNGIRYNSYDYVNRNAVDARLVFQFERGGKRYEIIREINALQRKHN--GKKAAIAAKPTSVKQEVEKILGIEHRTFIRTVFLPQGEIDKLLISPPSEITEIISDVFQSKET----------LEKLEKLLKEKMKKLENEISSGGAGGAGGSLEKKLKEMSDEYNNLDLLRKYLFDKSNFSRYFTGRVLEAVLKRTKAYLDILTNGRFDIDFDDEKGFIIKDWGIERPARGLSGGERALISISLAMSLAEVAS-GRLDAFFIDEGFSSLCTENKEKIASVLKELERLNKVIFITCDREFSEAFDRKLRITGGVVVNE..... 376
5 -59.8003qkr_A mol:protein length:203 DNA double-strand break repair rad50 ATPase  ali model follow..  29  1..MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHEWKHVTEPSSKAISAFMEKLIPYN--IFLNAIYIRQGQIDAILES-DEAREKVVREVLNLDKFETAYKKLSELKKTINNRIKEYRDILARTEG.................................................................................................................................................................................... 196
6 -54.5001e69_A mol:protein length:322 CHROMOSOME SEGREGATION SMC PROTEIN  ali model follow..  24  1..MRLKKLYLKGFKSFGRSLIGFSDRVTAIVGPNGSGKSNIIDAIKWVFGEQSRASEKFDMIFAGSENAYVELVFEENGEEITVARELKRTG-------ENTYYLNGSPVRLKDIRDRFAGTGLGVDFYSIVGQGQIDRIVNASPEELRLESSKHPTSLVPRGSYQRVNESFNRFISLL------FFGGEGRLNIVSEAKSILDAGFEISIR---------------------------------------------------------KPGRRDQKLSLLSGGEKALVGLALLFALMEI---KPSPFYVLDEVDSPLDDYNAERFKRLLKENSKHTQFIVITHNKIVMEAADLLHGVTMVNGVSAI.... 303
7 -52.5001w1w_A mol:protein length:430 STRUCTURAL MAINTENANCE OF CHROMOSOME 1  ali model follow..  17  2..GRLVGLELSNFKSYRGVTK-GESNFTSIIGPNGSGKSNMMDAISFVLGVRSRSNILKDLIYRGVLNDAASSNPQSAYVKAFYQKGNKLVELMRIISRNGDTIDGKTVSYKDYSIFLENENILIKAKNFLVFQGDVEQIAAQSPVELSRMFEEVSGSIQYKKEYEELKEKIEKLSKSATESIKNRRRIHGELKTYKSPGLEVLFQGPRGSRYDEAEGRFEVINNETEQLKAEEKKILNQFLKIKKKRKELFEKTFDYVSDHLDA-HATPPLKRFKDMEYLSGGEKTVAALALLFAINSY---QPSPFFVLDEVDAALDITNVQRIAAYIRRHRNPDQFIVISLKNTMFEKSDALVGVYRQENSSKI.... 420
8 -40.6003euj_A mol:protein length:483 Chromosome partition protein mukB, Linker  ali model follow..  11  6.RGKFRSLTLINWNGFFARTFDFDELVTTLSGGNGAGKSTTMAGFVTALIPDLTLLNFRNTTEAGSTSCYAVLETVNSRAQ-DLKEKFEETAVTFKPYHSITDYHSFMFDLASLYGGISSVITKSLRDYLLPENSGVRQAFQDMEAALRENSGGSGGSISAESVANILRKTIQREQNRILQLNQGLQNIAFGQVKGVRLVVNIRDTHSILLNALSDQHEQHKDLFESQKLSFSEAKRINPHIELGQRMPQTIGEELLDYRNYLDLEVETLRGAYSSALSTGEAIGTGMSILLMVVQSWEEESRRMRALLFLDQA-ARLDAMSINTLFELCERLD-----LLIAAPENISPERGTTYKLVRKANQEYVHVVG 478
9 -35.7001xew_X mol:protein length:182 SMC protein  ali model follow..  27  2..PYIEKLELKGFKSYGNVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSRASRISDLIFAGSKNEYAEVAIYFNNEDRGFPIDEDEVVIRRRVYPDGRSWLNGRRATRSEILDILTAAMISPDGYNIVLQGDITKFIKMSPLERRLLIDDISGIAEYDSKKEKALEE........................................................................................................................................................................................................ 182
10 -32.6001qhl_A mol:protein length:227 PROTEIN (CELL DIVISION PROTEIN MUKB)  ali model follow..  17  4.RGKFRSLTLINWNGFFARTFDLDELVTTLSGGNGAGKSTTMAAFVTALIPDLTLLHFRNTTEAGATS............................................................................................................................................................................................................................................................................................................... 70
11 -29.7002o5v_A mol:protein length:359 DNA replication and repair protein recF  ali model follow..  17  3.DVRLSALSTLNYRNLAPGTLNFPEGVTGIYGENGAGKTNLLEAAYLALTGQTDAPRIEQLIQAGETEAYVRADLQQGGSLSIQEVGLGRGRRQLKV------------DGVRARTGDLPR-----GGAVWIRPEDS-ELVFGPPSGRRAYLDSLLSLSRYERTVSQRNAALRGGEEWAMHVDVLLKLGTEIMLFRRRALTRLDELAREANAQLGSRKTLALTLTESTSPETYAADLRGRRAE---------ELARGSTVTGPHRDDLLLTLGDFPASDYASRGEGRTVALALRRAELELLREGEDPVLLLDDFTAELDPHRRQYLLDLAASVPQA--IVTGTELAPGAALTLRA................ 340
12 -28.6003qkr_B mol:protein length:179 DNA double-strand break repair rad50 ATPase  ali model follow..  30  1...........................................................................................................................................................................................AEKENRERVKKEIKDLEKAKDFTEELIEKVKKYKALAREAALSKIG-----ELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLA-GEISLLILDEPTPYLDEERRRKLITIMERYKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEV.. 177
13 -23.1003kta_B mol:protein length:173 Chromosome segregation protein smc  ali model follow..  30  55..............................................................................................................................................................................................................................................................................AGKDVKRIEAMSGGEKALTALAFVFAIQKF---KPAPFYLFDEIDAHLDDANVKRVADLIKESSKESQFIVITLRDVMMANADKIIGVSMRDGVSKV.... 148
14 -11.9001l7v_C mol:protein length:249 Vitamin B12 transport ATP-binding protein btu  ali model follow..  18  1MSIVMQLQDVAESTRLGPLSGEVRAGILHLVGPNGAGKSTLLARMAGMTSGKG--------------------SIQFAGQPLEAWSATKLALHRAYLSQQQTPPFA-------PVWHYLTLHQ--------------------HDKTRTELLNDVAGALALDDKLGR-------------------------------------------------------------------------------------------------------------STNQLSGGEWQRVRLAAVVLQITPQANPAGQLLLLDEPMNSLDVAQQSALDKILSALCQQGLIVMSSHDLNHTLRHAHRAWLLKGG---KMLASG 215
15 -11.8002ihy_A mol:protein length:279 ABC transporter, ATP-binding protein  ali model follow..  19  16IQLDQIGRMKQGKTILKKISWQIAKGKWILYGLNGAGKTTLLNILN-----AYEPATSGTVNLFGKMPGKVGYSA-------------------------------------ETVRQHIGFVSHSLLEKFQEGERVIDVVISGA----------FKSIGVYQDIDDEIRNEAHQLLKLVG------------------------------------------------------------------------------------------SAKAQQYIGYLSTGEKQRVMIARALM-------GQPQVLILDEPAAGLDFIARESLLSILDSLSDSYPMIYVTHFEEITANFSKILLLKD........... 232
16 -11.4002zu0_C mol:protein length:267 Probable ATP-dependent transporter sufC  ali model follow..  17  9VPRGSHMLSIKDLHVLRGLSLDVHPGVHAIMGPNGSGKSTLSATLA-------------------------------GREDYEVT--------GGTVEFKGKDLLA--LSPEDRAGEGIFMAFQYPVEIPGVSNQFF--LQTALNAVRSYRGQETLDRFDFQDLMEEKIALLKMPEDLLTRSVNV-----------------------------------------------------------------------------------------------FSGGEKKRNDILQMAVL-------EPELCILDESDSGLDIDALKVVADGVNSLRDGKRFIIVTHYQRILDYI................... 225
17 -11.0002nq2_C mol:protein length:253 Hypothetical ABC transporter ATP-binding prot  ali model follow..  15  4.ALSVENLGFY----FQQLNFDLNKGILAVLGQNGCGKSTLLDLLLGIHRPIQGKIEVYQSIGFVPQFFSSPFAYSV-------------------------------------------------LDIVLMGRSTHINTFAKPKSHDYQVAMQALDYLNLTHLAKR-------------------------------------------------------------------------------------------------------------EFTSLSGGQRQLILIARAIA-------SECKLILLDEPTSALDLANQDIVLSLLIDLAQSQTVVFTTHQPNQVVAIANKTLLLNKQNFKF..... 209
18 -10.7002pjz_A mol:protein length:263 Hypothetical protein ST1066  ali model follow..  20  2.......IQLKNVGSLENINLEVNGEKVIILGPNGSGKTTLLRAISGLL-------YSGNIFINGME----------------------------------------VRKIRNYIRYSTNLPEAYEIGVTVNDIVYLYEELKGLDRDLFLEMLKALKLGE-----------------------------------------------------------------------------------------------------------------LRRKLYKLSAGQSVLVRTSLALA-------SQPEIVGLDEPFENVDAARRHVISRYIKEYGK--EGILVTHELDMLNLYKEYKAYFLVGN........ 202
19 -10.5001sgw_A mol:protein length:214 putative ABC transporter  ali model follow..  22  3SKLEIRDLSVGDKPVLERITMTIEKGVVNFHGPNGIGKTTLLKTISTYLKPLKGEII------------------------------------------------------------YNGVPITKVKGKIFFLPEEIIVPRKISVEDYLKAVASLYGVKVNKNEIMDALESVEVLDLK-------------------------------------------------------------------------------------------------KKLGELSQGTIRRVQLASTLL-------VNAEIYVLDDPVVAIDEDSKHKVLKSILEILKEKGIVIIS-SREELSYCDVNENLHK----YSTKIDK 206
20 -10.5002d2e_A mol:protein length:250 SufC protein  ali model follow..  17  4LEIRDLWASIDGETILKGVNLVVPKGVHALMGPNGAGKSTLGKILA-----PEYTVERGEILLDGENILELSPD---------------------------ERARKGLFLAFQYPVEVPGVTIANFLRLA---------------------------LQAKLGREVGVAEFWTKVKKALELLDWDESYLSRYLNE-------------------------------------------------------------------------------------FSGGEKKRNEILQLLVL-------EPTYAVLDETDSGLDIDALKVVARGVNAMRGPNFALVITHYQRILNYI................... 209
21 -10.4001yqt_A mol:protein length:538 RNase l inhibitor  ali model follow..  15  12..SHMEQLEEDCVHRYGVNAFVVKEGVVGIVGPNGTGKSTAVKILAGQL--CGDNDSWDGVIRAFRGNELQNYFEKLKNGEIRPVVKPQYVDLIPKAVKGKVIELLKKADETGKLEEVLELENVLEREIQHLSGGELQRYFFDEPSSYLDIRQRLNAARAIRRLSEELRGYLKDENVRFRPYEIKFTKTGERVEIERETLVTYPRKTTFVKMLAGVEEPTEGKIEWDLTVAYKPQYIKADYEGTVYELLSKIDASKLNSNFYKTELLKPLGIIDDREVNELSGGELQRVAIAATLL-------RDADIYLLDEPSAYLDVEQRLAVSRAIRHLMEKNEALVVEHD--IDYVSDRLMVFE............ 470
22 -10.2002pcj_A mol:protein length:224 Lipoprotein-releasing system ATP-binding prot  ali model follow..  27  5.......LRAENIKKLKGISLSVKKGFVSIIGASGSGKSTLLYIL-----GLLDAPTEGKVFLEGKEVDYTN------------------------------------KELSLLRNRKLGFVFQFH-----------------------YLIPELTALENVIVPMLKMGKPKKEAKERGEYLLSELG-----------------------------------------------------------------------------------GDKLSRKPYELSGGEQQRVAIARALA-------NEPILLFADEPTGNLDSANTKRVMDIFLKINEGGTIVMVTHERELAELTHRTLEMK............ 213
23 -9.9801g6h_A mol:protein length:257 HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANS  ali model follow..  19  8LRTENIVKYFGEFKALDGVSISVNKGVTLIIGPNGSGKSTLINVITGFLKADEGRVYFENKDITNKEPAEL--------YHYGIVRTFQTPQ----------------------LKEMTVLENLLIGEICPGESPLNSLFYKKWIPKEEEMVEKAFKILEFLKLSHLYDRKAGE----------------------------------------------------------------------------------------------------------LSGGQMKLVEIGRALM-------TNPKMIVMDEPIAGVAPGLAHDIFNHVLELKAKGTFLIIEHRLDIVLNYIDHLYV----FNGQIIAEG 235
24 -9.9702iw3_A mol:protein length:986 ELONGATION FACTOR 3A  ali model follow..  15  430.......LCNCEFS-LNKTQLRLKRA-YGICGPNGCGKSTLMRAIAFGFTDEMIAMPISAL--SGGWKMKLALARAVLRNADILLLDEPTNHLDTVNVAWLVNYLNTCG-LDNVCEYIINYEGLKLRKY----KGNFTEFVKKCP-AAKAYEELSNTDLEFKFPEPGYLEGVKTKQKAIVKVTNMEFQYPGTSKPQITDINFQCSLSSRIAVIGPNGAGKSTLINVLTGELLPTSGEVGELVESHSKMVAEVDMKEALASGQFRPLTRKEIEESHSRIRGLSGGQKVKLVLAAGT--------QRPHLIVLDEPTNYLDRDSLGALSKALKEFEGG--VIIITHSAETKNLTEEVWAVKDGR......... 969
25 -9.9703bk7_A mol:protein length:607 ABC transporter ATP-binding protein  ali model follow..  15  84.......ISIVNLPEQLDEDCVHRYGVVGIVGPNGTGKTTAVKILA-DLLPKAVKGKVRELLKKVDEVGKFEEVVKELELENVLDRELHQLSGGELFYFFDEPSSYLDIRQRLKVARVIRRLANEGKAVLVVEHDDVIHVVYGEPGVYGIFSKPKGTRNGINEFLQGYLKDENVRFRPYEIRFTKLSERVDVERETLVEYPRLVKKTTFVKMLAGVEEPTEGKVEWDLTVAYKPQYIKAEYEGTVYELLSKIDSSKLNSNFYKTELLKPLGIIDDRNVEDLSGGELQRVAIAATLL-------RDADIYLLDEPSAYLDVEQRLAVSRAIRHLMEKNEALVVEHD--IDYVSDRLIVFE............ 546
26 -9.7002axp_A mol:protein length:173 hypothetical protein BSU20280  ali model follow..  10  3..........................LIILEGPDCCFKSTVAAKLSKELKYPIIKGSSFELAKSGNEKLFEHFNKLADEDNVIIDRFVYSNLVYAKKFKD-------YSILTERQLRFIEDKIKAKAKVVYLHAD--PSVIKKRLRVRGDEYIEGKDIDSILELYREVMSNAGLHTYSWDTGQWSSDEIAKDIIFLVEL............................................................................................................................................................................ 166
27 -9.7003ozx_A mol:protein length:538 RNase L inhibitor  ali model follow..  15  10...........KVNGFKLFGLPTPKNILGVLGKNGVGKTTVLKILAGEIGDPNSKVGKDEVLKRFRGKEIYNYFKELYSNELKIVHKIQYVEYASKFLKGTVNEKIDERGKKDEVKELLNMTNLWNKDANILSGGGLQRLVAASLLREADVYQPSSYLD---RERMNMAKAIRELLKNLDYLTDLIHIIYGESSVYGRVSKSYAARVGINNFLKGYLPAENMKIRPDEIKFMLKEVSDLDLSKDLKTKMKWTKIIKKLGDFQLVVDNGEAKEGEESNVNDLSGGELQKLYIAATLA-------KEADLYVLDQPSSYLDVEERYIVAKAIKRVTRERKTFIIDHDLSIHDYIADRIIVFKGE......... 462
28 -9.6401grq_A mol:protein length:178 CHLORAMPHENICOL 3-O PHOSPHOTRANSFERASE  ali model follow..  21  1......................MTTRMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGVDSLIE.................................................................................................................................................................................................................................................................................................................... 41
29 -9.3802yz2_A mol:protein length:266 Putative ABC transporter ATP-binding protein  ali model follow..  19  1MRIEVVNVSHIEKKALENVSLVINEGCLLVAGNTGSGKSTLLQIVAGLI-------------------------------------------------TSGDVLYDGERKKGYEIRRNIGI---------------------------------AFQYPEDQFFAERVFDEVAFAVKNFYPDRDPVPLVKKAMEFVGLDFDSFKD----------------------------------------------------------------------RVPFFLSGGEKRRVAIASVIVH-------EPDILILDEPLVGLDREGKTDLLRIVEKWKTLGTVILISHDETVINHVDRVVVLEK----GKKVFDG 220
30 -9.1003j16_B mol:protein length:608 Rli1p  ali model follow..  12  78NLEAHVTHRYSANSFKLHRLPTPRPGVLGLVGTNGIGKSTALKILA-AIIKPQYVDNIPRAIKGPVQKVGELLKLRMEKSPEDVKRYIKILQLENVLKRDGELQRFAIGMSCVQEADVYMFD-EPSSYLDVKQRLNAAQIIRSLLAPTKYVICVEHDLSVLDYLSDFVADATEDLQNDSASRAFSYPSLKKTQGDFVLNVEEGEFSDSEITTLIKLLAGALKPDEGQDIPKLNVSMKPQKIAPKFPGTVRQLFFKKIRGQFLNPQFQTDVVKP-DQEVQHLSGGELQRVAIVLALGI-------PADIYLIDEPSAYLDSEQRIICSKVIRRFILHNKAFIVEHD--ATYLADKVIVFEGIP......... 545

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.