From farmer@cse.ucsc.edu Tue Aug 22 21:10:12 2000 Return-Path: Received: from beta.cse.ucsc.edu (beta.cse.ucsc.edu [128.114.48.15]) by cyborg.bioinfo.pl (8.9.3/8.8.7) with SMTP id VAA02491 for Message-Id: <200008221916.MAA29212@beta.cse.ucsc.edu> Subject: T0124(target 99 alignment) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0124.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-966971784.t99align.a2m' Content-Disposition: attachment; filename="t99-results-966971784.t99align.a2m" >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREELLQKYSVLFLE PVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQHATEQTAKITELAREKQIAEL KALKESSESNIKDIKKKLEAKRLDRIQVMMRSTSDKAAQERLKKEINNSHIQEVVQTIKL LTEKTARYQQKLEEKQAENLRAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEV FP >gi|9438229|gb|AAF86613.1|_891:1166 (AY004175) phospholipase C beta 1 [Homo sapiens] etpseapsearttpaengvnhtttltpkppsqalhsqpapgsvkapakte -DLIQSVLTEVEAQTIEELKQQKSFVKLQKKHYKEMKDLVKRHHKKTTDL IKEHTTKYNEiqndylrrraaleksakkdskkksePSSPDHGSStieqdl aaldaemtqKLIDLKDKQQQQLLNLRQEQYYSEKYQKREHIKLLIQKLTD VAEECQNNQLKKLKEICEKEKKELKKKMDKKRQEKITEAK--SKDKSQME EEKTEMIRSYIQEVVQYIKRLEEAQSKRQEKLVEKHKEIRQQILDEKPKL QVELEQEYQDKFKRLPLEILEFVQEAMKG---kisedsnhgsaplslssd pgkvnhktpsseelggdipgkefdtpl >gi|9368448|emb|CAB98142.1|_896:1171 (AJ278313) phospholipase C-beta-1a [Homo sapiens] etpseapsearttpaengvnhtttltpkppsqalhsqpapgsvkapakte -DLIQSVLTEVEAQTIEELKQQKSFVKLQKKHYKEMKDLVKRHHKKTTDL IKEHTTKYNEiqndylrrraaleksakkdskkksePSSPDHGSStieqdl aaldaemtqKLIDLKDKQQQQLLNLRQEQYYSEKYQKREHIKLLIQKLTD VAEECQNNQLKKLKEICEKEKKELKKKMDKKRQEKITEAK--SKDKSQME EEKTEMIRSYIQEVVQYIKRLEEAQSKRQEKLVEKHKEIRQQILDEKPKL QVELEQEYQDKFKRLPLEILEFVQEAMKG---kisedsnhgsaplslssd pgkvnhktpsseelggdipgkefdtpl >gi|3043686|dbj|BAA25507.1|_378:653 (AB011153) KIAA0581 protein [Homo sapiens] etpseapsearttpaengvnhtttltpkppsqalhsqpapgsvkapakte -DLIQSVLTEVEAQTIEELKQQKSFVKLQKKHYKEMKDLVKRHHKKTTDL IKEHTTKYNEiqndylrrraaleksakkdskkksePSSPDHGSStieqdl aaldaemtqKLIDLKDKQQQQLLNLRQEQYYSEKYQKREHIKLLIQKLTD VAEECQNNQLKKLKEICEKEKKELKKKMDKKRQEKITEAK--SKDKSQME EEKTEMIRSYIQEVVQYIKRLEEAQSKRQEKLVEKHKEIRQQILDEKPKL QVELEQEYQDKFKRLPLEILEFVQEAMKG---kisedsnhgsaplslssd pgkvnhktpsseelggdipgkefdtpl >gi|130223|sp|P10687|PIP1_RAT_896:1171 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE BETA 1 (PLC-BETA-1) (PHOSPHOLIPASE C-BETA-1) (PLC-I) (PLC-154)gi|91896|pir||A28821 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase (EC 3.1.4.11) I - ratgi|206218|gb|AAA41885.1| (M20636) phospholipase C-1 [Rattus sp.] etsseapsetrttpaengvnhtatlapkppsqaphsqpapgsvkapakte -DLIQSVLTEVEAQTIEELKQQKSFVKLQKKHYKEMKDLVKRHHKKTTEL IKEHTTKYNEiqndylrrraaleksakkdskkksePSSPDHGSSaieqdl aaldaemtqKLIDLKDKQQQQLLNLRQEQYYSEKYQKREHIKLLIQKLTD VAEECQNNQLKKLKEICEKEKKELKKKMDKKRQEKITEAK--SKDKSQME EEKTEMIRSYIQEVVQYIKRLEEAQSKRQEKLVEKHKEIRQQILDEKPKL QMELEQEYQDKFKRLPLEILEFVQEAMKG---kvsedsnhgsappslasd pakvnlkspsseevqgenagrefdtpl >gi|130221|sp|P10894|PIP1_BOVIN_896:1171 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE BETA 1 (PLC-BETA-1) (PHOSPHOLIPASE C-BETA-1) (PLC-I) (PLC-154)gi|89334|pir||A28822 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase (EC 3.1.4.11) I - bovinegi|163522|gb|AAA30702.1| (J03137) phospholipase C [Bos taurus] etpseapsearptpaengvnhttsltpkppsqalhsqpapgsvkapakte -DLIQSVLTEVEAQTIEELKQQKSFVKLQKKHYKEMKDLVKRHHKKTTDL IKEHTTKYNEiqndylrrraalektakkdnkkksePSSPDHVSStieqdl aaldaemtqKLVDLKDKQQQQLLNLRQEQYYSEKYQKREHIKLLIQKLTD VAEECQNNQLKKLKEICEKEKKELKKKMDKKRQEKITEAK--SKDKSQME EEKTEMIRSYIQEVVQYIKRLEEAQSKRQEKLVEKHKEIRQQILDEKPKL QVELEQEYQDKFKRLPLEILEFVQEAMKG---kisedsnhssapplmtsd sgklnqkppsseelegenpgkefdtpl >gi|226908|prf||1611219A_896:1171 phospholipase C 154 [Bos taurus] etpseapsearptpaengvnhttsltpkppsqalhsqpapgsvkapakte -DLIQSVLTEVEAQTIEELKQQKSFVKLQKKHYKEMKDLVKRHHKKTTDL IKEHTTKYNEiqndylrrraalektakkdnkkksePSSPDHVSStieqdl aaldaemtqKLVDLKDKQQQQLLNLRQEQYYSEKYQKREHIKLLIQKLTD VAEECQNNQLKKLKEICEKEKKELKKKMDKKRQEKITEAK--SKDKSQME EEKTEMIRSYIQEVVQYIKRLEEAQSKRQEKLVEKHKEIRQQILDEKPKL QVELEQEYQDKFKRLPLEILEFVQEAMKG---kisedsnhssapplmtsd sgklnqkppsseelegenpgkefdtpl >gi|4099293|gb|AAD00571.1|_896:1171 (U85712) phospholipase C-beta-1a [Mus musculus] etsseapsetrttpaengvnhtaslapkppsqaphsqpapgsvkapakte -DLIQSVLTEVEAQTIEELKQQKSFVKLHKKHYKEMKDLVKRHHKKTTEL IKEHTTKYNEiqidylrrraaleksakkdskkksePSSPDHGSSaieqdl aaldaemtqKLIDLKDKQQQQLLNLRQEQYYSEKYQKREHIKLLIQKLTD VAEECQNNQLKKLKEICEKEKKELKKKMDKKRQEKITEAT--SKDKSQME EEKTEMIRSYIQEVVQYIKRLEEAQSKRQEKLVEKHNEIRQQILDEKPKL QTELEQEYQDKFKRLPLEILEFVQEAMKG---kisedsnhgsappslasd aakvnlkspsseeierenpgrefdtpl >gi|6807700|emb|CAB70666.1|_636:908 (AL137267) hypothetical protein [Homo sapiens] etpseapsearttpaengvnhtttltpkppsqalhsqpapgsvkapakte -DLIQSVLTEVEAQTIEELKQQKSFVKLQKKHYKEMKDLVKRHHKKTTDL IKEHTTKYNEiqndylrrraaleksakkdskkksePSSPDHGSStieqdl aaldaemtqKLIDLKDKQQQQLLNLRQEQYYSEKYQKREHIKLLIQKLTD VAEECQNNQLKKLKEICEKEKKELKKKMDKKRQEKITEAK--SKDKSQME EEKTEMIRSYIQEVVQYIKRLEEAQSKRQEKLVEKHKEIRQQILDEKPKG ------EGSSSFLSETCHEDPSVSPNFTPPNPqalkw >gi|9368450|emb|CAB98143.1|_896:1168 (AJ278314) phospholipase C-beta-1b [Homo sapiens] etpseapsearttpaengvnhtttltpkppsqalhsqpapgsvkapakte -DLIQSVLTEVEAQTIEELKQQKSFVKLQKKHYKEMKDLVKRHHKKTTDL IKEHTTKYNEiqndylrrraaleksakkdskkksePSSSDHGSStieqdl aaldaemtqKLIDLKDKQQQQLLNLRQEQYYSEKYQKREHIKLLIQKLTD VAEECQNNQLKKLKEICEKEKKELKKKMDKKRQEKITEAK--SKDKSQME EEKTEMIRSYIQEVVQYIKRLEEAQSKRQEKLVEKHKEIRQQILDEKPKG ------EGSSSFLSETCHEDPSVSPNFTPPNPqalkw >gi|4099295|gb|AAD00572.1|_896:1168 (U85713) phospholipase C-beta-1b [Mus musculus]gi|4099297|gb|AAD00573.1| (U85714) phospholipase C-beta-1b' [Mus musculus] etsseapsetrttpaengvnhtaslapkppsqaphsqpapgsvkapakte -DLIQSVLTEVEAQTIEELKQQKSFVKLHKKHYKEMKDLVKRHHKKTTEL IKEHTTKYNEiqidylrrraaleksakkdskkksePSSPDHGSSaieqdl aaldaemtqKLIDLKDKQQQQLLNLRQEQYYSEKYQKREHIKLLIQKLTD VAEECQNNQLKKLKEICEKEKKELKKKMDKKRQEKITEAT--SKDKSQME EEKTEMIRSYIQEVVQYIKRLEEAQSKRQEKLVEKHNEIRQQILDEKPKG ------EGPSSVLSEGCHEDPSVPPNFTPPNPqalkw >gi|1083573|pir||A53430_896:1168 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase (EC 3.1.4.11) beta-1b - rat etsseapsetrttpaengvnhtatlapkppsqaphsqpapgsvkapakte -DLIQSVLTEVEAQTIEELKQQKSFVKLQKKHYKEMKDLVKLHHKKTTEL IKEHTTKYNEiqndylrrraaleksakkdskkksePSSPDHGSSaieqdl aaldaemtqKLIDLKDKQQQQLLNLRQEQYYSEKYQKREHIKLLIQKLTD VAEECQNNQLKKLKEICEKEKKELKKKMDKKLQEKITEAK--SKDKSQME EEKTEMIRSYIQEVVQYIKRLEEAQSKRKEKLVEKHKEIRQQILDEKPKG ------EGSSSVLSESCHEDPSVPPNFTPPNPqalkw >gi|284352|pir||S27002_756:1017 phospholipase C (EC 3.1.4.3), phosphatidylinositol-specific - human (fragment)gi|38510|emb|CAA78903.1| (Z16411) phospholipase c [Homo sapiens] qetcqdtqsqqlgsqpssnptpspldasprrppgpttspastslsspgqr DDLIASILSEVAPTPLDELRGHKALVKLRSRQERDLRELRKKHQRKAVTL trrlldglaqAQAEGRCRLRPGALGGAADvedtkegedeakRYQEFQNRQ VQSLLELREAQVDAEAQRRLEHLRQALQRLREVVLDANTTQFKRLKEMNE REKKELQKILDRKRHNSISEAK--MRDKHKKEAELTEINRRHITESVNSI RRLEEAQKQRHDRLVAGQQQVLQQLAEEEPKLLAQLAQECQEQRARLPQE IRRSLLGEMPEGLGdgplvacasnghapgssghlsgadsesqeentql >gi|1730573|sp|Q01970|PIP3_HUMAN_939:1200 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE BETA 3 (PLC-BETA-3) (PHOSPHOLIPASE C-BETA-3)gi|7435175|pir||I38994 phospholipase C-beta-3 - humangi|836665|gb|AAA77683.1| (U26425) phospholipase C-beta-3 [Homo sapiens] qetcqdtqsqqlgsqpssnptpspldasprrppgpttspastslsspgqr DDLIASILSEVAPTPLDELRGHKALVKLRSRQERDLRELRKKHQRKAVTL trrlldglaqAQAEGRCRLRPGALGGAADvedtkegedeakRYQEFQNRQ VQSLLELREAQVDAEAQRRLEHLRQALQRLREVVLDANTTQFKRLKEMNE REKKELQKILDRKRHNSISEAK--MRDKHKKEAELTEINRRHITESVNSI RRLEEAQKQRHDRLVAGQQQVLQQLAEEEPKLLAQLAQECQEQRARLPQE IRRSLLGEMPEGLGdgplvacasnghapgssghlsgadsesqeentql >gi|4505867|ref|NP_000924.1|_750:1021 phospholipase C, beta 4gi|762826|gb|AAB02027.1| (L41349) phospholipase C beta 4 [Homo sapiens] ramgietsdiadvpsdtskndkkgkantakanvtpqssselrptttaalp SGVEAKKGIELIPqVRIEDLKQMKAYLKHLKKQQKELNSLKKKHAKEHST MQKLHCTQVDKIVAQYdkeksthekilekamkkkGGSNclemkketeiki qtltsdhksKVKEIVAQHTKEWSEMINTHSAEEQEIRDLHLSQQCELLKK LLINAHEQQTQQLKLSHDRESKEMRAHQAKISMENSKAIsqDKSIKNKAE RERRVRELNSSNTKKFLEERKRLAMKQSKEMDQLKKVQLEHLEFLEkqnE QAKEMQQMVKLEAEMDRRPATV---------------v >gi|543433|pir||A48047_904:1175 phospholipase C (EC 3.1.4.- ) beta-4 - ratgi|435757|gb|AAB28484.1| phospholipase C-beta 4, PLC-beta 4 [rats, brain, Peptide, 1176 aa] ramgietsdiadvpsdtskndkkgkanpakanvtpqssselrptttaalg SGQEAKKGIELIPqVRIEDLKQMKAYLKHLKKQQKELNSLKKKHAKEHST MQKLHCTQVDKIVAQYdkeksthekilekamkkkGGSNcleikketeiki qtltsdhksKVKEIVAQHTKEWSEMINTHSAEEQEIRDLHLSQQCELLRK LLINAHEQQTQQLKLSHDRESKEMRAHQAKISMENSKAIsqDKSIKNKAE RERRVRELNSSNTKKFLEERKRLAMKQSKEMDQLKKVQLEHLEFLEkqnE QAKEMQQMVKLEAEMDRRPATV---------------v >gi|7110695|ref|NP_032900.1|pPlcb3_940:1200 phospholipase C, beta 3gi|1730574|sp|P51432|PIP3_MOUSE 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE BETA 3 (PLC-BETA-3) (PHOSPHOLIPASE C-BETA-3)gi|1150880|gb|AAA85199.1| (U43144) phospholipase C beta3 [Mus musculus] tetyqetpcqqpgsqlpsnptpnpldasprwppgpttsstssslsspgqr DDLIASILSEVTPTPLEELRSHKAMVKLRSRQDRDLRELHKKHQRKAVAL trrlldglAQARAEGKCRPSPSALGKAtnsedvkeeeeakQYREFQNRQV QSLLELREAQADVETKRKLEHLRQAHQRLKEVVLDTHTTQFKRLKELNER EKKELQKILDRKRNNSISEAK--TREKHKKEVELTEINRRHITESVNSIR RLEEAQKQRHERLVAGQQQVLQQLEEEEPKLLAQLTQECQEQRERLPQEI RRCLLGETAEGLGdgplvacasnghapgsgghlssadsesqeentql >gi|4758938|ref|NP_004564.1|_874:1147 phospholipase C, beta 2gi|400793|sp|Q00722|PIP2_HUMAN 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE BETA 2 (PLC-BETA-2) (PHOSPHOLIPASE C-BETA-2)gi|346297|pir||A43346 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase (EC 3.1.4.11) beta-2 - humangi|190040|gb|AAA36453.1| (M95678) phospholipase C-beta-2 [Homo sapiens] tksvklkeamgglpekpfplaspvasqvngalaptsngspaaragareea ----MKEAAEPRTASLEELRELKGVVKLQRRHEKELRELERRGARRWEEL LQRGAAQLAELGPPGvggvgacklgpgkgsrkkrslpreesagaapgegp eGVDGRVRELKDRLELELLRQGEEQYECVLKRKEQHVAEQISKMMELARE KQAAELKALKETSENDTKEMKKKLETKRLERIQGMTKVTTDKMAQERLKR EINNSHIQEVVQVIKQMTENLERHQEKLEEKQAACLEQIREMEKQFQKEA LAEYEARMKGLEAEVKESVRACLRTCFPseakdkperacecppelceqdp liakadaqesrl >gi|304243|gb|AAA30700.1|_636:906 (L13937) phospholipase C [Bos taurus] amgietsdiadvpsdtskndkkgkantakanvtpqssselrptttaalga -GLEAKKGIELIPqVRIEDLKQMKAYLKHLKKQQKELSSLKKKHAKEHST MQKLHCTQVDKIVAQYdkeklthekilekamkkkGGSNclemkketeiki qtltsdhksKVKEIVAQHTKEWSDMINTHSAEEQEIRDLLLSQQCELLRK LLISAHEQQTQQLKLSHDRESKEMRAHQAKISMENSKAIsqDKSIKNKAE RERRVRELNSSNTKKFLEERKRLAMKQSKEMDQLKKVQLEHLEFVEkqnE QAKEMQQMVKLEAEMDRRPATV---------------v >gi|304245|gb|AAA30701.1|_648:918 (L13938) phospholipase C [Bos taurus] amgietsdiadvpsdtskndkkgkantakanvtpqssselrptttaalga -GLEAKKGIELIPqVRIEDLKQMKAYLKHLKKQQKELSSLKKKHAKEHST MQKLHCTQVDKIVAQYdkeklthekilekamkkkGGSNclemkketeiki qtltsdhksKVKEIVAQHTKEWSDMINTHSAEEQEIRDLLLSQQCELLRK LLISAHEQQTQQLKLSHDRESKEMRAHQAKISMENSKAIsqDKSIKNKAE RERRVRELNSSNTKKFLEERKRLAMKQSKEMDQLKKVQLEHLEFVEkqnE QAKEMQQMVKLEAEMDRRPATV---------------v >gi|304239|gb|AAC37304.1|_740:1010 (L13935) phospholipase C [Bos taurus] amgietsdiadvpsdtskndkkgkantakanvtpqssselrptttaalga -GLEAKKGIELIPqVRIEDLKQMKAYLKHLKKQQKELSSLKKKHAKEHST MQKLHCTQVDKIVAQYdkeklthekilekamkkkGGSNclemkketeiki qtltsdhksKVKEIVAQHTKEWSDMINTHSAEEQEIRDLLLSQQCELLRK LLISAHEQQTQQLKLSHDRESKEMRAHQAKISMENSKAIsqDKSIKNKAE RERRVRELNSSNTKKFLEERKRLAMKQSKEMDQLKKVQLEHLEFVEkqnE QAKEMQQMVKLEAEMDRRPATV---------------v >gi|1083064|pir||B38932_752:1022 phospholipase C (EC 3.1.4.3) beta-I form B - bovine (fragment)gi|304241|gb|AAA30699.1| (L13936) phospholipase C [Bos taurus] amgietsdiadvpsdtskndkkgkantakanvtpqssselrptttaalga -GLEAKKGIELIPqVRIEDLKQMKAYLKHLKKQQKELSSLKKKHAKEHST MQKLHCTQVDKIVAQYdkeklthekilekamkkkGGSNclemkketeiki qtltsdhksKVKEIVAQHTKEWSDMINTHSAEEQEIRDLLLSQQCELLRK LLISAHEQQTQQLKLSHDRESKEMRAHQAKISMENSKAIsqDKSIKNKAE RERRVRELNSSNTKKFLEERKRLAMKQSKEMDQLKKVQLEHLEFVEkqnE QAKEMQQMVKLEAEMDRRPATV---------------v >gi|1079311|pir||A48001_913:1169 phospholipase C (EC 3.1.4.3) beta, oocyte - African clawed froggi|405590|gb|AAA03065.1| (L20816) phospholipase C beta type [Xenopus laevis]gi|2706546|emb|CAA75861.1| (Y15901) phospholipase C beta type [Xenopus laevis] aalmgeneqpfnkdkidwdpiskppirsrddtpekikipiipvpsppaqr DDHIASVLTDIQAPSMEELKSQKSFEKLICRQYRELRQLRRKHLRKVSSL CKEQSTWVTPLQSLRrrkpfgrshrGVSGadqdaeqKLMDMQRDQQKRLL ELREIQHEQERKLKHSHLLQAVQKLQEVAISYHSTQLKKLKEINEKEKKE LQKILDRKRHNSITEAK--SRERQKKDVELTEINRRHINESVSSIRRLEE AQKRRQEKLQTAHQETLQRIKDEEPKLQAQLDEACQAEFCQLPQEVRRYL QEDGWVGSGsgppssshssppsitrswgsesgekdslhspgdssdeatrl >gi|2134446|pir||S68251_880:1154 phospholipase C, inositol-lipid specific (EC 3.1.4.-) isoform beta - turkeygi|1223920|gb|AAC60011.1| (U49431) phospholipase C beta [Meleagris gallopavo] nlkdgseverpdmqrnfsfpenngipestrifstpfangpagaaalvkdg NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRgkkrsmhsrktqkkrslttgdvgtcmqpvemaeKL DSQVVELKERLEMELIHLGEEYHDGIRRRKEQHATEQTAKITELAREKQI AELKALKESSESNIKDIKKKLEAKRLDRIQVMMRSTSDKAAQERLKKEIN NSHIQEVVQTIKLLTEKTARYQQKLEEKQAENLRAIQEKEGQLQQEAVAE YEEKLKTLTVEVQEMVKNYMKEVFPdgpeiqkeavlsipveeqgstkqle ekipgaevprltaatteppgaetdi >gi|423977|pir||A45493_921:1183 phospholipase C-beta 3 - rat (fragment) temcqetpsqqqgsqlssnpvpnplddsprwppgpttsptstslsspgqr DDLIASILSEVTPTPLEELRSHKAMVKLRSRQDRDLRELHKKHQRKAVAL trrlldglAQARAEGKCRPSSSAlsratNVEDvkeeekeaarQYREFQNR QVQSLLELREAQADAETERRLEHLKQAQQRLREVVLDAHTTQFKRLKELN EREKKELQKILDRKRNNSISEAK--TREKHKKEVELTEINRRHITESVNS IRRLEEAQKQRHERLLAGQQQVLQQLVEEEPKLVAQLTQECQEQRERLPQ EIRRCLLGETSEGLGdgplvacasnghaagsgghqsgadsesqeentql >gi|1172512|sp|P13217|PIPA_DROME_859:1094 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE (PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C)gi|157981|gb|AAA28724.1| (J03138) phospholipase C [Drosophila melanogaster] vpdgfedfmamlsdprgfagaakqqneqmkalgieeqsggaardagkake --EEKKEPPLVfEPVTLESLRQEKGFQKVGKKQIKELDTLRKKHAKERTS VQKTQNAAIDKLIKGKSKDDirndaNIKNSINDQTKQWTDMIARHRKEEW DMLRQHVQDSQDAMKALMLTVQAAQIKQLEDRHARDIKDLNAKQAKMSAD TAKEVqnDKTLKTKNEKDRRLREKRQNNVKRFMEEKKQIGVKQGRAMEKL KLAHS---KQIEEFSTDVQKLMDMYKIEEEAYKTQGKTEFC--------- a >gi|85099|pir||A31225_859:1094 phospholipase C (EC 3.1.4.3) - fruit fly (Drosophila melanogaster) vpdgfedfmamlsdprgfagaakqqneqmkalgieeqsggaardagkake --EEKKEPPLVfEPVTLESLRQEKGFQKVGKKQIKELDTLRKKHAKERTS VQKTQNAAIDKLIKGKSKDDirndaNIKNSINDQTKQWTDMIARHRKEEW DMLRQHVQDSQDAMKALMLTVQAAQIKQLEDRHARDIKDLNAKQAKMSAD TAKEVqnDKTLKTKNEKDRRLREKRQNNVKRFMEEKKQIGVKQGRAMEKL KLAHS---KQIEEFSTDVQKLMDMYKIEEEAYKTQGKTEFC--------- a >gi|7494881|pir||T33283_495:821 hypothetical protein B0348.3 - Caenorhabditis elegansgi|3168960|gb|AAC17811.1| (AF068714) contains similarity to C2 domains (Pfam: C2.hmm, score: 108.46) and to phophatidylinositol-specific phospholipase C, X domains (Pfam: PI-PLC-Y.hmm. score: 204.05) [Caenorhabditis elegans] dsdipdvpntrnmalrhvkqpprqngssadllanngqtgsargdqtssma SSTIRSPNEQPQPVavdkfkvdpiEVDDLRRDKAFAKLLKRFQKELDDLR KKHQKQRDSIQKQQQTNVDKlitnnrrstkkekgsrrsltasvssgcgsa sgtvtvsvcspsgascsgystggPSTPVACNSdgtgspatigspvpqdlv nndRVRSLVNTQTGEWSAMVRRHDEEEFELKKVQLKEQFDLLRKLMSEAQ KNQMLALKLRLEAEGKDLKQTQTKKSMEDAKVIqlDKGIKTKAERDRRVK ELNEKNLKMFVEERKRLAMKAQKHEEQLTKRHL---DQLEQLDKDFHKAL DAEIHANnfLNIPPRKIDKSIAFFSKEYLIqllnrktp >gi|5901838|gb|AAD55427.1|AF181641_1_859:1094 (AF181641) norpA [Drosophila melanogaster] vpdgfedfmamlsdprgfagaakqqneqmkalgieeqsggaardagkake --EEKKEPPLVfEPVTLESLRQEKGFQKVGKKQIKELDTLRKKHAKERTS VQKTQNAAIDKLIKGKSKDDirndaNIKNSINDQTKQWTDMIARHRKEEW DMLRQHVQDSQDAMKALMLTVQAAQIKQLEDRHARDIKDLNAKQAKMSAD TAKEVqnDKTLKTKNEKDRRLREKRQNNVKRFMEEKKQIGVKQGRAMEKL KLAHS---KQIEEFSTDVQKLMDMYKIEEEAYKTQGKTEFY--------- a >gi|3688530|emb|CAA09465.1|_882:1149 (AJ011035) phospholipase C beta 2 [Rattus norvegicus] kksvklkevtgslpeklfsgipvasqsngapvsagngstapgtkakeeat -----KEVAEPQTTSLEELRELKGVVKLQRRHEKELRELERRGARRWEEL LQRGAAQLAELQDPAascklrpgkgsrkkrivpceetivvprevleGPDP RVQDLKDRLEQELQQQGEEQYRSVLKRKEQHVTEQIAKMMELAREKQAAE LKSFKETSETDTKEMKKKLEAKRLERIQAMTKVTTDKVAQERLKREINNS HIQEVVQAVKQMTETLERHQEKLEEKQTACLEQIQAMEKQFQEKALAEYE AKMKGLEAEVKESMRACFKACFPteaeekperpceaseescpqeplvnkt dtqesrl >gi|3282557|gb|AAC24984.1|_456:716 (AF027571) phospholipase C-beta 4 isoform [Rattus norvegicus] ramgietsdiadvpsdtskndkkgkanpakanvtpqssselrptttaalg SGQEAKKGIELIPqVRIEDLKQMKAYLKHLKKQQKELNSLKKKHAKEHST MQKLHCTQVDKIVAQYdkeksthekilekamkkkGGSNcleikketeiki qtltsdhksKVKEIVAQHTKECSEMINTHSAEEQEIRDLHMSQQCELLRK LLINVHEQQTQQLKVSHDRESKEMRAHQAKICMENSKAIsqDKSIKNKAE RERRVRELNSSNTKKFLEERKRLAMKQSKEMDQLKKVQLEHLEFLEKQNE QLLKSCHAVSQ-----------------------tqgegdaadgeigsrd gpqtsnssmklqnan >gi|1082692|pir||S52099_939:1200 phospholipase C beta 3 - humangi|829153|emb|CAA85776.1| (Z37544) phospholipase C beta 3 [Homo sapiens] qetcqdtqsqqlgsqpssnptpspldasprrppgpttspastslsspgqr DDLIASILSEVAPTPLDELRGHKALVKLRSRQERDLRELRKKHQRKAVTL trrlldglaqAQAEGRCRLRPGALGGAADvedtkegedeakRYQEFQNRQ VQSLLELREAQVDAEAQRRLEHLRQALQRLREVVLDANTTQFKRLKEMNE SWPSWPRSVRSSGRGSP----RRSAGACWARCRRgeLTEINRRHITESVN SIRRLEEAQKQRHDRLVAGQQQVLQQLAEEEPKLLAQLAQECQEQRARLP QEIRRSLLGEMPEGLGdgplvacasnghapgssghlsgadsesqeentql >gi|7511518|pir||T37264_1102:1417 phospholipase C (EC 3.1.4.-) beta - Caenorhabditis elegansgi|6014683|gb|AAF01458.1|AF188477_1 (AF188477) phospholipase C beta [Caenorhabditis elegans] dsdipdvpntrnmalrhvkqpprqngssadllanngqtgsargdqtssma SSTIRSPNEQPQPVavdkfkvdpiEVDDLRRDKAFAKLLKRFQKELDDLR KKHQKQRDSIQKQQQTNVDKlitnnrrstkkekgsrrsltasvssgcgsa sgtvtvsvcspsgascsgystggPSTPVACNSdgtgspatigspvpqdlv nndRVRSLVNTQTGEWSAMVRRHDEEEFELKKVQLKEQFDLLRKLMSEAQ KNQMLALKLRLEAEGKDLKQTQTKKSMEDAKVIqlDKGIKTKAERDRRVK ELNEKNLKMFVEERKRLAMKAQKHEEQLTKRHL---DQLEQLDKDFHKAL DAEVgnykEEQLAAQPTSV-------------v >gi|6179894|gb|AAF05701.1|AF179426_1_1103:1430 (AF179426) phospholipase C beta homolog EGL-8 [Caenorhabditis elegans] dsdipdvpntrnmalrhvkqpprqngssadllanngqtgsargdqtssma SSTIRSPNEQPQPVavdkfkvdpiEVDDLRRDKAFAKLLKRFQKELDDLR KKHQKQRDSIQKQQPARRRNssiawiqtnvdklitnnrrstkkekgsrrs ltasvssgcgsasgtvtvsvcspsgascsgystggPSTPVACNSdgtgsp atigspvpqdlvnndRVRSLVNTQTGEWSAMVRRHDEEEFELKKVQLKEQ FDLLRKLMSEAQKNQMLALKLRLEAEGKDLKQTQTKKSMEDAKVIqlDKG IKTKAERDRRVKELNEKNLKMFVEERKRLAMKAQKHEEQLTKRHL---DQ LEQLDKDFHKALDAEVgnykEEQLAAQPTSV-------------v >gi|130222|sp|P25455|PIP1_DROME_987:1266 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE CLASSES I AND II (PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C)gi|103302|pir||B40879 phospholipase C (EC 3.1.4.3), neuronal, long splice form - fruit fly (Drosophila melanogaster)gi|158133|gb|AAA28820.1| (M60453) phospholipase C [Drosophila melanogaster] vdvtvdrtdggrgedsisivapsiqhqhsldqsvstsirqvessqfdvdl ----------VLAEPLEKILDHKSVKEKRLEMEKKLESLRKKHDKEKIKI aGQKSSPLEGKkpkfaitnklvkrlsnkslnclsphsepgveiPACPLdl gdsseesaaadagedlaGGSSsldgrtqesRLRSACREYTSQYRELQEKY HEAIYSAAE-----------KVLKTSQTGQTKQLKASLDKVTGEVMHQLQ EARRNEVKNLATVHRDRDELIRMKREVASSVVERGVAERVRLKQTFDRRT DELQKQHDSVRNALAEHRSKARQILDKEAESRSCVSSNGFL--VLFHGPH HHGctgsgssalsgnnltlnldagaagshsaispakshnsiaaaaemkt >gi|7296215|gb|AAF51507.1|_987:1266 (AE003589) Plc21C gene product [Drosophila melanogaster] vdvtvdrtdggrgedsisivapsiqhqhsldqsvstsirqvessqfdvdl ----------VLAEPLEKILDHKSVKEKRLEMEKKLESLRKKHDKEKIKI aGQKSSPLEGKkpkfaitnklvkrlsnkslnclsphsepgveiPACPLdl gdsseesaaadagedlaGGSSsldgrtqesRLRSACREYTSQYRELQEKY HEAIYSAAE-----------KVLKTSQTGQTKQLKASLDKVTGEVMHQLQ EARRNEVKNLATVHRDRDELIRMKREVASSVVERGVAERVRLKQTFDRRT DELQKQHDSVRNALAEHRSKARQILDKEAESRSCVSSNGFL--VLFHGPH HHGctgsgssalsgnnltlnldagaagshsaispakshnsiaaaaemkt >gi|103301|pir||A40879_987:1259 phospholipase C (EC 3.1.4.3), neuronal - fruit fly (Drosophila melanogaster)gi|158131|gb|AAA28819.1| (M60452) phospholipase C [Drosophila melanogaster] vdvtvdrtdggrgedsisivapsiqhqhsldqsvstsirqvessqfdvdl ----------VLAEPLEKILDHKSVKEKRLEMEKKLESLRKKHDKEKIKI aGQKSSPLEGKkpkfaitnklvkrlsnkslepgveiPACPLdlgdssees aaadagedlaGGSSsldgrtqesRLRSACREYTSQYRELQEKYHEAIYSA AE-----------KVLKTSQTGQTKQLKASLDKVTGEVMHQLQEARRNEV KNLATVHRDRDELIRMKREVASSVVERGVAERVRLKQTFDRRTDELQKQH DSVRNALAEHRSKARQILDKEAESRSCVSSNGFL--VLFHGPHHHGctgs gssalsgnnltlnldagaagshsaispakshnsiaaaaemkt >gi|4894766|gb|AAD32609.1|AF128539_1_881:1116 (AF128539) phospholipid phospholipase C beta isoform [Homarus americanus] ekreeqmkamgieasdidtkalkggggkaggakpaagakagacgkpgaca GGKKKKKFVEYEPINLETLRSQKNFLKATKKQQKELESMRKKHMKERLSI QKAQCSAIEKLAKGKkdvMDDPKIKSLVSEQMKQWSEMMEKHRKEEWEML KEHLKSQEDILKKLMEEEQAGQIKKMEAKHEQDMKDMKAQQAKAAMETAK DVnqDKTLKTKADRDRRLKEKNQNNTKRFIEERKISAMKQGKQKEKLKKV HD---QQMTELTKDI-QMAIQFYENTEA-------EYKMWNKMEFFC >gi|8778048|gb|AAF79180.1|_881:1115 (AF258528) phospholipase C [Loligo pealei] agagkkvsqgniaksafggakkaaaagkaatpaspppppaaadsefvqns ---KMKEESAVALPKLDALKSNKAYAKIISKRDKEVDSIKKKNDKAQSNM KTKMKAEEKK-----MKDShskaekkaeksgkeqhdqlvkenqdKFNQLH KENIDKYLATCSEHFNAESEICKKYIDSLNDCLKGVITSTQEDLKKKLQT IHDKEVESMNKELNKKSKEEQKNLGKETKDKEELARKKRELSKKLIDGIV AERNKLK--------ALKERQEKVLD-------KNVEELTKEYEKEKANA ENKLKEDI---------daklkkvkeews >gi|4521177|dbj|BAA76277.1|_1113:1357 (AB017512) PLC-betaH2 [Hydra magnipapillata] lcedeflkerkiddfkldkmflriakkngkevdilkqnhrkerkltesfy -DEEISKLQMYYDKTLES--ELKSFEKsLQKINTKEVQASYQK------- IVEDVSIKFDK-SSRKIIDSqmmelkekylektkiwktekvgKISVIVEE QKKALKIMIDEHIEKEARIKYSHSIQQIDLIGKLLKTAQDNDIKKLAEIN EKELSDLTKAQARDSIQSIKDlekefenskMDRINKEKIKRERDKLR--- --IEEFGMQRRKLVQNQQKRQEKLIEKHKNENKQFEDHRKEIIQLGYEPI IRHIRQAQTLI-------------slhqqkl >gi|4063009|gb|AAC98145.1|_903:1009 (AF031370) PLC-b4b [Rattus norvegicus]gi|4097344|gb|AAD10403.1| (U57836) PLC-b4b [Rattus norvegicus] ramgietsdiadvpsdtskndkkgkanpakanvtpqssselrptttaalg SGQEAKKGIELIPtVRIEDLKQMKAYLKHLKKQQKELNSLKKKHAKEHST MQKLHCTQVDKIVAQYdkeksthekilekamkkKGGSNCLEIKKETEIKI QTLTSDH------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----------kskgkqrdaspsg --simple mime boundary-- From farmer@cse.ucsc.edu Tue Aug 22 21:38:38 2000 Return-Path: Received: from beta.cse.ucsc.edu (beta.cse.ucsc.edu [128.114.48.15]) by cyborg.bioinfo.pl (8.9.3/8.8.7) with SMTP id VAA03051 for Message-Id: <200008221944.MAA01569@beta.cse.ucsc.edu> Subject: T0124(database hits) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0124.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-966971784.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 (updated Fri Aug 18 07:54:44 2000) Score method: average Summary of Database Hits: Average Target Template SeqID Reverse EValue Reverse EValue Reverse EValue SeqLabel 1qbkB -9.3 0.7647 -9.3 1 --------- --------- : Chain B, Structure Of The Karyopherin Beta2-Ran Gppnhp Nuclear Transport Complex 1tipA -8.45 1.789 -8.45 2.8 --------- --------- : Chain A, The Bisphosphatase Domain Of The Bifunctional Rat Liver 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatasegi|2914270|pdb|1TIP|B Chain B, The Bisphosphatase Domain Of The Bifunctional Rat Liver 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatase 1qlaA -6.66 10.7 -6.66 21 --------- --------- : Chain A, Respiratory Complex Ii-Like Fumarate Reductase From Wolinella Succinogenesgi|6730467|pdb|1QLA|D Chain D, Respiratory Complex Ii-Like Fumarate Reductase From Wolinella Succinogenes 2dorA -6.36 14.44 -6.36 21 --------- --------- : Chain A, Dihydroorotate Dehydrogenase A From Lactococcus Lactis Complexed With Orotategi|3660332|pdb|2DOR|B Chain B, Dihydroorotate Dehydrogenase A From Lactococcus Lactis Complexed With Orotate 1f4jA -6.23 16.44 -6.23 21 --------- --------- : Chain A, Structure Of Tetragonal Crystals Of Human Erythrocyte Catalasegi|9257060|pdb|1F4J|B Chain B, Structure Of Tetragonal Crystals Of Human Erythrocyte Catalase 1cl7H -6.2 16.94 -6.2 21 --------- --------- : Chain H, Anti Hiv1 Protease Fab 1ebfA -6.04 19.87 -6.04 21 --------- --------- : Chain A, Homoserine Dehydrogenase From S. Cerevisiae Complex With Nad+gi|7245385|pdb|1EBF|B Chain B, Homoserine Dehydrogenase From S. Cerevisiae Complex With Nad+ 1fbtA -6.04 19.87 -6.04 21 --------- --------- : Chain A, The Bisphosphatase Domain Of The Bifunctional Rat Liver 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatasegi|2392331|pdb|1FBT|B Chain B, The Bisphosphatase Domain Of The Bifunctional Rat Liver 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatase 119l 1e+06 8365 --------- --------- 1e+06 2.8 148lS 1e+06 8365 1e+06 21 --------- --------- : Chain S, Lysozyme (E.C.3.2.1.17) Mutant With Thr 26 Replaced By Glu, Cys 54 Replaced By Thr, And Cys 97 Replaced By Ala (T26e,C54t,C97a) Complexed With Substrate Cleaved From Cell Wall Of Escherichia Coli 193l 1e+06 8365 --------- --------- 1e+06 7.6 1a02F 1e+06 8365 --------- --------- 1e+06 2.8 1a02J 1e+06 8365 --------- --------- 1e+06 2.8 1a0aA 1e+06 8365 1e+06 2.8 1e+06 7.6 : Chain A, Crystal Structure Of Pho4 Bhlh Domain Complexed With Uasp2 (17)gi|2981653|pdb|1A0A|B Chain B, Crystal Structure Of Pho4 Bhlh Domain Complexed With Uasp2 (17) 1a0hA 1e+06 8365 --------- --------- 1e+06 2.8 1a0mA 1e+06 8365 1e+06 7.6 --------- --------- : Chain A, 1.1 Angstrom Crystal Structure Of A-Conotoxin [tyr15]-Epigi|4389389|pdb|1A0M|B Chain B, 1.1 Angstrom Crystal Structure Of A-Conotoxin [tyr15]-Epi 1a0nA 1e+06 8365 1e+06 7.6 --------- --------- : Chain A, Nmr Study Of The Sh3 Domain From Fyn Proto-Oncogene Tyrosine Kinase Complexed With The Synthetic Peptide P2l Corresponding To Residues 91-104 Of The P85 Subunit Of Pi3-Kinase, Family Of 25 Structuresgi|2982072|pdb|1AZG|A Chain A, Nmr Study Of The Sh3 Domain From Fyn Proto-Oncogene Tyrosine Kinase Kinase Complexed With The Synthetic Peptide P2l Corresponding To Residues 91-104 Of The P85 Subunit Of Pi3-Kinase, Minimized Average (Probmap) Structure 1a0oD 1e+06 8365 --------- --------- 1e+06 7.6 1a11 1e+06 8365 1e+06 7.6 --------- --------- : Nmr Structure Of Membrane Spanning Segment 2 Of The Acetylcholine Receptor In Dpc Micelles, 10 Structuresgi|4699861|pdb|1CEK|A Chain A, Three-Dimensional Structure Of The Membrane-Embedded M2 Channel-Lining Segment From The Nicotinic Acetylcholine Receptor By Solid-State Nmr Spectroscopy 1a13 1e+06 8365 1e+06 7.6 --------- --------- : G Protein-Bound Conformation Of Mastoparan-X, Nmr, 14 Structures --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-966971784.t99pairwise.a2m' Content-Disposition: attachment; filename="t99-results-966971784.t99pairwise.a2m" >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQH ATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENL RAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEVFP >1qbkB Chain B, Structure Of The Karyopherin Beta2-Ran Gppnhp Nuclear Transport Complex meyewkpdeqglqqil---------------------------------- ---QLLKESQSPDTTIQRTVQQKLEQlnqypdfnnylifvltklksedep trslsglilknnvkahfqnfpngvtdfikseclnnigdsspliratvgil ittiaskgelqnwpdllpklcslldsedyntcegafgalqkicedsaeil dsdvldrplnixipkflqffkhsspkirshavacvnqfiisrtqalxlhi dsftenlfalagdeepevrknvcralvxllevrmdrllphxhniveyxlq rtqdqdenvaleacefwltlaeqpickdvlvrhlpklipvlvngxkysdi diillkgdveedetipdseqdirprfhrsrtvaqqhdedgieeeddddde iddddtisdwnlrkcsaaaldvlanvyrdellphilpllkellfhhewvv kesgilvlgaiaegcxqgxipylpeliphliqclsdkkalvrsitcwtls ryahwvvsqppdtylkplxtellkrildsnkrvqeaacsafatleeeact elvpylayildtlvfafskyqhknllilydaigtladsVGHHLNKPEYIQ XLXPPLIQKWNXLKDED---------KDLFPLLECLSSVATALQSGFLPY CEPVYQRCVNLVQKTLAQAXLNNAQPDQYEAPDKDfxivalDLLSGLAEG LGGNIEQLVARSNILTLXYQCXQDKXPEVRQSSFALLGDLTKACFQHVKP CIADFXPILGTNLNPEFISVCNNATWaigeisiqxgiexqpyipxvlhql veiinrpntpktllentaitigrlgyvcpqevapxlqqfirpwctslrni rdneekdsafrgictxisvnpsgviqdfiffcdavaswinpkddlrdxfc kilhgfknqvgdenwrrfsdqfplplkerlaafygv >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQH ATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENL RAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEVFP >1tipA Chain A, The Bisphosphatase Domain Of The Bifunctional Rat Liver 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatasegi|2914270|pdb|1TIP|B Chain B, The Bisphosphatase Domain Of The Bifunctional Rat Liver 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatase mrsiylcrxgeseln----------------------------------- -------------------------LRGRIGGDSGLSARGKQYAYALANF IRSQGISSLKVWTSHMKRTIQTAEAL--GVPYEQWKALNEIDAGVCEEMT -------------------------------------------------- -------------------------------------------------- -------yeeiqehypeefalrdqdkyryrypkgesyedlvqrlepvime lerqenvlvichqavmrcllayfldkssdelpylkcplhtvlkltpvayg crvesiylnv >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQH ATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENL RAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEVFP >1qlaA Chain A, Respiratory Complex Ii-Like Fumarate Reductase From Wolinella Succinogenesgi|6730467|pdb|1QLA|D Chain D, Respiratory Complex Ii-Like Fumarate Reductase From Wolinella Succinogenes mkvqycdslviggglaglraavatqqkglstivlslipvkrshsaaaqgg mqaslgnskmsdgdnedlhfmdtvkgsdwgcdqkvarmfvntapkairel aawgvpwtri---------------------------------------- --HKGDRMAIINAQKTTITEedfrhglihsrdfggtkkwrtcytadatgh tmlfavaneclklgvsiqdrkeaialihqdgkcygavvrdlvtgdiiayv akgtliatggygriyknttnavvcegtgtaialetgiaqlgnmeavqfhp tplfpsgilltegcrgdggilrdvdghrfmpdyepekkelasrdvvsrrm iehirkgkgvqspygqhlwldisilgrkhietnlrdvqeiceyfagidpa ekwapvlpmqhysmggirtdyrgeaklkglfsageaacwdmhgfnrlggn svseaVVAGMIVGEYFAEHCA----------NTQVDLETKTLEKFVKGQE AYMKSLVESKGTEDVFKIKNRMKDVMDD---------------------- -------------------------------------------------- -------------------------------------nvgifrdgphlek svkeleelykksknvgiknkrlhanpeleeayrvpmmlkvalcvakgald rtesrgahnredypkrddinwlnrtlaswpnpeqtlptleyealdvneme iapryrgygakgnyienplsvkrqeeidkiqseleaagkdrhaiqealmp yelpakykarnerlgdk >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQH ATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENL RAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEVFP >2dorA Chain A, Dihydroorotate Dehydrogenase A From Lactococcus Lactis Complexed With Orotategi|3660332|pdb|2DOR|B Chain B, Dihydroorotate Dehydrogenase A From Lactococcus Lactis Complexed With Orotate mlnttfanakfanpfmnasgvhcmtiedleelkasqagay---------- ----------------------------------------ITKSSTLEKR egnplpryvdlelgsinsmglpnlgfdyyldyvlknqkenaqegpiffsi agmsaaeniamlkkiqesdfsgitelnlscpnvpgkpqlaydfeatekll kevftfftkplgvklppyfdlvhfdimaeilnqfpltyvnsvnsIGNGLF IDPeaesvvikpkdgfggiggayikptalaNVRAFYTRLKPEIQIIGTGG IETGQDAFE------HLLCGATMLQIGTALHKEGPAIFDRIIKELEEIMN QKGYQSIADF---------------------------------------- -------------------------------------------------- ---hgklksl >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQH ATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENL RAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEVFP >1f4jA Chain A, Structure Of Tetragonal Crystals Of Human Erythrocyte Catalasegi|9257060|pdb|1F4J|B Chain B, Structure Of Tetragonal Crystals Of Human Erythrocyte Catalase madsrdpasdqmq------------------------------------- -----HWKEQRAAQKADVLTTGAgnpvgdklnvitvgprgpllvqdvvft demahfdreripervvhakgagafgyfevthditkyskakvfehigkktp iavrfstvagesgsadtvrdprgfavkfytedgnwdlvgnntpiffirdp ilfpsfihsqkrnpqthlkdpdmvwdfwslrpeslhqvsflfsdrgipdg hrhmngygshtfklvnangeavyckfhyktdqgiknlsvedaarlsqedp dygirdlfnaiatgkypswtfyiqvmtfnqaetfpfnpfdltkvwphkdy plipvgklvlnrnpvnyfaeveqiafdpsnmppgieaspdkmlqgrlfay pdthrhrlgpnylhipvncpyrarvanyqrdgpmcmqdnqggapnyypns FGAPEQQPSalehsiqysgevrrfntanddnvtqvrafYVNVLNEEQRKR LCENIAGH------------------LKDAQIFIQKKAVKNFTEVHPDYG SHIQALLDKYNAEKPKNA-------------------------------- -------------------------------------------------- -----------ihtfvqsgshlaarekanl >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQH ATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENL RAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEVFP >1cl7H Chain H, Anti Hiv1 Protease Fab qiq----------------------------------------------- ---LQQSGPELKKPGETVKISCkatnyaftdysmhwvkqapggdlkyvgw intetdeptfaddfkgrfafsldtststaflQINNLKNEDTATYFCVRDR HDYGEI-------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----ftywgqgttvtvssakttppsvyplapgs >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQH ATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENL RAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEVFP >1ebfA Chain A, Homoserine Dehydrogenase From S. Cerevisiae Complex With Nad+gi|7245385|pdb|1EBF|B Chain B, Homoserine Dehydrogenase From S. Cerevisiae Complex With Nad+ stkvvnvavigagvvgsafldqllamkstitynlvllaeaersliskdfs plnvgsdwkaalaasttktlplddliahlktspkpvilvdntssayiagf ytkfvengisiatpnkkafssdlatwkalfsnkptngfvyheatvgaglp iisflreiiqtgdevekiegifsgtlsyifnefstsqandvkfsdvvkva kklgytepdprddlngldvarkvtivgrisgvevesptsfpvqs------ ----LIPKPLESVKSADEFLEKLSDYDKDLTQLKKEAATENKVLrfigkv dvaTKSVSVGIEKydyshPFASLKGSDNVISIK----------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- tkrytnpvviqgagagaavtaagvlgdvikiaqrl >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQH ATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENL RAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEVFP >1fbtA Chain A, The Bisphosphatase Domain Of The Bifunctional Rat Liver 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatasegi|2392331|pdb|1FBT|B Chain B, The Bisphosphatase Domain Of The Bifunctional Rat Liver 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatase rsiylcrhgeseln------------------------------------ ------------------------LRGRIGGDSGLSARGKQYAYALANFI RSQGISSLKVWTSHXKRTIQTAEAL--GVPYEQWKALNEIDAGVCEEXTY EEIQEHYPEEFALR--DQDKYRYRYPKGESYEDLVQRLEPVIXELE---- RQENVLVICHQAVXRCL--------------------------------- ------layfldkssdelpylkcplhtvlkltpvaygcrvesiylnv >T0124 nmkevtqlpepqtaslaelqqmklflkllkkqekelkelerkgskrreel lqkysvlflepvyprgldsqvvelkerlemelihlgeeyhdgirrrkeqh ateqtakitelarekqiaelkalkessesnikdikkkleakrldriqvmm rstsdkaaqerlkkeinnshiqevvqtiklltektaryqqkleekqaenl raiqekegql---------------------------------------- -------------------QQEAVAEYEEKLKTLTVEVQEMVK------- -------------------------------------------------- ----------------------nymkevfp >119l Lysozyme (E.C.3.2.1.17) Mutant With Cys 54 Replaced By Thr, Cys 97 Replaced By Ala, Ala 134 Replaced By Ser (C54t,C97a, A134s) MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAI GRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALI NMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLSKSRWYNQTPNRAKRVI TTFRTGTWDAYKnl >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQH ATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENL RAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEVFP >148lS Chain S, Lysozyme (E.C.3.2.1.17) Mutant With Thr 26 Replaced By Glu, Cys 54 Replaced By Thr, And Cys 97 Replaced By Ala (T26e,C54t,C97a) Complexed With Substrate Cleaved From Cell Wall Of Escherichia Coli x------------------------------------------------- -----------------------------------------XAEX----- -------------------------------------------------- -------------------------------------------------- -------------------------------------------x >T0124 nmkevtqlpepqtaslaelqqmklflkllkkqekelkelerkgskrreel lqkysvlflepvyprgldsqvvelkerlemelihlgeeyhdgirrrkeqh ateqtakitelarekqiaelkalkessesnik------DIKKKLEAKRLD RIQ----------------------------------------------- -------------------------------------------------- -----------vmmrstsdkaaqerlkkeinnshiqevvqtiklltekta ryqqkleekqaenlraiqekegqlqqeavaeyeeklktltvevqemvkny mkevfp >193l KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGS TDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVS DGNGMNAWVAWRNRCKGTDVQAWIRGCRL >T0124 -----NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSK RREellqkysvlflepvyprgldsqvvelkerlemelihlgeeyhdgirr rkeqhateqtakitelarekqiaelkalkessesnikdikkkleakrldr iqvmmrstsdkaaqerlkkeinnshiqevvqtiklltektaryqqkleek qaenlraiqekegqlqqeavaeyeeklktltvevqemvknymkevfp >1a02F Chain F, Structure Of The Dna Binding Domains Of Nfat, Fos And Jun Bound To Dna mkRRIRRERNKMAAAKSRNRRRELTDTLQAETDQLEDEKSALQTEIANLL KEKEKl >T0124 nmkevtqlpepqtaslaelqqmklflkllkkqekelkelerkgskrreel lqkysvlflepvyprgldsqvvelkerlemelihlgeeyhdgirrrkeqh ateqtakitelAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKkeinnshiqevvqtiklltektaryqqkleekqaenl raiqekegqlqqeavaeyeeklktltvevqemvknymkevfp >1a02J Chain J, Structure Of The Dna Binding Domains Of Nfat, Fos And Jun Bound To Dna mkaeRKRMRNRIAASKSRKRKLERIARLEEKVKTLKAQNSELASTANMLR EQVAQL >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQH ATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENL RAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEVFP >1a0aA Chain A, Crystal Structure Of Pho4 Bhlh Domain Complexed With Uasp2 (17)gi|2981653|pdb|1A0A|B Chain B, Crystal Structure Of Pho4 Bhlh Domain Complexed With Uasp2 (17) mkreshkhaeqarrnrlavalhelaslipaewkqqnvsaapskatt---- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----------------VEAACRYIRHLQQNGS------------------ --------------------------------------t >T0124 nmkevtqlpepqtaslaelqqmklflkllkkqekelkelerkgskrreel lqkysvlflepvyprgldsqvvelkerlemelihlgeeyhdgirrrkeqh ateqtakitelarekqiaelkalkessesnikdikkkleakrldriqvmm rstsdkaaqerlkkeinnshiqevvqti-----------------KLLTE KTARYQQKLEEKQAENLRAIQEKEG------------------------- -----------------------------------------------QLQ QEAVAEYEEKLKTLTVEVQEMVKNYMKEVF-------p >1a0hA Chain A, The X-Ray Crystal Structure Of Ppack-Meizothrombin Desf1: KringleTHROMBIN AND CARBOHYDRATEKRINGLETHROMBIN Interactions And Location Of The Linker Chaingi|3318970|pdb|1A0H|D Chain D, The X-Ray Crystal Structure Of Ppack-Meizothrombin Desf1: KringleTHROMBIN AND CARBOHYDRATEKRINGLETHROMBIN Interactions And Location Of The Linker Chain SPLLETCVPDRGREYRGRLAVTTHGSRCLAWSSEQAKALSKDQDFNPAVP LAENFCRNPDGDEEGAWCYVADQPGDFEYCDLNYCEEPVDGDLGDRLGED PDPDAAIEGRTSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKE LFESYIEGR >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQH ATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENL RAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEVFP >1a0mA Chain A, 1.1 Angstrom Crystal Structure Of A-Conotoxin [tyr15]-Epigi|4389389|pdb|1A0M|B Chain B, 1.1 Angstrom Crystal Structure Of A-Conotoxin [tyr15]-Epi gc------------------------------------------------ -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------CSDPRCNMNN---------------pdycx >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQH ATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENL RAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEVFP >1a0nA Chain A, Nmr Study Of The Sh3 Domain From Fyn Proto-Oncogene Tyrosine Kinase Complexed With The Synthetic Peptide P2l Corresponding To Residues 91-104 Of The P85 Subunit Of Pi3-Kinase, Family Of 25 Structuresgi|2982072|pdb|1AZG|A Chain A, Nmr Study Of The Sh3 Domain From Fyn Proto-Oncogene Tyrosine Kinase Kinase Complexed With The Synthetic Peptide P2l Corresponding To Residues 91-104 Of The P85 Subunit Of Pi3-Kinase, Minimized Average (Probmap) Structure xprpl--------------------------------------------- ---------------PVAPG------------------------------ -------------------------------------------------- -------------------------------------------------- -----------------------------------------------ssk t >T0124 nmkevtqlpepqtaslaelqqm-KLFLKLLKKQEKELKELE--------- ---------------------------------------rkgskrreell qkysvlflepvyprgldsqvvelkerlemelihlgeeyhdgirrrkeqha teqtakitelarekqiaelkalkessesnikdikkkleakrldriqvmmr stsdkaaqerlkkeinnshiqevvqtiklltektaryqqkleekqaenlr aiqekegqlqqeavaeyeeklktltvevqemvknymkevfp >1a0oD rqlaleakgetpsavtrlsvvaksepqdeqsrsqspRRIILSRLKAGEVD LLEEELGHLTTLTDVVKGADSLSAILPGDIAEDDITAVLCFVIEADQITF ETVevspkistppvlklaaeqaptgrverekttr >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQH ATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENL RAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEVFP >1a11 Nmr Structure Of Membrane Spanning Segment 2 Of The Acetylcholine Receptor In Dpc Micelles, 10 Structuresgi|4699861|pdb|1CEK|A Chain A, Three-Dimensional Structure Of The Membrane-Embedded M2 Channel-Lining Segment From The Nicotinic Acetylcholine Receptor By Solid-State Nmr Spectroscopy gsekmstaisvllaqavf-------------------------------- -------------------------------------------------- ----------------------------LLLTSQ---------------- -------------------------------------------------- -------------------------------------------------- ----------r >T0124 NMKEVTQLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREEL LQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQH ATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMM RSTSDKAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENL RAIQEKEGQLQQEAVAEYEEKLKTLTVEVQEMVKNYMKEVFP >1a13 G Protein-Bound Conformation Of Mastoparan-X, Nmr, 14 Structures ------------------------------INWKGIAAMAKK-------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ------------------------------------------llx --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-966971784.t99pairwise.casp.al' Content-Disposition: attachment; filename="t99-results-966971784.t99pairwise.casp.al" PFRMAT AL TARGET T0124 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 1qbk_B E 38 Q 17 L 39 L 18 E 40 L 19 R 41 K 20 K 42 E 21 G 43 S 22 S 44 Q 23 K 45 S 24 R 46 P 25 R 47 D 26 E 48 T 27 E 49 T 28 L 50 I 29 L 51 Q 30 Q 52 R 31 K 53 T 32 Y 54 V 33 S 55 Q 34 V 56 Q 35 L 57 K 36 F 58 L 37 L 59 E 38 E 60 Q 39 P 61 V 552 V 62 G 553 Y 63 H 554 P 64 H 555 R 65 L 556 G 66 N 557 L 67 K 558 D 68 P 559 S 69 E 560 Q 70 Y 561 V 71 I 562 V 72 Q 563 E 73 X 564 L 74 L 565 K 75 X 566 E 76 P 567 R 77 P 568 L 78 L 569 E 79 I 570 M 80 Q 571 E 81 K 572 L 82 W 573 I 83 N 574 H 84 X 575 L 85 L 576 G 86 K 577 E 87 D 578 E 88 E 579 Y 89 D 580 Q 99 K 581 H 100 D 582 A 101 L 583 T 102 F 584 E 103 P 585 Q 104 L 586 T 105 L 587 A 106 E 588 K 107 C 589 I 108 L 590 T 109 S 591 E 110 S 592 L 111 V 593 A 112 A 594 R 113 T 595 E 114 A 596 K 115 L 597 Q 116 Q 598 I 117 S 599 A 118 G 600 E 119 F 601 L 120 L 602 K 121 P 603 A 122 Y 604 L 123 C 605 K 124 E 606 E 125 P 607 S 126 V 608 S 127 Y 609 E 128 Q 610 S 129 R 611 N 130 C 612 I 131 V 613 K 132 N 614 D 133 L 615 I 134 V 616 K 135 Q 617 K 136 K 618 K 137 T 619 L 138 L 620 E 139 A 621 A 140 Q 622 K 141 A 623 R 142 X 624 L 143 L 625 D 144 N 626 R 145 N 627 I 146 A 628 Q 147 Q 629 V 148 P 630 M 149 D 631 M 150 Q 632 R 151 Y 633 S 152 E 634 T 153 A 635 S 154 P 636 D 155 D 637 K 156 K 638 A 157 D 639 A 158 D 646 Q 159 L 647 E 160 L 648 R 161 S 649 L 162 G 650 K 163 L 651 K 164 A 652 E 165 E 653 I 166 G 654 N 167 L 655 N 168 G 656 S 169 G 657 H 170 N 658 I 171 I 659 Q 172 E 660 E 173 Q 661 V 174 L 662 V 175 V 663 Q 176 A 664 T 177 R 665 I 178 S 666 K 179 N 667 L 180 I 668 L 181 L 669 T 182 T 670 E 183 L 671 K 184 X 672 T 185 Y 673 A 186 Q 674 R 187 C 675 Y 188 X 676 Q 189 Q 677 Q 190 D 678 K 191 K 679 L 192 X 680 E 193 P 681 E 194 E 682 K 195 V 683 Q 196 R 684 A 197 Q 685 E 198 S 686 N 199 S 687 L 200 F 688 R 201 A 689 A 202 L 690 I 203 L 691 Q 204 G 692 E 205 D 693 K 206 L 694 E 207 T 695 G 208 K 696 Q 209 A 697 L 210 C 698 Q 211 F 699 Q 212 Q 700 E 213 H 701 A 214 V 702 V 215 K 703 A 216 P 704 E 217 C 705 Y 218 I 706 E 219 A 707 E 220 D 708 K 221 F 709 L 222 X 710 K 223 P 711 T 224 I 712 L 225 L 713 T 226 G 714 V 227 T 715 E 228 N 716 V 229 L 717 Q 230 N 718 E 231 P 719 M 232 E 720 V 233 F 721 K 234 I 722 N 235 S 723 Y 236 V 724 M 237 C 725 K 238 N 726 E 239 N 727 V 240 A 728 F 241 T 729 P 242 W 730 TER END PFRMAT AL TARGET T0124 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 1tip_A P 61 L 16 V 62 R 17 Y 63 G 18 P 64 R 19 R 65 I 20 G 66 G 21 L 67 G 22 D 68 D 23 S 69 S 24 Q 70 G 25 V 71 L 26 V 72 S 27 E 73 A 28 L 74 R 29 K 75 G 30 E 76 K 31 R 77 Q 32 L 78 Y 33 E 79 A 34 M 80 Y 35 E 81 A 36 L 82 L 37 I 83 A 38 H 84 N 39 L 85 F 40 G 86 I 41 E 87 R 42 E 88 S 43 Y 89 Q 44 H 90 G 45 D 91 I 46 G 92 S 47 I 93 S 48 R 94 L 49 R 95 K 50 R 96 V 51 K 97 W 52 E 98 T 53 Q 99 S 54 H 100 H 55 A 101 M 56 T 102 K 57 E 103 R 58 Q 104 T 59 T 105 I 60 A 106 Q 61 K 107 T 62 I 108 A 63 T 109 E 64 E 110 A 65 L 111 L 66 E 114 G 67 K 115 V 68 Q 116 P 69 I 117 Y 70 A 118 E 71 E 119 Q 72 L 120 W 73 K 121 K 74 A 122 A 75 L 123 L 76 K 124 N 77 E 125 E 78 S 126 I 79 S 127 D 80 E 128 A 81 S 129 G 82 N 130 V 83 I 131 C 84 K 132 E 85 D 133 E 86 I 134 M 87 K 135 T 88 TER END PFRMAT AL TARGET T0124 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 1qla_A G 43 H 111 S 44 K 112 K 45 G 113 R 46 D 114 R 47 R 115 E 48 M 116 E 49 A 117 L 50 I 118 L 51 I 119 Q 52 N 120 K 53 A 121 Y 54 Q 122 S 55 K 123 V 56 T 124 L 57 T 125 F 58 I 126 L 59 T 127 E 60 E 128 P 61 V 414 V 62 V 415 Y 63 A 416 P 64 G 417 R 65 M 418 G 66 I 419 L 67 V 420 D 68 G 421 S 69 E 422 Q 70 Y 423 V 71 F 424 V 72 A 425 E 73 E 426 L 74 H 427 K 75 C 428 E 76 A 429 E 87 N 430 E 88 T 431 Y 89 Q 432 H 90 V 433 D 91 D 434 G 92 L 435 I 93 E 436 R 94 T 437 R 95 K 438 R 96 T 439 K 97 L 440 E 98 E 441 Q 99 K 442 H 100 F 443 A 101 V 444 T 102 K 445 E 103 G 446 Q 104 Q 447 T 105 E 448 A 106 A 449 K 107 Y 450 I 108 M 451 T 109 K 452 E 110 S 453 L 111 L 454 A 112 V 455 R 113 E 456 E 114 S 457 K 115 K 458 Q 116 G 459 I 117 T 460 A 118 E 461 E 119 D 462 L 120 V 463 K 121 F 464 A 122 K 465 L 123 I 466 K 124 K 467 E 125 N 468 S 126 R 469 S 127 M 470 E 128 K 471 S 129 D 472 N 130 V 473 I 131 M 474 K 132 D 475 D 133 D 476 TER END PFRMAT AL TARGET T0124 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 2dor_A L 51 I 41 Q 52 T 42 K 53 K 43 Y 54 S 44 S 55 S 45 V 56 T 46 L 57 L 47 F 58 E 48 L 59 K 49 E 60 R 50 P 61 I 195 V 62 G 196 Y 63 N 197 P 64 G 198 R 65 L 199 G 66 F 200 L 67 I 201 D 68 D 202 S 69 P 203 Q 70 N 231 V 71 V 232 V 72 R 233 E 73 A 234 L 74 F 235 K 75 Y 236 E 76 T 237 R 77 R 238 L 78 L 239 E 79 K 240 M 80 P 241 E 81 E 242 L 82 I 243 I 83 Q 244 H 84 I 245 L 85 I 246 G 86 G 247 E 87 T 248 E 88 G 249 Y 89 G 250 H 90 I 251 D 91 E 252 G 92 T 253 I 93 G 254 R 94 Q 255 R 95 D 256 R 96 A 257 K 97 F 258 E 98 E 259 T 105 H 260 A 106 L 261 K 107 L 262 I 108 C 263 T 109 G 264 E 110 A 265 L 111 T 266 A 112 M 267 R 113 L 268 E 114 Q 269 K 115 I 270 Q 116 G 271 I 117 T 272 A 118 A 273 E 119 L 274 L 120 H 275 K 121 K 276 A 122 E 277 L 123 G 278 K 124 P 279 E 125 A 280 S 126 I 281 S 127 F 282 E 128 D 283 S 129 R 284 N 130 I 285 I 131 I 286 K 132 K 287 D 133 E 288 I 134 L 289 K 135 E 290 K 136 E 291 K 137 I 292 L 138 M 293 E 139 N 294 A 140 Q 295 K 141 K 296 R 142 G 297 L 143 Y 298 D 144 Q 299 R 145 S 300 I 146 I 301 Q 147 A 302 V 148 D 303 M 149 F 304 TER END PFRMAT AL TARGET T0124 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 1f4j_A G 43 H _ S 44 W _ K 45 K _ R 46 E _ R 47 Q _ E 48 R _ E 49 A _ L 50 A _ L 51 Q _ Q 52 K _ K 53 A 24 Y 54 D 25 S 55 V 26 V 56 L 27 L 57 T 28 F 58 T 29 L 59 G 30 E 60 A 31 P 61 F 409 V 62 G 410 Y 63 A 411 P 64 P 412 R 65 E 413 G 66 Q 414 L 67 Q 415 D 68 P 416 S 69 S 417 Q 70 Y 447 V 71 V 448 V 72 N 449 E 73 V 450 L 74 L 451 K 75 N 452 E 76 E 453 R 77 E 454 L 78 Q 455 E 79 R 456 M 80 K 457 E 81 R 458 L 82 L 459 I 83 C 460 H 84 E 461 L 85 N 462 G 86 I 463 E 87 A 464 E 88 G 465 Y 89 H 466 I 108 L 467 T 109 K 468 E 110 D 469 L 111 A 470 A 112 Q 471 R 113 I 472 E 114 F 473 K 115 I 474 Q 116 Q 475 I 117 K 476 A 118 K 477 E 119 A 478 L 120 V 479 K 121 K 480 A 122 N 481 L 123 F 482 K 124 T 483 E 125 E 484 S 126 V 485 S 127 H 486 E 128 P 487 S 129 D 488 N 130 Y 489 I 131 G 490 K 132 S 491 D 133 H 492 I 134 I 493 K 135 Q 494 K 136 A 495 K 137 L 496 L 138 L 497 E 139 D 498 A 140 K 499 K 141 Y 500 R 142 N 501 L 143 A 502 D 144 E _ R 145 K _ I 146 P _ Q 147 K _ V 148 N _ M 149 A _ TER END PFRMAT AL TARGET T0124 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 1cl7_H L 51 L 4 Q 52 Q 5 K 53 Q 6 Y 54 S 7 S 55 G 8 V 56 P 9 L 57 E 10 F 58 L 11 L 59 K 12 E 60 K 13 P 61 P 14 V 62 G 15 Y 63 E 16 P 64 T 17 R 65 V 18 G 66 K 19 L 67 I 20 D 68 S 21 S 69 C 22 Q 70 Q 81 V 71 I 82 V 72 N 82A E 73 N 82B L 74 L 82C K 75 K 83 E 76 N 84 R 77 E 85 L 78 D 86 E 79 T 87 M 80 A 88 E 81 T 89 L 82 Y 90 I 83 F 91 H 84 C 92 L 85 V 93 G 86 R 94 E 87 D 95 E 88 R 96 Y 89 H 97 H 90 D 98 D 91 Y 99 G 92 G 100 I 93 E 100A R 94 I 100B TER END PFRMAT AL TARGET T0124 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 1ebf_A P 11 L 246 Q 12 I 247 T 13 P 248 A 14 K 249 S 15 P 250 L 16 L 251 A 17 E 252 E 18 S 253 L 19 V 254 Q 20 K 255 Q 21 S 256 M 22 A 257 K 23 D 258 L 24 E 259 F 25 F 260 L 26 L 261 K 27 E 262 L 28 K 263 L 29 L 264 K 30 S 265 K 31 D 266 Q 32 Y 267 E 33 D 268 K 34 K 269 E 35 D 270 L 36 L 271 K 37 T 272 E 38 Q 273 L 39 L 274 E 40 K 275 R 41 K 276 K 42 E 277 G 43 A 278 S 44 A 279 K 45 T 280 R 46 E 281 R 47 N 282 E 48 K 283 E 49 V 284 L 50 L 285 L 51 T 295 Q 52 K 296 K 53 S 297 Y 54 V 298 S 55 S 299 V 56 V 300 L 57 G 301 F 58 I 302 L 59 E 303 E 60 K 304 P 61 P 310 V 62 F 311 Y 63 A 312 P 64 S 313 R 65 L 314 G 66 K 315 L 67 G 316 D 68 S 317 S 69 D 318 Q 70 N 319 V 71 V 320 V 72 I 321 E 73 S 322 L 74 I 323 K 75 K 324 TER END PFRMAT AL TARGET T0124 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 1fbt_A P 61 L 15 V 62 R 16 Y 63 G 17 P 64 R 18 R 65 I 19 G 66 G 20 L 67 G 21 D 68 D 22 S 69 S 23 Q 70 G 24 V 71 L 25 V 72 S 26 E 73 A 27 L 74 R 28 K 75 G 29 E 76 K 30 R 77 Q 31 L 78 Y 32 E 79 A 33 M 80 Y 34 E 81 A 35 L 82 L 36 I 83 A 37 H 84 N 38 L 85 F 39 G 86 I 40 E 87 R 41 E 88 S 42 Y 89 Q 43 H 90 G 44 D 91 I 45 G 92 S 46 I 93 S 47 R 94 L 48 R 95 K 49 R 96 V 50 K 97 W 51 E 98 T 52 Q 99 S 53 H 100 H 54 A 101 X 55 T 102 K 56 E 103 R 57 Q 104 T 58 T 105 I 59 A 106 Q 60 K 107 T 61 I 108 A 62 T 109 E 63 E 110 A 64 L 111 L 65 E 114 G 66 K 115 V 67 Q 116 P 68 I 117 Y 69 A 118 E 70 E 119 Q 71 L 120 W 72 K 121 K 73 A 122 A 74 L 123 L 75 K 124 N 76 E 125 E 77 S 126 I 78 S 127 D 79 E 128 A 80 S 129 G 81 N 130 V 82 I 131 C 83 K 132 E 84 D 133 E 85 I 134 X 86 K 135 T 87 K 136 Y 88 K 137 E 89 L 138 E 90 E 139 I 91 A 140 Q 92 K 141 E 93 R 142 H 94 L 143 Y 95 D 144 P 96 R 145 E 97 I 146 E 98 Q 147 F 99 V 148 A 100 M 149 L 101 M 150 R 102 T 153 D 103 S 154 Q 104 D 155 D 105 K 156 K 106 A 157 Y 107 A 158 R 108 Q 159 Y 109 E 160 R 110 R 161 Y 111 L 162 P 112 K 163 K 113 K 164 G 114 E 165 E 115 I 166 S 116 N 167 Y 117 N 168 E 118 S 169 D 119 H 170 L 120 I 171 V 121 Q 172 Q 122 E 173 R 123 V 174 L 124 V 175 E 125 Q 176 P 126 T 177 V 127 I 178 I 128 K 179 X 129 L 180 E 130 L 181 L 131 T 182 E 132 R 187 R 133 Y 188 Q 134 Q 189 E 135 Q 190 N 136 K 191 V 137 L 192 L 138 E 193 V 139 E 194 I 140 K 195 C 141 Q 196 H 142 A 197 Q 143 E 198 A 144 N 199 V 145 L 200 X 146 R 201 R 147 A 202 C 148 I 203 L 149 TER END PFRMAT AL TARGET T0124 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 119l Q 211 K 60 Q 212 D 61 E 213 E 62 A 214 A 63 V 215 E 64 A 216 K 65 E 217 L 66 Y 218 F 67 E 219 N 68 E 220 Q 69 K 221 D 70 L 222 V 71 K 223 D 72 T 224 A 73 L 225 A 74 T 226 V 75 V 227 R 76 E 228 G 77 V 229 I 78 Q 230 L 79 E 231 R 80 M 232 N 81 V 233 A 82 K 234 K 83 TER END PFRMAT AL TARGET T0124 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 FIM_method_score geometric mean of match probabilities (6). % Single Track Model: /tmp/148lS.148lS.mod MODEL 1 PARENT 148l_S D 91 X 167 G 92 A 170 I 93 E _ R 94 X _ TER END PFRMAT AL TARGET T0124 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 193l D 133 E 7 I 134 L 8 K 135 A 9 K 136 A 10 K 137 A 11 L 138 M 12 E 139 K 13 A 140 R 14 K 141 H 15 R 142 G 16 L 143 L 17 D 144 D 18 R 145 N 19 I 146 Y 20 Q 147 R 21 TER END PFRMAT AL TARGET T0124 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 1a02_F N 1 E 145 M 2 R 146 K 3 N 147 E 4 K 148 V 5 M 149 T 6 A 150 Q 7 A 151 L 8 A 152 P 9 K 153 E 10 S 154 P 11 R 155 Q 12 N 156 T 13 R 157 A 14 R 158 S 15 R 159 L 16 E 160 A 17 L 161 E 18 T 162 L 19 D 163 Q 20 T 164 Q 21 L 165 M 22 Q 166 K 23 A 167 L 24 E 168 F 25 T 169 L 26 D 170 K 27 Q 171 L 28 L 172 L 29 E 173 K 30 D 174 K 31 E 175 Q 32 K 176 E 33 S 177 K 34 A 178 E 35 L 179 L 36 Q 180 K 37 T 181 E 38 E 182 L 39 I 183 E 40 A 184 R 41 N 185 K 42 L 186 G 43 L 187 S 44 K 188 K 45 E 189 R 46 K 190 R 47 E 191 E 48 K 192 TER END PFRMAT AL TARGET T0124 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 1a02_J A 112 R 267 R 113 K 268 E 114 R 269 K 115 M 270 Q 116 R 271 I 117 N 272 A 118 R 273 E 119 I 274 L 120 A 275 K 121 A 276 A 122 S 277 L 123 K 278 K 124 S 279 E 125 R 280 S 126 K 281 S 127 R 282 E 128 K 283 S 129 L 284 N 130 E 285 I 131 R 286 K 132 I 287 D 133 A 288 I 134 R 289 K 135 L 290 K 136 E 291 K 137 E 292 L 138 K 293 E 139 V 294 A 140 K 295 K 141 T 296 R 142 L 297 L 143 K 298 D 144 A 299 R 145 Q 300 I 146 N 301 Q 147 S 302 V 148 E 303 M 149 L 304 M 150 A 305 R 151 S 306 S 152 T 307 T 153 A 308 S 154 N 309 D 155 M 310 K 156 L 311 A 157 R 312 A 158 E 313 Q 159 Q 314 E 160 V 315 R 161 A 316 L 162 Q 317 K 163 L 318 TER END PFRMAT AL TARGET T0124 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 1a0a_A I 171 V 46 Q 172 E 47 E 173 A 48 V 174 A 49 V 175 C 50 Q 176 R 51 T 177 Y 52 I 178 I 53 K 179 R 54 L 180 H 55 L 181 L 56 T 182 Q 57 E 183 Q 58 K 184 N 59 T 185 G 60 A 186 S 61 TER END PFRMAT AL TARGET T0124 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 1a0h_A K 179 R 181 L 180 L 182 L 181 A 183 T 182 V 184 E 183 T 185 K 184 T 186 T 185 H 187 A 186 G 188 R 187 S 189 Y 188 R 190 Q 189 C 191 Q 190 L 192 K 191 A 193 L 192 W 194 E 193 S 195 E 194 S 196 K 195 E 197 Q 196 Q 198 A 197 A 199 E 198 K 200 N 199 A 201 L 200 L 202 R 201 S 203 A 202 K 204 I 203 D 205 Q 204 Q 206 E 205 D 207 K 206 F 208 E 207 N 209 G 208 P 210 Q 209 F 281 L 210 N 282 Q 211 E 283 Q 212 K 284 E 213 T 285 A 214 F 286 V 215 G 287 A 216 A 288 E 217 G 289 Y 218 E 290 E 219 A 291 E 220 D 292 K 221 C 293 L 222 G 294 K 223 L 295 T 224 R 296 L 225 P 297 T 226 L 298 V 227 F 299 E 228 E 300 V 229 K 301 Q 230 K 302 E 231 Q 303 M 232 V 304 V 233 Q 305 K 234 D 306 N 235 Q 307 Y 236 T 308 M 237 E 309 K 238 K 310 E 239 E 311 V 240 L 312 F 241 F 313 TER END PFRMAT AL TARGET T0124 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 1a0m_A Y 218 C 3 E 219 S 4 E 220 D 5 K 221 P 6 L 222 R 7 K 223 C 8 T 224 N 9 L 225 M 10 T 226 N 11 V 227 N 12 TER END PFRMAT AL TARGET T0124 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 FIM_method_score geometric mean of match probabilities (6). % Single Track Model: /tmp/1a0nA.1a0nA.mod MODEL 1 PARENT 1a0n_A P 61 P 97 V 62 V 98 Y 63 A 99 P 64 P 100 R 65 G 101 TER END PFRMAT AL TARGET T0124 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 1a0o_D K 23 R 161 L 24 I 162 F 25 I 163 L 26 L 164 K 27 S 165 L 28 R 166 L 29 L 167 K 30 K 168 K 31 A 169 Q 32 G 170 E 33 E 171 K 34 V 172 E 35 D 173 L 36 L 174 K 37 L 175 E 38 E 176 L 39 E 177 E 40 E 178 TER END PFRMAT AL TARGET T0124 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 1a11 L 111 L 19 A 112 L 20 R 113 L 21 E 114 T 22 K 115 S 23 Q 116 Q 24 TER END PFRMAT AL TARGET T0124 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 1a13 K 31 I 1 Q 32 N 2 E 33 W 3 K 34 K 4 E 35 G 5 L 36 I 6 K 37 A 7 E 38 A 8 L 39 M 9 E 40 A 10 R 41 K 11 K 42 K 12 TER END --simple mime boundary-- From farmer@cse.ucsc.edu Tue Aug 22 21:45:13 2000 Return-Path: Received: from beta.cse.ucsc.edu (beta.cse.ucsc.edu [128.114.48.15]) by cyborg.bioinfo.pl (8.9.3/8.8.7) with SMTP id VAA03385 for Message-Id: <200008221951.MAA00686@beta.cse.ucsc.edu> Subject: T0124(target 99 secondary structure prediction) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0124.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-966971784.t99secstr.fasta' Content-Disposition: attachment; filename="t99-results-966971784.t99secstr.fasta" >T0124 LLLHHHHLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLHHHHHHHHHHLLLLLL --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-966971784.t99secstr.casp.ss' Content-Disposition: attachment; filename="t99-results-966971784.t99secstr.casp.ss" PFRMAT SS TARGET T0124 AUTHOR UCSC Target99 server METHOD This prediction was derived from the following methods METHOD by averaging the corresponding probabilities: METHOD Method 0: METHOD TARGET T0124 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-beta-29043/target-align-29043.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 20.7233 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: T0124 METHOD model_file: /projects/compbio/tmp/sam-nn-tmp.beta.32592/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 Aug 22 12:48:42 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-beta-29043/target-align-29043.a2m METHOD METHOD guide seq name: T0124 METHOD ###end 0 MODEL 1 N C 0.678 M C 0.521 K C 0.434 E H 0.424 V H 0.458 T H 0.407 Q H 0.423 L C 0.477 P C 0.466 E C 0.462 P C 0.48 Q C 0.547 T C 0.571 A C 0.565 S C 0.586 L H 0.73 A H 0.758 E H 0.768 L H 0.772 Q H 0.758 Q H 0.728 M H 0.761 K H 0.781 L H 0.771 F H 0.798 L H 0.802 K H 0.812 L H 0.796 L H 0.774 K H 0.779 K H 0.787 Q H 0.767 E H 0.803 K H 0.839 E H 0.833 L H 0.853 K H 0.855 E H 0.862 L H 0.848 E H 0.836 R H 0.834 K H 0.802 G H 0.686 S H 0.732 K H 0.758 R H 0.737 R H 0.744 E H 0.732 E H 0.738 L H 0.754 L H 0.745 Q H 0.737 K H 0.693 Y H 0.626 S H 0.55 V H 0.519 L H 0.467 F H 0.452 L C 0.444 E C 0.465 P C 0.505 V C 0.522 Y C 0.578 P C 0.593 R C 0.58 G C 0.612 L C 0.625 D C 0.635 S C 0.575 Q H 0.486 V H 0.552 V H 0.65 E H 0.694 L H 0.734 K H 0.756 E H 0.785 R H 0.811 L H 0.802 E H 0.811 M H 0.831 E H 0.83 L H 0.833 I H 0.831 H H 0.83 L H 0.814 G H 0.802 E H 0.812 E H 0.815 Y H 0.778 H H 0.763 D H 0.782 G H 0.795 I H 0.802 R H 0.806 R H 0.802 R H 0.799 K H 0.795 E H 0.816 Q H 0.816 H H 0.804 A H 0.807 T H 0.832 E H 0.845 Q H 0.842 T H 0.849 A H 0.861 K H 0.862 I H 0.86 T H 0.858 E H 0.855 L H 0.841 A H 0.83 R H 0.817 E H 0.796 K H 0.773 Q H 0.766 I H 0.78 A H 0.777 E H 0.789 L H 0.821 K H 0.845 A H 0.841 L H 0.831 K H 0.813 E H 0.799 S H 0.739 S H 0.609 E H 0.763 S H 0.753 N H 0.721 I H 0.781 K H 0.805 D H 0.818 I H 0.837 K H 0.829 K H 0.843 K H 0.814 L H 0.796 E H 0.747 A H 0.743 K H 0.671 R H 0.597 L H 0.693 D H 0.671 R H 0.668 I H 0.731 Q H 0.73 V H 0.728 M H 0.671 M H 0.558 R H 0.585 S H 0.529 T H 0.468 S H 0.462 D C 0.495 K H 0.677 A H 0.694 A H 0.723 Q H 0.72 E H 0.735 R H 0.747 L H 0.729 K H 0.756 K H 0.748 E H 0.742 I H 0.744 N H 0.669 N H 0.703 S H 0.681 H H 0.691 I H 0.752 Q H 0.78 E H 0.791 V H 0.776 V H 0.8 Q H 0.813 T H 0.816 I H 0.834 K H 0.834 L H 0.83 L H 0.822 T H 0.807 E H 0.798 K H 0.772 T H 0.728 A H 0.646 R H 0.708 Y H 0.795 Q H 0.838 Q H 0.879 K H 0.878 L H 0.871 E H 0.856 E H 0.867 K H 0.856 Q H 0.846 A H 0.853 E H 0.863 N H 0.856 L H 0.857 R H 0.863 A H 0.856 I H 0.846 Q H 0.835 E H 0.825 K H 0.777 E H 0.724 G H 0.758 Q H 0.788 L H 0.81 Q H 0.846 Q H 0.854 E H 0.839 A H 0.821 V H 0.811 A H 0.818 E H 0.79 Y H 0.778 E H 0.766 E H 0.756 K H 0.704 L H 0.663 K H 0.6 T H 0.536 L H 0.45 T C 0.454 V H 0.471 E H 0.486 V H 0.509 Q H 0.53 E H 0.58 M H 0.581 V H 0.573 K H 0.583 N H 0.533 Y H 0.453 M C 0.512 K C 0.469 E C 0.497 V C 0.526 F C 0.597 P C 0.679 END --simple mime boundary--