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KOG4577
Query: [K] KOG4577 Transcription factor LIM3, contains LIM and HOX domains, from COG0312

Results of FFAS03 search in COG0312
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 MMQSATVPAEGAVKGLPEMLGVPMQQIPQCAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCFSRAGSVYCKEDFFKRFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKEDYETAKQNDDSEAGAKRPRTTITAKQLETLKNAYKNSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRHRWGQFYKSVKRSRGSSKQEKESSAEDCGVSDSELSFREDQILSELGHTNRIYGNVGDVTGGQLMNGSFSMDGTGQSYQDLRDGSPYGIPQSPSSISSLPSHAPLLNGLDYTVDSNLGIIAHAGQGVSQTLRAMAGGPTSDISTGSSVGYPDFPTSPGSWLDEMDHPPFLast
1 -102.000[K] KOG4577 Transcription factor LIM3, contains LIM and HOX domains  ali  100  1MMQSATVPAEGAVKGLPEMLGVPMQQIPQCAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCFSRAGSVYCKEDFFKRFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKEDYETAKQNDDSEAGAKRPRTTITAKQLETLKNAYKNSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRHRWGQFYKSVKRSRGSSKQEKESSAEDCGVSDSELSFREDQILSELGHTNRIYGNVGDVTGGQLMNGSFSMDGTGQSYQDLRDGSPYGIPQSPSSISSLPSHAPLLNGLDYTVDSNLGIIAHAGQGVSQTLRAMAGGPTSDISTGSSVGYPDFPTSPGSWLDEMDHPPF 390
2 -70.300[R] KOG0490 Transcription factor, contains HOX domain  ali follow..  34  1.........................MMVHCAGCERPILDRFLLNVLDRAWHIKCVQCCECKTNLSEKCFSREGKLYCKNDFFRRFGTKCAGCAQGISPSDLVRKARSKVFHLNCFTCMVCNKQLSTGEELYVIDENKFVCKDDYLSENEEQNSGTKRRGPRTTIKAKQLETLKAAFAATPKPTRHIREQLAQETGLNMRVIQVWFQNRRSKERRMKQLSALGARRHAFFRSPRRMRP---------LGGRLDESEMLGSTPYTYYGDYQGDYYAPGSNYDFFAHGPPSQAQSPADSSFLAASGPGSTPLGALEPPLAGPHAADNPRFTDMISHPDTPSPEPGLPGTLHPMPGEVFSGGPSPPFPMSGTSGYSGPLSHPNPELNE...... 398
3 -60.300[TZ] KOG1044 Actin-binding LIM Zn-finger protein Limatin involved in axon guidance  ali follow..  16  31ACTICKRPFPPGLCAQPMSSSPKETFSSNCAGCGRDIKNGQALLALDKQWHLGCFKCKSCGKVLTGEYISKDGAPYCEKDYQGLFGVKCEACHQFI--TGKVLEAGDKHYHPSCARCSRCNQMFTEGEEMYLQGSTVWHPDCKQSTKTE-EKLRPTRTSSESIYSRPGSSIPGSPGHTIYAKVDNEILDYKDLAAIPKVKAIYDIERPDLITYEPFYTSGYDDKQERQSLGESPRTLSPTPSAEGYQDVRDRMIHRSTSQGSINSPVYSRHSYTPTTSRSPQHFHRPGNEPSSGRNSPLPYRPDSLPLTPTYA--------------QAPKHFHVPDQGINIYRKPPIYKQHRALAAQSKSSEDIIKFSKFPAAQAPDPSETPKIETDHW 417
4 -53.800[T] KOG1701 Focal adhesion adaptor protein Paxillin and related LIM proteins  ali follow..  15  374HSGQLGPSSVAPKKMLYDMENPPADYFGRCARCGENVVGETGCTAMDQVFHVDCFTCIICNNKLRGQFYAVEKKAYCEPCYINTL-EQCNVCSKPIM--ERILRATGKAYHPHCFTCVMCHRSLDGIPFTVAGGLIHCIEDFHKKFAPRCSVCKEPIMPAPGQEETVRIVALDRDFHVHCYRCEDCGGLLSEGDCYPLDGHILCKTCNSARIRVLTAKAST......................................................................................................................................................................... 610
5 -50.000[TZR] KOG1704 FOG: LIM domain  ali follow..  12  148KCEKMLQGSPDKFQLPKLKRPPIKMQYDSNIFDFQVIFGDECLEAEGRSWHFHHFQCAQCNDVLADQYMQRANKPVCLKCFHSSSSTSCTTCRLSFSSDTPHMSQGDLHWHAECFCCCVCSKNLLGVKYSRVGESLFCGYQTCGLDEDRLGSPHRSTKVVRIPASPRVAPRHPHVIQQNLTTTMTIQKPSVVIQNQRPKPPQRAPPPPSENIYETVLPCSSNNSPNFDKKYSHELPTSPNHHNYYSKTPNNLLTGYPEMDGYSTSSSSDSDDEQLYISNIMAAASLSRVPAKSSSRKSKKNEPMMMSGGGVRMAKKKKSS...................................................................... 484
6 -43.000[TZ] KOG2272 Focal adhesion protein PINCH-1, contains LIM domains  ali follow..  14  35VCAQCFRPFQDGFEGRKYCERDFHVFAPCCNKCGEFVIGR-VIKAMSASWHPQCFRCQLCAKELADCGFIKMNELYCLRCHDKMGIPICGACRRPI--EERVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKRGLAYCETHYHQLFGNLCFVCNQ-------VIGGDVFTALNKAWCVHHFACSVCDTKMTKSKFYEYDEKPVCKKCYDRFPNELRRRLRTAHEMTMKKNT............................................................................................................................................................... 335
7 -29.100[K] KOG0775 Transcription factor SIX and related HOX domain proteins  ali follow..  12  1.........................................MSMLPSFGFTQEQVAC-VCEV------------LQQGGNLERLFLWSLPACDHLHKNESVLKAKAVVAFHRGNFRELYKSHQFSPHNHPKLQQLWLKAHYVEAEKLRGRPRTIWDGEETSYCFKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEAKERENTENNNSSSNKQNQLSPLEGGKPLMSSSEEEFSPPQSPDQNSVLLLQGNMGHARSSNYSLPGLTASQPSHGLQTHQHQLQDSLLGPLTSSLVDLGS......................................................................... 284
8 -22.600[K] KOG3802 Transcription factor OCT-1, contains POU and HOX domains  ali follow..  17  166............................................LREPPDHGELGSHHCQDHSDEETPTSDELEQFAKQFKQRRIKLGFTQADV-----GLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLNKWLEEADSSTGSPTSIDKRKRKKRTSIEVSVKGVLETHFLKCPKPAAQEISSLADSLQLEKEVVRVWFCNRRQKEKRMTPPGDQQPHEVYSHTVKTDTSCH........................................................................................................................................................ 359
9 -18.400[K] KOG1168 Transcription factor ACJ6/BRN-3, contains POU and HOX domains  ali follow..  18  220.....................................................................PRELEAFAER---KQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALEEAEAQAKNKRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAG................................................................................................................................................................ 386
10 -17.200[R] KOG4299 PHD Zn-finger protein  ali follow..  11  265YCSACHGP------GNFLC----------CETC-------------PNSFHFTCIDCNECKHHSLYNELDEQEEILCFRCHKSALVSQCDYC--------------NSYWHPDCWKCPNH.............................................................................................................................................................................................................................................................................. 456
11 -16.700[K] KOG2251 Homeobox transcription factor  ali follow..  16  43.........................................................................................................................................................PRKQRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQNGGQNKSESGTSGQFTPPSSTSVPTIASSSAPVSIWSPASISPLSDPLSTSSSCMQRSYPMTYTQASGYSQGYAGSTSYFGGMDCGSYLTPMHHQLPGPGATLSPMGTNAVTSHLNQSPASLSTQGYGASSLGFNSTTDCLDYKDQTASWKLNFNADCLDYKDQTSSWKF 294
12 -16.100[R] KOG3608 Zn finger proteins  ali follow..  179.WAMCHKHMGNKYRLIEHISTHSNKKQVACFHCGELFRTKTTLFD-----HLR-FQCAQCFKFFATKKLLKSHVVRHVNCY------KCTMCDMTCSSASSLTTHI-RYRHLK-LKCSECDTRCVRESDLAKHVQIVHSKTVHQCEHPDCHYSVRTYTQMRRHFLEVH--------NPILYACHCCERFFKSGKSLSAHLMKKHGFRLPSGHKRTYRVDENGFYRLETTRLESLEVTQQILSPQVNDSLAKPGTGSCYEIVDPTNTEFERIIVSNDP................................................................................................................. 447
13 -15.900[K] KOG2252 CCAAT displacement protein and related homeoproteins  ali follow..  10  281.......................HIAQPRRIYSTQDSNDPLNAEIGDDIYIDTKDLCKRIAFELKNH-----PQAIFAERILCRSQGTLSDLLRNPKPWNKLKSGRETFRRMYNWVAAILDMKTEDVNRASGMSPPTPAQNVRTHRRSTSDHDGPVSKRPRLVFTDIQKRTLQAIFKETQRPSREMQQTIAEHLRLDLSTVANFFMNARRRSRLGGNIDEPTPFQQVKNISPPPVGDTSDALLNGDDHVPLLNTVMAEMYKEGAIATSNHSAEQREMIERGFGVSIPGPSHSGELLNGDSHEDDEELDELNDSELAYEEDVEIGDEEEEDEEQANGDILPTPKVEELEEKTVIKEEAPDDGEYGATKLA..................... 630
14 -15.700[O] KOG4275 Predicted E3 ubiquitin ligase  ali follow..  2PCESCGVEFT--------------RRKRACFDCK-------------RYYCANCIACKRCSV-FAQRPLSRTDLLKLKIFYLQSKHISTEGCLEKEELVGLVLTHVAQV---------------------------------DRSRGSNASSNSPGRGQANPIDSLKQSCQNFFSNLSDNISDSLASFDSKVTTKPPESRQPEVPTHIFEQPRVSTREIPTYASAVNGGPQHVHVQQQATTTNGGSQSSSSPSTSTQSSNNRDASSSSQAHVAHQEARNEEQEDAQSKSDCECSDEEIMATFSERVSISLKTDTSGRRVNAAAEPSPVDLANVDNGPAGNTAPSPGCSKPGSSSSKADASSQSSFEELGAIGGISDESKANTDTNSS... 336
15 -15.700[R] COG5141 PHD zinc finger-containing protein  ali follow..  16  213FCDNCNTSVHQNCYGIPFCKKC-PHEVICCAFC--PDRDGAFCTTLDGRWHTICLVCCICKLRWGT----------C----------QCSNCY--------------AAYHITC-METYCDKHTPPD....................................................................................................................................................................................................................................................................... 366
16 -15.700[K] KOG0486 Transcription factor PTX1, contains HOX domain  ali follow..  15  89.........................................................................................................................................................KKRQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELCKNGFGPQFNGLMQPYDDMYPGYSYNNWAAKGLTSASLSTKSFPFFNSMNVNPLSSQSMFSPPNSISSMSMSSSMVPSAVTGVPGSSLNSLNNLNNLSSPNSAVPTPACPYAPPTPPYVYRDTCNSSLASLRLKAKQHSSFGYASVQNPASNLSACQYADRP..... 323
17 -15.400[D] KOG2186 Cell growth-regulating nucleolar protein  ali follow..  5............................QCDDCGENLKKPRLPR------H-MCFSCIDCGNMFGQVSV--HYHNQCITE-AEKYGPMVRS-SKQKHDFDINAELFNSQW-----FCSLCNATMTCEQDYFAHKKHQEKANEVADMDYSKQQSEHPAVDKNNLTQQPDLDIYVGLSNDYPWFCSLCDINATSEQTLLAHANGKKHRVKVERFDAEQQKRQSTQHSTVDKKDYSKQQIEVDINVGLSNCYPWFCSLCNVKATCQQNLLSHANGRKHRENVELFDATQQQQLEKTTVDKKDTTVNASDGNSEQKKVDLLVS....................................................................... 292
18 -15.300[R] COG5048 FOG: Zn-finger  ali follow..  526.ITRKLTTLPRGSIDK---VKEMPDKTFECLGCTKTFKRRYNIRSHIQT-HLE-YSCDHCDKAFVRN-LIRHKKSHQEKAY------ACP-CGKKFNREDALVVHRSRMICSG-YENVVIKRSPRKRGRPRKDG--------------------------TSSVSSSPIKENINKDHNGQLM--KLEDQLRRERSYDGNGTGIMVSPMKTNQR................................................................................................................................................................................. 709
19 -15.100[K] KOG2462 C2H2-type Zn-finger protein  ali follow..  11  121.CPECGKKYSTSSNLARHRQTHRSIMDKKCPYCEKVYVSMPAYSMHVRT-HNQGCECQFCGKRFSRPWLLQGHI----RTHTGEKPFKCGVCEKAFADKSNLRAHIQTHSNTKPHTCARCGKAFALKSYLYKHEESSCMKNRGG--PGSGAASGNRPPSSPKRQQAEVTSGTISALAPGSPAAAVCAASDSAKSTLANKLLQKEKDRRQAAMAFQGFPAGPE........................................................................................................................................................................ 338
20 -15.100[R] KOG1819 FYVE finger-containing proteins  ali follow..  25  566.......................DEDCEQCTACSMPFN------FVRRRHH-----CRNC------------GRIFCHK---------CSCNTISIPEHGYDRKPV---------SSPQSNLSLLTRQD..................................................................................................................................................................................................................................................................... 631
21 -15.000[R] COG5236 Uncharacterized conserved protein, contains RING Zn-finger  ali follow..  11  63LCVICARKLT----HHKTCHICGFRNKKSCLICRTENEEVMFTDRIDGDIHLKCLICATHKHAFELEIFTQNGHPMCAFCSGKRFYSKCHICDKMNPASPQYFKDYNQL-HFK-YVCTTCELELQAHILQEHGNILKGKPKFFQSELSTFISAPSRVIRERDDYDLPSISSLPGSSSGSRTDVRSASSPEESRLRLAERAKYYLENSKEDFNKSKGRLSAEKLLESYKLLFTKPNADVYLLIHNLAETFPKNSSKYNNLNAIYEQREQTLARQTSLPSLSSDSSLSMSIGRGHWGGTNDGGSAGAALGVRNIKNLPTLKSPSASYDPFATTVKKNTLRPVQNIKRTTPQSVSYRTSTNTVAFSPTYLESKKGSSSTSLNNSKDKLKSLNL 573
22 -14.700[O] KOG0802 E3 ubiquitin ligase  ali follow..  11  342.....................................LHAALPDATSEELRAYDDECAICREPMAKA-----KRLHC-----------------------------NHLFHLGCLSCPTCRKPLFVGR----------------------------------------------------------------------------------TENEVNPRTVEVSSDEQLARQLERQNNPVHALATGLFPAEVPDSVENDTSRNLGLDPSWLQTWSSQGSDVAGPSTTSRTVGLGRVQMMMRHLASVGESYAQTALDDAAWSLWPMNPSQASTSSTTVPPGNGGRTGGLHLRTVSNTTNESLTNILAMAETVREVMPHVPDEIIFQVN.... 586
23 -14.600[K] KOG1244 Predicted transcription factor Requiem/NEURO-D4  ali follow..  15  272YCDFCLGDSKINKK------TGQPEELVSCSDCGRSFTPVMMAAVKTYRWQIECKCCNICGTS-------NDDQLLF-----------CDDC--------------DRGYHMYCWSCHLCLDLLKEKASIYQNQNS.............................................................................................................................................................................................................................................................. 390
24 -14.600[R] KOG3138 Predicted N-acetyltransferase  ali follow..  14.CRYCESP--------------EDDNYLECQECRR--------------VHIKCFTCVKCVLD-------------------KAKESVIPSD---LEPIKEVIVRQRIPWTLTLYNLSIKQKGLGHHGFFHWRTHSFVDKNWNYIFGPNVRRRKQWTGSVSGALSHNSPEYFQSGLDVFQENG-KLAKPFQTPRSVLKEYEKKQQLRLQMRIEKRLPAADETSCSSEISVADHAQDNPPLIKAEAEKPSSTEGCARTIPYMGRLPKIQTQPSPLSQETLPGPPILQENIAPPSQKEEEPQNQPMSMVQAGLMDFLAESLESDDFTMFGNLPGIMPPPLIGAGKNDFFMTEPLLHAPLNNEGLFDMDTNFAIPNTADETKPISTEEPA... 375
25 -14.500[O] KOG2231 Predicted E3 ubiquitin ligase  ali follow..  47ACVVCFKNVE----DHPVCYECSTRQQNECPICRHVLSKVLFTLDKLPYRELE-HPCPKCDAPLRNHVRSEHKLLYCD---------LCVETLNIFTFERRCYTQAELQLHNT--LCEYCNKRYVDRDELF---------RHLRREHYFCHFCDADGCNE------NDYADLAEHFRAEHFLCEQFVGAFRNEIEYKAHVANVHGKSLNKQQAKQTRTLQVEITLGPRGRSGQTEQGITSVRTRNDEHNDYQNDLPSITQRHVSIDAGNEEQFPTLRGASTAPSVSLVRPPPPSMRNLSGTSGLARTKENFPALGGGNGGGVTGPTSSSIAARAAQSQHPVAAVFKKPTSAAGSGSRSGPPGNGMLLHVSNRSAAVPKKAATPQVD.... 472
26 -14.200[O] KOG0006 E3 ubiquitin-protein ligase (Parkin protein)  ali follow..  14  210.CITCTDVRSPVLVFQCNSRHVI------CLDCVTRLNDRQFVHDPQLGYSLPC-CPNSHFRILGEEQYNRYQQYGAEECVLQMGGVLCPGCGAGLLPEPDQRKVTCEG--LGC--CRECKEAYHEGEC--------------AVFEASGTTTQAYRVDERAAEQARWEAASKETIKKTTKPCPRCHVPVEKNGGCMH................................................................................................................................................................................................ 405
27 -13.600[KL] COG5151 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1  ali follow..  13  297LCA-CHSIPSRGGFHCPRCKAKVCTLPIECPSCSLVLLSTHLARSYHHLFPLKNWSCFACQLPFPKPPVSPFDES-CKNHF-------CLDCDVFA--------------HEQLHECYGCQCS........................................................................................................................................................................................................................................................................... 419
28 -13.600[KL] KOG2807 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1  ali follow..  13  297LCA-CHSIPSRGGFHCPRCKAKVCTLPIECPSCSLVLLSTHLARSYHHLFPLKNWSCFACQLPFPKPPVSPFDES-CKNHF-------CLDCDVFA--------------HEQLHECYGCQCS........................................................................................................................................................................................................................................................................... 419
29 -13.600[R] KOG0494 Transcription factor CHX10 and related HOX domain proteins  ali follow..  15  133.........................................................................................................................................................KRKKRRHRTIFTQYQIDELEKAFQDSHYPDIYAREVLAGKTELQEDRIQVWFQNRRAKWRK-TEKTWGKSTIMAEYGLYGAMVRHSLPLPETITKSAEAADPQQSAAPWLLGMHKKSMEAAAHLESVEKCDMSDSDDDDRPVTPPVQRQVKNEYKPRIIEHVQQQAPQHQSSLNFDTSLVVSSSLSQLHFQDSQMIPNNNASLKLYHDYNNP......................... 343
30 -13.500[K] KOG0484 Transcription factor PHOX2/ARIX, contains HOX domain  ali follow..  19  87.........................................................................................................................................................KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREELALKIDLTEARVQVWFQNRRAKFRKQERAASAKGAAGAAGAKKGEARCSSEDDDSKESTCSPTPDSTASLPPPPAPGLASPRLSPSPLPVALGSGPGPGPGPQPLKGALWAGVAGGGGGGPGAGAAELLKAWQPAESGPGPFSGVLSSFHRKPGPALKTN......................................... 282
31 -13.400[R] KOG4323 Polycomb-like PHD Zn-finger protein  ali follow..  17  192LCSVCQRGHSPLSNRIVF-----------CDGC-------------NSPYHQLCH-----HPPIDDA--DVDAEWFCM---------KC............................................................................................................................................................................................................................................................................................................. 243
32 -13.100[K] KOG4218 Nuclear hormone receptor betaFTZ-F1  ali follow..  18  40.............................CPVCGDKVSG----------YHYGLLTCESCK------FFVQNNKRYCIENIDKTQRKRCPYCR------------------QKCLSVGMKLEAVRADR...................................................................................................................................................................................................................................................................... 114
33 -12.900[K] KOG0844 Transcription factor EVX1, contains HOX domain  ali follow..  14  180.........................................................................................................................................................SDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMTWPHPADPAFYTYMMSHAAAAGGLPYPFPSHLPLPYYSPVGLGAASAASAAASPFSGSLRPLDTFRVLSQPYPRPELLCAFRHPPLYPGPAHGLGASAGGPCSCLACHSGPANGLAPRAAAASDFTCASTSRSDSFLTFAPSVLSKASSVALDQREEVPLT.......... 406
34 -12.900[T] KOG4825 Component of synaptic membrane glycine-, glutamate- and thienylcyclohexylpiperidine-binding glycoprotein (43kDa)  ali follow..  14  757.CGERSESFTEEGLDLHYWKHC--LMLTRCDHCKQ------VVEISSLTEHLEC-KCYRCSEAVFKEELPRHKHKDCNPAKPEKLANRCPLCHENFSPGEEAWKA-----HL-----AGCTMNLRKTH--ILQKAPALQPGKSSAVAASGPLGSKAGSKIPTPKGGLSKSSSRTYAK..................................................................................................................................................................................................................... 924
35 -12.900[K] KOG4216 Steroid hormone nuclear receptor  ali follow..  17  98.............................CKICGDKSSG----------IHYGVITCEGCK------FFQQSNATYCPRQIDRTSRNRCQHCR------------------QKCLAVGMSRDAVKFGRM..................................................................................................................................................................................................................................................................... 173
36 -12.700[O] COG5243 HRD ubiquitin ligase complex, ER membrane component  ali follow..  13  348ICIICMDELIHSPNQQTWKNKNKKPKRLPC----------------GHILHLSCLTCPICRLPVFDE................................................................................................................................................................................................................................................................................................................................... 406
37 -12.700[K] KOG0483 Transcription factor HEX, contains HOX and HALZ domains  ali follow..  15  66.........................................................................................................................................................SSTAAEKKRRLGVEQVKALEKNFEIDNKLEPERKVKLAQELGLQPRQVAIWFQNRRARWKTKQLERDYGVLKSNFDALKRNRDSLQRDNDSLLGQIKELKAKLNVEGVKGIEENGALKAVEAN--------------QSVMANNEVLELSHRSPSPPPHIPTDAPTSELAFEMFSIFPRTENFRDDPADSSDSSAVLNEEYSPNTVEAAGAVAATTVEMSTMGCFSQFVKMEEHEDL 288
38 -12.700[O] KOG3970 Predicted E3 ubiquitin ligase  ali follow..  15  3............................LC-KCPK--------RKVTNLF---CYE-NVCEFCLVDNHPNCVVQSYLTWLTDQDYDPNCSLCKTTLAEGDTIRLNCLHLLHWKCFRCPCCSQEV.......................................................................................................................................................................................................................................................................... 104
39 -12.600[K] KOG0485 Transcription factor NKX-5.1/HMX1, contains HOX domain  ali follow..  12  116.........................................................................................................................................................DDRKKRPRTAFSAAQIKALETEFERGKYLSVAKRTALAKQLQLTETQIKIWFQNRRTKWKRKYTSDVETLASHYYAQLQTPTGPTPIQSIMLNGSGSAAPMASATTATGSPMRPYATSGGMPPLPGPSVMESARNAILARGQPLNFALPFGVAKPPAGGVPAASYIPRCKPYATSYVDYAASLPTNESYLQMKYATLPPEAESGASNGLAELERVFGDANANFLQQRSTPVAG.... 367
40 -12.400[O] COG0068 Hydrogenase maturation factor  ali follow..  13  104..........................AATCPECQREIFDP-----FSRFYRYPFTNCTHC----GPRLSIIRAIPYDRCNTSMSAFVMCPECEDSYH------DVENRRFHAQPVACHTCGPKA------------WLERADGKPVTASMFSMLDDVDAVCTLLQKGEIVAIKGIFHLACDATQAAVEKLRQRKRRYDKPFALMARDINVIEK................................................................................................................................................................................. 266
41 -12.400[K] KOG0850 Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains  ali follow..  17  126.........................................................................................................................................................PKKVRKPRTIYSSYQLAALQRRFQKAQYLALPERAELAAQLGLTQTQVKIWFQNRRSKFKKLYKNGEVPLEHSPNNSDSMACNSPPSPALWDTSSHSTPAPARSQLPPPLPYSASPSYLDDPTNSWYHAQNLSGPHLQQQPPQPATLHHASPGPPPNPGA............................................................................. 285
42 -12.300[O] KOG4628 Predicted E3 ubiquitin ligase  ali follow..  10  212.................................KSMLKKLPVLRYTKNNANNKYDTCVIC---LED--FIEDDKL-CS-----------------------------HPYHTHCIVCPICKRKVFTKGEARASRSR-------QPSLDNVTDTDDDTTPLLQQQQSNGRQVGQVSSASSAGGAAGSSSSVAAAAVAGTTRHGTFRRGHAGRNPFEESQSSDDENALLASTVRPATSSGAHERINPFDRAPNLPAHLAEQLTESRRSVWSRINFASFFRRQPAVISVAAPPYLERVESGTSAMGLPVTGTIAVASPASNNILNPNLSGSFKDEDDMPPHRSIYEPIAISTPAADSATVDDSAFLQTPT-QGGIGVAALPHSASDR----QF 534
43 -12.200[O] COG3058 Uncharacterized protein involved in formate dehydrogenase formation  ali follow..  13  189YCPVCGSM---PVSSMVQIGTTQGLRYLHCNLC-------------ETEWHVVRVKCSNCEQS------GKLHYWSLDDEQAAIKAESCDDCGTYLK..................................................................................................................................................................................................................................................................................................... 263
44 -12.100[O] KOG3579 Predicted E3 ubiquitin ligase  ali follow..  21  478............................CCTLCHERLEDTHFVQCPSVPSHKFCFPCS--RQSIKQQ---ASGEVYCPS------GEKCPLVGSNVP------------W---AFMQGEIATILAGDVKVKKERDS.............................................................................................................................................................................................................................................................. 560
45 -12.100[R] KOG3002 Zn finger protein  ali follow..  12  57.CPVCTNLMYPPIHGHTLCSSCKLRVQNTCPTCRYELGNIR--LALEKVAESLEVPCRYCQDIFP----KLKHEQHCRFRSYSCPYA-GSECSVTGDIPTLV--------HLKD-MHDGCTFNH.......................................................................................................................................................................................................................................................................... 181
46 -12.100[R] KOG0492 Transcription factor MSH, contains HOX domain  ali follow..  28  139.........................................................................................................................................................HKTNRKPRTPFTTSQLLALERKFRQKQYLSIAERAEFSSSLNLTETQVKIWFQNRSAKAKRLQEAELEKLKMAAKPMLPSS............................................................................................................................................................ 219
47 -12.000[K] KOG0847 Transcription factor, contains HOX domain  ali follow..  24  166.........................................................................................................................................................NMQKKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMSESQVKVWFQNRRTKWRKKEAADNALVKRGASGDKSPCSLSP........................................................................................................................................................ 250
48 -12.000[P] COG3303 Formate-dependent nitrite reductase, periplasmic cytochrome c552 subunit  ali follow..  15  161.CWTCKGP-KDYFNAKWAKGGPEIVNSIGCADC-----------------HDT--ICANCHVEFTDWTHSLSKAPMLKAQHPDF-GVTCVDCHMPKVQGADGKVYTDHQIQNP--TCANCHDQ........................................................................................................................................................................................................................................................................... 375
49 -12.000[R] KOG0489 Transcription factor zerknullt and related HOX domain proteins  ali follow..  32  316.........................................................................................................................................................NSKSRRRRTAFTSEQLLELEREFHAKKYLSLTERSQIATSLKLSEVQVKIWFQNRRAKWKRVKAGLTSHGLGR.................................................................................................................................................................... 388
50 -11.900[K] KOG0848 Transcription factor Caudal, contains HOX domain  ali follow..  21  183.........................................................................................................................................................TRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKERKINKKKLQQQQQQQPPQPPPPPPQPPQPQPGPLRSVPEPLSPVSSLQASVSGSVPGVLGPTGGVLNPTVTQ.......................................................................................................... 313
51 -11.800[K] KOG0842 Transcription factor tinman/NKX2-3, contains HOX domain  ali follow..  23  125.........................................................................................................................................................AGKKRKRRVLFSKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKMKRARAEKGMEVTPLPSPR................................................................................................................................................................ 201
52 -11.800[K] KOG0843 Transcription factor EMX1 and related HOX domain proteins  ali follow..  28  319.........................................................................................................................................................ERQQKRVRTMFNLEQLEELEKVFAKQHNLVGKKRAQLAARLKLTENQVRVWFQNRRVKYQKQQKLRAAVTSAEAASLDEPSSSSIASIQSDDAES.............................................................................................................................................. 413
53 -11.800[S] COG4306 Uncharacterized protein conserved in bacteria  ali follow..  9ICTNGHVATTA-------ADQKHELWEAFCSHSGEATILQ----------------YPKCSASIRGD---DYVEGVLGFGGDYEPPTFCNNCGSRFPWAERKIAGTVELV........................................................................................................................................................................................................................................................................................ 92
54 -11.800[K] KOG2482 Predicted C2H2-type Zn-finger protein  ali follow..  13  163.CMFCNEEFLGNRSVILHMAREHAFNIGQCLYCEKTFRDKNTLKD-----HMR-AVCLFCEKQAET---IEKLYVHMEDAHEFDLLKIKSELGLNFYQQVKLVNFIRR--QVHQCRCYGCHVKFKSKADL.................................................................................................................................................................................................................................................................... 360
55 -11.700[K] KOG2461 Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains  ali follow..  10  484.SSHNDSSFNGV--PNYVQQQENGKTRYACKDCNKTFGQLSNLKVHVRT-HTG-FKCEICTKEFTQLAHLQGERPHCDKRFSSTSN-TCDVCDAKFTQYVHLRLHKRLHANERPYSCGTCGKKYISPSGLRTHWKTTTCKEEDMKDSMEIDEGSMSGSGYGNLGIFENTLNSELKRP-----LMPIETIYSKYNLPNASLLGQGPSGMQEQQAPPPTSQQQQHMMYGNTMGHMGQGS......................................................................................................................................................... 746
56 -11.700[O] COG5540 RING-finger-containing ubiquitin ligase  ali follow..  15  311...................STRRATFGVECVICLESFTKGDKVVALKHEFHRPCIACPTCNTEV...................................................................................................................................................................................................................................................................................................................................... 366
57 -11.600[O] KOG0828 Predicted E3 ubiquitin ligase  ali follow..  21  699.CAICMSDVPIYIEEIPETHKV-DQHSYMVTPC-------------NHVFHTSCLQCPVCRSPL...................................................................................................................................................................................................................................................................................................................................... 755
58 -11.600[R] KOG0488 Transcription factor BarH and related HOX domain proteins  ali follow..  22  163.........................................................................................................................................................PPKRKKPRTSFSRVQICELEKRFHRQKYLASAERAALAKSLKMTDAQVKTWFQNRRTKWRRQTAEEREAERQQASRLMLQLQHDAFQKS.................................................................................................................................................... 251
59 -11.500[O] KOG4265 Predicted E3 ubiquitin ligase  ali follow..  24  272.......................SDNSNECVVCLSDLRDTLILPCR----HL-CL-CTSCADTLRYQ------------------ANNCPICRLFPGPPADPGGAEEA.......................................................................................................................................................................................................................................................................................... 332
60 -11.500[O] KOG0823 Predicted E3 ubiquitin ligase  ali follow..  19  116.CNICLEKAED----------------PILTCCG----------------HLFCWGC------FYQLPLIYLNI------------KECPVCDGEVTDAEVI................................................................................................................................................................................................................................................................................................ 166
61 -11.400[O] KOG0801 Predicted E3 ubiquitin ligase  ali follow..  20  178.......................TKDAGECVICLEELLQGDTIARLLCIYHKSCISCPEHPAD....................................................................................................................................................................................................................................................................................................................................... 227
62 -11.300[O] KOG1734 Predicted RING-containing E3 ubiquitin ligase  ali follow..  295VCAVCGGRLDDSE----------HVHDADAVVTTKMVEDEDEKLYKGHVFHEFCITCPYCKERVDLQRMFKNPW----EKPHLFYGKLLDWIRYLVCWQPLIVTAVQGLTTW...................................................................................................................................................................................................................................................................................... 405
63 -11.200[OU] COG5082 Arginine methyltransferase-interacting protein, contains RING Zn-finger  ali follow..  11  62KCNNCSQR-----HLKKDCPH------IICSYCGAT--------------HYHC-QCSKCDEV-------------CPH---KWKKVQCTLCKSK-DDNEKAKPKVLPFHTIYCYNCGGCKEK........................................................................................................................................................................................................................................................................... 180
64 -11.200[DR] KOG4739 Uncharacterized protein involved in synaptonemal complex formation  ali follow..  21  5............................QCNHCGIKPNQTKLYLT----------AC---------------GHVFCQNCTKAAFNSQCYLCKKPLKVDE.................................................................................................................................................................................................................................................................................................. 51
65 -11.100[S] KOG4020 Protein DRE2, required for cell viability  ali follow..  17  300ACKNCTCGLAEELEKEKSREQMSSQPKSACGNCY------------------DAFRCASC---LGMPAFKPGEKV........................................................................................................................................................................................................................................................................................................................... 357
66 -11.100[O] KOG1100 Predicted E3 ubiquitin ligase  ali follow..  22  282........................VGMSMCRSCGKGEASVLLLPCR----HM-CL-CSVCGSSL----------------------NTCPICKSPKTASLHVNLS............................................................................................................................................................................................................................................................................................. 334
67 -11.000[O] KOG1815 Predicted E3 ubiquitin ligase  ali follow..  136TCGICFDSYPPEK-GHPFCTTCWTGYISTCPSCLAAVGHDMVDKLASEDEKEKIMMFPACARLAFAGMILANSK-------------PCPRCKRPIEKNQ----------HMTCTPCWLCLGAWMDGQSRQKAMADLQQAQMQNVRLVMFFRILLLSESLRLFISKLSDKQCTPESQLKFILEAECRRVLKWTYAYG-----YYLPEHEHAKRQFFEYLQGEAESGLERLHQCVEKDLVQFLIAEGPSKDFNDFRTKLAGLTSVTKNYFENLVKALENGLADVDSHAACSSKSTSSKSTGCSSKTRELVDPRQGTKPELIVCNCTMHTLEEKPKLHAHSGILIL----MYSVKEYEKDEQRRVKPIK------------------SHFHL 565
68 -10.900[O] KOG3800 Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor  ali follow..  3.CKKCKSNEYTNKQLVMMINECGHPL---CKNC------------VDNIFALNSGNCHVCNRVLRKNNFREQ---YQERKFFEPLKFPVKIKISNFRRFKNFKNFFYEF-----------SIRYSNSPSFSWSNPEFSAQNSKIAPSNSKFQFFRFETVVYNLVFETNVNETNAEIQAFEEKHKEQIDRNKRRLDDDQKWIEDQLREERAMKARMTDHMEMDAKEQEAASAVTDTRKIMDELRDSNVAAEVILDRERKKQIEKELEEKEEQEKRKRRNKEMLQTRKRAAENMSFNTVIRVAGRAYVHQVGHENSEEIEKMQLFHSKFQIFKSIFRFSPLELVINGPPMPNVSEIEALGYLAHIRQPTAEYIAGGYTPMLGCSRALFEA-F 403
69 -10.900[O] KOG1814 Predicted E3 ubiquitin ligase  ali follow..  14  174.CNVCFDEFNGTD-GHVSCQSCLRDYYTKCLDCGKDAEKRRYENDSNIIFRSFCAICQKC------------DFAFCAEKWVLLNGQRCPTCDRVVERID----------HMNCLCCFLCGAYLMEQNPYKHFND............................................................................................................................................................................................................................................................... 411
70 -10.900[O] KOG1571 Predicted E3 ubiquitin ligase  ali follow..  25  285........................SQDQLCVVCSTNPKEIILLPC-----HV-CL-CEDCAQKISV---------------------TCPVCRGSIVSKAAAFIA............................................................................................................................................................................................................................................................................................. 338
71 -10.800[O] KOG0800 FOG: Predicted E3 ubiquitin ligase  ali follow..  20  90...................KESFTVMDSQCSVCLGDYQPNDKLQQIKHTFHMDCITCPLCRLAL...................................................................................................................................................................................................................................................................................................................................... 145
72 -10.800[K] COG5175 Transcriptional repressor  ali follow..  33.CPLCIEPMDITDKNFFPCPCGYQ----ICQFCYNNIRQNPELNG----------RCPACRRHLSGTRVIQKNLVYVSEKYFGQYGK--------INK---IVVNRKTPHSNNTTSEHYHHHSPGYGVYITFGSK-------------------DDAARCIAQVDGTYMRLIKAAYGTT----KYCSSYLRGLP-CPNPNCMFLHEPGEEADSFNKRELHNKQQAQQQSGGTAFTRSGIHNNISTSTAGSNTNLLSENFTGTPSPAAMRAQLHHDSHTNAGTPVLTPAPVPAGSNPWGVTQSATPVTSINLSKNSSSINLPTLNDSLGHHTTPTTENTITSTTTTTNTNATSHSHGSKKKQSLAAEEYKDPYDALGNAVDFLDARL.... 434
73 -10.800[O] KOG3268 Predicted E3 ubiquitin ligase  ali follow..  10  307.CGICYAYQLDGTIPDQVC---------DNSQC-------------GQPFHQICLECPYCSKPITLKMSGRKH............................................................................................................................................................................................................................................................................................................................. 375
74 -10.800[S] KOG4623 Uncharacterized conserved protein  ali follow..  11  42............................NCWFCNG---NVRVPYQDRNSW-----TCPSCEQ------FTKDG------DYNRDITSQCDQCAQRLKVEKVYRERLEKQFRL----CSSCERHV---NKVLHEKKKMVLSSKFLNYIIKGASLLKQPHFNRLAAAQKQALLLWSGYAMGIEFLDPYISGISFILVGSFVTLVLLATNRTNLLSQVNRDESACESFHRLCADECDDETLSMLSQQLSGYSDISNSNLSMRTASVCHSPAPTISQRTIQAPASLLSLDSLHLSKQRMEQQAWSSNYGDASTVVAPRVQPAMMFQQKPMRPLESQWYRHGQSNLAQGNTFTRSTQNLLMPSRLPSINRNVGGADVSAWVAANQSVNQ...... 566
75 -10.700[C] COG0348 Polyferredoxin  ali follow..  15  194...............HGWCG--------LC-GAAYGVIGAKGLFRIKVEHRQQCDNCMDCYNVCPEPQVLRDPLHAKKSESPLVLSKDCISCGR-------------------CIVCPEKVFIFTTRFNHSVNHSG.............................................................................................................................................................................................................................................................. 290

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.

Ye Y, Godzik A. Database searching by flexible protein structure alignment. Protein Sci. 2004 Jul;13(7):1841-50.