From farmer@cse.ucsc.edu Tue May 9 19:53:09 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 TAA01021 for Message-Id: <200005091756.KAA12026@alpha.cse.ucsc.edu> Subject: T1001(target 99 alignment) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T1001.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" >T1001 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMIREGFVEQNEI PEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRYLFT SSTLTRDFIEIGRDAGLWGRRSRLRLSGKPLLLTELFLPASPLY >gi|281803|pir||S25660_39:202 4-hydroxybenzoate synthetase - Escherichia coligi|43234|emb|CAA40681.1| (X57434) 4-hydroxybenzoate synthetase [Escherichia coli]gi|396374|gb|AAC43133.1| (U00006) chorismate lyase [Escherichia coli]gi|1790472|gb|AAC77009.1| (AE000477) chorismate lyase [Escherichia coli] mrllrfccvldhlicftspvntflrynaftlcngefgmSHPALTQLRALR YCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMIREGFVEQNEIPE ELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLSGPELALQKLGKT PLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKPLLLTELFLPASP LY >gi|136659|sp|P26602|UBIC_ECOLI_2:165 CHORISMATE--PYRUVATE LYASEgi|43231|emb|CAA47181.1| (X66619) chorismate-pyruvate lyase [Escherichia coli]gi|148100|gb|AAA24711.1| (M93136) chorismate lyase [Escherichia coli]gi|148107|gb|AAA24716.1| (M93413) chorismate lyase [Escherichia coli]gi|347888|gb|AAA17027.1| (M96268) chorismate lyase [Escherichia coli]gi|450008|prf||1920311A chorismate-pyruvate lyase [Escherichia coli] mSHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTM IREGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTL SGPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGK PLLLTELFLPASPLY >gi|6014666|gb|AAF01449.1|AF187880_4_8:180 (AF187880) unknown [Pseudomonas sp. YH102] mevayrfSQPHLEWNSYGHWRSSIAAT---QREWLFDRSSLTRRLRTLsD NEFEVIPLREA--AGPMLPEECRvlGLQPGVTGWIREVYLAGFGRPWVYA RSVISHCDVEGSDSALLQLGNIPLGSLLFGENPYKRSEIEVCRYPdacna ssrpayPLWARRSVFSRRQSRVLVHEMFLPALWEEls >gi|7379648|emb|CAB84215.1|_2:156 (AL162754) hypothetical protein NMA0944 [Neisseria meningitidis] mEHLFEEWLPDLP--ADVSDGIGLPMSRLLKARSLTAALRALPHLFSVEL LKLG-----ELETECGGR------LVREVLLKLDGIPVVAARSECRIG-- SAFWQNILDCGTRPLGERLFQADlEGARSAFEFavfgeGCGRYFAARRSR FSHHGEEMLLTEYFLPELKRFig >gi|7225962|gb|AAF41147.1|_2:156 (AE002428) hypothetical protein [Neisseria meningitidis] mEHLFGKWLPDLP--AAISDGISLPMVRLLHTRSLTAALRALPHTFSVEL LKLG-----ELETECGGR------LVREVLLKLDRIPVVEARSECRIG-- SAFWQNILDCGTRPLGERLFQADlEGARSAFEFavageGCGRYFAARRSR FSRHGEEMLLTEYFLPELKRFig --simple mime boundary-- From farmer@cse.ucsc.edu Tue May 9 20:17:07 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 UAA01412 for Message-Id: <200005091820.LAA00021@alpha.cse.ucsc.edu> Subject: T1001(database hits) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T1001.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 1sesA -10.28 0.7583 --------- --------- -10.28 0.76 1cpt -8.49 4.541 --------- --------- -8.49 4.5 1be3A -8.37 5.12 --------- --------- -8.37 5.1 1tcoA -8.1 6.706 -8.1 6.7 --------- --------- : mol:protein length:375 Serine/Threonine Phosphatase B2 1qpoA -7.77 9.327 --------- --------- -7.77 9.3 1maeL -7.73 9.708 -7.73 9.7 --------- --------- : mol:protein length:124 Methylamine Dehydrogenase (Madh) (E.C. 1.4.9 1mafL -7.73 9.708 -7.73 9.7 --------- --------- : mol:protein length:124 Methylamine Dehydrogenase (Madh) (E.C. 1.4.9 2bbkL -7.73 9.708 -7.73 9.7 --------- --------- : mol:protein length:125 Methylamine Dehydrogenase (Madh) (E.C. 1.4.9 2bbkM -7.73 9.708 -7.73 9.7 --------- --------- : mol:protein length:125 Methylamine Dehydrogenase (Madh) (E.C. 1.4.9 2madL -7.73 9.708 -7.73 9.7 --------- --------- : mol:protein length:124 Methylamine Dehydrogenase (Madh) (E.C. 1.4.9 2mtaL -7.73 9.708 -7.73 9.7 --------- --------- : mol:protein length:125 Methylamine Dehydrogenase (E.C. 1.4.99.3) Co 1auiA -7.72 9.805 -7.72 9.8 --------- --------- : mol:protein length:521 Serine/Threonine Phosphatase 2B 1cg2A -7.72 9.805 --------- --------- -7.72 9.8 2bmhA -7.41 13.37 --------- --------- -7.41 13 1phg -7.09 18.4 --------- --------- -7.09 18 1oxa -6.82 24.1 --------- --------- -6.82 24 1bu7A -6.75 25.85 --------- --------- -6.75 26 4nosA -6.73 26.37 -6.73 26 --------- --------- : mol:protein length:427 Inducible Nitric Oxide Synthase 4nosB -6.73 26.37 -6.73 26 --------- --------- : mol:protein length:427 Inducible Nitric Oxide Synthase 4nosC -6.73 26.37 -6.73 26 --------- --------- : mol:protein length:427 Inducible Nitric Oxide Synthase --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results.t99pairwise.a2m' Content-Disposition: attachment; filename="t99-results.t99pairwise.a2m" >T1001 shpaltqlralryck----------------------------EIPALDP QLLDWLLLEDSMTKRFEQQGKTVSvtmiREGFVEQNEIPEELPLLPKESR YWLREILLCADGEPWLAGRTV------VPVStLSGPELALQKLGKTPLGr ylftsSTLTRDFIEIGRDAGLWGR-RSRLRLSGKPLLLTELFL------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------------------------------------------pas ply >1sesA mol:protein length:421 Seryl-tRNA Synthetase (E.C. 6.1.1.11) (Serin MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQELKKRLQEVQTE RNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQ VPLPPWPGAPVGGEEANREIKRVGGPPEFSFPPLDHVALMEKNGWWEPRI SQVSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREKAFL GTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILPYEALPLRYAG YAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLE NAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCS ALLDWQARRANLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDG RVRVPQALIPYMGKEVLEPC-g >T1001 shpALTQLRALRYCKEIPALDPQLLDWLLLEDSMtKRFEQQGKTVSVTMI --------------REGFVEQNEIPEELPLLPKESR-------------Y WLREILLCADGEPWLAGRTVVPvSTLSGPELAL----------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------------qklgktplgrylftsstltrdfieigrdaglwg rrsrlrlsgkpllltelflpasply >1cpt mol:protein length:412 Cytochrome P450-Terp - Chain _ md--ARATIPEHIARTVILPQGYADDEVIYPAFKWLRDEQPLAMAHIEGY DPMWIATKHADVMQIGKQPGLFSNAEGSEILYDQNNEAFMRSISGGCPHV IDSLTSMDPPTHTAYRGLTLNWFQPASIRKLEENIRRIAQASVQRLLDFD GECDFMTDCALYYPLHVVMTALGVPEDDEPLMLKLTQDFFGVEAARRFHE TIATFYDYFNGFTVDRRSCPKDDVMSLLANSKLDGNYIDDKYINAYYVAI ATAGHDTTSSSSGGAIIGLSRNPEQLALAKSDPALIPRLVDEAVRWTAPV KSFMRTALADTEVRGQNIKRGDRIMLSYPSANRDEEVFSNPDEFDITRFP NRHLGFGWGAHMCLGQHLAKLEMKIFFEELLPKLKSVELSGPPRLVATNF VGGPKNVPIRFTK-a >T1001 shpaltqlralryckeipaldpqlldwllledsmtkrfeqqgktvsvtmi regfveq------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------------------NEIPEELPLLPK----ESRYWLREILL CADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRYLF---TSSTLTRD FIEIGRDAGL---------------------------------------- -------------------------------------------------- -------------------------------------------------- ---wgrrsrlrlsgkpllltelflpasply >1be3A mol:protein length:446 Cytochrome Bc1 Complex TATYAQALQSVPETQVSQLDNGLRVASEQSSQPTCTVGVWIDAGSRYESE KNNGAGYFVEHLAFKGTKNRPGNALEKEVESMGAHLNAYSTREHTAYYIK ALSKDLPKAVELLADIVQNCSLEDSQIEKERDVILQELQENDTSMRDVVF NYLHATAFQGTPLAQSVEGPSENVRKLSRADLTEYLSRHYKAPRMVLAAA GGLEHRQLLDLAQKHFSGLSGTYDEDAVPTLSPCRFTGSQICHREDGLPL AHVAIAVEGPGWAHPDNVALQVANAIIGHYDCTYGGGAHLSSPLASIAAT NKLCQSFQTFNICYADTGLLGAHFVCDHMSIDDMMFVLQGQWMRLCTSAT ESEVLRGKNLLRNALVSHLDGTTPVCEDIGRSLLTYGRRIPLAEWESRIA EVDARVVREVCSKYFYDQCPAVAGFGPIEQLPDYNRIRSGMFWLRF >T1001 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMI REGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLS GPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKP LLLTELFLPASPLY >1tcoA mol:protein length:375 Serine/Threonine Phosphatase B2 vkavpfppshrltakevfdndgkprvdilkahlmkegrleetvalriite gasilrqeknlldidapvtvcgdihgqffdlmklfevggspant------ -------------------------------------------------- -------------------------------------------------- ---------RYLFLGDYVDRGYFSIECVLYLWA----------------- --------lkilypktlfllrgnhecrhlteyftfkqeckikyservyda cmdafdclplaalmnqqflcvhgglspeintlddirkldrfkeppaygpm cdilwsdpledfgnektqehfthntvrgcsyfysypavceflqhnnllsi lraheaqdagyrmyrksqttgfpslitifsapnyldvynnkaavlkyenn vmnirqfncsphpywlpnfmdvftwslpfvgekvtemlvnvlnicsddel gseedgfdgataaar >T1001 shpaltqlralryckeipaldpqlldwllledsmtkrfeqqgktvsvtmi regfveqneipeelpllpkesry--------------------------- ------------------------------------------WLREILLC ADGEPWLAGRtvvPVSTLSGPELALQKLGKTPLGRYLFTSSTLTR----- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----------dfieigrdaglwgrrsrlrlsgkpllltelflpasply >1qpoA mol:protein length:284 Quinolinate Acid Phosphoribosyl Transferase g-LSDWELAAARAAIARGLDEDLRYGPDVTTLATVPASATTTASLVTREA GVVAGLDVALLTLNEVLGTNGYRVLDRVEDGARVPPGEALMTLEAQTRGL LTAERTMLNLVGHLSGIATATAAWVDAVRGTKAKIRDTRKTLPGLRALQK YAVRTGGGVNHRLGLGDAALIKDNHVAAAGSVVDALRAVRNAAPDLPCEV EVDSLEQLDAVLPEKPELILLDNFAVWQTQTAVQRRDSRAPTVMLESSGG LSLQTAATYAETGVDYLAVGALTHSVRVLDIGLDM >T1001 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMI REGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLS GPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKP LLLTELFLPASPLY >1maeL mol:protein length:124 Methylamine Dehydrogenase (Madh) (E.C. 1.4.9 vdprakwqpqdndiqacdywrhcsidgnicdcsggsltncp--------- -------------------------------------------------- -----PGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTE GELPVYRPEFAND------------------------------------- -----iiwcfgaeddamtyhctispivgka >T1001 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMI REGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLS GPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKP LLLTELFLPASPLY >1mafL mol:protein length:124 Methylamine Dehydrogenase (Madh) (E.C. 1.4.9 vdprakwqpqdndiqacdywrhcsidgnicdcsggsltncp--------- -------------------------------------------------- -----PGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTE GELPVYRPEFAND------------------------------------- -----iiwcfgaeddamtyhctispivgka >T1001 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMI REGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLS GPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKP LLLTELFLPASPLY >2bbkL mol:protein length:125 Methylamine Dehydrogenase (Madh) (E.C. 1.4.9 tdprakwvpqdndiqacdywrhcsidgnicdcsggsltncp--------- -------------------------------------------------- -----PGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTE GELPVYRPEFAND------------------------------------- -----iiwcfgaeddamtyhctispivgkas >T1001 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMI REGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLS GPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKP LLLTELFLPASPLY >2bbkM mol:protein length:125 Methylamine Dehydrogenase (Madh) (E.C. 1.4.9 tdprakwvpqdndiqacdywrhcsidgnicdcsggsltncp--------- -------------------------------------------------- -----PGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTE GELPVYRPEFAND------------------------------------- -----iiwcfgaeddamtyhctispivgkas >T1001 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMI REGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLS GPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKP LLLTELFLPASPLY >2madL mol:protein length:124 Methylamine Dehydrogenase (Madh) (E.C. 1.4.9 vdprakwqpqdndiqacdywrhcsidgnicdcsggsltncp--------- -------------------------------------------------- -----PGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTE GELPVYRPEFAND------------------------------------- -----iiwcfgaeddamtyhctispivgka >T1001 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMI REGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLS GPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKP LLLTELFLPASPLY >2mtaL mol:protein length:125 Methylamine Dehydrogenase (E.C. 1.4.99.3) Co tdprakwvpqdndiqacdywrhcsidgnicdcsggsltncp--------- -------------------------------------------------- -----PGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTE GELPVYRPEFAND------------------------------------- -----iiwcfgaeddamtyhctispivgkas >T1001 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMI REGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLS GPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKP LLLTELFLPASPLY >1auiA mol:protein length:521 Serine/Threonine Phosphatase 2B msepkaidpklsttdrvvkavpfppshrltakevfdndgkprvdilkahl mkegrleesvalriitegasilrqeknlldidapvtvcgdihgqffdlmk lfevggspant--------------------------------------- -------------------------------------------------- --------------------------RYLFLGDYVDRGYFSIECVLYLWA -------------------------lkilypktlfllrgnhecrhlteyf tfkqeckikyservydacmdafdclplaalmnqqflcvhgglspeintld dirkldrfkeppaygpmcdilwsdpledfgnektqehfthntvrgcsyfy sypavceflqhnnllsilraheaqdagyrmyrksqttgfpslitifsapn yldvynnkaavlkyennvmnirqfncsphpywlpnfmdvftwslpfvgek vtemlvnvlnicsddelgseedgfdgataaarkevirnkiraigkmarvf svlreesesvltlkgltptgmlpsgvlsggkqtlqsatveaieadeaikg fspqhkitsfeeakgldrinermpprrdampsdanlnsinkaltsetngt dsngsnssniq >T1001 shpaltqlralryckeip-------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------------------------ALDPQLLDWLLLEDSMTKRFE QQGKTVSVTMIReGFVEQNEIPEELPLL---------------------- -------------------------------------------------- -------------------------------------------------- --------pkesrywlreillcadgepwlagrtvvpvstlsgpelalqkl gktplgrylftsstltrdfieigrdaglwgrrsrlrlsgkpllltelflp asply >1cg2A mol:protein length:393 Carboxypeptidase G2 alaq-KRDNVLFQAATDEQPAVIKTLEKLVNIETGTGDAEGIAAAGNFLE AELKNLGFTVTRSKSAGLVVGDNIVGKIKGRGGKNLLLMSHMDTVYLKGI LAKAPFRVEGDKAYGPGIADDKGGNAVILHTLKLLKEYGVRDYGTITVLF NTDEEKGSFGSRDLIQEEAKLADYVLSFEPTSAGDEKLSLGTSGIAYVQV NITGKASHAGAAPELGVNALVEASDLVLRTMNIDDKAKNLRFNWTIAKAG NVSNIIPASATLNADVRYARNEDFDAAMKTLEERAQQKKLPEADVKVIVT RGRPAFNAGEGGKKLVDKAVAYYKEAGGTLGVEERTGGGTDAAYAALSGK PVIESLGLPGFGYHSDKAEYVDISAIPRRLYMAARLIMDL---gagk >T1001 shpaltq-LRALRYCKEIPALDPQLLDW-LLLEDSMTKRFEQQGKTVSVT M-------------IREGFVEQNEIPEELPLLPKESRYWLRE-ILLCADG EPWLAGRTVVpVSTLSGPEL------------------------------ -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------alqklgktplgrylftsstltrdfieigrdaglwgrr srlrlsgkpllltelflpasply >2bmhA mol:protein length:455 Cytochrome P450 (Bm-3) (E.C. 1.14.14.1) (Hem TIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTR YLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAH NILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTL DTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDE NKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLD DENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVD PVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKG DELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRAC IGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEG------- -----fvvkakskkipl >T1001 shpaltqlralrycke--------IPALDPQLLDWLLLEdSMTKRFEQQG KTVSVTM---------------------IREGFvEQNEIPEEL-PLLPKE SRYWLREILLCADGEPWLAGRTVV-------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------------------pvstlsgpelalqklgktplgrylfts stltrdfieigrdaglwgrrsrlrlsgkpllltelflpasply >1phg mol:protein length:414 Cytochrome P450-Cam (E.C. 1.14.15.1) (Campho ttetiqsnaNLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNV PDLVWTRCNGGHWIATRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIP TSMDPPEQRQFRALANQVVGMPVVDKLENRIQELACSLIESLRPQGQCNF TEDYAEPFPIRIFMLLAGLPEEDIPHLKYLTDQMTRPDGSMTFAEAKEAL YDYLIPIIEQRRQKPGTDAISIVANGQVNGRPITSDEAKRMCGLLLVGGL DTVVNFLSFSMEFLAKSPEHRQELIERPERIPAACEELLRRFSLVADGRI LTSDYEFHGVQLKKGDQILLPQMLSGLDERENACPMHVDFSRQKVSHTTF GHGSHLCLGQHLARREIIVTLKEWLTRIPDFSIAPGAQIQHKSGIVSGVQ ALPLVWDP------attkav >T1001 shpaltqlralryckeipaldpqlldwllledsmtkrfeqqgktvsvt-- -------------------------------------------MIREGFv EQNEIPEELP--------------LLPKESRYWLREILLCADGEPWLAGR TVVPvSTLSGPELA------------------------------------ -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ---lqklgktplgrylftsstltrdfieigrdaglwgrrsrlrlsgkpll ltelflpasply >1oxa mol:protein length:403 Cytochrome P450 Eryf atvpdlesdsf-----------HVDWYSTYAELRETAPVTPVRFLGQDAW LVTGYDEAKAALSDLRLSSDPKKKYPGVEVEFPAYLGFPEDVRNYFATNM GTSDPPTHTRLRKLVSQEFTVRRVEAMRPRVEQITAELLDEVGDSGVVDI VDRFAHPLPIKVICELLGVDEAARGAFGRWSSEILVMDPERAEQRGQAAR EVVNFILDLVERRRTEPGDDLLSALISVQDDDDGRLSADELTSIALVLLL AGFEASVSLIGIGTYLLLTHPDQLALVRADPSALPNAVEEILRYIAPPET TTRFAAEEVEIGGVAIPQYSTVLVANGAANRDPSQFPDPHRFDVTRDTRG HLSFGQGIHFCMGRPLAKLEGEVALRALFGRFPALSLGIDADDVVWRRSL LLRGIDHLPVRL--dg >T1001 shpaltq-LRALRYCKEIPALDPQLLDW-LLLEDSMTKRFEQQGKTVSVT M-------------IREGFVEQNEIPEELPLLPKEsRYWLREILLCA--D GEPWLAGRTVVPvSTLSGPEL----------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- --------------alqklgktplgrylftsstltrdfieigrdaglwgr rsrlrlsgkpllltelflpasply >1bu7A mol:protein length:455 Cytochrome P450 ti--KEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRV TRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKK AHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRL TLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAY DENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEP LDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVL VDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLE KGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQR ACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEG----- -------fvvkakskkipl >T1001 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMI REGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLS GPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKP LLLTELFLPASPLY >4nosA mol:protein length:427 Inducible Nitric Oxide Synthase prhvriknwgsgmtfqdtlhhkakgiltcrsksclgsimtpksltrgprd kptppdellpqaiefvnqyygsfkeakieehlarveavtkeiettgtyql tgdelifatkqawrnaprcigriqwsnlqvfdarscstaremfehicrhv rystnngnirsaitvfpqrsdgkhdfrvwnaqliryagyqmpdgsirgdp anveftqlcidlgwkpkygrfdvvplvlqangrdpelfeippdlvlevam ehpkye-------------------------------------------- -----------------------------WFRELELKWYALPAVA----- -------------------------------------------------- --------------------nmllevgglefpgcpfngwymgteigvrdf cdvqrynileevgrrmglethklaslwkdqavveiniavihsfqkqnvti mdhhsaaesfmkymqneyrsrggcpadwiwlvppmsgsitpvfhqemlny vlspfyyyqveawkthvwqdekrrp >T1001 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMI REGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLS GPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKP LLLTELFLPASPLY >4nosB mol:protein length:427 Inducible Nitric Oxide Synthase prhvriknwgsgmtfqdtlhhkakgiltcrsksclgsimtpksltrgprd kptppdellpqaiefvnqyygsfkeakieehlarveavtkeiettgtyql tgdelifatkqawrnaprcigriqwsnlqvfdarscstaremfehicrhv rystnngnirsaitvfpqrsdgkhdfrvwnaqliryagyqmpdgsirgdp anveftqlcidlgwkpkygrfdvvplvlqangrdpelfeippdlvlevam ehpkye-------------------------------------------- -----------------------------WFRELELKWYALPAVA----- -------------------------------------------------- --------------------nmllevgglefpgcpfngwymgteigvrdf cdvqrynileevgrrmglethklaslwkdqavveiniavihsfqkqnvti mdhhsaaesfmkymqneyrsrggcpadwiwlvppmsgsitpvfhqemlny vlspfyyyqveawkthvwqdekrrp >T1001 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMI REGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLS GPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKP LLLTELFLPASPLY >4nosC mol:protein length:427 Inducible Nitric Oxide Synthase prhvriknwgsgmtfqdtlhhkakgiltcrsksclgsimtpksltrgprd kptppdellpqaiefvnqyygsfkeakieehlarveavtkeiettgtyql tgdelifatkqawrnaprcigriqwsnlqvfdarscstaremfehicrhv rystnngnirsaitvfpqrsdgkhdfrvwnaqliryagyqmpdgsirgdp anveftqlcidlgwkpkygrfdvvplvlqangrdpelfeippdlvlevam ehpkye-------------------------------------------- -----------------------------WFRELELKWYALPAVA----- -------------------------------------------------- --------------------nmllevgglefpgcpfngwymgteigvrdf cdvqrynileevgrrmglethklaslwkdqavveiniavihsfqkqnvti mdhhsaaesfmkymqneyrsrggcpadwiwlvppmsgsitpvfhqemlny vlspfyyyqveawkthvwqdekrrp --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 T1001 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 1sesA A 29 E 16 L 30 I 17 L 31 P 18 A 32 A 19 L 33 L 20 D 34 D 21 R 35 P 22 E 36 Q 23 V 37 L 24 Q 38 L 25 E 39 D 26 L 40 W 27 K 41 L 28 K 42 L 29 R 43 L 30 L 44 E 31 Q 45 D 32 E 46 S 33 V 47 M 34 Q 48 T 35 T 49 K 36 E 50 R 37 R 51 F 38 N 52 E 39 Q 53 Q 40 V 54 Q 41 A 55 G 42 K 56 K 43 R 57 T 44 V 58 V 45 P 59 S 46 K 60 R 51 A 61 E 52 P 62 G 53 P 63 F 54 E 64 V 55 E 65 E 56 K 66 Q 57 E 67 N 58 A 68 E 59 L 69 I 60 I 70 P 61 A 71 E 62 R 72 E 63 G 73 L 64 K 74 P 65 A 75 L 66 L 76 L 67 G 77 P 68 E 78 K 69 E 79 E 70 A 80 S 71 K 81 R 72 R 82 Y 73 L 83 W 74 E 84 L 75 E 85 R 76 A 86 E 77 L 87 I 78 R 88 L 79 E 89 L 80 K 90 C 81 E 91 A 82 A 92 D 83 R 93 G 84 L 94 E 85 E 95 P 86 A 96 W 87 L 97 L 88 L 98 A 89 L 99 G 90 Q 100 R 91 V 101 T 92 P 102 V 93 A 109 V 94 P 110 P 95 V 111 V 96 G 112 S 97 G 113 L 99 E 114 S 100 E 115 G 101 A 116 P 102 N 117 E 103 R 118 L 104 E 119 A 105 I 120 L 106 K 121 Q 107 R 122 K 108 V 123 L 109 G 124 G 110 G 125 K 111 P 126 T 112 P 127 P 113 E 128 L 114 F 129 G 115 S 130 S 122 F 131 T 123 P 132 L 124 P 133 T 125 L 134 R 126 D 135 D 127 H 136 F 128 V 137 I 129 A 138 E 130 L 139 I 131 M 140 G 132 E 141 R 133 K 142 D 134 N 143 A 135 G 144 G 136 W 145 L 137 W 146 W 138 E 147 G 139 P 148 R 140 I 150 R 141 S 151 S 142 Q 152 R 143 V 153 L 144 S 154 R 145 G 155 L 146 S 156 S 147 R 157 G 148 S 158 K 149 Y 159 P 150 A 160 L 151 L 161 L 152 K 162 L 153 G 163 T 154 D 164 E 155 L 165 L 156 A 166 F 157 L 167 L 158 TER END PFRMAT AL TARGET T1001 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 1cpt A 3 T 6 R 4 Q 7 A 5 L 8 T 6 R 9 I 7 A 10 P 8 L 11 E 9 R 12 H 10 Y 13 I 11 C 14 A 12 K 15 R 13 E 16 T 14 I 17 V 15 P 18 I 16 A 19 L 17 L 20 P 18 D 21 Q 19 P 22 G 20 Q 23 Y 21 L 24 A 22 L 25 D 23 D 26 D 24 W 27 E 25 L 28 V 26 L 29 I 27 L 30 Y 28 E 31 P 29 D 32 A 30 S 33 F 31 M 34 K 32 K 36 W 33 R 37 L 34 F 38 R 35 E 39 D 36 Q 40 E 37 Q 41 Q 38 G 42 P 39 K 43 L 40 T 44 A 41 V 45 M 42 S 46 A 43 V 47 H 44 T 48 I 45 M 49 E 46 I 50 M 61 R 51 Q 62 E 52 I 63 G 53 G 64 F 54 K 65 V 55 Q 66 E 56 P 67 Q 57 G 68 N 58 L 69 E 59 F 70 I 60 S 71 P 61 N 72 E 62 A 73 E 63 E 74 L 64 G 75 P 65 S 76 L 66 E 77 L 67 I 78 P 68 L 79 K 69 Y 80 E 70 D 81 S 71 Q 82 R 72 P 96 Y 73 H 97 W 74 V 98 L 75 I 99 R 76 D 100 E 77 S 101 I 78 L 102 L 79 T 103 L 80 S 104 C 81 M 105 A 82 D 106 D 83 P 107 G 84 P 108 E 85 T 109 P 86 H 110 W 87 T 111 L 88 A 112 A 89 Y 113 G 90 R 114 R 91 G 115 T 92 L 116 V 93 T 117 V 94 L 118 P 95 N 119 S 97 W 120 T 98 F 121 L 99 Q 122 S 100 P 123 G 101 A 124 P 102 S 125 E 103 I 126 L 104 R 127 A 105 K 128 L 106 TER END PFRMAT AL TARGET T1001 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 1be3A S 217 N 58 G 218 E 59 L 219 I 60 S 220 P 61 G 221 E 62 T 222 E 63 Y 223 L 64 D 224 P 65 E 225 L 66 D 226 L 67 A 227 P 68 V 228 K 69 P 233 E 70 C 234 S 71 R 235 R 72 F 236 Y 73 T 237 W 74 G 238 L 75 S 239 R 76 Q 240 E 77 I 241 I 78 C 242 L 79 H 243 L 80 R 244 C 81 E 245 A 82 D 246 D 83 G 247 G 84 L 248 E 85 P 249 P 86 L 250 W 87 A 251 L 88 H 252 A 89 V 253 G 90 A 254 R 91 I 255 T 92 A 256 V 93 V 257 V 94 E 258 P 95 G 259 V 96 P 260 S 97 G 261 T 98 W 262 L 99 A 263 S 100 H 264 G 101 P 265 P 102 D 266 E 103 N 267 L 104 V 268 A 105 A 269 L 106 L 270 Q 107 Q 271 K 108 V 272 L 109 A 273 G 110 N 274 K 111 A 275 T 112 I 276 P 113 I 277 L 114 G 278 G 115 H 279 R 116 Y 280 Y 117 D 281 L 118 C 282 F 119 G 286 T 120 G 287 S 121 A 288 S 122 H 289 T 123 L 290 L 124 S 291 T 125 S 292 R 126 P 293 D 127 L 294 F 128 A 295 I 129 S 296 E 130 I 297 I 131 A 298 G 132 A 299 R 133 T 300 D 134 N 301 A 135 K 302 G 136 L 303 L 137 TER END PFRMAT AL TARGET T1001 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 1tcoA R 95 R 116 Y 96 Y 117 L 97 L 118 F 98 F 119 L 99 T 120 G 100 S 121 D 101 S 122 Y 102 T 123 V 103 L 124 D 104 T 125 R 105 R 126 G 106 D 127 Y 107 F 128 F 108 I 129 S 109 E 130 I 110 I 131 E 111 G 132 C 112 R 133 V 113 D 134 L 114 A 135 Y 115 G 136 L 116 L 137 W 117 W 138 A 118 G 139 TER END PFRMAT AL TARGET T1001 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 1qpoA G 70 W 74 Y 71 L 75 R 72 R 76 V 73 E 77 L 74 I 78 D 75 L 79 R 76 L 80 V 77 C 81 E 78 A 82 D 79 D 83 G 80 G 84 A 81 E 85 R 82 P 86 V 83 W 87 P 84 L 88 P 85 A 89 G 86 G 90 E 87 R 91 A 88 P 95 L 89 V 96 M 90 S 97 T 91 T 98 L 92 L 99 E 93 S 100 A 94 G 101 Q 95 P 102 T 96 E 103 R 97 L 104 G 98 A 105 L 99 L 106 L 100 Q 107 T 101 K 108 A 102 L 109 E 103 G 110 R 104 K 111 T 105 T 112 M 106 P 113 L 107 L 114 N 108 G 115 L 109 R 116 V 110 Y 117 G 111 L 118 H 112 F 119 L 113 T 120 S 114 S 121 G 115 S 122 I 116 T 123 A 117 L 124 T 118 T 125 A 119 R 126 TER END PFRMAT AL TARGET T1001 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 1maeL P 42 P 65 G 43 L 66 T 44 L 67 K 45 P 68 L 46 K 69 A 47 E 70 T 48 S 71 A 49 R 72 S 50 Y 73 W 51 W 74 V 52 L 75 A 53 R 76 S 54 E 77 C 55 I 78 Y 56 L 79 N 57 L 80 P 58 C 81 T 59 A 82 D 60 D 83 G 61 G 84 Q 62 E 85 S 63 P 86 Y 64 W 87 L 65 L 88 I 66 A 89 A 67 G 90 Y 68 R 91 R 69 T 92 D 70 V 93 C 71 V 94 C 72 P 95 G 73 V 96 Y 74 S 97 N 75 T 98 V 76 L 99 S 77 S 100 G 78 G 101 R 79 P 102 C 80 E 103 P 81 L 104 C 82 A 105 L 83 L 106 N 84 Q 107 T 85 K 108 E 86 L 109 G 87 G 110 E 88 K 111 L 89 T 112 P 90 P 113 V 91 L 114 Y 92 G 115 R 93 R 116 P 94 Y 117 E 95 L 118 F 96 F 119 A 97 T 120 N 98 S 121 D 99 S 122 TER END PFRMAT AL TARGET T1001 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 1mafL P 42 P 65 G 43 L 66 T 44 L 67 K 45 P 68 L 46 K 69 A 47 E 70 T 48 S 71 A 49 R 72 S 50 Y 73 W 51 W 74 V 52 L 75 A 53 R 76 S 54 E 77 C 55 I 78 Y 56 L 79 N 57 L 80 P 58 C 81 T 59 A 82 D 60 D 83 G 61 G 84 Q 62 E 85 S 63 P 86 Y 64 W 87 L 65 L 88 I 66 A 89 A 67 G 90 Y 68 R 91 R 69 T 92 D 70 V 93 C 71 V 94 C 72 P 95 G 73 V 96 Y 74 S 97 N 75 T 98 V 76 L 99 S 77 S 100 G 78 G 101 R 79 P 102 C 80 E 103 P 81 L 104 C 82 A 105 L 83 L 106 N 84 Q 107 T 85 K 108 E 86 L 109 G 87 G 110 E 88 K 111 L 89 T 112 P 90 P 113 V 91 L 114 Y 92 G 115 R 93 R 116 P 94 Y 117 E 95 L 118 F 96 F 119 A 97 T 120 N 98 S 121 D 99 S 122 TER END PFRMAT AL TARGET T1001 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 2bbkL P 42 P 65 G 43 L 66 T 44 L 67 K 45 P 68 L 46 K 69 A 47 E 70 T 48 S 71 A 49 R 72 S 50 Y 73 W 51 W 74 V 52 L 75 A 53 R 76 S 54 E 77 C 55 I 78 Y 56 L 79 N 57 L 80 P 58 C 81 T 59 A 82 D 60 D 83 G 61 G 84 Q 62 E 85 S 63 P 86 Y 64 W 87 L 65 L 88 I 66 A 89 A 67 G 90 Y 68 R 91 R 69 T 92 D 70 V 93 C 71 V 94 C 72 P 95 G 73 V 96 Y 74 S 97 N 75 T 98 V 76 L 99 S 77 S 100 G 78 G 101 R 79 P 102 C 80 E 103 P 81 L 104 C 82 A 105 L 83 L 106 N 84 Q 107 T 85 K 108 E 86 L 109 G 87 G 110 E 88 K 111 L 89 T 112 P 90 P 113 V 91 L 114 Y 92 G 115 R 93 R 116 P 94 Y 117 E 95 L 118 F 96 F 119 A 97 T 120 N 98 S 121 D 99 S 122 TER END PFRMAT AL TARGET T1001 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 2bbkM P 42 P 65 G 43 L 66 T 44 L 67 K 45 P 68 L 46 K 69 A 47 E 70 T 48 S 71 A 49 R 72 S 50 Y 73 W 51 W 74 V 52 L 75 A 53 R 76 S 54 E 77 C 55 I 78 Y 56 L 79 N 57 L 80 P 58 C 81 T 59 A 82 D 60 D 83 G 61 G 84 Q 62 E 85 S 63 P 86 Y 64 W 87 L 65 L 88 I 66 A 89 A 67 G 90 Y 68 R 91 R 69 T 92 D 70 V 93 C 71 V 94 C 72 P 95 G 73 V 96 Y 74 S 97 N 75 T 98 V 76 L 99 S 77 S 100 G 78 G 101 R 79 P 102 C 80 E 103 P 81 L 104 C 82 A 105 L 83 L 106 N 84 Q 107 T 85 K 108 E 86 L 109 G 87 G 110 E 88 K 111 L 89 T 112 P 90 P 113 V 91 L 114 Y 92 G 115 R 93 R 116 P 94 Y 117 E 95 L 118 F 96 F 119 A 97 T 120 N 98 S 121 D 99 S 122 TER END PFRMAT AL TARGET T1001 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 2madL P 42 P 65 G 43 L 66 T 44 L 67 K 45 P 68 L 46 K 69 A 47 E 70 T 48 S 71 A 49 R 72 S 50 Y 73 W 51 W 74 V 52 L 75 A 53 R 76 S 54 E 77 C 55 I 78 Y 56 L 79 N 57 L 80 P 58 C 81 T 59 A 82 D 60 D 83 G 61 G 84 Q 62 E 85 S 63 P 86 Y 64 W 87 L 65 L 88 I 66 A 89 A 67 G 90 Y 68 R 91 R 69 T 92 D 70 V 93 C 71 V 94 C 72 P 95 G 73 V 96 Y 74 S 97 N 75 T 98 V 76 L 99 S 77 S 100 G 78 G 101 R 79 P 102 C 80 E 103 P 81 L 104 C 82 A 105 L 83 L 106 N 84 Q 107 T 85 K 108 E 86 L 109 G 87 G 110 E 88 K 111 L 89 T 112 P 90 P 113 V 91 L 114 Y 92 G 115 R 93 R 116 P 94 Y 117 E 95 L 118 F 96 F 119 A 97 T 120 N 98 S 121 D 99 S 122 TER END PFRMAT AL TARGET T1001 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 2mtaL P 42 P 65 G 43 L 66 T 44 L 67 K 45 P 68 L 46 K 69 A 47 E 70 T 48 S 71 A 49 R 72 S 50 Y 73 W 51 W 74 V 52 L 75 A 53 R 76 S 54 E 77 C 55 I 78 Y 56 L 79 N 57 L 80 P 58 C 81 T 59 A 82 D 60 D 83 G 61 G 84 Q 62 E 85 S 63 P 86 Y 64 W 87 L 65 L 88 I 66 A 89 A 67 G 90 Y 68 R 91 R 69 T 92 D 70 V 93 C 71 V 94 C 72 P 95 G 73 V 96 Y 74 S 97 N 75 T 98 V 76 L 99 S 77 S 100 G 78 G 101 R 79 P 102 C 80 E 103 P 81 L 104 C 82 A 105 L 83 L 106 N 84 Q 107 T 85 K 108 E 86 L 109 G 87 G 110 E 88 K 111 L 89 T 112 P 90 P 113 V 91 L 114 Y 92 G 115 R 93 R 116 P 94 Y 117 E 95 L 118 F 96 F 119 A 97 T 120 N 98 S 121 D 99 S 122 TER END PFRMAT AL TARGET T1001 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 1auiA R 112 R 116 Y 113 Y 117 L 114 L 118 F 115 F 119 L 116 T 120 G 117 S 121 D 118 S 122 Y 119 T 123 V 120 L 124 D 121 T 125 R 122 R 126 G 123 D 127 Y 124 F 128 F 125 I 129 S 126 E 130 I 127 I 131 E 128 G 132 C 129 R 133 V 130 D 134 L 131 A 135 Y 132 G 136 L 133 L 137 W 134 W 138 A 135 G 139 TER END PFRMAT AL TARGET T1001 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 1cg2A G 215 A 19 V 216 L 20 N 217 D 21 A 218 P 22 L 219 Q 23 V 220 L 24 E 221 L 25 A 222 D 26 S 223 W 27 D 224 L 28 L 225 L 29 V 226 L 30 L 227 E 31 R 228 D 32 T 229 S 33 M 230 M 34 N 231 T 35 I 232 K 36 D 233 R 37 D 234 F 38 K 235 E 39 A 236 Q 40 K 237 Q 41 N 238 G 42 L 239 K 43 R 240 T 44 F 241 V 45 N 242 S 46 W 243 V 47 T 244 T 48 I 245 M 49 A 246 I 50 K 247 R 51 A 248 G 53 G 249 F 54 N 250 V 55 V 251 E 56 S 252 Q 57 N 253 N 58 I 254 E 59 I 255 I 60 P 256 P 61 A 257 E 62 S 258 E 63 A 259 L 64 T 260 P 65 L 261 L 66 N 262 L 67 TER END PFRMAT AL TARGET T1001 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 2bmhA I 2 L 8 K 3 R 9 E 4 A 10 M 5 L 11 P 6 R 12 Q 7 Y 13 P 8 C 14 K 9 K 15 T 10 E 16 F 11 I 17 G 12 P 18 E 13 A 19 L 14 L 20 K 15 D 21 N 16 P 22 L 17 Q 23 P 18 L 24 L 19 L 25 L 20 D 26 N 21 W 27 D 23 L 28 K 24 L 29 P 25 L 30 V 26 E 31 Q 27 D 32 A 28 S 33 L 29 M 34 M 30 T 35 K 31 K 36 I 32 R 37 A 33 F 38 D 34 E 39 E 35 Q 40 L 36 Q 41 G 37 G 42 E 38 K 43 I 39 T 44 F 40 V 45 K 41 S 46 F 42 V 47 E 43 T 48 A 44 M 49 I 58 I 50 K 59 R 51 E 60 E 52 A 61 G 53 C 62 F 54 D 63 V 55 E 64 E 56 S 65 Q 57 R 66 N 58 F 67 E 59 D 68 I 60 K 69 P 61 N 70 E 62 L 71 E 63 S 72 L 64 Q 73 P 65 A 74 L 66 L 75 L 67 K 76 P 68 F 77 K 69 V 78 E 70 R 79 S 71 D 80 R 72 F 81 Y 73 A 82 W 74 G 83 L 75 D 84 R 76 G 85 E 77 F 87 I 78 T 88 L 79 S 89 L 80 W 90 C 81 T 91 A 82 H 92 D 83 E 93 G 84 K 94 E 85 N 95 P 86 W 96 W 87 K 97 L 88 K 98 A 89 A 99 G 90 H 100 R 91 N 101 T 92 I 102 V 93 L 103 V 94 L 104 V 96 P 105 S 97 S 106 T 98 F 107 L 99 S 108 S 100 Q 109 G 101 Q 110 P 102 A 111 E 103 M 112 L 104 TER END PFRMAT AL TARGET T1001 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 1phg V 18 I 17 P 19 P 18 E 20 A 19 H 21 L 20 L 22 D 21 V 23 P 22 F 24 Q 23 D 25 L 24 F 26 L 25 D 27 D 26 M 28 W 27 Y 29 L 28 N 30 L 29 P 31 L 30 S 32 E 31 N 33 S 33 L 34 M 34 S 35 T 35 A 36 K 36 G 37 R 37 V 38 F 38 Q 39 E 39 E 40 Q 40 A 41 Q 41 W 42 G 42 A 43 K 43 V 44 T 44 L 45 V 45 Q 46 S 46 E 47 V 47 S 48 T 48 N 49 M 49 I 71 I 50 R 72 R 51 E 73 E 52 A 74 G 53 Y 75 F 54 E 76 E 56 D 77 Q 57 Y 78 N 58 R 79 E 59 H 80 I 60 F 81 P 61 S 82 E 62 S 83 E 63 E 84 L 64 P 86 P 65 F 87 L 66 I 88 L 67 P 89 P 68 R 90 K 69 E 91 E 70 A 92 S 71 G 93 R 72 E 94 Y 73 A 95 W 74 Y 96 L 75 D 97 R 76 F 98 E 77 I 99 I 78 P 100 L 79 T 101 L 80 S 102 C 81 M 103 A 82 D 104 D 83 P 105 G 84 P 106 E 85 E 107 P 86 Q 108 W 87 R 109 L 88 Q 110 A 89 F 111 G 90 R 112 R 91 A 113 T 92 L 114 V 93 A 115 V 94 TER END PFRMAT AL TARGET T1001 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 1oxa E 46 M 49 A 47 I 50 K 48 R 51 A 49 E 52 A 50 G 53 L 51 F 54 S 52 E 56 D 53 Q 57 L 54 N 58 R 55 E 59 L 56 I 60 S 57 P 61 S 58 E 62 D 59 E 63 P 60 L 64 K 61 P 65 G 76 L 66 F 77 L 67 P 78 P 68 E 79 K 69 D 80 E 70 V 81 S 71 R 82 R 72 N 83 Y 73 Y 84 W 74 F 85 L 75 A 86 R 76 T 87 E 77 N 88 I 78 M 89 L 79 G 90 L 80 T 91 C 81 S 92 A 82 D 93 D 83 P 94 G 84 P 95 E 85 T 96 P 86 H 97 W 87 T 98 L 88 R 99 A 89 L 100 G 90 R 101 R 91 K 102 T 92 L 103 V 93 V 104 V 94 S 105 P 95 Q 106 S 97 E 107 T 98 F 108 L 99 T 109 S 100 V 110 G 101 R 111 P 102 R 112 E 103 V 113 L 104 E 114 A 105 TER END PFRMAT AL TARGET T1001 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 1bu7A K 3 R 9 E 4 A 10 M 5 L 11 P 6 R 12 Q 7 Y 13 P 8 C 14 K 9 K 15 T 10 E 16 F 11 I 17 G 12 P 18 E 13 A 19 L 14 L 20 K 15 D 21 N 16 P 22 L 17 Q 23 P 18 L 24 L 19 L 25 L 20 D 26 N 21 W 27 D 23 L 28 K 24 L 29 P 25 L 30 V 26 E 31 Q 27 D 32 A 28 S 33 L 29 M 34 M 30 T 35 K 31 K 36 I 32 R 37 A 33 F 38 D 34 E 39 E 35 Q 40 L 36 Q 41 G 37 G 42 E 38 K 43 I 39 T 44 F 40 V 45 K 41 S 46 F 42 V 47 E 43 T 48 A 44 M 49 I 58 I 50 K 59 R 51 E 60 E 52 A 61 G 53 C 62 F 54 D 63 V 55 E 64 E 56 S 65 Q 57 R 66 N 58 F 67 E 59 D 68 I 60 K 69 P 61 N 70 E 62 L 71 E 63 S 72 L 64 Q 73 P 65 A 74 L 66 L 75 L 67 K 76 P 68 F 77 K 69 V 78 E 70 R 79 R 72 D 80 Y 73 F 81 W 74 A 82 L 75 G 83 R 76 D 84 E 77 G 85 I 78 L 86 L 79 F 87 L 80 T 88 C 81 S 89 A 82 H 92 D 83 E 93 G 84 K 94 E 85 N 95 P 86 W 96 W 87 K 97 L 88 K 98 A 89 A 99 G 90 H 100 R 91 N 101 T 92 I 102 V 93 L 103 V 94 L 104 P 95 P 105 S 97 S 106 T 98 F 107 L 99 S 108 S 100 Q 109 G 101 Q 110 P 102 A 111 E 103 M 112 L 104 TER END PFRMAT AL TARGET T1001 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 4nosA W 257 W 74 F 258 L 75 R 259 R 76 E 260 E 77 L 261 I 78 E 262 L 79 L 263 L 80 K 264 C 81 W 265 A 82 Y 266 D 83 A 267 G 84 L 268 E 85 P 269 P 86 A 270 W 87 V 271 L 88 A 272 A 89 TER END PFRMAT AL TARGET T1001 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 4nosB W 257 W 74 F 258 L 75 R 259 R 76 E 260 E 77 L 261 I 78 E 262 L 79 L 263 L 80 K 264 C 81 W 265 A 82 Y 266 D 83 A 267 G 84 L 268 E 85 P 269 P 86 A 270 W 87 V 271 L 88 A 272 A 89 TER END PFRMAT AL TARGET T1001 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 4nosC W 257 W 74 F 258 L 75 R 259 R 76 E 260 E 77 L 261 I 78 E 262 L 79 L 263 L 80 K 264 C 81 W 265 A 82 Y 266 D 83 A 267 G 84 L 268 E 85 P 269 P 86 A 270 W 87 V 271 L 88 A 272 A 89 TER END --simple mime boundary-- From farmer@cse.ucsc.edu Tue May 9 20:21:29 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 UAA01548 for Message-Id: <200005091825.LAA08040@alpha.cse.ucsc.edu> Subject: T1001(target 99 secondary structure prediction) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T1001.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" >T1001 LLLHHHHHHHLLHHHHLLLLLLLHHHHHHHHHHHHHHHHHLLLLEEEEEEELLLLLLLLLLHHLLLLLLLLHHHHHHHHHHLLLLLEEEEEEEEELLLLLLHHHHHHHLLLLLLLLHHLLLLLLLLLEEEELLLLLHHHHHHHHHHLLLHEEHHHHLLLLLLLL --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 T1001 AUTHOR UCSC Target99 server METHOD This prediction was derived from the following methods METHOD by averaging the corresponding probabilities: METHOD Method 0: METHOD TARGET T1001 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-27626/target-align-27626.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 4.70987 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: T1001 METHOD model_file: ./tmp.alpha.20268/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: Tue May 9 11:23:36 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-27626/target-align-27626.a2m METHOD METHOD guide seq name: T1001 METHOD ###end 0 MODEL 1 S C 0.65 H C 0.619 P C 0.5 A H 0.502 L H 0.575 T H 0.562 Q H 0.571 L H 0.483 R H 0.469 A H 0.489 L C 0.462 R C 0.443 Y H 0.479 C H 0.477 K H 0.485 E H 0.446 I C 0.448 P C 0.533 A C 0.509 L C 0.575 D C 0.657 P C 0.557 Q C 0.503 L H 0.462 L H 0.606 D H 0.636 W H 0.673 L H 0.645 L H 0.569 L H 0.503 E H 0.617 D H 0.662 S H 0.679 M H 0.747 T H 0.755 K H 0.807 R H 0.799 F H 0.786 E H 0.731 Q H 0.625 Q C 0.51 G C 0.64 K C 0.626 T C 0.427 V E 0.513 S E 0.566 V E 0.585 T E 0.563 M E 0.537 I E 0.48 R E 0.382 E C 0.405 G C 0.537 F C 0.482 V C 0.466 E C 0.543 Q C 0.592 N C 0.589 E C 0.546 I C 0.524 P C 0.443 E H 0.477 E H 0.454 L C 0.554 P C 0.592 L C 0.614 L C 0.636 P C 0.662 K C 0.551 E C 0.518 S C 0.476 R H 0.479 Y H 0.513 W H 0.554 L H 0.591 R H 0.607 E H 0.609 I H 0.58 L H 0.586 L H 0.583 C H 0.485 A C 0.492 D C 0.668 G C 0.754 E C 0.727 P C 0.517 W E 0.538 L E 0.558 A E 0.509 G E 0.438 R E 0.405 T E 0.489 V E 0.526 V E 0.496 P E 0.419 V C 0.388 S C 0.445 T C 0.514 L C 0.533 S C 0.574 G C 0.461 P H 0.535 E H 0.681 L H 0.722 A H 0.711 L H 0.714 Q H 0.644 K H 0.596 L C 0.48 G C 0.73 K C 0.76 T C 0.705 P C 0.636 L C 0.58 G C 0.542 R C 0.449 Y H 0.396 L H 0.372 F C 0.42 T C 0.547 S C 0.587 S C 0.633 T C 0.573 L C 0.568 T C 0.512 R C 0.415 D C 0.368 F E 0.424 I E 0.51 E E 0.529 I E 0.477 G C 0.501 R C 0.574 D C 0.609 A C 0.529 G C 0.478 L H 0.457 W H 0.452 G H 0.47 R H 0.482 R H 0.544 S H 0.542 R H 0.533 L H 0.488 R H 0.452 L H 0.486 S C 0.514 G C 0.576 K C 0.553 P H 0.382 L E 0.421 L E 0.45 L H 0.442 T H 0.508 E H 0.54 L H 0.478 F C 0.445 L C 0.561 P C 0.52 A C 0.494 S C 0.491 P C 0.489 L C 0.479 Y C 0.557 END --simple mime boundary--