From farmer@cse.ucsc.edu Fri May 12 12:27:39 2000 Return-Path: Received: from alpha.cse.ucsc.edu (alpha.cse.ucsc.edu [128.114.48.14]) by cyborg.bioinfo.pl (8.9.3/8.8.7) with SMTP id MAA09513 for Message-Id: <200005121031.DAA31720@alpha.cse.ucsc.edu> Subject: T0087(target 99 alignment) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0087.target99@cafasp.bioinfo.pl --simple mime boundary Content-type: text/plain; charset=us-ascii The following is the Target99 alignment in the formats you requested. Citation: K. Karplus, C. Barrett, and R. Hughey, Hidden Markov Models for Detecting Remote Protein Homologies, Bioinformatics, 1998, vol. 14, no. 10, pp. 846-856. http://www.cse.ucsc.edu/resesarch/compbio/HMM-apps -------------------------------------------------------- For questions or problems, please see the SAM-T99 FAQ at http://www.cse.ucsc.edu/research/compbio/HMM-apps/sam-t99-faq.html or email us at sam-info@cse.ucsc.edu --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results.t99align.a2m' Content-Disposition: attachment; filename="t99-results.t99align.a2m" >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVLDYFGIQAPPV VKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHRVANFETANPLYMRLEPVGSA SSIVYRLYKENGVAIPKEIAGVMLSGLISDTLLLKSPTTHASDPAVAEDLAKIAGVDLQE YGLAMLKAGTNLASKTAAQLVDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIK ASQAANGYSDFVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >gi|7674163|sp|O68579|PPX1_STRMU_1:310 PUTATIVE EXOPOLYPHOSPHATASEgi|2952533|gb|AAC05778.1| (AF051356) putative exopolyphosphatase [Streptococcus mutans]gi|3403205|gb|AAC29042.1| (AF050517) unknown [Streptococcus mutans] MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >gi|1743856|gb|AAB39104.1|_1:310 (U57759) intrageneric coaggregation-relevant adhesin [Streptococcus gordonii] MSKILVFGHQNPDSDAIGSSYAFAYLArEAYGLDTEAVALGEPNEETAFV LDYFGVAAPRVITSAKAEGAEQVILTDHNEFQQSVADIAEVEVYGVVDHH RVANFETANPLYMRLEPVGSASSIVYRMFKEHSVAVSKEIAGLMLSGLIS DTLLLKSPTTHPTDKAIAPELAELAGVNLEEYGLAMLKAGTNLASKSAEE LIDIDAKTFELNGNNVRVAQVNTVDIAEVLERQAEIEAAIEKAIADNGYS DFVLMITDIINSNSEILAIGSNMDKVEAAFNFVLENNHAFLAGAVSRKKQ VVPQLTESFN-a >gi|586817|sp|P37487|YYBQ_BACSU_1:305 HYPOTHETICAL 34.0 KDA PROTEIN IN COTF-TETB INTERGENIC REGIONgi|2126990|pir||S65980 conserved hypothetical protein yybQ - Bacillus subtilisgi|467340|dbj|BAA05186.1| (D26185) unknown [Bacillus subtilis]gi|2636602|emb|CAB16092.1| (Z99124) similar to hypothetical proteins [Bacillus subtilis] MEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYAL DYFKQESPRLVETAANEVNG-VILVDHNERQQSIKDIEEVQVLEVIDHHR IANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISD SLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEEL ISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDL FLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQV VPVLTD----amae >gi|7447473|pir||D69344_5:319 exopolyphosphatase (ppx1) homolog - Archaeoglobus fulgidusgi|2649851|gb|AAB90480.1| (AE001052) exopolyphosphatase (ppx1) [Archaeoglobus fulgidus] mehv---VYVVGHKNPDTDSVCSAIAFAYLWNkwkeggnvakmmKIEAEA KPVIQGDVNPETKYVLEKFGFEVPEIMTN--GEGKK-VALVDHSEKAQTV DGIDKAEVVAIVDHHKIGDVTTPQPILFVNLPVGCTATVIKLLFDKTGVE IPKDIAGILLSSILSDTVIFKSATTTELDKEVAEELAKIAGIdDLTKFGV EIKAKLSAVDDLTAMDIIKRDYKDFDMSGKKVGVGQIELVDLSLIESRID EIYEAMKKMKEEGGYAGIFLMLTDIMKEGTELLVVTDYPEVVEKAFGKKL EGKSVWLDGVMSRKKQVVPPLEKAF--ael >gi|2496072|sp|Q58025|Y608_METJA_3:307 HYPOTHETICAL PROTEIN MJ0608gi|2128021|pir||H64375 hypothetical protein homolog MJ0608 - Methanococcus jannaschiigi|1591318|gb|AAB98601.1| (U67509) exopolyphosphatase (ppx1) [Methanococcus jannaschii] mr----YVVGHKNPDTDSIASAIVLAYFLD-----CYPARLGDINPETEF VLRKFGVMEPELIES--AKGKE-IILVDHSEKSQSFDDLEEGKLIAIIDH HKVG-LTTTEPILYYAKPVGSTATVIAELYFKdaidliggKKKELKPDLA GLLLSAIISDTVLFKSPTTTDLDKEMAKKLAEIAGIsNIEEFGMEILKAK SVVGKLKPEEIINMDFKNFDFNGKKVGIGQVEVIDVSEVESKKEDIYKLL EEKLKNEGYDLIVFLITDIMKEGSEALVVGNK-EMFEKAFNVKVEGNSVF LEGVMSRKKQVVPPLERAYNG >gi|7471265|pir||A75258_2:312 conserved hypothetical protein - Deinococcus radiodurans (strain R1)gi|6460400|gb|AAF12113.1|AE002086_5 (AE002086) conserved hypothetical protein [Deinococcus radiodurans] m---LAVFGHLNPDTDAISAAMVYARLLTRQGTEAQAYRLGEPNFETAYV LRELGLEAPPLLTE-LPAGSK-VALVDHNESAQSLPALGELDVTRVVDHH KLGDLTTINPPYLRFEPVGCTGTILLKLHREAGLSVEPQDAKLMLSAILS DTLHFRSPTTTQDDRDAVAFLAPVAGVnDVEAYALAMFAAKSDLGNTPAE TLLRMDYKVFPFGDpvqpQNWGIGVIETTNPAYVFGRQQELLAAMDQVKA EDTLSGMLLSVVDILNETnRTLVLGATEAKVLREAFGAEAEGQVADLGNR ISRKKQIVPTLEKYFAPea >gi|7462213|pir||D72359_24:561 conserved hypothetical protein - Thermotoga maritima (strain MSB8)gi|4981105|gb|AAD35672.1|AE001733_9 (AE001733) conserved hypothetical protein [Thermotoga maritima] mvtfsiriissdriflvaevkal-ERVYVIGHKNPDTDSVCSAIGYAHFK NNVEKGKTFIPARSGdlTNESLFVLKYFGMNPPLHIETLEPtvedlelkn pifvtpdtsaydvamlmesrgiknvpvvskekmigvvtesniarvyvrrl kieplvihpvpfdqlvrilkaevvcdymkektvsgkvhiavdalhvllgk ieigdvvivgdnepaqiallekgaklmivvnnapvsnrvleiakeknaav lrvkfdafsaaklinlslpvtlvmskkfptvtkkdtleevkeivftskir aafvedekgrlcgvitrtdllkDVRKKVILVDHNEITQAPEGVEKAEILE IIDHHRLGGLSTLNPVFFYNEPVGSTSTIVAEFFLKNGVKMEREIAGILL SGIVSDTLFFKLSTTTEKDRKMANFLADVAKLDLEKFAKKLLKEGMKIpE DVDPAELLKRDVKVYEMGEESFAVSQIMTSDFSTLLKEKERFMNTLKTLK GEFGVKHFFVLFTNPVEEASLLMMDGDQ-KLVEKAFNAEKKDGLFLLKGV MSRKKDFVPKIGE----vlrrer >gi|7448979|pir||B75216_162:471 hypothetical protein PAB0174 - Pyrococcus abyssi (strain Orsay)gi|5457686|emb|CAB49177.1| (AJ248283) hypothetical protein [Pyrococcus abyssi] eeyemevkvdyiinprtaiikavvetvekigekknafkllqklneikert -DSLLIVMHDNPDPDSMASASALAVIAQSVGLRPQIVYGGDItHHQNRAM VNVLGMEFKKVLRgSYEIKRYDAIAIVDAQPNGNItILDDDDLKRVEIiV DHHqilqNLREKLSPNCFVDIRTDVNATSSIMVEYLKALEIPITDTLATA LFYGMYIDTK--KFSKLSRVDISAIEFLTGKVNY------ELLDKIEFPD ISTETAEILARAILNRKMYK------NVIISNVGFIANRDAIAEAADFLL RLEGITTVLVFGIVDdrIEISARTRDVRVNIGKVMKEAFGEIGSGGGHAQ MGGAriplgifklAKDKTSLLRLVE----eaitekflealgmkevt >gi|7448980|pir||H71452_162:471 hypothetical protein PH0279 - Pyrococcus horikoshiigi|3256668|dbj|BAA29351.1| (AP000001) 488aa long hypothetical protein [Pyrococcus horikoshii] eeyemdvkidyvinprtaivknvvetiekigekknalkllnklneikekt -DTLLIVMHDNPDPDCMASASALAVIAQSIGLKTQIVYGGDItHHQNRAM VNVLGMEFRKVSRgSYEIKRHKAIAIVDAQPNGNItILDEEDLNKIEIiI DHHqilqNLREKLPPNCFVDIRTDVNATSSIMAEYLKALEIPITETLATA LFYGMYIDTK--KFSKLSRVDINAIEFLTGKVNY------ELLDKIEFPD ISTETAEILARAILNRKIYK------NVIISNVGFIANRDAIAEAADFLL RLEGITTVLVFGIVDdrIEISARTRDVRVNIGNVMKEAFGEIGSGGGHPQ AGGAriplgifklARDKTSLLRLVE----eaitekflealgmkevs >gi|2498554|sp|P75144|MGPA_MYCPN_21:302 MGPA PROTEINgi|2146160|pir||S73340 hypothetical protein 4 - Mycoplasma pneumoniae (strain ATCC 29342)gi|1673660|gb|AAB95662.1| (AE000002) Mycoplasma pneumoniae, hypothetical 28K protein; similar to GenBank Accession Number JS0068, from M. pneumoniae mnsqvhrkgsiaeavsaiqaHDKIVIFHHIRPDGDCLGAQHGLARLIQTN FPHKQVFCVGDPKHNFPWLEMVFTPK-----EQITPELMQQalAVIVDAN YKERIecrdLLDQNQFKAVLRIDHHPNEDD--LNtTHNFVDASYIAAAEQ VVDLAVQAKWKLSPPAATALYLGIYTDSNRFLYSNTSWRTLYLGSMLYR- AQANIAKIHDELN-------HTSLKDI---QFKQYVFKNFQTFQNVIYFV --------------ADKKFQKKLKVTPLECARVNILANIEQFHIWLFFIE EGKNHYRVEFRSNGINVREVALKYGGGGHIQASG---avlkskrdiirvv qdcqkqiav >gi|1346531|sp|P22746|MGPA_MYCGE_59:338 MGPA PROTEINgi|1361725|pir||A64221 MgPa operon hypothetical protein MG190 - Mycoplasma genitaliumgi|3844787|gb|AAC71409.1| (U39698) mgpA protein (mgpA) [Mycoplasma genitalium] nhcvirdyllsvchlwhcasdhyhyqwrgtfiifvmkkgsiteainaikq FDKIVIFHHVRPDGDCLGAQQGLFHLIKANFKNKEVKCVGNNNNLFSFIN MTFTNQ---IDESFLKEALA--IVVDANYKNRIelreLLDKNLFKAVLRI DHHPNEDD--LNtSFNFVEESYVACCEQIVEMATVAKWTIPPVAATLLYI GIYTDSNRFLYSNTSYRTLYLAAILYK-AKADIRIVHDHLN-------HT SLADL---KFKKYVYNHFKTQGQVIYFICTKKIQKRLRMTADQCAR---- ------VNLLSNIAD----YKIWLFFIEQANNEIRIDLRSNGINVRDIAI KYGGGGHNNASG---aiitnkkqisdvvsdcvkkivyn >gi|3025197|sp|Q59027|YG33_METJA_167:460 HYPOTHETICAL PROTEIN MJ1633gi|2128983|pir||G64503 hypothetical protein MJ1633 - Methanococcus jannaschiigi|1592223|gb|AAB99654.1| (U67603) conserved hypothetical protein [Methanococcus jannaschii] nilesgakdiakevedaklkrklmqlksvliegkkrcmklekteeekkap ---LLILTHINPDPDAIASAMALKTLAERWGVDSDIAYGGNIgYDENKAM INLLGIKLLNVEDIDLDNYCV-IAVIDTSTSKQLPIELPN--IDIIIDHH NNTDL--TAKYMDVRPEVGATASILTQYLMELDIEPSRNLATALFYGIQS DTDYFKR-ETSKLDFEAAAYLQSYIDA------SILNMIENPEISTEVME VLAKAVMNRRVVK-----GNIALAYVGEISNRDALPKAADFLLKMEGIST TFVFGIVGdeIHISARTKDLRLNLGEILNKAFGG---GGHQTAAAAKipl gifkaVSDKEALRKLVE----eairakilevigikeeek >gi|2496409|sp|Q49428|Y371_MYCGE_19:263 HYPOTHETICAL PROTEIN MG371gi|1361596|pir||A64241 hypothetical protein homolog MG371 - Mycoplasma genitaliumgi|3844959|gb|AAC71598.1| (U39719) conserved hypothetical protein [Mycoplasma genitalium] misidpqfiknfskkvkqFDKFSLFVHVNPDFDAFGSAFAFKTFLNTFFS EKKAYVMGSYNIN-ADGRELFPFEQTDINDDFVKESLA--IIFDTSNQER VLTQKHKLAKETVrIDHHPRTEK--FADMEWIDSSFSATAEMIGYLILQM GYKLNDEIASYLYAGIITDTQRFWGPTTTPQTFALTAKLME-TGFNRNKV HDAVY----------LKPLLEHKYFSYVLSKAKITKNGL----------- -------AYALIKKGAYKHF-----GVVSPLPMVHALNNI---------- -----------------KGVKIWTTVYFNesikkwigsirsrnipinnfa qmfnggghkyaaafvldeknqfmklvqim >gi|7492568|pir||T38544_32:377 probable exopolyphosphatase - fission yeast (Schizosaccharomyces pombe)gi|2408065|emb|CAB16267.1| (Z99165) putative exopolyphosphatase [Schizosaccharomyces pombe] mklgrflengreqirnlllnastvssapsfs----FVSGNESADLDSCAS SIVYAYCLQRKQLGRIVVPFFNIPRKELRLRPELSYLLNLASISSddivf lddivkLPKRIFSnpIYLVDHNSLDRKDLENFNGSIAGIIDHHKDE-GGS LHADPRIIEECGSCCTLVCRYFMPVIRSLYDskvselhqtatNLAVLALG PILIDTGNLKNEKTTDTDVKIVNDLCSFVPKDwvRDEFFDTLKEKKKSCK GFSFDDLLRRDLKQYFPDGIVVNYASV-GKGLDWIKKKRLGWEDELKSFA EvqnsdlvivglslskndEFGRQLILYKRTergaGLADSFLKLSKQNLGL EIIEEKDNGDL--SMWNQRNSAASRKKVVPLLMDS---vkqvask >gi|6321995|ref|NP_012071.1|PPX1|_31:394 Cytosolic exopolyphosphatase; Ppx1pgi|730369|sp|P38698|PPX1_YEAST EXOPOLYPHOSPHATASE (METAPHOSPHATASE)gi|626143|pir||S46691 exopolyphosphatase (EC 3.6.1.11) - yeast (Saccharomyces cerevisiae)gi|458943|gb|AAB68368.1| (U00030) Ppx1p: Cytosolic exopolyphosphatase [Saccharomyces cerevisiae] msplrktvpeflahlkslpiskiasndvlt----ICVGNESADMDSIASA ITYSYCQyiynegtysEEKKKGSFIVPIIDIPREDLSLRRDVMYVLEKLK IKEeelffiedlksLKQNVSQgtelnSYLVDNNDTPKNLKNYID-NVVGI IDHHFDL-QKHLDAEPRIVKVSGSCSSLVFNYWyekLQGDREVVMNIAPL LMGAILIDTSNMRR-KVEESDKLAIERCQAVLSGavnevsaqgleDSSEF YKEIKSRKNDIKGFSVSDILKKDYKQFNFQGKGHKGLEI---GLSSIVKR mswlfnehggEADFVNQCRRFQAERGLDVLVLLTSwrKAGDSHRELVILG DSNvvreliervsdKLQLQLFGGNLDGGVAMFKQLNveATRKQVVPYLEE AYSNlee >gi|453695|gb|AAA65933.1|_31:394 (L28711) exopolyphosphatase [Saccharomyces cerevisiae] msplrktvpeflahlkslpiskiasndvlt----ICVGNESADMDSIASA ITYSYCQyiynegtysEEKKKGSFIVPIIDIPREDLSLRRDVMYVLEKLK IKEeelffiedlksLKQNVSQgtelnSYLVDNNDTPKNLKNYID-NVVGI IDHHFDL-QKHLDAEPRIVKVSGSCSSLVFNYWyekLQGDREVVMNIALL LMGAILIDTSNMRR-KVEESDKLAIERCQAVLSGavnevsaqgleDSSEF YKEIKSRKNDIKGFSVSDILKKDYKQFNFQGKGHKGLEI---GFSSIVKR mswlfnehggEADFVNQCRRFQAERGLDVLVLLTSwrKAGDSHRELVILG DSNvvreliervsdKLQLQLFGGNLDGGVAMFKQLNveATRKQVVPYLEE AYSNlee >gi|7448978|pir||D69503_156:450 conserved hypothetical protein AF2029 - Archaeoglobus fulgidusgi|2648507|gb|AAB89226.1| (AE000963) conserved hypothetical protein [Archaeoglobus fulgidus] pkkkeefeeaganlvvlvadavkqafmdkikkmetlkkieklkrimeslr GKRLGIFTHDNPDPDSMSSAYALREIAKQFDVIADILYYGEIlhqkNRAM VNLLEIPMIRAPEVDLSHYDAF----AIVDSSGPGVNNSIPPDIDISIVI DHHPAEKV--VAEFVDLREDVGATATILTEYIKELKITPSKILATALFFG IKSETDEFKR-NTRTADFLACAFLYPFVDQ------DLIEKIESPSISTE TLDILGTAIKNRQVYS------SFLISFAGFINDRDALPQAADFLLKLEG ISTVVVFGVIkDtVYVSARNKDVRIHMGEVLRRAFGDVGsAGGHAHAAGA QIPLGIFGETNEKD---llakliteaitkrllsavgmeqs >gi|2496410|sp|P75229|Y371_MYCPN_19:263 HYPOTHETICAL PROTEIN MG371 HOMOLOGgi|2146233|pir||S73619 hypothetical protein G12_orf325 - Mycoplasma pneumoniae (strain ATCC 29342)gi|1673964|gb|AAB95941.1| (AE000027) Mycoplasma pneumoniae, hypothetical 28K protein (P1 operon) homolog; similar to GenBank Accession Number JS0068, from M. pneumoniae minidphfihnltnklktFDNFSLYVHVNPDFDAFGAAFAFKAFLAVYFP HKKAYVMGSHNIK-ADGKDLFPFEAAPIDDAFVKNSLA--IIFDTSNQER VLTQKHKLAKETVrIDHHPKTES--FADLEWIDPAFSAAAEMVGYLILQM GYELNAEMAAYIYAGIITDTQRFSSSATTPQTFALTAKLLE-TGFNRNKV HDAVY----------LKPLLEHKYFSYVLNKAKITPNGL----------- -------AYALLKKGTYKQF-----GVVSPLPMVHALNNI---------- -----------------KGVKIWTTCYFNedikkwigsirsrsipinnfa qmfgggghkyaaafvlddkrqfmklveim >gi|7462295|pir||G72233_11:309 conserved hypothetical protein - Thermotoga maritima (strain MSB8)gi|4982166|gb|AAD36662.1|AE001804_6 (AE001804) conserved hypothetical protein [Thermotoga maritima] mdeivkvlsqHDRILVVGHIMPDGDCVSSVLSLTLGLEKLGKEVKA---- ----AVDYKIPYVFEKFPYIDKiEENPNFDPElLVVVDASSPDRIGKFQD LLDKVpsVVIDHHSTNTN--FGNWNWVDPSFAATAQMIFRINKALGVEYD SNLATLNYLGIATDTGFFRHSNADVRVFEDAYKLVK-MGADAHFVAKEIL ENKRFEQFKLFAEVLErlqllengkiaysyIDYDTYLRHN------CTDE DSAGFVGElRSIRGVEVAVLFMEFPRGKIHVSMRSkDWFNVNEVAFELGG GG--HPRAAGVTFEGK---------KIEEVIPRVINH---llkkfkegve sesekipegdvlgg >gi|7477397|pir||H70693_35:318 hypothetical protein Rv2837c - Mycobacterium tuberculosis (strain H37RV)gi|1648883|emb|CAB03672.1| (Z81331) hypothetical protein Rv2837c [Mycobacterium tuberculosis] mttidprselvdgrrragarvdavgaaallsaaa--RVGVVCHVHPDADT IGAGLALALVLDGCGKRVEV------SFAAPATLPESLRSLPGCHLLVRP EVMRRdvdlVVTVDIPSVDRLGALgdlTDSGRELLVIDHHASNDL--FGT ANFIDPSADSTTTMVAEILDAWGKPIDPRVAHCIYAGLATDTGSFRW--A SVRGYRLAARLVE-IGVDNATVSRTLM----DSHPFTWLPLLSRVLGSAQ LVSEAVGGRGLVYVvvdNREWVAARSEE-----------------VESIV DIVRTTQQAEVAAVFKEVEPHRWSVSMRAKTVNLAAVASGFGGGGHRLAA GY--tttgsiddavaslraalg >gi|7469901|pir||S74940_64:380 hypothetical protein sll0639 - Synechocystis sp. (strain PCC 6803)gi|1652055|dbj|BAA16980.1| (D90902) hypothetical protein [Synechocystis sp.] lsvpessivsspqqisaqrsiasadvvspripaantaqiiklqhhleghq GQRLILVIQDFPDPDALSSAWAFQLIAAQYEIQCDIVYAGTLsHQENIAL VKLTGLPAKRWGPQMLKDIDLSdyqgCVLVDsqgTNSQLMPLVQEANIPV VVIIDHHsPQDEVEAEGAFVDIRPSSRSTATILTEYLQGGMLDFNSsnpt hvKCATALMHGLRSDTINLLQ--AQEAEFMAAAYLSRIYDA------QLL NAVLQSARSKRVMEVIERSLQNRVVQN------NFSLAGVGYLRyeERDA IPQAADFLVSEENVHTALVYGIVhDrandielVIGSLRTNKLTLDPDEFL KDSLGMDGTGRYYGGGRDMaGGFEIPVGFLT-----gcndqaeytklkwe vfdrqlkqkffrlinpdhrvvhs >gi|7462978|pir||B72344_3:297 tRNA nucleotidyl transferase-related protein - Thermotoga maritima (strain MSB8)gi|4981239|gb|AAD35797.1|AE001742_12 (AE001742) tRNA nucleotidyl transferase-related protein [Thermotoga maritima] mr----VITTHRSPDFDAFASCVAAKKLLD----DHIIVLPSNPARNLSD FLKVYSDRFEFVWDhEFEGEITE-LVIVDAPSLDRIpesIRKKAQGAKIT VYDHHVDE-----SPYDGIVSKVGATITILVELIREKNIPLDPTEATLFM IALYDDTGNLLFSSTTPRDLEIAKFLLE-NGANLDEVALYTREELTPRQM ELLDDLIE-NARDYEVNGVPITISMIECEdfvgGLGLIVSKAWEMMgKET FIAIVKMGKKIYVIGRTSSPD--------VDLGSLMKDLGGGGHtraASA TITGKEIDEVLKEVLNRLHDH---vvpllrardimsspvkvvlsnmtike vdrlmkqtghsgfpvvegnrlvgi >gi|7445472|pir||F70440_17:299 conserved hypothetical protein aq_1630 - Aquifex aeolicusgi|2983973|gb|AAC07520.1| (AE000748) hypothetical protein [Aquifex aeolicus] mtkenipivdflknvk-GSILILTHENPDGDSLGSGLALYKFLKKKGKEV YI--------GSKDGVPHFLDFLPGVEDVINPDGKFYdvGIVVDASGFYR VGKEV-KVGKRIRIDHHVGGEF--YGMHDYIDPTAPATAALVYEIIKNWD ETaIDKDIATCIYTGLATDTGFFRYSNTNEKTFELAKELVS-YGADPYYV YTMVMEREKVNKMKLIAKVLEtlqlhedgkvagiTVFKKFLDET------ GTTYEDTEGLVnyPRSIEGVKVAYALIEKP--------EEGVWKVSLRAK GNVNVGKIAERLGGG----GHKYASGAKIK--------------tnsyee alkklleaikeelklekvya >gi|7430137|pir||B70177_21:297 conserved hypothetical protein BB0619 - Lyme disease spirochetegi|2688546|gb|AAC66977.1| (AE001163) conserved hypothetical protein [Borrelia burgdorferi] mfcgrfanfimrdvinfikkYNNFVIIGHKDPDFDCIGSSLALSSFLSRI GKNSILLNEGPFiRKEIVPFKDKFLSEWPNIEISEY-----SVIILDCSI LDRIGDEfifYVKNMPTLVIDHHMSGEK--LECEGYIDPFAPSTTFLIEK LIREFGHDLTKEEAWYILVGFCTDTGFFKFiSRSDPEPFEMVARLVS-KG ISLKEVYSYIETTKSLKSIETLKLMLNslesywngKVLFTFLSSSSSGKD GGVSGV------------------------NELFYMILSNVEN------- -NEILGILKEMEDGSI------IVGLRSKDSFDVGKLAEDFGGgghknas gfrikqgsleivknrmlayikdniyl >gi|7516499|pir||D72622_13:305 hypothetical protein APE1437 - Aeropyrum pernix (strain K1)gi|5105120|dbj|BAA80434.1| (AP000061) 341aa long hypothetical protein [Aeropyrum pernix] mealkevageaeGEKSAVITHRNADPDAVGAALVVREVLRALRMNPCLYS PEGISRQSKRLLEAVGEEFGPLCSPDENPLIA--VVVDAANLSQIaGAEs LFRAARLKVvIDHHERGSIHEEADVALVDPGAGSSSELAVKTAVEAGTPL RPSVATAALGGIVYDTGRFLR--ASKLSFEAAAHLLS-MGADYGKVLEAG RQRGRRDRGDLSLRLAKLKAFSRLKIGRACSELLIAVTHIGSFEsdvAKS LVDEAADVAVAVAERTSEF---RLSVRVSPLALEKGVTaraIASMLAEKF GGEG--GGHDEAGMA----------------hipytaafsaedmavkafn lisgrlgwmcvktlekg >gi|7514584|pir||D71323_41:319 conserved hypothetical protein TP0436 - syphilis spirochetegi|3322722|gb|AAC65424.1| (AE001221) conserved hypothetical protein [Treponema pallidum] mfsssppsslpksvsspspcaartgdrgrglsgliefidaHRAFAVVGHE KPDGDCVGSSLALASFLRRIGKEVELLSAGPFKRR--EIAAYATLFRPSL SAQIRPSDQTAVIVVDCSELSRVGAElASQLAPFARafIDHHETCGD--H CAHSFVVKTAPSTTTLVQTLIETMAGSLEAAEARALFLGLATDTGFFRHl DEHSADTFASAARLVR-AGANPKDTFLAMN-------------------- ----GGRSLASRML----IARVLSRLTPYYGGALMTSYET-CEDAVQLGL DVRDSDa--LYQLIQSIQGVEAIVVVRQESPTHCSVGFRSRGSIDVSVIA ARFGGgghrcaaglriegtvdellprfvaafeaqmrapaagaqvrs >gi|6175243|gb|AAF04914.1|U67085_1_5:339 (U67085) TcD37 homolog [Homo sapiens] awhe-------GNEACDLDSTVSALALAfYLAKTTEAEEVFVPVLNIKRS ELPLRGDIVFFLQKVHIPEsilifrdeidlhalYQAGQLTLILVDHHILS KSDTALEE-AVAEVLDHRPIE-PKHCPPCHVSVELVGSCATLVTERILQG APEIlDRQTAALLHGTIILDCVNMDLkiGKATPKDSKYVEKLEALFPDlp KRNDIFDSLQKVKFDVSGLTTEQMLRKDQKTIYRQGVKVAISAI-YMDLE AFLQRSNLLADLHAFCQAHS-YDVLVAMTIffNthnepvrqLAIFCPHVA LQTTICEVLERSHSPPLKltpassthpNLHAYLQGNTqVSRKKLLPLLQE ----alsayfdsmkipsgqpetadvsreqvdkeldrasnslisglsqdee dppl >gi|7494008|pir||T02817_25:378 exopolyphosphatase XPP - Leishmania majorgi|1407725|gb|AAC24640.1| (AE001274) XPP; L2759.9 [Leishmania major] msgvindflrrclkkvagkvqplt----VVQGNEGGDMDSIVGCIYLAML FDKQPKFGFenPVPALNFPQEDFGLRNDVTNLFKELGIDAsllmsvqrgq iahnlvdIAALNASVVLYDHNKLRENQSDLAS-RVVGVVDHHFDEQQYLK TaSKLRVLRTVGSACTLVTELYRECGEDVv---CPTLLTAPIVLDTVNFE PaqKKVTPEDIAAYEWLRA-KEVadsaDAAALFEKLSKWKDDVLALSVPQ ILRRDYKQFSFKARTQKGVMSAgtssvpcackqleaHFSVDLIVAEAAKY VEQHQLDVLivafagkvggKHTREVAFCAKPDVISFFaPFVAEAPDGVSF TVITKCQTVDGSYEYASYSLsdpsISRKKLVPALSEF---laegtrslce >gi|7518105|pir||C75065_18:315 hypothetical protein PAB1366 - Pyrococcus abyssi (strain Orsay)gi|5458929|emb|CAB50416.1| (AJ248287) hypothetical protein [Pyrococcus abyssi] mrgerklknllkslkrd-EGIILLCHHNADPDSLGSAIAFSnFLLDRGLR NVRIGVAQSIa----SYSRRLLKFSRVPIERN--PKISERvVFIFDTSSL EQLePIKIPPNAKLIVIDHHVEKENPIPADISVIDPKRTSTAEIVWELFK KLGYK-DEDSAKVLLAAIISDTSSFRY--ANAKTFKTVSEILELYDFSIS EVSQLVA--------------------------------PVSDENVE--Q SKRIAVLKACQRMEIHKVRKFIIVtskvsayealackvflqlgadvaivg sEKDGVRISARakdYLVKKGLHLGKLMEKVGPIIGGSGGGHPGAAgANGK ENLDEAIKF---lvkevqrflkgvgdg >gi|7518694|pir||B71167_18:314 hypothetical protein PH0534 - Pyrococcus horikoshiigi|3256940|dbj|BAA29623.1| (AP000002) 329aa long hypothetical protein [Pyrococcus horikoshii] mkgerklkklleslnrd-EGIILLCHHNADPDSLGSAIAFSnFLLSKGFS RIRIGVAQSIa----SYSRRLVALSRVPIEKDPVIKENV-IFIFDTSSIE QLePIEVPP-AKIVVIDHHVEKENPIPADVAIIDPTRTSTAEIVWELFKK FNYS-DENSAKALLAGIISDTSNFRY--ANAKTFKAVYEILELYDFSIPE VSQLVA--------------------------------PVSDENVD--QS RRIAILKACQRMEIHKVKKFVIVtskvsayealackvflqlgadvaivgs EKDGVRISARakdYLVKQGLHLGKIMEKVGPIIKGSGGGHAGAAgANGKE NLDEAIKF---lvkevqkflkgvgng >gi|7520820|pir||D70337_6:360 poly A polymerase - Aquifex aeolicusgi|2983086|gb|AAC06692.1| (AE000689) poly A polymerase [Aquifex aeolicus] mvcpk----VVILSEGADLDSLSAAYGVL----KLYPDAYLLKPKHLSKK AGEVFKKYRDKFRVIEDL--PDCFE-LVLVDTHFLPE-GLPRERIKRIIV YDHHPIGDV---KEFEGKIEKVGAATTLVVEEIKEKGIDINPRDATLLAF GIYEDTGNFTYEGTTPRDALALAFLLE-KGANLREIREVVMETYTPEQie avgkivqsiekvfingrqisfatavleryqpdintllyeikdlkeSDAFF VIIEAEGKTYVFGR-----SQSEDVDVGEILshfgggghreagavKLENV SAERIKELIKAFLKRKYVKLKVrDIMNTPPFVLEEHVSVKdaLTELSERG IANAPVINREGKLvgIISKKALLKLVKLYPDepielfvnrdfytlspdap vweaeeiltkfgqklipvvedgtvvgvvtrl >gi|3024962|sp|Q58395|Y988_METJA_10:307 HYPOTHETICAL PROTEIN MJ0988gi|2128620|pir||D64423 hypothetical protein MJ0988 - Methanococcus jannaschiigi|1591650|gb|AAB98990.1| (U67541) conserved hypothetical protein [Methanococcus jannaschii] melleylkr-DEVLFLCHHNADPDAVGSCVALKYLASQLNPNGKFrISAD SVSKLSRNILNEIGER---VDIEIYPKLPETVFIVDTASINQLKVNFDEL KEREVilIDHHKKTDLADICKYYIIKEDYPSTSEIIAEIFKELNIFPPKN VRIALLCGIVYDTKHLKL--ANSKTFELISYLIK--DISFQKI-LYLLSQ ESDVskrtahlKACSRMEI-------REFDKLRIALSHVSsheascakti vsiGADVAFVVavrkkEKEIRVSARCRKHVSKY----------------- --VHLGNLMEKIGKELGGSGgghsEAGGLNAPYDKSKSKEKV-------- -ikevlnlcykrfveeykkakqn >gi|7430136|pir||F69999_12:258 conserved hypothetical protein ytqI - Bacillus subtilisgi|2293259|gb|AAC00337.1| (AF008220) YtqI [Bacillus subtilis]gi|2635390|emb|CAB14885.1| (Z99118) similar to hypothetical proteins [Bacillus subtilis] mktelirtislYDTIILHRHVRPDPDAYGSQCGLTEILRETYPEKNIFAV GTPepSLSFLYSLDEVDNE--------TYEGAL-VIVCDTANQERIDDQr YPSGAKLMKIDHHPNEDP--YGDLLWVDTSASSVSEMIYELYlegKEHGW KLNTKAAELIYAGIVGDTGRFLFPNTTEKTLKYAGELIQ-YPFSSSELFN QLYETKLN--------VVKLNGFIFQNVSLSENGAAS------------- -----------------------------------VFIKKDTLEKFGTTA seASQLVGTLGNISGIRAWVFFVEED---dqirvrfrskgpvinglarky nggghplasgasiyswdeadriladletl >gi|6899406|gb|AAF30828.1|AE002139_1_16:247 (AE002139) conserved hypothetical [Ureaplasma urealyticum] mqkdlltklieqtygFNKITIFVHTNPDCDALGSAFALARILKlnTFGTR VKIVGVNALNPN--DFKNFFTFDPNEVDDEFIKDSIA--FIVDTANQERV LSQKHRLAKKTIlVDHHVKT--ITYTDLEYINDQSIAACEMIAYSLMHTN LNFDLKTLNYLLLGITTDSNRLMYDKVSDFTYEIMSWFFK-NNVKHYQIY QQLYERNLNDILFDNELV-----KTIKTQG------QVAYLNID------ -------------------------------------------------- ---PQWNQKYHFTRWGDKVYLLSN----iknypiwfivyfdentntykvs lrsnkykvrlvasqfnggghdlaagcsl >gi|7471305|pir||A75470_29:258 conserved hypothetical protein - Deinococcus radiodurans (strain R1)gi|6458543|gb|AAF10405.1|AE001937_1 (AE001937) conserved hypothetical protein [Deinococcus radiodurans] mtaensatpdyrrnvgavadallahpgp---IVVLSHENPDGDALGSVLG LSRALRTLGKTVLAPMTVPHy----LSFLPQPGELTAPLESW--PQGALA aVLDVDNNDPVRVaGADLTQFDGPVVnVDHHGTN--LRRADAGVVDPSKP AAAMMVADVIDALGAPWSEAVATPLMLGLNTDTGNFAFDSVSAETFECAA RLRA-HGARIGWLNDQMRQNPQSYYLLLREVL---GKLEFLHGG-----R VVQTR-----VDEEMLARAGATWEQVENYVSML----------------- ------------------------------------------rnaegaql avmakdygdrvkfslrsrgpvsaqniavalgggghvpaagat >gi|586814|sp|P37484|YYBT_BACSU_338:570 HYPOTHETICAL 74.3 KD PROTEIN IN RPLI-COTF INTERGENIC REGIONgi|2126987|pir||S65976 yybT protein - Bacillus subtilisgi|467336|dbj|BAA05182.1| (D26185) unknown [Bacillus subtilis]gi|2636598|emb|CAB16088.1| (Z99124) yybT [Bacillus subtilis] algrggdqvaiklpngkvkfyggktnpmekrtrvrarvishalkeivtes -SNVIIMGHKFPDMDSIGAAIGILKVAQANNKDGFIVIDPNQiGSSVQRL IGEIKKYEELWSRFITPEEAMEisnddtlLVIVDTHKPSLVMEErlVNKI EHIVVIDHHRRGEEFIRDPLLVYMEPYaSSTAELVTELLeyQPKRLKINM IEATALLAGIIVDTKSFSL-RTGSRTFDAASYLRA-KGADTVLVQKFLK- -------------------------------ET----VDSYIKRAKL--- ----------IQHTVLYKDNIAI--------------------------- -----------ASLPENEEEYFDqvliaqaadsllsmseveasfavarrd eqtvcisarslgevnvqiimeal >gi|7470790|pir||S75598_3:208 poly(A) polymerase - Synechocystis sp. (strain PCC 6803)gi|1653244|dbj|BAA18159.1| (D90912) polyA polymerase [Synechocystis sp.] md----LILCHQTADFDVLGAAVGLA----KLHPGSRIVLTGGSHPTVRQ FLALHRNEFPLIELrSVNPDKIRSLYIVDNQQGDRLGKAadwltLPHLRQ VAIYDHHLNS-PRDIEADIWELEAVGASTTLIVEKLQRADISLSMVEASV MALGIHVDTGSLTFTQTTVRDVKALAWLME-QGANLRLIAE--------- -----------------------------YADPGFPPPLQFLFAEAMQNL HKEMVR-------------------------------------------- ------------------gywlgsvllttenfvpglshlterllsltecd alllghvydkgkdktknd >gi|7519590|pir||E71279_37:180 hypothetical protein TP0803 - syphilis spirochetegi|3323118|gb|AAC65775.1| (AE001251) T. pallidum predicted coding region TP0803 [Treponema pallidum] mgalacdytyspspkrdlsiaaknavvrnilqeiaiHGSFLLLGHEHPDE DCIASLVAFALLLTRCNKRVEICCQGPIRVQISFLIDICLYNGIAVHLdt QTVPRMPDALVILDTPNPGMIYAPpscrllLSDSTIRKIeLDHHLFANAA CCGdPGYSLIARASSTCEIIAYLCYKLARN-------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ------haqrtalgirnlysrnvvlsiltgmigdaktgaylisrkdraly tyftqr --simple mime boundary-- From farmer@cse.ucsc.edu Fri May 12 13:05:04 2000 Return-Path: Received: from alpha.cse.ucsc.edu (alpha.cse.ucsc.edu [128.114.48.14]) by cyborg.bioinfo.pl (8.9.3/8.8.7) with SMTP id NAA09808 for Message-Id: <200005121108.EAA23718@alpha.cse.ucsc.edu> Subject: T0087(database hits) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0087.target99@cafasp.bioinfo.pl --simple mime boundary Content-type: text/plain; charset=us-ascii The following are search results using the SAM-T99 method for a sequence query against a database. If there are no hits associated with this output, then your score cutoff was too conservative. Citation: K. Karplus, C. Barrett, and R. Hughey, Hidden Markov Models for Detecting Remote Protein Homologies, Bioinformatics, 1998, vol. 14, no. 10, pp. 846-856. http://www.cse.ucsc.edu/resesarch/compbio/HMM-apps -------------------------------------------------------- For questions or problems, please see the SAM-T99 FAQ at http://www.cse.ucsc.edu/research/compbio/HMM-apps/sam-t99-faq.html or email us at sam-info@cse.ucsc.edu --simple mime boundary Content-type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="t99-results.t99dbhits.txt" The E-value is an estimate of approximately how many sequences would score this well by chance in the database searched. For SAM-T99, E-values less than about 0.01 are roughly equivalent, as sequences that score that well have most likely already been included in the SAM-T99 multiple alignment. Database: PDB Score method: average Summary of Database Hits: Average Target Template SeqID Reverse EValue Reverse EValue Reverse EValue SeqLabel 1gln -11.15 0.3177 -11.15 0.32 --------- --------- : mol:protein length:468 Glutamyl-tRNA Synthetase 1agnA -8.47 4.633 --------- --------- -8.47 4.6 2ohxA -8.22 5.948 --------- --------- -8.22 6 1bw9A -7.35 14.19 --------- --------- -7.35 14 1xxaA -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxaB -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxaC -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxaD -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxaE -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxaF -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxbA -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxbB -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxbC -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxbD -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxbE -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxbF -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxcA -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxcB -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxcC -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor 1xxcD -6.93 21.59 -6.93 22 --------- --------- : mol:protein length:78 Arginine Repressor --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results.t99pairwise.a2m' Content-Disposition: attachment; filename="t99-results.t99pairwise.a2m" >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1gln mol:protein length:468 Glutamyl-tRNA Synthetase mvvtriapsptgdphvgtayialfnyawarrnggrfivriedtdraryvp gaeerilaalkwlglsydegpdvaaptgpyrqserlplyqkyaeellkrg wayrafetpeeleqirkekggydgrarnippeeaeerarrgeph------ ---------------------------------------------VIRLK VPRPGTTEVKDELRGVVVYDNQEIPDVVLLksdgYPTYHLANVVDDHLMG ----VTDVIRAEEWLVST-------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- --------pihvllyrafgweaprfyhmpllrnpdktkiskrkshtsldw ykaegflpealrnylclmgfsmpdgreiftleefiqaftwervslggpvf dleklrwmngkyirevlsleevaervkpflreaglsweseaylrravelm rprfdtlkefpekarylftedypvsekaqrkleeglpllkelyprlraqe ewteaaleallrgfaaekgvklgqvaqplraaltgsletpglfeilallg keralrrlerala >T0087 mskilvfghqnpdsdaigssmayaylkrqlgvdaqavalgnpneetafvl dyfgiqapp----------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- --------------VVKSAQAEGAKQVILTDHNEfqqsiadiREVEVVEV VDHHRVANFETAN-------------PLYMRLEPVGS---ASSIVYRLYK ENGVAIPKEIAGVMLSGLISDTLLLKSPTTHAS----------------- ----------------------------------------dpavaedlak iagvdlqeyglamlkagtnlasktaaqlvdidaktfelngsqvrvaqvnt vdinevlerqneieeaikasqaangysdfvlmitdilnsnseilalgnnt dkveaafnftlknnhaflagavsrkkqvvpqltesfng >1agnA mol:protein length:373 Human Sigma Alcohol Dehydrogenase g-TAGKVIKCKAAVLWEQKQPFSIEEIEVAPPKTKEVRIKILATGICRTD DHVIKGTMVSKFPVIVGHEATGIVESIGEGVTTVKPGDKVIPLFLPQCRE CNACRNPDGNLCIRSDITGRGVLADGTTRFTCKGKPVHHFMNTSTFTEYT VVDESSVAKIDDAAPPEKVCLIGCGFSTGYGAAVKTGKVKPGSTCVVFGL GGVGLSVIMGCKSAGASRIIGIDLNKDKFEKAMAVGATECISPKDSTKPI SEVLSEMTGNNVGYTFEVIGHLETMIDALASCHMNYGTSVVVGVPPSAKM LTYDPMLLFTGRTWKGCVFGGLKSRDDVPKLVTEFLAKKFDLDQLITHVL PFKKISEGFELLNSGQSIRTVLTF >T0087 mskilvfghqnpdsdaigssmayaylkrqlgvdaqavalgnpneetafvl dyfgiqapp----------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ---------------VVKSAQAEGAKQVILTDHNEFQQSIA--------- -------------------------------------------------- -------------------------------------------------- ---------------------------------direvevvevvdhhrva nfetanplymrlepvgsassivyrlykengvaipkeiagvmlsglisdtl llksptthasdpavaedlakiagvdlqeyglamlkagtnlasktaaqlvd idaktfelngsqvrvaqvntvdinevlerqneieeaikasqaangysdfv lmitdilnsnseilalgnntdkveaafnftlknnhaflagavsrkkqvvp qltesfng >2ohxA mol:protein length:374 Alcohol Dehydrogenase (Holo Form) (E.C. 1.1. STAGKVIKCKAAVLWEEKKPFSIEEVEVAPPKAHEVRIKMVATGICRSDD HVVSGTLVTPLPVIAGHEAAGIVESIGEGVTTVRPGDKVIPLFTPQCGKC RVCKHPEGNFCLKNDLSMPRGTMQDGTSRFTCRGKPIHHFLGTSTFSQYT VVDEISVAKIDAASPLEKVCLIGCGFSTGYGSAVKVAKVTQGSTCAVFGL GGVGLSVIMGCKAAGAARIIGVDINKDKFAKAKEVGATECVNPQDyKKPI QEVLTEMSNG-GVDFSFEVIGRLDTMVTALSCCQEAYGVSVIVGVPPDSQ NLSMNPMLLLSGRTWKGAIFGGFKSKDSVPKLVADFMAKKFALDPLITHV LPFEKINEGFDLLRSGESIRTILTF >T0087 mskilvfghqnpdsdaigssmayaylkrqlgvdaqavalgnpneetafvl dyfgiqapp----------------------------------------- -------------------------------------------------- -------------------------------------------------- ------------------------------------------------VV KSAQAEGAkQVILTDHNEFQQSIADIREVEVVEVVDHHRV---------- -------------------------------------------------- -------------------------------------------------- ----------anfetanplymrlepvgsassivyrlykengvaipkeiag vmlsglisdtlllksptthasdpavaedlakiagvdlqeyglamlkagtn lasktaaqlvdidaktfelngsqvrvaqvntvdinevlerqneieeaika sqaangysdfvlmitdilnsnseilalgnntdkveaafnftlknnhafla gavsrkkqvvpqltesfng >1bw9A mol:protein length:356 Phenylalanine Dehydrogenase msidsa-----LNWDGEMTVTRFDSMTGAHFVIRLDSTQLGPAAGGTRAA QYSNLADALTDAGKLAGAMTLKMAVSNLPMGGGKSVIALPAPRHSIDPST WARILRIHAENIDKLSGNYWTGPDVNTNSADMDTLNDTTEFVFGRSLERG GAGSSAFTTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSLASLA AEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCDVFAPCAMGGVI TTEVARTLDCSVVAGAANNVIADEAASDILHARGILYAPDFVANAGGAIH LVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAARTLAGRR AREA--stttata >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxaA mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxaB mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxaC mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxaD mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxaE mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxaF mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxbA mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxbB mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxbC mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxbD mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxbE mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxbF mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxcA mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxcB mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxcC mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- >T0087 MSKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVL DYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHR VANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISD TLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQL VDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSD FVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQV VPQLTESFNG >1xxcD mol:protein length:78 Arginine Repressor msplknlvld---------------------------------------- -------------------------------------------------- --------------IDYNDAVVVIHTSPGAAQLIARLLDSLG------KA EGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL------------ -------------------------------------------------- -------------------------------------------------- -------------------- --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results.t99pairwise.casp.al' Content-Disposition: attachment; filename="t99-results.t99pairwise.casp.al" PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1gln V 145 Y 52 I 146 F 53 R 147 G 54 L 148 I 55 K 149 Q 56 V 150 A 57 P 151 P 58 R 152 P 59 P 153 V 60 G 154 V 61 T 155 K 62 T 156 S 63 E 157 A 64 V 158 Q 65 K 159 A 66 D 160 E 67 E 161 G 68 L 162 A 69 R 163 K 70 G 164 Q 71 V 165 V 72 V 166 I 73 V 167 L 74 Y 168 T 75 D 169 D 76 N 170 H 77 Q 171 N 78 E 172 E 79 I 173 F 80 P 174 Q 81 D 175 Q 82 V 176 S 83 V 177 I 84 L 178 A 85 L 179 D 86 Y 184 I 87 P 185 R 88 T 186 E 89 Y 187 V 90 H 188 E 91 L 189 V 92 A 190 V 93 N 191 E 94 V 192 V 95 V 193 V 96 D 194 D 97 D 195 H 98 H 196 H 99 L 197 R 100 M 198 V 101 G 199 A 102 V 200 A 107 T 201 N 108 D 202 P 109 V 203 L 110 I 204 Y 111 R 205 M 112 A 206 R 113 E 207 L 114 E 208 E 115 W 209 P 116 L 210 V 117 V 211 G 118 S 212 S 119 T 213 A 120 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1agnA V 206 V 60 I 207 V 61 M 208 K 62 G 209 S 63 C 210 A 64 K 211 Q 65 S 212 A 66 A 213 E 67 G 214 G 68 A 215 A 69 S 216 K 70 R 217 Q 71 I 218 V 72 I 219 I 73 G 220 L 74 I 221 T 75 D 222 D 76 L 223 H 77 N 224 N 78 K 225 E 79 D 226 R 88 K 227 E 89 F 228 V 90 E 229 E 91 K 230 V 92 A 231 V 93 M 232 E 94 A 233 V 95 V 234 V 96 G 235 D 97 A 236 H 98 T 237 H 99 E 238 R 100 C 239 V 101 I 240 A 102 S 241 N 103 P 242 F 104 K 243 E 105 D 244 T 106 S 245 A 107 T 246 N 108 N 260 P 109 V 261 L 110 G 262 Y 111 Y 263 M 112 T 264 R 113 F 265 L 114 E 266 E 115 V 267 P 116 I 268 V 117 G 269 G 118 H 270 S 119 M 274 A 120 I 275 S 121 D 276 S 122 A 277 I 123 L 278 V 124 A 279 Y 125 S 280 R 126 C 281 L 127 H 282 Y 128 M 283 K 129 N 284 E 130 Y 285 N 131 G 286 G 132 T 287 V 133 S 288 A 134 V 289 I 135 V 290 P 136 V 291 K 137 G 292 E 138 V 293 I 139 P 294 A 140 P 295 G 141 S 296 V 142 A 297 M 143 K 298 L 144 M 299 S 145 L 300 G 146 T 301 L 147 Y 302 I 148 D 303 S 149 P 304 D 150 M 305 T 151 L 306 L 152 L 307 L 153 F 308 L 154 T 309 K 155 G 310 S 156 R 311 P 157 T 312 T 158 W 313 T 159 K 314 H 160 G 315 A 161 C 316 S 162 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 2ohxA V 207 V 60 I 208 V 61 M 209 K 62 G 210 S 63 C 211 A 64 K 212 Q 65 A 213 A 66 A 214 E 67 G 215 G 68 A 216 A 69 A 217 K 70 R 218 Q 71 I 219 V 72 I 220 I 73 G 221 L 74 V 222 T 75 D 223 D 76 I 224 H 77 N 225 N 78 K 226 E 79 D 227 F 80 K 228 Q 81 F 229 Q 82 A 230 S 83 K 231 I 84 A 232 A 85 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1bw9A L 191 V 60 A 192 V 61 S 193 K 62 L 194 S 63 A 195 A 64 A 196 Q 65 E 197 A 66 A 198 E 67 G 199 G 68 A 200 A 69 Q 201 Q 71 L 202 V 72 L 203 I 73 V 204 L 74 A 205 T 75 D 206 D 76 T 207 H 77 D 208 N 78 T 209 E 79 E 210 F 80 R 211 Q 81 V 212 Q 82 A 213 S 83 H 214 I 84 A 215 A 85 V 216 D 86 A 217 I 87 L 218 R 88 G 219 E 89 H 220 V 90 T 221 E 91 A 222 V 92 V 223 V 93 A 224 E 94 L 225 V 95 E 226 V 96 D 227 D 97 V 228 H 98 L 229 H 99 S 230 R 100 T 231 V 101 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxaA I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxaB I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxaC I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxaD I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxaE I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxaF I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxbA I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxbB I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxbC I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxbD I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxbE I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxbF I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxcA I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxcB I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxcC I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END PFRMAT AL TARGET T0087 AUTHOR UCSC T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xxcD I 11 E 105 D 12 T 106 Y 13 A 107 N 14 N 108 D 15 P 109 A 16 L 110 V 17 Y 111 V 18 M 112 V 19 R 113 I 20 L 114 H 21 E 115 T 22 P 116 S 23 V 117 P 24 G 118 G 25 S 119 A 26 A 120 A 27 S 121 Q 28 S 122 L 29 I 123 I 30 V 124 A 31 Y 125 R 32 R 126 L 33 L 127 L 34 Y 128 D 35 K 129 S 36 E 130 L 37 N 131 G 38 G 132 K 39 I 139 A 40 A 140 E 41 G 141 G 42 V 142 I 43 M 143 L 44 L 144 G 45 S 145 T 46 G 146 I 47 L 147 A 48 I 148 G 49 S 149 D 50 D 150 D 51 T 151 T 52 L 152 I 53 L 153 F 54 L 154 T 55 K 155 T 56 S 156 P 57 P 157 A 58 T 158 N 59 T 159 G 60 H 160 F 61 A 161 T 62 S 162 V 63 D 163 K 64 P 164 D 65 A 165 L 66 V 166 Y 67 A 167 E 68 E 168 A 69 D 169 I 70 L 170 L 71 A 171 E 72 K 172 L 73 I 173 F 74 A 174 D 75 G 175 Q 76 V 176 E 77 D 177 L 78 L 178 TER END --simple mime boundary-- From farmer@cse.ucsc.edu Fri May 12 13:14:02 2000 Return-Path: Received: from alpha.cse.ucsc.edu (alpha.cse.ucsc.edu [128.114.48.14]) by cyborg.bioinfo.pl (8.9.3/8.8.7) with SMTP id NAA09850 for Message-Id: <200005121117.EAA32736@alpha.cse.ucsc.edu> Subject: T0087(target 99 secondary structure prediction) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0087.target99@cafasp.bioinfo.pl --simple mime boundary Content-type: text/plain; charset=us-ascii The following is the Target99 secondary structure prediction in the formats you requested. Citation: K. Karplus, C. Barrett, and R. Hughey, Hidden Markov Models for Detecting Remote Protein Homologies, Bioinformatics, 1998, vol. 14, no. 10, pp. 846-856. http://www.cse.ucsc.edu/resesarch/compbio/HMM-apps -------------------------------------------------------- For questions or problems, please see the SAM-T99 FAQ at http://www.cse.ucsc.edu/research/compbio/HMM-apps/sam-t99-faq.html or email us at sam-info@cse.ucsc.edu --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results.t99secstr.fasta' Content-Disposition: attachment; filename="t99-results.t99secstr.fasta" >T0087 LLLEEEEELLLLLLLHHHHHHHHHHHHHHLLLLLEEEELLLLLHHHHHHHHHHHLLLLLLLLLLLLLLLLEEEEELLLLLLHLHLLLLLLLEEEEELLLLLLLLLLLLLLEEELLLLLLHHHHHHHHHHHHLLLLLHHHHHHHHHHHHHLLLLLLLLLLLHHHHHHHHHHHHHHLLLHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHEELLLLLLLEEEEEEELHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEELLLLLHHHHHHHHLHHHHHHHHLLLLLLLLLLLHLLHHLLHHHHHHHHHHHHLL --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results.t99secstr.casp.ss' Content-Disposition: attachment; filename="t99-results.t99secstr.casp.ss" PFRMAT SS TARGET T0087 AUTHOR UCSC Target99 server METHOD This prediction was derived from the following methods METHOD by averaging the corresponding probabilities: METHOD Method 0: METHOD TARGET T0087 METHOD Using neural net overrep-2260-IDaa13-5-9-7-10-5-9-11-ehl-seeded2-trained.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 9 METHOD 7 10 METHOD 5 9 METHOD 11 3 (1 EHL ) METHOD The input amino acid frequencies were determined from METHOD alignment /projects/compbio/tmp/hmm-target99-alpha-8086/target-align-8086.a2m METHOD with weighted counts, using EntropyWeight(1.4 bits/column, 10) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 27.037 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: T0087 METHOD model_file: ./tmp.alpha.23167/model.mod METHOD database_files: /projects/compbio/bin/scripts/hmm-target99-dir/pcc/data/overrep-2260.verify.mixed.seq /projects/compbio/bin/scripts/hmm-target99-dir/pcc/data/overrep-2260.verify.mixed.2d METHOD scoring_mode: local METHOD null_model: reverse METHOD scoring_algorithm: EM METHOD adjust_score: 2 METHOD date: Fri May 12 04:14:25 2000 METHOD Method 2: METHOD ###begin 0 METHOD METHOD Protein secondary structure prediction by universal HMM METHOD HMM file: /projects/compbio/bin/scripts/hmm-target99-dir/pcc/scripts/gdac.test.initreest.38state.abb.isites.gd.updated.ghmm-128reest-1-128-105-0.07gd METHOD Alignment file: /projects/compbio/tmp/hmm-target99-alpha-8086/target-align-8086.a2m METHOD METHOD guide seq name: T0087 METHOD ###end 0 MODEL 1 M C 0.658 S C 0.633 K C 0.437 I E 0.669 L E 0.73 V E 0.739 F E 0.694 G E 0.561 H C 0.514 Q C 0.669 N C 0.805 P C 0.771 D C 0.787 S C 0.508 D C 0.489 A H 0.616 I H 0.678 G H 0.678 S H 0.709 S H 0.751 M H 0.754 A H 0.751 Y H 0.763 A H 0.766 Y H 0.771 L H 0.758 K H 0.751 R H 0.711 Q H 0.638 L C 0.484 G C 0.658 V C 0.672 D C 0.603 A C 0.449 Q E 0.54 A E 0.616 V E 0.611 A E 0.527 L C 0.47 G C 0.605 N C 0.688 P C 0.645 N C 0.654 E H 0.485 E H 0.512 T H 0.581 A H 0.611 F H 0.598 V H 0.603 L H 0.597 D H 0.6 Y H 0.589 F H 0.519 G H 0.448 I C 0.444 Q C 0.482 A C 0.535 P C 0.531 P C 0.481 V C 0.439 V C 0.437 K C 0.403 S C 0.436 A C 0.433 Q C 0.523 A C 0.461 E C 0.451 G C 0.474 A C 0.47 K C 0.422 Q E 0.519 V E 0.704 I E 0.752 L E 0.743 T E 0.655 D C 0.499 H C 0.679 N C 0.667 E C 0.631 F C 0.528 Q C 0.459 Q H 0.425 S C 0.418 I H 0.421 A C 0.46 D C 0.474 I C 0.451 R C 0.517 E C 0.513 V C 0.527 E C 0.496 V E 0.432 V E 0.562 E E 0.62 V E 0.637 V E 0.525 D C 0.475 H C 0.578 H C 0.583 R C 0.584 V C 0.58 A C 0.59 N C 0.587 F C 0.525 E C 0.486 T C 0.506 A C 0.541 N C 0.612 P C 0.57 L C 0.435 Y E 0.368 M E 0.463 R E 0.413 L C 0.465 E C 0.531 P C 0.542 V C 0.509 G C 0.555 S C 0.456 A H 0.639 S H 0.708 S H 0.722 I H 0.738 V H 0.755 Y H 0.765 R H 0.778 L H 0.77 Y H 0.764 K H 0.751 E H 0.7 N H 0.472 G C 0.631 V C 0.637 A C 0.615 I C 0.571 P C 0.601 K H 0.664 E H 0.691 I H 0.7 A H 0.709 G H 0.702 V H 0.697 M H 0.689 L H 0.659 S H 0.594 G H 0.543 L H 0.512 I H 0.477 S H 0.438 D C 0.49 T C 0.509 L C 0.499 L C 0.486 L C 0.481 K C 0.512 S C 0.562 P C 0.662 T C 0.651 T C 0.656 H C 0.677 A H 0.589 S H 0.611 D H 0.665 P H 0.77 A H 0.782 V H 0.789 A H 0.819 E H 0.826 D H 0.818 L H 0.806 A H 0.775 K H 0.751 I H 0.712 A H 0.495 G C 0.613 V C 0.622 D C 0.652 L H 0.699 Q H 0.735 E H 0.744 Y H 0.746 G H 0.75 L H 0.762 A H 0.762 M H 0.745 L H 0.709 K H 0.693 A H 0.581 G H 0.491 T C 0.502 N C 0.473 L C 0.465 A C 0.47 S C 0.476 K C 0.485 T C 0.486 A H 0.725 A H 0.761 Q H 0.765 L H 0.756 V H 0.741 D H 0.711 I H 0.64 D H 0.572 A H 0.559 K H 0.488 T H 0.41 F E 0.365 E E 0.4 L C 0.376 N C 0.505 G C 0.567 S C 0.524 Q C 0.445 V C 0.403 R C 0.431 V E 0.381 A E 0.432 Q E 0.506 V E 0.542 N E 0.556 T E 0.523 V E 0.429 D C 0.548 I H 0.512 N H 0.575 E H 0.624 V H 0.623 L H 0.611 E H 0.619 R H 0.686 Q H 0.705 N H 0.739 E H 0.737 I H 0.751 E H 0.782 E H 0.79 A H 0.782 I H 0.765 K H 0.761 A H 0.745 S H 0.727 Q H 0.705 A H 0.672 A H 0.548 N C 0.507 G C 0.548 Y C 0.479 S E 0.391 D E 0.541 F E 0.607 V E 0.633 L E 0.62 M E 0.569 I E 0.515 T E 0.392 D C 0.504 I C 0.407 L C 0.417 N C 0.464 S C 0.483 N H 0.448 S H 0.499 E H 0.534 I H 0.547 L H 0.541 A H 0.529 L H 0.504 G H 0.432 N C 0.435 N H 0.559 T H 0.62 D H 0.674 K H 0.669 V H 0.647 E H 0.664 A H 0.64 A H 0.579 F C 0.418 N C 0.566 F C 0.54 T C 0.475 L C 0.503 K C 0.579 N C 0.602 N C 0.578 H C 0.445 A C 0.358 F C 0.357 L H 0.385 A C 0.409 G C 0.418 A H 0.4 V H 0.398 S C 0.403 R C 0.479 K H 0.45 K H 0.505 Q H 0.471 V H 0.511 V H 0.583 P H 0.628 Q H 0.666 L H 0.667 T H 0.671 E H 0.664 S H 0.614 F H 0.441 N C 0.589 G C 0.663 END --simple mime boundary--