From farmer@cse.ucsc.edu Sat May 20 21:01:13 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 VAA15619 for Message-Id: <200005201905.MAA09924@alpha.cse.ucsc.edu> Subject: T0093(target 99 alignment) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0093.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" >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRH KTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKI RIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNLPEVK >gi|549584|sp|P33899|YIBK_ECOLI_1:156 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YIBKgi|1073422|pir||S47827 yibK protein - Escherichia coligi|466744|gb|AAB18583.1| (U00039) alternate gene name yibK [Escherichia coli]gi|1790034|gb|AAC76630.1| (AE000438) orf, hypothetical protein [Escherichia coli] MLNIVLYEPEIPPNTGNIIRLCANTGFRLHIIEPMGFAWDDKRLRRAGLD YHEFTAVTRHHDYRAFLEAENPQRLFALTTKGTPAHSAVSYQDGDYLMFG PETRGLPASILDALPAEQKIRIPMVPDSRSMNLSNAVSVVVYEAWRQLGY PGAVLR----d >gi|1176303|sp|P44868|YIBK_HAEIN_1:160 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE HI0766gi|1074511|pir||E64158 hypothetical protein HI0766 - Haemophilus influenzae (strain Rd KW20)gi|1573774|gb|AAC22424.1| (U32760) rRNA methylase, putative [Haemophilus influenzae Rd] MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >gi|7225492|gb|AAF40722.1|_1:152 (AE002383) RNA methyltransferase, TrmH family [Neisseria meningitidis] MFTIVLYQPEIPPNTGNIIRLCANTGADLHLVKPLGFPLDSAKMKRAGLD YHEFASLTVHENFDDCLKALAGRRIFALTTKGTARPDETAFQKGDVLLFG PETRGLPADILDSLPAAQKIRLPMQPGSRSMNLSNTVAVILFEAWRQHGY AG--------gv >gi|7380837|emb|CAB85429.1|_1:152 (AL162758) putative tRNA/rRNA methyltransferase [Neisseria meningitidis] MFTIVLYQPEIPPNTGNIIRLCANTGADLHLVKPLGFPLDSAKMKRAGLD YHEFASLTVYENFDDCLKALAGRRIFALTTKGTARPDETAFQKGDVLLFG PETRGLPADILDSLPAAQKIRLPMQPGSRSMNLSNTVAVILFEAWRQHGY AG--------gv >gi|7475809|pir||G69608_6:159 rRNA methylase homolog cspR - Bacillus subtilisgi|2633216|emb|CAB12721.1| (Z99108) rRNA methylase homolog [Bacillus subtilis] mniva-LHVVLYHPEIPANTGNIARTCAATNTTLHLIRPLGFSTDDKMLK RAGLDYWEFVNVVYHDSLEELFEAYKKGKFFFITKFGQQPHTSFDYtdlD EDYFFVFGRETSGLPKDLIQNN-MDRCLRLPMTEHVRSLNLSNTAAILVY EALRQQNYRDL-------k >gi|7469033|pir||C71503_1:147 probable rRNA methylase - Chlamydia trachomatis (serotype D, strain UW3/Cx)gi|3328978|gb|AAC68142.1| (AE001324) rRNA Methylase (SpoU family) [Chlamydia trachomatis] -MRIVLHNPDIPQNTGNIGRTCVALGAELILVRPLGFSLADKFVKRAGMD YWERLSLSVVDSLEEALLGVPKERIFCLTTKGSSYYGERELPLDGTYIFG AESKGLPQTVLDAYS-SQCLYIPMIEGTRSLNLATSVGIVMYEVARQNY- ----------ktlf >gi|1381681|gb|AAB02738.1|_3:156 (U58864) CspR [Bacillus subtilis] ma-LHVVLYQPEIPANTGNIARTCAATNTTLHLIRPLGFSTDDKMLKRAG LDYWEFVNVVYHDSLEELFEAYKKGKFFFITKFGQQPHTSFDYtdlDEDY FFVFGRETSGLPKDLIQNN-MDRCLRLPMTEHVRSLNLSNTAAILVYEAL RQQNYRDL-------k >gi|7468542|pir||E72052_1:146 rRNA methylase - Chlamydia pneumoniae (strain CWL029)gi|4376959|gb|AAD18799.1| (AE001648) rRNA Methylase [Chlamydophila pneumoniae] -MRVVLHCPDIPQNTGNIGRTCVALGAELILVRPLGFSLADKFVKRAGMD YWDKLQLTVVDSIEEALHDVPEDQIFCLSTKGSASYTEFSLPSSGTYVFG SESKGLPKEILKKYY-KNCLRIPMQQDIRSLNLATSVGIVLYEVVRQK-- ----------tvalqknptv >gi|666878|gb|AAB41347.1|_3:147 (L39892) spoU [Chlamydophila caviae] mk---VVLYNPDIPQNTGNIGRTCIALGAELILVRPLGFSLLDKFVKRAG MDYWDKVNLSVVDSLDEALSGVDQNKVFCLSTKGSQYYGDVSLPMDGVYV FGSESKGLPEDVLKKYY-NHCYYLPMRPGIRSLNLATTVGVVLFEAVRQN N-----------qsacirngd >gi|418440|sp|P32813|YGL3_BACST_3:156 HYPOTHETICAL 18.2 KD PROTEIN IN GLDA 3'REGION (ORF3)gi|80208|pir||JS0680 hypothetical protein 3 (gldA 5' region) - Bacillus stearothermophilusgi|142979|gb|AAA22478.1| (M65289) ORF3 is homologous to an ORF downstream of the spoT gene of E.coli; ORF3 [Bacillus stearothermophilus] ma-LHVVLFQPEIPANTGNIARTCAATNTALHLIRPLGFSTDDKMLRRAG LDYWEFVNIHYYDSLDHFFQQNQNGDFYYITKFGKRYYTSYDFsdpSKEI FFIFGRETTGLPKELLAENE-DRCLRIPMTENVRALNLSNTAAILVYEAL RQQSFHGL-------s >gi|2222703|emb|CAB09926.1|_16:169 (Z97179) rRNA methylase [Mycobacterium leprae] mirkphtkprvmiskMFRLLFYTPRIPPNTGNAIRTAAVTGCALHLVEPI GFDLSNPKLRRAGLDYHDLASVTVHTSLSEAWNALSPARVFAFSTLANTL FTDVSYQAGDVLMFGPEPTGLDAATLADDHITQQVRIPMLSGRRSLNLSN AAAVAVYEAWRQHGYAGLV------ >gi|7474350|pir||S71440_3:144 hypothetical protein 3 - Bacillus circulans (fragment)gi|563845|emb|CAA86559.1| (Z46432) orf [Bacillus circulans subsp. alkalophilus] ma-LHIVLVEPEIPANTGNIARTCAATGTHLHLVRPLGFNTDDKTLKRAG LDYWYAVHIEYHDSFEELQQKYPEGRFFYTSTKATKRYCDIAFQDGDFLV FGKETKGLPPELLAANP-DSCIRMPMTDKVRSLNLSNSAAIIVYEA---- ------------ >gi|7448027|pir||D72218_90:241 conserved hypothetical protein - Thermotoga maritima (strain MSB8)gi|4982318|gb|AAD36806.1|AE001812_16 (AE001812) conserved hypothetical protein [Thermotoga maritima] evekrgikysfeseerlknlsgtkkhqgvvfdigeyryssveeileaktp PLIVLLDQIQDPHNLGAIVRTSVGAGANGIIIPKDKSVKVTETVVKVSAG TVFRARIAVVTNLARTIEELKEKGVWTYASdIDGTPIYEEDFTFPTAFVF GNEGEGIRRLVREKC--DRVVTIPMENDIDSLNVSVSVGVVLFEAVRQRR MKGA-------g >gi|3915412|sp|P74516|Y992_SYNY3_1:153 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE SLR0992gi|7469603|pir||S76491 hypothetical protein - Synechocystis sp. (strain PCC 6803)gi|1653708|dbj|BAA18620.1| (D90915) hypothetical protein [Synechocystis sp.] MVKLVLVNPQIPPNTGNIARTCAATGTELHLVGPLGFELGDRYLKRAGLD YWPYVDLHYHNSCEEFITHWRGQGGNLLGFsvTGTVNFWDYTYQSTDWLM MGSETDGLPQMMRDLS--TQLLCIPMpHSEVRSLNLASSAAIALFEAGRQ LRSLG-------- >gi|7478931|pir||E70971_1:154 probable rRNA methylase - Mycobacterium tuberculosis (strain H37RV)gi|2661644|emb|CAA15751.1| (AL009198) spoU [Mycobacterium tuberculosis] MFRLLFVSPRIAPNTGNAIRTCAATGCELHLVEPLGFDLSEPKLRRAGLD YHDLASVTVHASLAHAWEALSPARVFAFTAQATTLFTNVGYRAGDVLMFG PEPTGLDEATLADTHITGQVRIPMLAGRRSLNLSNAAAVAVYEAWRQHGF AGAV------ >gi|586908|sp|Q06753|YACO_BACSU_97:248 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YACOgi|2127060|pir||S66124 conserved hypothetical protein yacO - Bacillus subtilisgi|467483|dbj|BAA05329.1| (D26185) unknown [Bacillus subtilis]gi|2632363|emb|CAB11872.1| (Z99104) similar to hypothetical proteins [Bacillus subtilis] kqgitiqyvprkkldqmvtgqhqgvvaqvaayeyaelddlykaaeekneq PFFLILDELEDPHNLGSIMRTADAVGAHGIVIPKRRAVGLTTTVAKASTG AIEHIPVARVTNLARTLEEMKERGIWVVGTdaSAREDFRNMDGNMPLALV IGSEGKGMGRLVKEKC--DFLIKLPMAGKVTSLNASVAAGLLMYEVYRKR NPVG--------e >gi|6968342|emb|CAB73162.1|_1:150 (AL139076) putative RNA methylase [Campylobacter jejuni] MFNIVLVHPRIPQNTGSIGRMCFNAGFKLHIVKPIVFDISQKAVRRAGLD YWDKLEPIIWENLEEFLNEnmIYKNRFFFATTKSQKAYFDAEFQKNDFLF FGSESYGLPMELMQLNW-ENAITIPMKSYGRSLNLATSVGIISYEALRQN F-----------rnfas >gi|732016|sp|P39290|YJFH_ECOLI_95:242 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFHgi|1361164|pir||S56405 hypothetical 26.6K protein (vacB-aidB intergenic region) - Escherichia coligi|537021|gb|AAA97076.1| (U14003) ORF_o243 [Escherichia coli]gi|1790623|gb|AAC77137.1| (AE000490) orf, hypothetical protein [Escherichia coli] sqgvviqlanrqyldeksdgavhqgiiarvkpgrqyqendlpdliasldq PFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACG AAESVPLIRVTNLARTMRMLQEENIWIVGTagEADHTLYQSKMTGRLALV MGAEGEGMRRLTREHC--DELISIPMAGSVSSLNVSVATGICLFEAVRQR ------------s >gi|2500863|sp|P75257|Y346_MYCPN_6:161 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE MG346 HOMOLOGgi|2146304|pir||S73647 hypothetical protein ygl3 - Mycoplasma pneumoniae (strain ATCC 29342)gi|1673994|gb|AAB95969.1| (AE000029) Mycoplasma pneumoniae, hypothetical protein (ygl3) homolog; similar to Swiss-Prot Accession Number P32813, from B. stearothermophilus myksa-INIVLFCPEIPNNTGNIVRSCTAFKANLHLIKPYGFFLNDKRMV RAGLNCWDKVQMFEHKSWEHFIETTPPnKAIWLLTKsgttTPDQINMQTD NREQLYFVFGQETKGLPQTLMEQYS-QNQVRIPIWNPVRSINLSNTVACV LYEYAKQNHYFNL-------dkqca >gi|3915411|sp|P74328|Y955_SYNY3_217:366 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE SLR0955gi|7469455|pir||S76163 hypothetical protein - Synechocystis sp. (strain PCC 6803)gi|1653509|dbj|BAA18422.1| (D90914) hypothetical protein [Synechocystis sp.] ngtvvdevdnfrlnqithnanhqgiaaqvapyhywelgdlidkaksqsta PVLIIIDSITDPHNLGAIIRTAEAFGAQGMVLPQRRVAGITSTVMKVAAG ALEHFPVARVVNLSRALETLKESGFWIYGTvaGKQTALHQADLREPMGLV IGSEGEGLSLLTQKHC--DHLITIPLAGKTPSLNASVAAAISLYEIFRQR GF----------drptlshtasdlrevsed >gi|3915481|sp|P74261|YG73_SYNY3_120:271 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE SLR1673gi|7469350|pir||S75896 hypothetical protein - Synechocystis sp. (strain PCC 6803)gi|1653441|dbj|BAA18355.1| (D90913) rRNA methylase [Synechocystis sp.] vladrlmaqsvhsylvsgevlakmastvnpdgvvatltmdqfwrspppha RLGLVLERLQDPGNLGTILRTAAATGVEGIWLTADCVDPTSPKVLRSSAG SSLLLPQQQLQSLPPLLEKFHTQGLQLIATvpQATQTLWEIDFQRPTIVI FGSEGQGLSAPVLELT--THQVAIPQAPQVESLNVAIAVGVMLYEARRQQ WAAS--------tpg >gi|1176354|sp|P44906|YJFH_HAEIN_95:243 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE HI0860gi|1074541|pir||E64160 hypothetical protein HI0860 - Haemophilus influenzae (strain Rd KW20)gi|1573875|gb|AAC22519.1| (U32767) conserved hypothetical protein [Haemophilus influenzae Rd] slgigvqfvnrqtldkkadgevhqgviarvqaakelnendldeilankqn PLLLVLDGVTDPHNLGACLRTADAAGAVAVIVPKDKSAQLTSIARKVACG AAETVPLIRVTNLSRTLRDLQQnHNIWVVGTagEATETIYQSKLTGPLAL VMGAEGEGMRRLTREHC--DQLISIPMAGSVSSLNVSVATGVCLFEIVRQ R------------lgs >gi|4104449|gb|AAD02043.1|_2:152 (AF035964) unknown [Brucella abortus] mELRVALYQPDIPGNTGTILRMAACLGFAVDLIEPAGFDISDRALKRAGM DYLEQAALTRHPDWNRFDAWRKNAGRGLVLlsTKAAIPYTGYQFQENDIL LFGRESAGVPEAIHDNA--DERLLIPMVRSARSLNLAVSVAMTTGEALRQ IRSK---------idshsgk >gi|1723153|sp|P47588|Y346_MYCGE_6:161 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE MG346gi|1361592|pir||C64238 hypothetical protein homolog MG346 - Mycoplasma genitaliumgi|3844929|gb|AAC71571.1| (U39716) rRNA methylase, putative [Mycoplasma genitalium] myksv-INIVLFCPEIPNNTGNIVRSCTAFKANLHLIKPYGFFLNDKRMV RAGLNCWDKIQLFEHKSWEHFLQAtTENKTIWLLTKSGDKTPDQIcmtnK LPNELYFVFGQETKGLPKTIMDNFK-QNQIRIPIWNSVRSINLANAVVCI LYEYSKQNQYSNL-------dkqca >gi|7226378|gb|AAF41528.1|_56:200 (AE002463) RNA methyltransferase, TrmH family [Neisseria meningitidis]gi|7226416|gb|AAF41563.1| (AE002466) RNA methyltransferase, TrmH family [Neisseria meningitidis] vrkltavlpedgffsvsdgilkkissltcaddvlalidipdagalpaggd --CVVLDGVQDPGNVGTVLRSAAAAGIGAVILGKGCADAWSPKVLRAGMG AHFLSEIYPQADLEIWLVRYK---GRVFATalreEKQAVLYGEDLCEPTA WVFGNEGAGVGKAVLDRA--DKCVRIPMHDATESLNVAMAATICLFEQMR QR------------aay >gi|7380020|emb|CAB84598.1|_114:258 (AL162755) putative RNA methyltransferase [Neisseria meningitidis] vrkltavlpedgffsvsdgilkkissltcaddvlalidipdagalpaggd --CVVLDGVQDPGNVGTVLRSAAAAGIGAVILGKGCADAWSPKVLRAGMG AHFLSEIYPQADLEIWLVRYK---GRVFATalreEKQAVLYGEDLCEPTA WVFGNEGAGVGKAVLDRA--DKCVRIPMHDATESLNVAMAATICLFEQMR QR------------aay >gi|6687040|emb|CAB64790.1|_96:243 (AJ242786) YjfH protein [Burkholderia sp.] asanarliaadasrlnalsgekrhqgvvarvteatrahsletlldtiegq PLLLALDGVTDPHNLGACLRVADGAGAHAVIAPRRRAAGLTAAAAKAANG AAETVPYLTVINLARALRALKNAGIQVIGTadDATTSLFDIQLDGALALV MGAEGAGMRRLTREAC--DEVVRIPLAGHVQSLNVSVASGICLFEAVRQR ------------lkrl >gi|134838|sp|P19396|TRMH_ECOLI_19:175 TRNA (GUANOSINE-2'-O-)-METHYLTRANSFERASE (TRNA [GM18] METHYLTRANSFERASE)gi|78514|pir||JV0043 SpoU protein - Escherichia coligi|147866|gb|AAB00161.1| (M24503) spoU gene product [Escherichia coli]gi|290501|gb|AAA62004.1| (L10328) spoU [Escherichia coli]gi|1790083|gb|AAC76675.1| (AE000442) putative RNA methylase [Escherichia coli] mnptryaricemlarrqpDLTVCMEQVHKPHNVSAIIRTADAVGVhEVHA VWPG---SRMRTMASAAAGSNSWVQVKTHRTIGDAVAHLKGQGMQILATh lsDNAVDFREIDYTRPTCILMGQEKTGITQEALALA--DQDIIIPMIGMV QSLNVSVASALILYEAQRQRQNAGMYLREN--smlpeaeqqrllfeggyp vlakvakrkglpyphvnqqgeieadadwwatm >gi|6899082|gb|AAF30530.1|AE002113_4_91:237 (AE002113) rRNA methylase [Ureaplasma urealyticum] ityeivneawfkqfdhslnhqniafklvkknfqktslesflklikdkkna -LVLILDEIEDPRNFGAIIRTANGFGVDAIIYKKHHQASINDLVIKTSMG AINYIYMIEVNNLSNTIKNLQDEGFWVYATslLKSQPYEKVDYANKTVFI VGNENKGVSPLILKNA--DQSIRIDMFGDVQSLNVGVATGIILAHYRTKI ------------kp >gi|7477670|pir||A70607_161:308 hypothetical protein Rv3579c - Mycobacterium tuberculosis (strain H37RV)gi|1877310|emb|CAB07153.1| (Z92774) hypothetical protein Rv3579c [Mycobacterium tuberculosis] sgiaivellradldrmtanhlhqgialqvppynyahpddllaaaldqppa -LLVALDNLSDPRNLGAIVRSVAAFGGHGVLIPQRRSASVTAVAWRTSAG AAARIPVARATNLTRTLKGWADRGVRVIGLdaGGGTALDDVDGTDSLVVV VGSEGKGLSRLVRQNC--DEVVSIPMAAQAESLNASVAAGVVLAEIARQR R-----------rprepreqtqnrmi >gi|7473863|pir||A75448_116:264 rRNA methylase - Deinococcus radiodurans (strain R1)gi|6458745|gb|AAF10591.1|AE001953_5 (AE001953) rRNA methylase [Deinococcus radiodurans] earelfpevtgatelsraafekvsgrenpdgvlgvaplpaprlpqpgddt -VVVVLHGLEKPGNVGAILRTADAAGAAGVLVLGRGADPYGPNVIRASQG AVFSVPTAV-LGEDAALGWLAEHNFRTVAcTpDAPADYWDTPLTGRVALL LGTEHAGLPAEWRAAH---QAVRVPMHGQADSLNVATAAALVLYEALRQR RPAD--------a >gi|7481299|pir||T36832_120:274 probable rRNA methylase - Streptomyces coelicolorgi|3581852|emb|CAA20808.1| (AL031541) putative rRNA methylase [Streptomyces coelicolor A3(2)] gaarevgarvhlaadaviedisttvtpqglvgvcrfldtpfdeilaarpk -LVAVLAHVRDPGNAGTVLRCADAAGAEAVVLTDASVDLYNPKAVRASVG SLFHLPVAVGVPVERAVAGLREAGVRVLAAdgaGEDDLDTELDAgtmGGP TAWVFGNEAWGLPEETRALT--DAVLRVPIHGKAESLNLATAAAVCLYAS ARAQRAAG--------gcrsvtes >gi|2500862|sp|P75424|Y252_MYCPN_97:238 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE MG252 HOMOLOGgi|2146299|pir||S73807 hypothetical protein yacO - Mycoplasma pneumoniae (strain ATCC 29342)gi|1674172|gb|AAB96129.1| (AE000047) Mycoplasma pneumoniae, hypothetical protein (yacO) (rRNA methylase) homolog; similar to Swiss-Prot Accession Number Q06753, from B. subtilis lryemhssqwfhqqfrhinhqefvcvinpnqmlktieqliqitdskstst --LVMLHEIQDPHNFGAILRTCMAAEVDGIIFKKHNQAPINSTVIRTSMG TVFYQNLVQVTNLSYAITTLQKHGFWTVATtlderLKPKDYRQVDFDKRI -LLVGNEDKGLNALLLKNA--DLKVKIPMNPKLNSLNVSVAVGIILF--- ---------------gwks >gi|7468541|pir||C72066_116:263 rRNA methylase - Chlamydia pneumoniae (strain CWL029)gi|4376820|gb|AAD18670.1| (AE001638) rRNA Methylase [Chlamydophila pneumoniae] lkrnstkilycldstlaqlsfkehhdsfvaviqkrvwnkedfliqrknaq PFYLIIEQVEKPGNVGAILRIADGAGVDGVILCNPIVDLYNPNVVRSSLG AVFSLPILS-ISREEGKELFKQEGWTVFVTspRAETMYFSKNYLGPTALV FGSEKDGLTEDWFSED--FSEIALPMLGESDSLNLATSVAAVAYEVVRQR W-----------vn >gi|7473864|pir||C75301_22:185 rRNA methylase SpoU - Deinococcus radiodurans (strain R1)gi|6460013|gb|AAF11758.1|AE002054_3 (AE002054) rRNA methylase SpoU [Deinococcus radiodurans] maptperyakirrvlskrqpt-LTVLMDEVNKPHNLSAIIRTCDAVGVpE AHAVPPKHGTLasfEGHTYEATSGSAHKWVKVHPHADAVSAVRELQAQGF QVLAThlsQRSVDYREPDYTKPTCVLLGAEKWGVSDEAAEAA--DANIVI PMFGMVQSLNVSVAAATILFEAQRQRLAAGMYEEPQLSpeelhrlsfewg ypdlapgyrergeaypalgeegellrepvsrpe >gi|7473665|pir||G75542_11:155 probable RNA methyltransferase - Deinococcus radiodurans (strain R1)gi|6457905|gb|AAF09819.1|AE001885_3 (AE001885) RNA methyltransferase, putative [Deinococcus radiodurans] mtdaeasgpl-LHVVLFEPEKAGNVGNVARTCSVLGAELHLIRPFGFHLH DREFRRAVMDYLQGVTLHEYAGWSDFQAQLPDaARVFAFSTHATEYHTRA GFKRGDYLLFGPESRGLPVWLRDALP---KLKLPQPGRGRSLNLSVAVGA AAFEAGRQI------------erw >gi|7477844|pir||G70619_109:260 probable 23s rrnamethyltransferase - Mycobacterium tuberculosis (strain H37RV)gi|1838995|emb|CAB06638.1| (Z85982) tsnR [Mycobacterium tuberculosis] lllaaheasvhlvteraakalsdtvtpaglvavcdlpatrledvlagspq -LIAVTVEIREPGNAGTVIRIADAMGAAAVILAGRSVDPYNGKCLRASTG SIFAIPVVVAPDVGAAIADLRAAGLQVLATavDGEMALDDADRllAEPTA WLFGPEAHGLSAEIAALA--DHRVHILMSGGAESLNVAAAAAICLYESAR ALGRR--------- >gi|7469036|pir||F71519_117:268 probable rRNA methylase - Chlamydia trachomatis (serotype D, strain UW3/Cx)gi|3328830|gb|AAC68000.1| (AE001313) rRNA Methylase (SpoU family) [Chlamydia trachomatis] tslgieklycskdileklsfkenpenfiavfekkelscqeflglqrknqa PFYLIVEQAEKPGNIGALLRIADGAGVDGVILCDPVVDLYNPNVIRSSLG TVFTMPVWQ-ASLKEVLDLVHQQEWQVFTTtpSAQTFYFDQDFCQPMVVV FGSEKDGLSPDWLNGS--FCNIALPMLGKADSLNLSSSVAAVAYEVVRQR SIRNL-------l >gi|7242757|emb|CAB77330.1|_165:313 (AL160331) putative tRNA/rRNA methyltransferase [Streptomyces coelicolor A3(2)] gginlmeaprpeldrmtnglnhqglvlqvppyeyahpedlvaaahdegid PLIVALDGVTDPRNLGAVVRSVSAFGGHGVVVPERRAAGMTAGAWKTSAG TAARTPVARATNLTRALEQYQKAGITVVGLaadGEAELGDLAALDGPVVI VVGSEGKGLSRLVGETC--DFRVRIPMPGGAESLNAGVAAGIVLYEAARR R------------s >gi|7448026|pir||A70463_94:239 rRNA methylase - Aquifex aeolicusgi|2984156|gb|AAC07690.1| (AE000761) rRNA methylase [Aquifex aeolicus] krgvkvqrisrkkveelagtkktqgvvallspvnyvsphelfkeciekks -FFIVIDHITDPQNVGNLLRTCEVLGGVGALISKDRTSPINETVVKASSG AVFHLKISKVSSLSRELKNFQKMGGWVFAVeKGGKDIREVDIPLPVALVL GSEDKGVSKSVLDIS--DQIVTIPMKGKVTSLNVGSAGAIAMWETAKKI- -----------l >gi|6899239|gb|AAF30677.1|AE002123_10_1:169 (AE002123) rRNA methylase [Ureaplasma urealyticum] MLNIVLFEPEIILNTGNIARMCVGFDANLHLVRPYGFILDKKRfhkdFIR ASTNHLNALKLYEYDDFNEFINKNNISGDEIYFfTrygTKTPCDYQYQNi iQHNVYLVFGKESTGIDHNILKKYP-HNWIRIPTSINLRSLNIANSVAMG IYEVVRQNNFKDLFKYEPHKkfe >gi|3915369|sp|O51468|Y516_BORBU_79:226 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE BB0516gi|7448025|pir||C70164 rRNA methylase (yacO) homolog - Lyme disease spirochetegi|2688440|gb|AAC66889.1| (AE001154) rRNA methylase (yacO) [Borrelia burgdorferi] intneldkilknkdhrgfalklkleknknvktqtkdfenlletfkkkena -FILLLDEIEDPQNFGAILRTAEQFSIDLVITTQKRSAKDNSTVLRTSSG ASQYVKKMTVTNINNTINLLKNYGFWIYTGdIKGQDINKIKInDKKIALI LGNEGKGVHKLIKENS--DFLIRIPTSGKIDSLNVSVSTGILIFEIKRQL N-----------ll >gi|3915169|sp|O67577|TRMH_AQUAE_25:184 PROBABLE TRNA (GUANOSINE-2'-O-)-METHYLTRANSFERASE (TRNA [GM18] METHYLTRANSFERASE)gi|7451695|pir||H70443 rRNA methylase SpoU - Aquifex aeolicusgi|2983982|gb|AAC07528.1| (AE000749) rRNA methylase SpoU [Aquifex aeolicus] mvmeylvlekrlkrlrevlekrqkDLIVFADNVKNEHNFSAIVRTCDAVG Vl--------YLYYYHAEGKKAkinegiTQGSHKWVFIEKVDNPVQKLLE FKNRGFQIVATwlsKESVNFREVDYTKPTVLVVGNELQGVSPEIVEIA-- DKKIVIPMYGMAQSLNVSVATGIILYEAQRQREEKGMYSRPSLSeeeiqk ilkkwayedvikerkrtlsts >gi|7475810|pir||G69984_106:247 rRNA methylase homolog ysgA - Bacillus subtilisgi|1770029|emb|CAA99602.1| (Z75208) hypothetical protein [Bacillus subtilis]gi|2635330|emb|CAB14825.1| (Z99118) similar to rRNA methylase [Bacillus subtilis] etripsdletgiqcymlsedafsavtetetpqqiaavchmpeeklatark --VLLIDAVQDPGNLGTMIRTADAAGLDAVVLGDGTADAFNGKTLRSAQG SHFHIPVVR-RNLPSYVDELKAEGVKVYGTalQNGAPYQEIPQSESFALI VGNEGAGVDAALLEKT--DLNLYVPLYGQAESLNVAVAAAILVYHLR--- ------------g >gi|1723134|sp|P47494|Y252_MYCGE_97:238 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE MG252gi|1361843|pir||H64227 rRNA methylase - Mycoplasma genitaliumgi|3844850|gb|AAC71472.1| (U39704) rRNA methylase, putative [Mycoplasma genitalium] infqihstnwfnnqyrdinhqelvavldtnqllipldqlvkvvenkkcst --LVMLDEIQDPYNFGAILRTCLASEVDGIIFKKNNQVPINNTVMKTSMG SVFYQNLVQVANLSYTITKLKEIGFWTVVStldpiWKPIDYRKVDFAKKI -LIVGNEDRGVNQLITKNA--DCRIKIPMNNKINSLNVSVALGIILF--- ---------------awkn >gi|6899305|gb|AAF30736.1|AE002130_3_115:257 (AE002130) rRNA methylase [Ureaplasma urealyticum] etifkytlydniqiykvsgniikklsvniepspilavvkikqemcdindn --ILLLDNIQDPGNLGTILRTCFAFNIKQVIFNNC-VDLYNPKTIKASMG AIFKINFLRFNDSKLALNFLLKNKFYLIATildKNAISLNEITIKQKYCL MVGNEGHGLVQTFIDHA--HIKTMIKM-NQTESLNVAVAAAIFLYELNK- ------------- >gi|465634|sp|P33635|YFIF_ECOLI_197:343 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YFIFgi|7449751|pir||D65036 hypothetical 37.8 kD protein in ung 3' region - Escherichia coli (strain K-12)gi|1788935|gb|AAC75634.1| (AE000344) orf, hypothetical protein [Escherichia coli] maanrkayhvvdeaeltkasgtehhggvcflikkrngttvqqwvsqagaq DCVLALENESNPHNLGGMMRSCAHFGVKGVVVQDA-ALLESGAAIRTAEG GAEHVQPITGDNIVNVLDDFRQAGYTVVTTssEQGKPLFKTSLPAKMVLV LGQEYEGLPDAARDPN--DLRVKIDGTGNVAGLNISVATGVLLGEWWRQN ------------ka >gi|3253066|dbj|BAA29043.1|_1:156 (D86335) SpoU homologue [Pyrococcus sp.] MISVVLVEPEGPANIGMIARTMKNFGFsRLVLINPN---LTEESYAYAVH ARDVLENALILDSFEKALELFD---FTVGTTgkpgkrfiphRAPLMPWEL vglikDYPGEVGIFFGRESIGLKNEELDAM--DVTLTIPTSEEYPVMNLA QAAAVVLYELSKKR------------pepyvealkpatreekealvrtwe kllntldypkdaerrdvfvkvfqrav >gi|5032157|ref|NP_005637.1|_1463:1612 TAR (HIV) RNA-binding protein 1gi|2136327|pir||S62356 TRP-185 protein - humangi|1184692|gb|AAC50379.1| (U38847) TAR RNA loop binding protein [Homo sapiens]gi|1586092|prf||2203267A TRP-185 protein [Homo sapiens] digtnlveadnqaewtdvqkkiipwnsrvsdldlellfqdraarlgksis RLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSL-QCISDKQFQHLSVS AEQWLPLVEVKPPQliDYLQQKKTEGYTIIGveqTAKSLDLTQYCFPEKS LLLLGNEREGIPANLIQQL--DVCVEIPQQGIIRSLNVHVSGALLIWEYT RQQ------------llshgdtkp >gi|1731374|sp|Q10543|Y881_MYCTU_134:285 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE RV0881gi|7476540|pir||F70780 hypothetical protein Rv0881 - Mycobacterium tuberculosis (strain H37RV)gi|1314020|emb|CAA97388.1| (Z73101) hypothetical protein Rv0881 [Mycobacterium tuberculosis] agvgapyyrasadvmarvigfhlnrgvlaaagrvpepsvaqvvagartva ----VLEGVNDHENLGSIFRNAAGLSVDAVVFGTGCADPLYRRAVRVSMG HALLVPYARAADWPTELMTLKESGFRLLAmTphgNACKLPEAIAAvsHER IALLVGAEGPGLTAAALRIS--DVRVRIPMSRGTDSLNVATAAALAFYER TRSGHHIG--------pgt >gi|6015729|emb|CAB57556.1|_1:155 (Y18930) hypothetical protein [Sulfolobus solfataricus] MIRVVLVEPEGEYNIGFVARLCKNFLVdELYIVNPR--ANISEAFRFSAG GREILEKAKIVNTFDKAINDVD---IKIATSsiadnngdilRKSIRPWEI LPliqGKKIALIFGRESVGLTREEIFKC--DFLLYIPANPSYPVLNLSHA VGIVLYEIWKNR------------elltnpqtstisdqsiklidkyteil ykllkrsdddykmyialkraiikg >gi|7464733|pir||G71924_87:223 hypothetical protein jhp0500 - Helicobacter pylori (strain J99)gi|4155040|gb|AAD06078.1| (AE001483) putative [Helicobacter pylori J99] falkkacpniikvdnkkaqslakggnhqgvlakvelplaaslkeikkaqk --LLVLCGITDVRNIGGIFRSAYCLGMDGVILDFA-REFAYEGIVRSSLG LMYDLPFSVMPNTLDLINELKTSGFLCLGaSMQGSSQAENLSLKKCALFL GSEHEGLSKKILAKM--DAILSVKMRRDFDSLNVSVAAGILM-------- -----------dkin >gi|1199536|emb|CAA64900.1|_331:482 (X95644) ORF 2310 [Saccharomyces cerevisiae]gi|1903285|emb|CAA98679.1| (Z74159) ORF YDL112w [Saccharomyces cerevisiae] lwldkrdtntesvnnaniscdtsplqtksgawetvldldnkksndvvtrs ELIVVSSLVDKPPNLGGICRLCDVLGVGLLTVQDI-KVKNHPQFKNVAVT ADRWMPMEEValDEIASFMKEKKKEGYTLIGLeqtdKSVKLDNNFQFPKK SLILLGTEAFGIPGTLLSEL--DLCLEIQQFGVIRSMNIQTATAVIVHSY TVQHM----------- >gi|7448028|pir||A64589_87:223 conserved hypothetical protein HP0553 - Helicobacter pylori (strain 26695)gi|2313669|gb|AAD07619.1| (AE000569) conserved hypothetical protein [Helicobacter pylori 26695] falkkacpniikvdnkkaqslakggnhqgvlakvelplavslkevkkaqk --LLVLCGITDVGNIGGIFRSAYCLGMGGVILDFA-KELAYEGIVRSSLG LMYDLPFSVMPNTLDLINELKTSGFLCLGaSMQGSSQIENLSLKKCALFL GSEHEGLSKKILAKM--DTILSVKMRRDFDSLNVSVAAGILM-------- -----------dkin >gi|136456|sp|P18644|TSNR_STRAZ_118:268 RRNA (ADENOSINE-2'-O-)-METHYLTRANSFERASE (23S RRNA [AM1067] 2'-O-METHYLTRANSFERASE) (23S RRNA METHYLASE) (THIOSTREPTON-RESISTANCE METHYLASE)gi|282558|pir||S28369 rRNA methylase - Streptomyces cyaneusgi|46771|emb|CAA26234.1| (X02392) rRNA methylase [Streptomyces cyaneus]gi|1403525|emb|CAA67009.1| (X98363) Thiostrepton resistance protein [Cloning vector pIJ2581]gi|7380884|dbj|BAA93040.1| (AB040452) rRNA methylase [Shuttle vector pRES19] lcgrqnipvrlidssivnqlfkgerkaktfgiarvprparfgdiasrrgd --VVVLDGVKIVGNIGAIVRTSLALGAsGIILVDSDITSIADRRLQRASR GYVFSLPVVL-SGREEAIAFIRDSGMQLMTLkaDGDISVKELgDNPDRLA LLFGSEKGGPSDLFEEAS--SASVSIPMMSQTESLNVSVSLGIALHERID RNLAAN--------r >gi|695296|gb|AAB41449.1|_1:115 (L40369) spoU [Chlamydia trachomatis] ---------------------------------PLGFSLADKFVKRAGMD YWERLSLSVVDSLEEALLGVPKERIFCLTTKGSSYYGERELPLDGTYIFG AESKGLSQTVLDAYS-SQCLYIPMIEGTRSLNLATSVGIVMYEVARQNY- ----------ktlf >gi|7485251|pir||T01767_82:257 hypothetical protein A_IG002P16.25 - Arabidopsis thalianagi|2191177|gb|AAB61063.1| (AF007270) belongs to the SPOU family of rRNA methylases. [Arabidopsis thaliana] kgklslsinsfsskiqshalrgvgigesdkknplprgagegvkedarskl -LHVVLVSPQIPGNTGCIARTCAASAVGLHLVGvnvddlichlfllqPLG FQVDDARVKRAGGR----------KTNDSFYKKRNKDTFKIATiTsnwva enNGYNLMQDFSYRSGDYLLFGSETSGLPPEALSDC--NhepyggGTLRI PMvETYVRCLNLSVSVGIALYEASRQLNYEQIECAPQGCvngeepllted ifa >gi|6320091|ref|NP_010171.1|TRM3_1285:1436 tRNA (Gm18) ribose methylase; Trm3pgi|2132435|pir||S67655 probable membrane protein YDL112w - yeast (Saccharomyces cerevisiae)gi|1431162|emb|CAA98680.1| (Z74160) ORF YDL112w [Saccharomyces cerevisiae] lwldkrdtntesvnnaniscdtsplqtksgawetvldldnkksndvvtrs ELIVVSSLVDKPPNLGGICRLCDVLGVGLLTVQDI-KVKNHPQFKNVAVT ADRWMPMEEValDEIASFMKEKKKEGYTLIGLeqtdKSVKLDNNFQFPKK SLILLGTEAFGIPGTLLSEL--DLCLEIQQFGVIRSMNIQTATAVIVHSY TVQHM----------- >gi|1709266|sp|P52391|NHS_STRAS_118:260 23S RRNA METHYLTRANSFERASE (23S RRNA METHYLASE)gi|80684|pir||JQ0686 nosiheptide resistance protein - Streptomyces actuosusgi|1654411|gb|AAB17875.1| (U75434) 23S rRNA methyltransferase [Streptomyces actuosus] lcrqreipvrlidvsivnqlfkaerkakvfgiarvprparladiaerggd --VVVLDGVKIVGNIGAIVRTSLALGAaGIVLVDSDLATIADRRLLRASR GYVFSLPVVL-ADREEAVSFLRDNDIALMVldTDGDLGVKDLGDrADRMA LVFGSEKGGPSGLFQEAS--AGTVSIPMLSSTESLNVSVSVGIALHER-- --------------sarnfavrraaaqa >gi|7293773|gb|AAF49141.1|_235:402 (AE003516) CG14100 gene product [Drosophila melanogaster] tkiykvpqhdlktwsslvtppglmaifdrpsdkgleknlaeqqrlgsqpf PITVVCDNIREPNNLGSIIRTCAALPCSQVVVTHGCCDPWESKALRGGCG GQFRVPIRDDVTWDELALTippEAADDCHVFIaeTnqrkrenNQTIDYAD IKGlGAHNLLIIGGESHGVSEEAYRFL--NlvggkgKCIYIPLAAGIDSL NVASALTLLLFELRRKLIHQ---------aseke >gi|7022703|dbj|BAA91694.1|_209:409 (AK001443) unnamed protein product [Homo sapiens] klkgvslikvkfedikdwsdlvtpqgimgifakpdhvkmtypktqlqhsl PLLLICDNLRDPGNLGTILRSAAGAGCSKVLLTKGCVDAWEPKVLRAGMG AHFRMPIINNLEWEtvpnylppdtrvyvadncglyaqaemsnkasdhgwv cdqrvmKFHKYEEEEDVETGASQDWLPHVEVQSydsdwtEAPAAVVIGGE TYGVSLESLQLA--EstggKRLLIPVVPGVDSLNSAMAASILLFEGKRQL RGR---------aedlsrdrsyh >gi|7473664|pir||E75501_13:163 probable RNA methyltransferase - Deinococcus radiodurans (strain R1)gi|6458273|gb|AAF10156.1|AE001916_2 (AE001916) RNA methyltransferase, putative [Deinococcus radiodurans] mssaapsptaqs-LAVVLVSPKTPGNIGAAARAMLNMGAsDLRIVAPRCD YLDSQAVAMAVHAGDLLRSAKIYPTLREALADRD---LSVGTSariradl PAPRHPAQVRGlvreAAAPALVFGPEETGLINSDLEQC--QVTVRIPT-G DYASLNLAQAVLLVCYEFLQ--------------gqddvpehsrqtatre dmeamyghlqdtmhligytdavrgrhtmrlwram >gi|7429550|pir||C69114_11:170 conserved hypothetical protein MTH1849 - Methanobacterium thermoautotrophicum (strain Delta H)gi|2622984|gb|AAB86315.1| (AE000937) conserved protein [Methanobacterium thermoautotrophicum] mealkmlaen-ISVVFVEPETPGNIGFLARAMKNFGLrTLILINP--CEL EDEAYYQAMHARDIVEGALIYRDLSEMIDSLEPD-FLVGTTgvpggsynv driplRPSQLADAIRPSSGTFILFGREGDGLSNEEIGLC--DMVVSVPTS EEYPIMNITHAAAIIFYELFRDREFR---------cegleeasaleksll leemddilslidipehkqrvasrvfrnitgrafit >gi|3915341|sp|O51081|Y052_BORBU_34:181 HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE BB0052gi|7451696|pir||D70106 spoU protein (spoU) homolog - Lyme disease spirochetegi|2687923|gb|AAC66431.1| (AE001118) spoU protein (spoU) [Borrelia burgdorferi] mdddvlkrigvlskfitdekkariekvlnlrtnYLTFVLEDIFQSQNASA TIRTGEILGLsDVHVIEKKNKHTLNPDV---TLGSSQWINLNKYKNAKFA IDRLKSDGYSIVATslnPKSINLENLTINNKMAIFFGTELTGLSAEVLGA A--DLYVKIPMYGFTQSYNISVAVAIVMYSLLMRLR-----------kss idyllneaeksnlrlkyyrqvvknyqfienlins >gi|2127985|pir||C64484_4:161 hypothetical protein HI0380 homolog - Methanococcus jannaschiigi|1592115|gb|AAB99481.1| (U67588) conserved hypothetical protein [Methanococcus jannaschii] miiMISVILVNPKYSGNVGSIARVMMNFGFeELRIVGDK-SIINNEAYMM AVHAREILDNAKFYNTFDEAIGDLD----FVIATsgarggdrnlkrvpit PKELADKILEVKGNIGIVFGREDDGLRNEEIDKC--DLLVSIPTSEKYPI MNLSHAVAVILYEIYTKK------------vrnkfldinmreaskedkel lirkfnefidknekipehkkelckiifkrl >gi|3046324|gb|AAC24483.1|_5:161 (AF010139) unknown [Azotobacter vinelandii] mlqs-IRVVLVNTSHPGNIGGAARAMRNMGLsRLYLVAPE-DFPSSEAVA RASGATDILDNAQVVATLEEALVGCT---LALGTSardrripwplldpre CAATCLEQVGQGAEVALVFGREYAGLTNEELQRC--QFHVHIPSDPSFSS LNLAAAVQVLVYEVRMAW------------laaegvpskqeklettamln sqpatmdelelfyghlestlveigfldpek >gi|1903046|emb|CAB07516.1|_1:113 (Z93102) hypothetical 13.6 kd protein [Bacillus subtilis] ------------------------------------------MLKRAGLD YWEFVNVVYHDSLEELFEAYKKGKFFFITKFGQQPHTSFDYtdlDEDYFF VFGRETSGLPKDLIQNN-MDRCLRLPMTEHVRSLNLSNTAAILVYEALRQ QNYRDL-------k >gi|7429552|pir||S76714_2:148 hypothetical protein - Synechocystis sp. (strain PCC 6803)gi|1208490|dbj|BAA10658.1| (D64004) hypothetical protein [Synechocystis sp.] m-------EPQGERNVGAIARAMKNMGLeELILVNPRCDYRSVEAQTMAV HAKDVLAQAKVVDDLATALGDRQ----RIIATsarerilqspmetPRQAL PWLLAPNLKSALVFGREDSGLTNEELNQA--HRFVRIPVHPQYPSLNLSQ AVMVCTYELYQ--------------aslametnnqvpgdrledgstmpla tnaqldsycqhlektllnievlyph >gi|7481298|pir||T36705_119:251 probable rRNA methylase - Streptomyces coelicolorgi|5102788|emb|CAB45203.1| (AL079308) putative rRNA methylase [Streptomyces coelicolor A3(2)] vlaglltevsreayaslvarphptavaalavrpsraaglealartprrap --VVVLDQPRNLGNAGAVIRLAAGFGATGVVTTGT-LDPWHPTVVRGGAG LHFATVVER---------------LEVAGLppgplfaldPEGEDIRGLEL PDDALLAFGSERSGLTPELRARA--DRLVALPMRPQVSSYNLATSVAMTL YHW----------------sagggaprvp >gi|7445204|pir||C72640_2:151 hypothetical protein APE0555 - Aeropyrum pernix (strain K1)gi|5104208|dbj|BAA79523.1| (AP000060) 235aa long hypothetical protein [Aeropyrum pernix] m-------ETEGAVNLGFVARLAENFEAdEIYLVSPR--ASLEEAKRYAA RAAWRLDAARVVSNLEEALRGVS---ASLCTSshmsdrdalRAPLAPWEA AEvlaatPGTVAIVFGRESVGLTRGEIALC--SLYSSIPASPRYPSLNLS NAAAIYLYEVYKARR-----------ggavarggvdeelikllrayaaal asrlvhreraeevavslvriasksvm >gi|3023080|gb|AAC12641.1|_1:61 (AF054517) putative rRNA methylase [Synechococcus PCC7002] -------------------------------------------------- -------------------------------------EFTYQDDDWLLFG SETKASPQXLLQRC--DATLTIPInKTHVRSLNLSVSAAVGLFEVRRQLG -----------l >gi|2274931|emb|CAA74647.1|_1:24 (Y14275) hypothetical protein X [Eubacterium acidaminophilum] -------------------------------------------------- -------------------------------------------------- -----------------------------SLNLSNSVAIVVYEALRQLGY PGL-------e --simple mime boundary-- From farmer@cse.ucsc.edu Sat May 20 21:22:01 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 VAA15920 for Message-Id: <200005201925.MAA20871@alpha.cse.ucsc.edu> Subject: T0093(database hits) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0093.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 1d8cA -11.8 0.1664 -11.8 0.17 --------- --------- : mol:protein-het length:723 Malate Synthase G 1rkd -11.57 0.2094 --------- --------- -11.57 0.21 1bhgA -8.76 3.477 --------- --------- -8.76 3.5 1a0p -6.69 27.53 --------- --------- -6.69 27 1bct -6.55 31.66 -6.55 32 --------- --------- : mol:protein length:69 Bacteriorhodopsin (Fragment 163-231) (NMR, 14 1cdoA -6.55 31.66 -6.55 32 --------- --------- : mol:protein length:374 Alcohol Dehydrogenase 1cdoB -6.55 31.66 -6.55 32 --------- --------- : mol:protein length:374 Alcohol Dehydrogenase 1ede -6.53 32.3 --------- --------- -6.53 32 1glcG -6.49 33.61 --------- --------- -6.49 33 1dbgA -6.37 37.89 -6.37 38 --------- --------- : mol:protein length:506 Chondroitinase B 1dboA -6.37 37.89 -6.37 38 --------- --------- : mol:protein length:506 Chondroitinase B 1ap9 -6.2 44.9 -6.2 45 --------- --------- : mol:protein length:248 Bacteriorhodopsin 1at9 -6.2 44.9 -6.2 45 --------- --------- : mol:protein-het length:247 Bacteriorhodopsin 1bac -6.2 44.9 -6.2 45 --------- --------- : mol:protein-het length:248 Rhodopsin (7-Helix Bundle) Complex With 1bad -6.2 44.9 -6.2 45 --------- --------- : mol:protein-het length:248 Bacteriorhodopsin (7-Helix Bundle) With 1bm1 -6.2 44.9 -6.2 45 --------- --------- : mol:protein-het length:247 Bacteriorhodopsin 1brd -6.2 44.9 -6.2 45 --------- --------- : mol:protein-het length:248 Bacteriorhodopsin - Chain _ 1brrA -6.2 44.9 -6.2 45 --------- --------- : mol:protein-het length:247 Bacteriorhodopsin 1brrB -6.2 44.9 -6.2 45 --------- --------- : mol:protein-het length:247 Bacteriorhodopsin 1brrC -6.2 44.9 -6.2 45 --------- --------- : mol:protein-het length:247 Bacteriorhodopsin --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results.t99pairwise.a2m' Content-Disposition: attachment; filename="t99-results.t99pairwise.a2m" >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1d8cA mol:protein-het length:723 Malate Synthase G xaqtitqsrlridanfkrfvdeevlpgtgldaaafwrnfdeivhd----- -------------------------LAPENRQLLAERDRIQAALDEWHRS NPGPVKDKAAYKSFLRELGYLVPQPERVTV----------------ETTG IDSEITSQA--GPQLVVPAXNARYALNAANARWGSLYDAL---------- -----ygsdiipqegaxvsgydpqrgeqviawvrrfldeslplengsyqd vvafkvvdkqlriqlkngkettlrtpaqfvgyrgdaaaptcillknnglh ielqidangrigkddpahindviveaaistildcedsvaavdaedkilly rnllglxqgtlqekxekngrqivrklnddrhytaadgseislhgrsllfi rnvghlxtipviwdsegneipegildgvxtgaialydlkvqknsrtgsvy ivkpkxhgpqevafanklftrietxlgxapntlkxgixdeerrtslnlrs ciaqarnrvafintgfldrtgdexhsvxeagpxlrknqxkstpwikayer nnvlsglfcglrgkaqigkgxwaxpdlxadxysqkgdqlragantawvps ptaatlhalhyhqtnvqsvqaniaqtefnaefepllddlltipvaenanw saqeiqqeldnnvqgilgyvvrwveqgigcskvpdihnvalxedratlri ssqhianwlrhgiltkeqvqaslenxakvvdqqnagdpayrpxagnfans cafkaasdliflgvkqpngytepllhawrlrekesh >T0093 mldivlyepeipqnTGNIIRLCANT------------------------- --GFRLHLIEPLG-----------------FTWDDKRLRRSGLDYHEFAE IKRHKTFE----------------------AFLESEKPkrLFAL------ -------TTKGCPAHSQVKFKLGDYLMFGP-ETRGIPMSILNE-mpmeqk irIPMTAN------------------------------------------ -------------------SRSMNLSNSVAVTV---------YEAWRQLG YKGAVNLPE--------vk------------- >1rkd mol:protein length:309 Ribokinase mqnAGSLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVA AGRSGANIAFIACTGDDSIGESVRQQLATDNIDITPVSVIKGESTGVALI FVNGEGENVIGIHAGANAALSPALVEAQRERIANASALLMQLESPLESVM AAAKIAHQNKTIVALNPAPARELPDELLALVDIITPNETEAEKLTGIRVE NDEDAAKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRVPGFRVQAVDT IAAGDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREE IDAFLDRQR >T0093 -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----MLDIVLYEPE-ipqnTGNIIRLCAN-TGFRLHLIEPLG------- ------------FTWDDKRLRRSG-LDYHEFA---------EIKRHKTFE AFLESEKPKRLFALTTKGCPAHSqVKFKLGDYLMFGPETRG--------- ---IPMSILNEMPMEQKIRIPMTANSRSMN--------------LSNSVA VTVYEAWRQLG---YKGAVNLPEV-------------------------- ----------k------ >1bhgA mol:protein length:613 Beta-Glucuronidase lGLQGGMLYPQESPSRECKELDGLWSFRADFSDNRRRGFEEQWYRRPLWE SGPTVDMPVPSSFNDISQDWRLRHFVGWVWYEREVILPERWTQDLRTRVV LRIGSAHSYAIVWVNGVDTLEHEGGYLPFEADISNLVQVGPLPSRLRITI AINNTLTPTTLPPGTIQYLTDTSKYPKGYFVQNTYFDFFNYAGLQRSVLL YTTPTTYIDDITVTTSVEQDSGLVNYQISVKGSNLFKLEVRLLDAENKVV ANGTGTQGQLKVPGVSLWWPYLMHERPAYLYSLEVQLTAQTSLGPVSDFY TLPVGIRTVAVTKSQFLINGKPFYFHGVNKHEDADIRGKGFDWPLLVKDF NLLRWLGANAFRTSHYPYAEEVmQMCDR-YGIVVIDECPGVGLALPQFFN NVSLHHHMQVMEEVVRRDKNHPAVVMWSVANEPASHLESAGYYLKMVIAH TKSLDPSRPVTFVSNSNYAADKGAPYVDVICLNSYYSWYHDYGHLELIQL QLATQFENWYKKYQKPIIQSEYGAETIAGFHQDPPLMFTEEYQKSLLEQY HLGLDQKRRKYVVGELIWNFADFMTEQSPTRVLGNKKGIFTRQRQPKSAA FLLRERYWKIANEt >T0093 mld----------------------------------------------- --------------------------------------------IVLYEP EI-------------PQNTGNIIRLCANTGFRLHliEPLGFTWDDKRLRR SGLDYHEFAEIKRH--------KTFEAFLE--------SEKPKRLFA--- ---LTT------------------KGCPAHSQVKFKLGDYLMFGPETRGI PM--------SILNEMPMEQKI----ripmtansrsmnlsnsvavtvyea wrqlgykgavnlpevk >1a0p mol:protein length:290 Site-Specific Recombinase Xerd QDLARIEQFLDALWLEKNLAENTLNAYRRDLSMMVEWLHHRGLTLATAQS DDLQALLAERLEGgykatssARLLSAVRRLFQYLYREKFREDDPSAHLas pklpqrlpKDLSEAQVERLLQAPLIDQPLELRDKAMLEVLYATGLRVSEL VGLTMSDISLRQGVVRVIGKGNKERLVPLGEEAVYWLETYLEHGRPWLLN GVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLRHAFAT HLLNHGADLRVVQMLLghSDLSTTQIYTHVATERLRQLHQ >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1bct mol:protein length:69 Bacteriorhodopsin (Fragment 163-231) (NMR, 14 mrpevastfkvlrnvtvvlwsay--------------------------- -------------------------------------------------- ----------------PVVWLIGSEGAGIVPLNIETL------------- ---------------------------------lfmvldvsakvgfglil lrsraifg >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1cdoA mol:protein length:374 Alcohol Dehydrogenase atvgkvikckaav------------------------------------- -------------AWEANKPLVIEEIEVDVPHANEIRIKIIATgvchTDL YHLFEGKHKDGFPVVLGHEGAGI--------------------------- ---------------------------vesvgpgvtefqpgekviplfis qcgecrfcqspktnqcvkgwanespdvmspketrftckgrkvlqflgtst fsqytvvnqiavakidpsapldtvcllgcgvstgfgaavntakvepgstc avfglgavglaavmgchsagakriiavdlnpdkfekakvfgatdfvnpnd hsepisqvlskmtnggvdfslecvgnvgvmrnalesclkgwgvsvlvgwt dlhdvatrpiqliagrtwkgsmfggfkgkdgvpkmvkayldkkvkldefi thrmplesvndaidlmkhgkcirtvlsl >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1cdoB mol:protein length:374 Alcohol Dehydrogenase atvgkvikckaav------------------------------------- -------------AWEANKPLVIEEIEVDVPHANEIRIKIIATgvchTDL YHLFEGKHKDGFPVVLGHEGAGI--------------------------- ---------------------------vesvgpgvtefqpgekviplfis qcgecrfcqspktnqcvkgwanespdvmspketrftckgrkvlqflgtst fsqytvvnqiavakidpsapldtvcllgcgvstgfgaavntakvepgstc avfglgavglaavmgchsagakriiavdlnpdkfekakvfgatdfvnpnd hsepisqvlskmtnggvdfslecvgnvgvmrnalesclkgwgvsvlvgwt dlhdvatrpiqliagrtwkgsmfggfkgkdgvpkmvkayldkkvkldefi thrmplesvndaidlmkhgkcirtvlsl >T0093 mldivlyepeipqntg---------------------------------- ------------------------------NIIRLCANTGFRLHLIEPLG FTWDDKRLRRSGLDYHEFAE------------------------------ -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- --------------------------ikrhktfeaflesekpkrlfaltt kgcpahsqvkfklgdylmfgpetrgipmsilnempmeqkiripmtansrs mnlsnsvavtvyeawrqlgykgavnlpevk >1ede mol:protein length:310 Haloalkane Dehalogenase (E.C. 3.8.1.5) At pH MINAIRTPDQRFSNLDQYPFSPNYLDDLPGYPGLRAHYLDEGNSDAEDVF LCLHGEPTWSYLYRKMIPVFAESGARVIAPDFFGFGKSDKPVDEEDYTFE FHRNFLLALIERLDLRNITLVVQDWGGFLGLTLPMADPSRFKRLIIMNAC LMTDPVTQPAFSAFVTQPADGFTAWKYDLVTPSDLRLDQFMKRWAPTLTE AEASAYAAPFPDTSYQAGVRKFPKMVAQRDQACIDISTEAISFWQNDWNG QTFMAIGMKDKLLGPDVMYPMKALINGCPEPLEIADAGHFVQEFGEQVAR EALKHFAET-e >T0093 mldivlyepeipqntGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD ---------YHEFAEIKRHKTFEAFLEse----KPKRL------------ -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----FALTTKGCPAHSQVKFKLGDYLMFGPETR----------------- ---GIPMSIl----------------------NEMPME------------ -------------------------------------------QKIRIPM TAN-----------------------SRSMNLSNSVAVTVYEAWRQLGYK GAV----------------------------------------------- -NLPEVK >1glcG mol:protein length:501 Glycerol Kinase (E.C. 2.7.1.30) Complexed Wi tekKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPM EIWATQSSTLVEVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNA IVWQCRRTAEICEHLKRDGLEDYIRSNTGLVIDPYFSGTKVKWILDHVEG SRERARRGELLFGTVDTWLIWKMTQGRVHVTDYTNASRTMLFNIHTLDWD DKMLEVLDIPREMLPEVRRSSEVYGQTNIggkggtrIPISGIAGDQQAAL FGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNY ALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTG LGAPYWDPYARGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSG IRLHALRVDGGAVANNFLMQFQSDILGTRVERPEVREVTALGAAYLAGLA VGFWQNLDELQEKAVIEREFRPGIETTERNYRYAGWKKAVKRAMAWEEhd E >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1dbgA mol:protein length:506 Chondroitinase B mkmlnklagyllpimvllnvapclgqvvasnetlyqvvkevkpgglvqia dgtykdvqlivsnsgksglpitikalnpgkvfftgdakvelrgehlileg iwfkdgnraiqawkshgpglvaiygsynritacvfdcfdeansayittsl tedgkvpqhcridhcsftdkitfdqvinlnntaraikdgsvggpgmyhrv d--HCFFSNPQKPGNAGGGIRIGYYRNDiGRCLVDSNLFMRQDSEA---- -------------------------------------------------- -------------------------------------------------- ------------eiitsksqenvyygntylncqgtmnfrhgdhqvainnf yigndqrfgyggmfvwgsrhviacnyfelsetiksrgnaalylnpgamas ehalafdmliannafinvngyaihfnplderrkeycaanrlkfetphqlm lkgnlffkdkpyvypffkddyfiagknswtgnvalgvekgipvnisanrs aykpvkikdiqpiegialdlnaliskgitgkplswdevrpywlkempgty altarlsadraakfkavikrnkeh >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1dboA mol:protein length:506 Chondroitinase B mkmlnklagyllpimvllnvapclgqvvasnetlyqvvkevkpgglvqia dgtykdvqlivsnsgksglpitikalnpgkvfftgdakvelrgehlileg iwfkdgnraiqawkshgpglvaiygsynritacvfdcfdeansayittsl tedgkvpqhcridhcsftdkitfdqvinlnntaraikdgsvggpgmyhrv d--HCFFSNPQKPGNAGGGIRIGYYRNDiGRCLVDSNLFMRQDSEA---- -------------------------------------------------- -------------------------------------------------- ------------eiitsksqenvyygntylncqgtmnfrhgdhqvainnf yigndqrfgyggmfvwgsrhviacnyfelsetiksrgnaalylnpgamas ehalafdmliannafinvngyaihfnplderrkeycaanrlkfetphqlm lkgnlffkdkpyvypffkddyfiagknswtgnvalgvekgipvnisanrs aykpvkikdiqpiegialdlnaliskgitgkplswdevrpywlkempgty altarlsadraakfkavikrnkeh >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1ap9 mol:protein length:248 Bacteriorhodopsin qaqitgrpewiwlalgtalmglgtlyflvkgmgvsdpdakkfyaittlvp aiaftmylsmllgygltmvpfggeqnpiywaryadwlfttplllldlall vdadqgtilalvgadgimigtglvgaltkvysyrfvwwaistaamlyily vlffgftskaesmrpevastfkvlrnvtvvlwsay--------------- -------------------------------------------------- ----------------------------PVVWLIGSEGAGIVPLNIETL- ---------------------------------------------lfmvl dvsakvgfglillrsraifgeaeapepsagdgaaats >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1at9 mol:protein-het length:247 Bacteriorhodopsin xaqitgrpewiwlalgtalmglgtlyflvkgmgvsdpdakkfyaittlvp aiaftmylsmllgygltmvpfggeqnpiywaryadwlfttplllldlall vdadqgtilalvgadgimigtglvgaltkvysyrfvwwaistaamlyily vlffgftskaesmrpevastfkvlrnvtvvlwsay--------------- -------------------------------------------------- ----------------------------PVVWLIGSEGAGIVPLNIETL- ---------------------------------------------lfmvl dvsakvgfglillrsraifgeaeapepsadgaaats >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1bac mol:protein-het length:248 Rhodopsin (7-Helix Bundle) Complex With xaqitgrpewiwlalgtalmglgtlyflvkgmgvsdpdakkfyaittlvp aiaftmylsmllgygltmvpfggeqnpiywaryadwlfttplllldlall vdadqgtilalvgadgimigtglvgaltkvysyrfvwwaistaamlyily vlffgftskaesmrpevastfkvlrnvtvvlwsay--------------- -------------------------------------------------- ----------------------------PVVWLIGSEGAGIVPLNIETL- ---------------------------------------------lfmvl dvsakvgfglillrsraifgeaeapepsagdgaaats >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1bad mol:protein-het length:248 Bacteriorhodopsin (7-Helix Bundle) With xaqitgrpewiwlalgtalmglgtlyflvkgmgvsdpdakkfyaittlvp aiaftmylsmllgygltmvpfggeqnpiywaryadwlfttplllldlall vdadqgtilalvgadgimigtglvgaltkvysyrfvwwaistaamlyily vlffgftskaesmrpevastfkvlrnvtvvlwsay--------------- -------------------------------------------------- ----------------------------PVVWLIGSEGAGIVPLNIETL- ---------------------------------------------lfmvl dvsakvgfglillrsraifgeaeapepsagdgaaats >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1bm1 mol:protein-het length:247 Bacteriorhodopsin xaqitgrpewiwlalgtalmglgtlyflvkgmgvsdpdakkfyaittlvp aiaftmylsmllgygltmvpfggeqnpiywaryadwlfttplllldlall vdadqgtilalvgadgimigtglvgaltkvysyrfvwwaistaamlyily vlffgftskaesmrpevastfkvlrnvtvvlwsay--------------- -------------------------------------------------- ----------------------------PVVWLIGSEGAGIVPLNIETL- ---------------------------------------------lfmvl dvsakvgfglillrsraifgeaeapepsadgaaats >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1brd mol:protein-het length:248 Bacteriorhodopsin - Chain _ xaqitgrpewiwlalgtalmglgtlyflvkgmgvsdpdakkfyaittlvp aiaftmylsmllgygltmvpfggeqnpiywaryadwlfttplllldlall vdadqgtilalvgadgimigtglvgaltkvysyrfvwwaistaamlyily vlffgftskaesmrpevastfkvlrnvtvvlwsay--------------- -------------------------------------------------- ----------------------------PVVWLIGSEGAGIVPLNIETL- ---------------------------------------------lfmvl dvsakvgfglillrsraifgeaeapepsagdgaaats >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1brrA mol:protein-het length:247 Bacteriorhodopsin xaqitgrpewiwlalgtalmglgtlyflvkgmgvsdpdakkfyaittlvp aiaftmylsmllgygltmvpfggeqnpiywaryadwlfttplllldlall vdadqgtilalvgadgimigtglvgaltkvysyrfvwwaistaamlyily vlffgftskaesmrpevastfkvlrnvtvvlwsay--------------- -------------------------------------------------- ----------------------------PVVWLIGSEGAGIVPLNIETL- ---------------------------------------------lfmvl dvsakvgfglillrsraifgeaeapepsadgaaats >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1brrB mol:protein-het length:247 Bacteriorhodopsin xaqitgrpewiwlalgtalmglgtlyflvkgmgvsdpdakkfyaittlvp aiaftmylsmllgygltmvpfggeqnpiywaryadwlfttplllldlall vdadqgtilalvgadgimigtglvgaltkvysyrfvwwaistaamlyily vlffgftskaesmrpevastfkvlrnvtvvlwsay--------------- -------------------------------------------------- ----------------------------PVVWLIGSEGAGIVPLNIETL- ---------------------------------------------lfmvl dvsakvgfglillrsraifgeaeapepsadgaaats >T0093 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLD YHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY KGAVNLPEVK >1brrC mol:protein-het length:247 Bacteriorhodopsin xaqitgrpewiwlalgtalmglgtlyflvkgmgvsdpdakkfyaittlvp aiaftmylsmllgygltmvpfggeqnpiywaryadwlfttplllldlall vdadqgtilalvgadgimigtglvgaltkvysyrfvwwaistaamlyily vlffgftskaesmrpevastfkvlrnvtvvlwsay--------------- -------------------------------------------------- ----------------------------PVVWLIGSEGAGIVPLNIETL- ---------------------------------------------lfmvl dvsakvgfglillrsraifgeaeapepsadgaaats --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 T0093 AUTHOR UCSC SAM-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 1d8c_A L 31 L 46 I 32 A 47 E 33 P 48 P 34 E 49 L 35 N 50 G 36 R 51 F 37 Q 52 T 38 L 53 W 39 L 54 D 40 A 55 D 41 E 56 K 42 R 57 R 43 D 58 L 44 R 59 R 45 I 60 R 46 Q 61 S 47 A 62 G 48 A 63 L 49 L 64 D 50 D 65 Y 51 E 66 H 52 W 67 E 53 H 68 F 54 R 69 A 55 S 70 E 56 N 71 I 57 P 72 K 58 G 73 R 59 P 74 H 60 V 75 K 61 K 76 T 62 D 77 F 63 K 78 E 64 A 79 A 65 A 80 F 66 Y 81 L 67 K 82 E 68 S 83 S 69 F 84 E 70 L 85 K 71 R 86 P 72 E 87 K 73 L 88 R 74 G 89 L 75 Y 90 F 76 L 91 A 77 V 92 L 78 P 93 T 79 Q 94 T 80 P 95 K 81 E 96 G 82 R 97 C 83 V 98 P 84 T 99 A 85 V 100 E 102 E 101 T 103 T 102 R 104 T 103 G 105 G 104 I 106 I 105 P 107 D 106 M 108 S 107 S 109 E 108 I 110 I 109 L 111 T 110 N 112 S 111 E 113 Q 112 M 114 A 113 E 117 G 114 Q 118 P 115 K 119 Q 116 I 120 L 117 R 121 V 118 I 122 V 119 P 123 P 120 M 124 A 121 T 125 X 122 A 126 N 123 N 127 A 124 S 128 R 125 R 129 Y 126 S 130 A 127 M 131 L 128 N 132 N 129 L 133 A 130 S 134 A 131 N 135 N 132 S 136 A 133 V 137 R 134 A 138 W 135 V 139 G 136 T 140 S 137 V 141 L 138 Y 142 Y 139 E 143 D 140 A 144 A 141 W 145 L 142 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1rkd T 15 A 4 G 16 G 5 N 17 S 6 I 18 L 7 I 19 V 8 R 20 V 9 L 21 L 10 C 22 G 11 A 23 S 12 N 24 I 13 T 25 N 14 G 26 G 42 F 27 K 43 R 28 G 44 L 29 A 45 H 30 N 46 L 31 Q 47 I 32 A 48 E 33 V 49 P 34 A 50 L 35 A 51 G 36 G 52 F 37 G 70 T 38 E 71 W 39 S 72 D 40 V 73 D 41 R 74 K 42 Q 75 R 43 Q 76 L 44 L 77 R 45 A 78 R 46 T 79 S 47 D 80 G 48 N 81 L 49 I 82 D 50 D 83 Y 51 I 84 H 52 T 85 E 53 P 86 F 54 V 87 A 55 S 88 E 56 V 89 I 57 I 90 K 58 K 91 R 59 G 92 H 60 E 93 K 61 S 94 T 62 T 95 F 63 G 96 E 64 V 97 A 65 L 120 F 66 S 121 L 67 P 122 E 68 A 123 S 69 L 124 E 70 V 125 K 71 E 126 P 72 A 127 L 75 Q 128 F 76 R 129 A 77 E 130 L 78 R 131 T 79 P 145 T 80 L 146 K 81 E 147 G 82 S 148 C 83 V 149 P 84 M 150 A 85 A 151 H 86 A 152 S 87 A 153 Q 88 K 154 V 89 I 155 K 90 A 156 F 91 H 157 K 92 Q 158 L 93 N 159 G 94 K 160 D 95 T 161 Y 96 I 162 L 97 V 163 M 98 A 164 F 99 L 165 G 100 N 166 P 101 P 167 E 102 P 169 T 103 A 170 R 104 R 171 G 105 E 172 I 106 L 173 P 107 P 174 M 108 D 175 S 109 E 176 I 110 L 177 L 111 L 178 N 112 A 179 E 113 L 180 I 122 D 182 P 123 I 183 M 124 I 184 T 125 T 185 A 126 P 186 N 127 N 187 S 128 D 249 R 129 T 250 S 130 I 251 M 131 A 252 N 132 A 253 L 133 G 254 S 134 D 255 N 135 T 256 S 136 F 257 V 137 N 258 A 138 G 259 V 139 A 260 T 140 L 261 V 141 I 262 Y 142 P 272 E 143 E 273 A 144 A 274 W 145 I 275 R 146 R 276 Q 147 F 277 L 148 A 278 G 149 H 279 Y 150 A 280 K 151 A 281 G 152 A 282 A 153 A 283 V 154 I 284 N 155 A 285 L 156 V 286 P 157 T 287 E 158 R 288 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1bhg_A M 1 G 377 L 2 A 378 D 3 N 379 I 4 A 380 V 5 F 381 L 6 R 382 Y 7 T 383 E 8 S 384 P 9 H 385 E 10 Y 386 T 15 Y 388 G 16 A 389 N 17 E 390 I 18 E 391 I 19 V 392 R 20 Q 394 L 21 M 395 C 22 C 396 A 23 D 397 N 24 R 398 T 25 Y 399 G 26 G 400 F 27 I 401 R 28 V 402 L 29 V 403 H 30 I 404 L 31 D 405 I 32 E 406 E 33 C 407 P 34 P 408 L 35 G 409 G 36 V 410 F 37 M 430 T 38 E 431 W 39 E 432 D 40 V 433 D 41 V 434 K 42 R 435 R 43 R 436 L 44 D 437 R 45 K 438 R 46 N 439 S 47 H 440 G 48 P 441 L 49 V 443 D 50 V 444 Y 51 M 445 H 52 W 446 E 53 S 447 F 54 V 448 A 55 A 449 E 56 A 459 I 57 G 460 K 58 Y 461 R 59 Y 462 H 60 L 463 K 61 K 464 T 62 M 465 F 63 V 466 E 64 I 467 A 65 A 468 F 66 H 469 L 67 T 470 E 68 K 471 S 69 S 472 E 70 L 473 K 71 D 474 P 72 P 475 K 73 S 476 R 74 R 477 L 75 P 478 F 76 V 479 A 77 T 480 L 78 F 481 T 79 V 482 T 80 S 483 K 81 N 484 G 82 S 485 C 83 N 486 P 84 Y 487 A 85 A 488 H 86 A 489 S 87 D 490 V 89 K 491 K 90 G 492 F 91 A 493 K 92 P 494 L 93 Y 495 G 94 V 496 D 95 D 497 Y 96 V 498 L 97 I 499 M 98 C 500 F 99 L 501 G 100 N 502 P 101 S 503 E 102 Y 504 T 103 Y 505 R 104 S 506 G 105 W 507 I 106 Q 520 P 107 L 521 M 108 A 522 S 109 T 523 I 110 Q 524 L 111 F 525 N 112 E 526 E 113 N 527 M 114 W 528 P 115 Y 529 M 116 K 530 E 117 K 531 Q 118 Y 532 K 119 Q 533 I 120 K 534 R 121 P 535 I 122 I 536 P 123 I 537 M 124 Q 538 T 125 S 539 A 126 E 540 N 127 Y 541 S 128 G 542 R 129 A 543 S 130 E 544 M 131 T 545 N 132 I 546 L 133 Y 561 S 134 Q 562 N 135 K 563 S 136 S 564 V 137 L 565 A 138 L 566 V 139 E 567 T 140 Q 568 V 141 Y 569 Y 142 H 570 E 143 L 571 A 144 G 572 W 145 L 573 R 146 D 574 Q 147 Q 575 L 148 K 576 G 149 R 577 Y 150 V 581 K 151 V 582 G 152 G 583 A 153 E 584 V 154 L 585 N 155 I 586 L 156 W 587 P 157 N 588 E 158 F 589 V 159 A 590 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1a0p I 4 K 111 V 5 D 112 L 6 L 113 Y 7 S 114 E 8 E 115 P 9 A 116 E 10 Q 117 I 11 V 118 P 12 E 132 Q 13 L 133 N 14 R 134 T 15 D 135 G 16 K 136 N 17 A 137 I 18 M 138 I 19 L 139 R 20 E 140 L 21 V 141 C 22 L 142 A 23 Y 143 N 24 A 144 T 25 T 145 G 26 G 146 F 27 L 147 R 28 R 148 L 29 V 149 H 30 S 150 E 33 E 151 P 34 L 152 L 35 V 153 G 36 G 154 F 37 L 155 T 38 T 156 W 39 M 157 D 40 S 158 D 41 D 159 K 42 I 160 R 43 S 161 L 44 L 162 R 45 R 163 R 46 Q 164 S 47 G 165 G 48 V 166 L 49 V 167 D 50 R 168 Y 51 V 169 H 52 I 170 E 53 G 171 F 54 K 172 A 55 G 173 E 56 N 174 I 57 K 175 K 58 E 176 R 59 R 177 H 60 L 178 K 61 Y 187 T 62 W 188 F 63 L 189 E 64 E 190 A 65 T 191 F 66 Y 192 L 67 L 193 E 68 E 194 S 69 G 203 E 70 V 204 K 71 S 205 P 72 I 206 K 73 D 207 R 74 V 208 L 75 L 209 F 76 F 210 A 77 P 211 L 78 M 218 T 79 T 219 T 80 R 220 K 81 E 239 G 82 K 240 C 83 L 241 P 84 S 242 A 85 P 243 H 86 H 244 S 87 V 245 Q 88 L 246 V 89 R 247 K 90 H 248 F 91 A 249 K 92 F 250 L 93 A 251 G 94 T 252 D 95 H 253 Y 96 L 254 L 97 L 255 M 98 N 256 F 99 H 257 G 100 G 258 P 101 A 259 E 102 D 260 T 103 L 261 R 104 R 262 G 105 V 263 I 106 V 264 P 107 Q 265 M 108 M 266 S 109 Q 277 I 110 I 278 L 111 Y 279 N 112 T 280 E 113 H 281 M 114 V 282 P 115 A 283 M 116 T 284 E 117 E 285 Q 118 R 286 K 119 L 287 I 120 R 288 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1bct G 94 P 186 D 95 V 187 Y 96 V 188 L 97 W 189 M 98 L 190 F 99 I 191 G 100 G 192 P 101 S 193 E 102 E 194 T 103 G 195 R 104 A 196 G 105 G 197 I 106 I 198 P 107 V 199 M 108 P 200 S 109 L 201 I 110 N 202 L 111 I 203 N 112 E 204 E 113 T 205 M 114 L 206 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1cdo_A Y 51 A 14 H 52 W 15 E 53 E 16 F 54 A 17 A 55 N 18 E 56 K 19 I 57 P 20 K 58 L 21 R 59 V 22 H 60 I 23 K 61 E 24 T 62 E 25 F 63 I 26 E 64 E 27 A 65 V 28 F 66 D 29 L 67 V 30 E 68 P 31 S 69 H 32 E 70 A 33 K 71 N 34 P 72 E 35 K 73 I 36 R 74 R 37 L 75 I 38 F 76 K 39 A 77 I 40 L 78 I 41 T 79 A 42 T 80 T 43 K 81 T 48 G 82 D 49 C 83 L 50 P 84 Y 51 A 85 H 52 H 86 L 53 S 87 F 54 Q 88 E 55 V 89 G 56 K 90 K 57 F 91 H 58 K 92 K 59 L 93 D 60 G 94 G 61 D 95 F 62 Y 96 P 63 L 97 V 64 M 98 V 65 F 99 L 66 G 100 G 67 P 101 H 68 E 102 E 69 T 103 G 70 R 104 A 71 G 105 G 72 I 106 I 73 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1cdo_B Y 51 A 14 H 52 W 15 E 53 E 16 F 54 A 17 A 55 N 18 E 56 K 19 I 57 P 20 K 58 L 21 R 59 V 22 H 60 I 23 K 61 E 24 T 62 E 25 F 63 I 26 E 64 E 27 A 65 V 28 F 66 D 29 L 67 V 30 E 68 P 31 S 69 H 32 E 70 A 33 K 71 N 34 P 72 E 35 K 73 I 36 R 74 R 37 L 75 I 38 F 76 K 39 A 77 I 40 L 78 I 41 T 79 A 42 T 80 T 43 K 81 T 48 G 82 D 49 C 83 L 50 P 84 Y 51 A 85 H 52 H 86 L 53 S 87 F 54 Q 88 E 55 V 89 G 56 K 90 K 57 F 91 H 58 K 92 K 59 L 93 D 60 G 94 G 61 D 95 F 62 Y 96 P 63 L 97 V 64 M 98 V 65 F 99 L 66 G 100 G 67 P 101 H 68 E 102 E 69 T 103 G 70 R 104 A 71 G 105 G 72 I 106 I 73 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1ede N 17 K 65 I 18 M 66 I 19 I 67 R 20 P 68 L 21 V 69 C 22 F 70 A 23 A 71 N 24 E 72 T 25 S 73 G 26 G 74 F 27 A 75 R 28 R 76 L 29 V 77 H 30 I 78 L 31 A 79 I 32 P 80 E 33 D 81 P 34 F 82 L 35 F 83 G 36 G 84 F 37 F 85 T 38 G 86 W 39 K 87 D 40 S 88 D 41 D 89 K 42 K 90 R 43 P 91 L 44 V 92 R 45 D 93 R 46 E 94 S 47 E 95 G 48 D 96 L 49 Y 97 D 50 T 98 Y 51 F 99 H 52 E 100 E 53 F 101 F 54 H 102 A 55 R 103 E 56 N 104 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1glc_G G 16 K 4 N 17 Y 5 I 18 I 6 I 19 V 7 R 20 A 8 L 21 L 9 C 22 D 10 A 23 Q 11 N 24 G 12 T 25 T 13 G 26 T 14 F 27 S 15 R 28 S 16 L 29 R 17 H 30 A 18 L 31 V 19 I 32 V 20 E 33 M 21 P 34 D 22 L 35 H 23 G 36 D 24 F 37 A 25 T 38 N 26 W 39 I 27 D 40 I 28 D 41 S 29 K 42 V 30 R 43 S 31 L 44 Q 32 R 45 R 33 R 46 E 34 S 47 F 35 G 48 E 36 L 49 Q 37 D 50 I 38 Y 51 D 48 H 52 P 49 E 53 M 50 F 54 E 51 A 55 I 52 E 56 W 53 I 57 A 54 K 58 T 55 R 59 Q 56 H 60 S 57 K 61 S 58 T 62 T 59 F 63 L 60 E 64 V 61 A 65 E 62 F 66 V 63 L 67 L 64 E 68 A 65 K 71 S 70 P 72 S 71 K 73 D 72 R 74 Q 73 L 75 I 74 F 76 A 248 A 77 A 249 L 78 L 250 T 79 F 251 T 80 G 252 K 81 Q 253 G 82 L 254 C 83 C 255 P 84 V 256 A 85 K 257 H 86 E 258 S 87 G 259 Q 88 M 260 V 89 A 261 K 90 K 262 F 91 N 263 K 92 T 264 L 93 Y 265 G 94 G 266 D 95 T 267 Y 96 G 268 L 97 C 269 M 98 F 270 F 99 M 271 G 100 L 272 P 101 M 273 E 102 N 274 T 103 T 275 R 104 G 276 G 105 E 297 I 106 V 298 P 107 N 299 M 108 Y 300 S 109 A 301 I 110 L 302 N 112 D 325 E 113 A 326 M 114 Y 327 P 115 D 328 M 116 S 329 E 117 E 330 Q 118 Y 386 K 119 Q 387 I 120 T 388 R 121 R 389 I 122 D 390 P 123 V 391 M 124 L 392 T 125 E 393 A 126 A 394 N 127 M 395 S 128 M 419 R 129 Q 420 S 130 F 421 M 131 Q 422 N 132 S 423 L 133 D 424 S 134 I 425 N 135 L 426 S 136 G 427 V 137 T 428 A 138 R 429 V 139 V 430 T 140 E 431 V 141 R 432 Y 142 P 433 E 143 E 434 A 144 V 435 W 145 R 436 R 146 E 437 Q 147 V 438 L 148 T 439 G 149 A 440 Y 150 L 441 K 151 G 442 G 152 A 443 A 153 A 444 V 154 Y 445 N 155 M 494 L 156 A 495 P 157 W 496 E 158 E 497 V 159 E 498 K 160 E _ TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1dbg_A D 3 H 202 I 4 C 203 V 5 F 204 L 6 F 205 Y 7 S 206 E 8 N 207 P 9 P 208 E 10 Q 209 I 11 K 210 P 12 P 211 Q 13 G 212 N 14 N 213 T 15 A 214 G 16 G 215 N 17 G 216 I 18 G 217 I 19 I 218 R 20 R 219 L 21 I 220 C 22 G 221 A 23 Y 222 N 24 Y 223 T 25 R 224 G 26 N 225 F 27 D 226 R 28 G 228 L 29 R 229 H 30 C 230 L 31 L 231 I 32 V 232 E 33 D 233 P 34 S 234 L 35 N 235 G 36 L 236 F 37 F 237 T 38 M 238 W 39 R 239 D 40 Q 240 D 41 D 241 K 42 S 242 R 43 E 243 L 44 A 244 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1dbo_A D 3 H 202 I 4 C 203 V 5 F 204 L 6 F 205 Y 7 S 206 E 8 N 207 P 9 P 208 E 10 Q 209 I 11 K 210 P 12 P 211 Q 13 G 212 N 14 N 213 T 15 A 214 G 16 G 215 N 17 G 216 I 18 G 217 I 19 I 218 R 20 R 219 L 21 I 220 C 22 G 221 A 23 Y 222 N 24 Y 223 T 25 R 224 G 26 N 225 F 27 D 226 R 28 G 228 L 29 R 229 H 30 C 230 L 31 L 231 I 32 V 232 E 33 D 233 P 34 S 234 L 35 N 235 G 36 L 236 F 37 F 237 T 38 M 238 W 39 R 239 D 40 Q 240 D 41 D 241 K 42 S 242 R 43 E 243 L 44 A 244 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1ap9 G 94 P 186 D 95 V 187 Y 96 V 188 L 97 W 189 M 98 L 190 F 99 I 191 G 100 G 192 P 101 S 193 E 102 E 194 T 103 G 195 R 104 A 196 G 105 G 197 I 106 I 198 P 107 V 199 M 108 P 200 S 109 L 201 I 110 N 202 L 111 I 203 N 112 E 204 E 113 T 205 M 114 L 206 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1at9 G 94 P 186 D 95 V 187 Y 96 V 188 L 97 W 189 M 98 L 190 F 99 I 191 G 100 G 192 P 101 S 193 E 102 E 194 T 103 G 195 R 104 A 196 G 105 G 197 I 106 I 198 P 107 V 199 M 108 P 200 S 109 L 201 I 110 N 202 L 111 I 203 N 112 E 204 E 113 T 205 M 114 L 206 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1bac G 94 P 186 D 95 V 187 Y 96 V 188 L 97 W 189 M 98 L 190 F 99 I 191 G 100 G _ P 101 S _ E 102 E _ T 103 G _ R 104 A _ G 105 G _ I 106 I _ P 107 V _ M 108 P _ S 109 L _ I 110 N 202 L 111 I 203 N 112 E 204 E 113 T 205 M 114 L 206 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1bad G 94 P 186 D 95 V 187 Y 96 V 188 L 97 W 189 M 98 L 190 F 99 I 191 G 100 G _ P 101 S _ E 102 E _ T 103 G _ R 104 A _ G 105 G _ I 106 I _ P 107 V _ M 108 P _ S 109 L _ I 110 N 202 L 111 I 203 N 112 E 204 E 113 T 205 M 114 L 206 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1bm1 G 94 P 186 D 95 V 187 Y 96 V 188 L 97 W 189 M 98 L 190 F 99 I 191 G 100 G 192 P 101 S 193 E 102 E 194 T 103 G 195 R 104 A 196 G 105 G 197 I 106 I 198 P 107 V 199 M 108 P 200 S 109 L 201 I 110 N 202 L 111 I 203 N 112 E 204 E 113 T 205 M 114 L 206 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1brd G 94 P 186 D 95 V 187 Y 96 V 188 L 97 W 189 M 98 L 190 F 99 I 191 G 100 G 192 P 101 S _ E 102 E _ T 103 G _ R 104 A _ G 105 G _ I 106 I _ P 107 V _ M 108 P _ S 109 L _ I 110 N 202 L 111 I 203 N 112 E 204 E 113 T 205 M 114 L 206 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1brr_A G 94 P 186 D 95 V 187 Y 96 V 188 L 97 W 189 M 98 L 190 F 99 I 191 G 100 G 192 P 101 S 193 E 102 E 194 T 103 G 195 R 104 A 196 G 105 G 197 I 106 I 198 P 107 V 199 M 108 P 200 S 109 L 201 I 110 N 202 L 111 I 203 N 112 E 204 E 113 T 205 M 114 L 206 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1brr_B G 94 P 186 D 95 V 187 Y 96 V 188 L 97 W 189 M 98 L 190 F 99 I 191 G 100 G 192 P 101 S 193 E 102 E 194 T 103 G 195 R 104 A 196 G 105 G 197 I 106 I 198 P 107 V 199 M 108 P 200 S 109 L 201 I 110 N 202 L 111 I 203 N 112 E 204 E 113 T 205 M 114 L 206 TER END PFRMAT AL TARGET T0093 AUTHOR UCSC SAM-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 1brr_C G 94 P 186 D 95 V 187 Y 96 V 188 L 97 W 189 M 98 L 190 F 99 I 191 G 100 G 192 P 101 S 193 E 102 E 194 T 103 G 195 R 104 A 196 G 105 G 197 I 106 I 198 P 107 V 199 M 108 P 200 S 109 L 201 I 110 N 202 L 111 I 203 N 112 E 204 E 113 T 205 M 114 L 206 TER END --simple mime boundary-- From farmer@cse.ucsc.edu Sat May 20 21:26:39 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 VAA15960 for Message-Id: <200005201930.MAA29969@alpha.cse.ucsc.edu> Subject: T0093(target 99 secondary structure prediction) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0093.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" >T0093 LEEEEEELLLLLLLHHHHHHHHHHHLLEEEEELLLLLLLLLHHHHHHHLLHHHHLLEEEELLHHHHHHHHHHLLEEEEELLLLLLHHHLLLLLLEEEEELLLLLLLLHHHHHHLLLLLEEEELLLLLLHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLL --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 T0093 AUTHOR UCSC Target99 server METHOD This prediction was derived from the following methods METHOD by averaging the corresponding probabilities: METHOD Method 0: METHOD TARGET T0093 METHOD Using neural net overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-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 EHL2 ) METHOD The input amino acid frequencies were determined from METHOD alignment /projects/compbio/tmp/hmm-target99-alpha-31977/target-align-31977.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 47.5325 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: T0093 METHOD model_file: ./tmp.alpha.17499/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: Sat May 20 12:28:28 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-31977/target-align-31977.a2m METHOD METHOD guide seq name: T0093 METHOD ###end 0 MODEL 1 M C 0.607 L E 0.525 D E 0.637 I E 0.688 V E 0.689 L E 0.632 Y E 0.498 E C 0.558 P C 0.632 E C 0.657 I C 0.758 P C 0.703 Q C 0.651 N C 0.638 T H 0.591 G H 0.617 N H 0.639 I H 0.67 I H 0.683 R H 0.698 L H 0.705 C H 0.707 A H 0.696 N H 0.672 T H 0.554 G C 0.64 F C 0.649 R E 0.481 L E 0.614 H E 0.658 L E 0.67 I E 0.6 E C 0.458 P C 0.584 L C 0.55 G C 0.502 F C 0.478 T C 0.473 W C 0.48 D C 0.515 D C 0.512 K H 0.643 R H 0.639 L H 0.644 R H 0.635 R H 0.642 S H 0.603 G H 0.528 L C 0.468 D C 0.501 Y H 0.459 H H 0.442 E H 0.434 F H 0.358 A C 0.38 E C 0.419 I E 0.48 K E 0.499 R E 0.474 H E 0.386 K C 0.458 T C 0.558 F H 0.724 E H 0.752 A H 0.763 F H 0.752 L H 0.754 E H 0.72 S H 0.683 E H 0.592 K H 0.51 P H 0.478 K C 0.584 R C 0.639 L E 0.433 F E 0.622 A E 0.672 L E 0.653 T E 0.553 T C 0.449 K C 0.628 G C 0.646 C C 0.594 P C 0.542 A C 0.538 H H 0.466 S H 0.479 Q H 0.484 V C 0.4 K C 0.486 F C 0.561 K C 0.625 L C 0.631 G C 0.585 D E 0.502 Y E 0.631 L E 0.691 M E 0.688 F E 0.629 G C 0.48 P C 0.601 E C 0.549 T C 0.482 R C 0.573 G C 0.717 I C 0.702 P C 0.662 M H 0.635 S H 0.658 I H 0.658 L H 0.647 N H 0.628 E H 0.6 M C 0.547 P C 0.624 M C 0.577 E C 0.597 Q C 0.455 K E 0.529 I E 0.612 R E 0.606 I E 0.49 P C 0.529 M C 0.577 T C 0.606 A C 0.573 N C 0.544 S C 0.494 R H 0.435 S H 0.514 M H 0.566 N H 0.572 L H 0.631 S H 0.657 N H 0.7 S H 0.712 V H 0.712 A H 0.713 V H 0.701 T H 0.699 V H 0.712 Y H 0.744 E H 0.748 A H 0.751 W H 0.735 R H 0.731 Q H 0.695 L H 0.617 G H 0.505 Y H 0.454 K C 0.455 G C 0.533 A C 0.493 V C 0.462 N C 0.483 L C 0.606 P C 0.643 E C 0.646 V C 0.657 K C 0.696 END --simple mime boundary--