From farmer@cse.ucsc.edu Wed Jul 5 20:34:25 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 UAA29287 for Message-Id: <200007051838.LAA16534@beta.cse.ucsc.edu> Subject: t0105(target 99 alignment) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: t0105.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-962822209.t99align.a2m' Content-Disposition: attachment; filename="t99-results-962822209.t99align.a2m" >t0105 DENINFKQSELPVTCGEVKGTLYKERFKQGTSKKCIQSEDKKWFTPREFEIEGDRGASKN WKLSIRCGGYTLKVLMENKFLPEPPSTRKKVTIK >gi|3309565|gb|AAC79677.1|_179:271 (AF049460) nuclear DEAF-1 related transcriptional regulator protein 8 [Homo sapiens] tekatlivvhtdgsivettglkgpaapltpgpqspptplapgqekggtky NWDPSVYDSELPVRCRNISGTLYKNRLGSGGRGRCIKQGE-NWYSPTEFE AMAGRASSKDWKRSIRYAGRPLQCLIQDGILNPHAASCTCAACCddmtls gpvrlfvpykrrkkenelpttpvkkdspknitllpataattftv >gi|3309567|gb|AAC79678.1|_193:285 (AF049461) nuclear DEAF-1 related transcriptional regulator protein [Pan troglodytes] tekatlivvhtdgsivettglkgpaapltpgpqspptplapgqekggtky NWDPSVYDSELPVRCRNISGTLYKNRLGSGGRGRCIKQGE-NWYSPTEFE AMAGRASSKDWKRSIRYAGRPLQCLIQDGILNPHAASCTCAACCdnmtls gpvrlfvpykrrkkenelpttpvkkdspknitllpataattftv >gi|3309563|gb|AAC79676.1|_193:285 (AF049459) nuclear DEAF-1 related transcriptional regulator protein [Homo sapiens] tekatlivvhtdgsivettglkgpaapltpgpqspptplapgqekggtky NWDPSVYDSELPVRCRNISGTLYKNRLGSGGRGRCIKQGE-NWYSPTEFE AMAGRASSKDWKRSIRYAGRPLQCLIQDGILNPHAASCTCAACCddmtls gpvrlfvpykrrkkenelpttpvkkdspknitllpataattftv >gi|3309569|gb|AAC79679.1|_193:285 (AF055884) nuclear DEAF-1 related transcriptional regulator [Rattus norvegicus] tekatlivvhtdgsivettglkgpaapltpgpqspptplapgqekggtky NWDPSVYDSELPVRCRNISGTLYKSRLGSGGRGRCIKQGE-NWYSPTEFE AMAGRASSKDWKRSIRYAGRPLQCLIQDGILNPHAASCTCAACCddmtls gpvrlfvpykrrkkenelpttpvkkdspknitllpataattftv >gi|8393248|ref|NP_058570.1|_194:286 deformed epidermal autoregulatory factor 1 (Drosophila)gi|4063898|gb|AAC98511.1| (AF102818) deformed epidermal autoregulatory factor 1 [Mus musculus] tekatlivvhtdgsivettglkgpaapltpgpqspptplapgqekggtky NWDPSVYDSELPVRCRNISGTLYKSRLGSGGRGRCIKQGE-NWYSPTEFE AMAGRASSKDWKRSIRYAGRPLQCLIQDGILNPHAASCTCAACCddmtls gpvrlfvpykrrkkenelpttpvkkdspknitllpataattftv >gi|1389895|gb|AAC35994.1|_125:217 (U59659) suppressin [Rattus norvegicus] tekatlivdhtdgsivettglkgpaapltpgpqspptpltpgqekggtky NWDPSVYDSELPVRCRNISGTLYKSRLGSGGRGRCIKQGE-NWYSPTEFE AMAGRASSKDWKRSIRYAGRPLQCLIQDGILNPHAASCTCAACCddmtls gpvrlllpykrrkkenvscprlvkkdspknitllpataattftv >gi|3293440|gb|AAC25714.1|_125:217 (AF068892) truncated suppressin [Homo sapiens] tekatlivvhtdgsivettglkgpaapltpgpqspptplapgqekggtky NWDPSVYDSDLPVRCRNISGTLYKNRLGSGGRGRCIKQGE-NWYSPTEFE AMAGRASSKDWKRSIRYAGRPLQCLIQDGILNPHAASCTCAACCddmtls gpvrlfvpykrrkkenelpttpvkkdspknitllpataattftv >gi|3293442|gb|AAC25715.1|_125:217 (AF068893) suppressin [Homo sapiens] tekatlivvhtdgsivettglkgpaapltpgpqspptplapgqvkggtny NWDPSVCDNDLPVRCRNISGTLYKNKLGSGGRGRCIKQGE-NWYSPTEFE AMAGRASSKDWKRSIRYAGRPLQCLIQDGILNPHAASCTCAACCddmtls gpvrlfvpykrrkkenelpttpvkkdspknitllpataattftv >gi|2246694|gb|AAB62704.1|_125:217 (AF007165) suppressin [Homo sapiens] tekatlivvhtdgsivettglkgpaapltpgpqspptplapgqekggtky NWDPSVYDSELPVRCRNISGTLYKNRLGSGGRGRCIKQGE-NWYSPTEFE AMAGRTSSKDWKRSIRYAGRPLQCLIQDGILNPHAASCTCAACCddmtls gplrlfvpykrrkkenelpttpvkkdspknitllpataattftv >gi|3293444|gb|AAC25716.1|_125:217 (AF068894) suppressin [Homo sapiens] tekatlivvhtdgsivettglkgpaapltpgpqspptplapgqekggtky NWDPSVYDSELPVRCRNISGTLYKNKLGSGGRGRCIKQGE-NWYSPTEFE AMAGRASSKDWKRSIRYAGRPLQCLIQDGILNPHAASCTCAACCddmtls gpvrlfvpykrrkkenelpttpvkkdspknitllpataattftv >gi|3293446|gb|AAC25717.1|_125:217 (AF068895) suppressin [Homo sapiens] tekatlivvhtdgsivettglkgpaapltpgpqspptplapgqekggtiy NWDPSVYDSELPVRCRNISGTLYKNKLGSGGRGRCIKQGE-NWYSPTEFE AMAGRASSKDWKRSIRYAGRPLQCLIQDGILNPHAASCTCAACCddmtls gpvrlfvpykrrkkenelpttpvkkdspknitllpataattftv >gi|6175041|sp|P23497|SP10_HUMAN_595:684 NUCLEAR AUTOANTIGEN SP-100 (SPECKLED 100 KDA)gi|1173656|gb|AAC50743.1| (U36501) SP100-B [Homo sapiens] glqrgrkkdrprkhltlnnkvqkkrwqqrgrkantrplkrrrkrgpripk DENINFKQSELPVTCGEVKGTLYKERFKQGTSKKCIQSEDKKWFTPREFE IEGDRGASKNWKLSIRCGGYTLKVLMENKFLPEPPSTRKK----vtik >gi|3252911|gb|AAC39790.1|_595:687 (AF056322) SP100-HMG nuclear autoantigen [Homo sapiens] glqrgrkkdrprkhltlnnkvqkkrwqqrgrkantrplkrrrkrgpripk DENINFKQSELPVTCGEVKGTLYKERFKQGTSKKCIQSEDKKWFTPREFE IEGDRGASKNWKLSIRCGGYTLKVLMENKFLPEPPSTRKKRIL-eshnnt lvdpceehkkknpdasvkfseflkkcsetwktifakekgkfedm >gi|7021843|dbj|BAA91410.1|_76:168 (AK000892) unnamed protein product [Homo sapiens] pedtktqvilqlqpvqqgiyeagsenntavvavethtihkieegidtgti -EANEDMEIAYPITCGESKAILLWKKFvCPGINVKCVKFND-QLISPKHF VHLAGKSTLKDWKRAIRLGGIMLRKMMDSGQIDFYQHDKVCSNTCrstkf dllissarapvpgqqtsvvqtptsadgsitqiaiseesmeeagle >gi|5764636|gb|AAD51352.1|AF173868_1_76:168 (AF173868) DNA binding protein p96PIF [Homo sapiens] pedtktqvilqlqpvqqgiyeagsenntavvavethtihkieegidtgti -EANEDMEIAYPITCGESKAILLWKKFvCPGINVKCVKFND-QLISPKHF VHLAGKSTLKDWKRAIRLGGIMLRKMMDSGQIDFYQHDKVCSNTCrstkf dllissarapvpgqqtsvvqtptsadgsitqiaiseesmeeagle >gi|5729846|ref|NP_006573.1|_86:178 glucocorticoid modulatory element binding protein 1gi|5081374|gb|AAD39355.1|AF099013_1 (AF099013) glucocorticoid modulatory element binding protein-1 [Homo sapiens] qlqpvqqglfidghfynriyeagsenntavvavethtihkieegidtgti -EANEDMEIAYPITCGESKAILLWKKFvCPGINVKCVKFND-QLISPKHF VHLAGKSTLKDWKRAIRLGGIMLRKMMDSGQIDFYQHDKVCSNTCrstkf dllissarapvpgqqtsvvqtptsadgsitqiaiseesmeeagle >gi|8118043|gb|AAF72874.1|AF210433_1_76:168 (AF210433) glucocorticoid modulatory element binding protein 1; GMEB-1 [Mus musculus] pedtktqvilqlqpvqqgiyeagsensaavvavethsihkieegidassi -EGNEDMEIAYPITCGESKAVLLWKKFvCPGINVKCVKFND-QLISPKHF VHLAGKSTLKDWKRAIRLGGIMLRKMMDSGQIDFYQHDKVCSNTCrstkf dllissarapvpgqqtsvvqtptsadgnitqiaiseesmeeagle >gi|6599186|emb|CAB63765.1|_56:150 (AL133646) hypothetical protein [Homo sapiens] alrdpdsilsslhftrgdltednmetenaaaaaaaaftassqlkeavlma EEGENLEAEIVyPITCGDSRANLIWRKFvCPGINVKCVQYDE-HVISPKE FVHLAGKSTLKDWKRAIRMNGIMLRKIMDSGELDFYQHDKVCSNTCrstk idlsgarvslssptsaeyipltpaaadvngspatitietcedpgdw >gi|7643907|gb|AAF65539.1|AF205780_1_81:175 (AF205780) GMEB-2b [Rattus norvegicus] vktvlvttnlaphggdltednmetenaaaaaaaaftassqlkeavlvkma EEGENLEAEIVyPITCGDSRANLIWRKFvCPGINVKCVQYDE-HVISPKE FVHLAGKSTLKDWKRAIRMNGIMLRKIMDSGELDFYQHDKVCSNTCrstk idlsgarvslssptsteyipltpaaadvngspatitietcedpgdw >gi|7643903|gb|AAF65537.1|AF205778_1_81:175 (AF205778) GMEB-2' [Rattus norvegicus] vktvlvttnlaphggdltednmetenaaaaaaaaftassqlkeavlvkma EEGENLEAEIVyPITCGDSRANLIWRKFvCPGINVKCVQYDE-HVISPKE FVHLAGKSTLKDWKRAIRMNGIMLRKIMDSGELDFYQHDKVCSNTCrstk idlsgarvslssptsteyipltpaaadvngspatitietcedpgdw >gi|3746541|gb|AAC64001.1|_80:174 (AF059273) glucocorticoid modulatory element binding protein 2 [Rattus norvegicus] evktvlvttnlaphggdltednmetenaaaaacaftassqlkeavlvkma EEGENLEAEIVyPITCGDSRANLIWRKFvCPGINVKCVQYDE-HVISPKE FVHLAGKSTLKDWKRAIRMNGIMLRKIMDSGELDFYQHDKVCSNTCrstk idlsgarvslssptsteyipltpaaadvngspatitietcedpgdw >gi|6912568|ref|NP_036516.1|_81:175 glucocorticoid modulatory element binding protein 2gi|5764634|gb|AAD51351.1|AF173867_1 (AF173867) DNA binding protein p79PIF [Homo sapiens] vktvlvttnlaphggdltednmetenaaaaaaaaftassqlkeavlvkma EEGENLEAEIVyPITCGDSRANLIWRKFvCPGINVKCVQYDE-HVISPKE FVHLAGKSTLKDWKRAIRMNGIMLRKIMDSGELDFYQHDKVCSNTCrstk idlsgarvslssptsaeyipltpaaadvngspatitietcedpgdw >gi|6331220|dbj|BAA86583.1|_82:176 (AB033095) KIAA1269 protein [Homo sapiens] vktvlvttnlaphggdltednmetenaaaaaaaaftassqlkeavlvkma EEGENLEAEIVyPITCGDSRANLIWRKFvCPGINVKCVQYDE-HVISPKE FVHLAGKSTLKDWKRAIRMNGIMLRKIMDSGELDFYQHDKVCSNTCrstk idlsgarvslssptsaeyipltpaaadvngspatitietcedpgdw >gi|7643905|gb|AAF65538.1|AF205779_1_81:175 (AF205779) GMEB-2a [Rattus norvegicus] vktvlvttnlaphggdltednmetenaaaaaaaaftassqlkeavlvkma EEGENLEAEIVyPITCGDSRANLIWRKFvCPGINVKCVQYDE-HVISPKE FVHLAGKSTLKDWKRAIRMNGIMLRKIMDSGELDFYQHDKVCSNTCrstk idlsgarvslssptsteyipltpaaadvngspatitietcedpgdw >gi|6005880|ref|NP_009168.1|_466:554 nuclear body protein Sp140gi|6094325|sp|Q92881|SP14_HUMAN NUCLEAR AUTOANTIGEN SP-140 (SPECKLED 140 KD)gi|1669498|gb|AAC50817.1| (U63420) Sp140 protein [Homo sapiens] vvssekkanvnlkdlskirgrkrgkpgtrftqsdraaqkrvrsrasrkhk DETVDFKAPLLPVTCGGVKGILHKKKLQQGILVKCIQTEDGKWFTPTEFE IKGGHARSKNWRLSVRCGGWPLRWLMENGFLPDPPRIRY-----rkkkri lksqnnssvdpcmrnldecevcrdggelfccdtcsrvfhedchi >gi|6166538|sp|Q13342|LY10_HUMAN_580:668 LYSP100 PROTEIN (LYMPHOID-RESTRICTED HOMOLOG OF SP100)gi|1173654|gb|AAB18617.1| (U36500) LYSP100-B [Homo sapiens] vvssekkanvnlkdlskirgrkrgkpgtrftqsdraaqkrvrsrasrkhk DETVDFKAPLLPVTCGGVKGILHKKKLQQGILVKCIQTEDGKWFTPTEFE IKGGHARSKNWRLSVRCGGWPLRWLMENGFLPDPPRIRY-----rkkkri lksqnnssvdpcmrnldecevcrdggelfccdtcsrvfhedchi >gi|2340123|gb|AAC53509.1|_360:453 (U83633) alternatively spliced; lacks nucleotides 1 to 91 and exon 11 [Mus caroli] rggkkrerlgsylirnikipmktswktavlarsantssqrrrkrgpripr EENADFGGAELPVVCGNVQGFLNKEKFKQGIYVRSIRSETGRLFTPMDFE IEGNCEKAKNWRQTIRCKGWTLRELIQKGVLQDPPRKKKENPRNprqmkr qvnal >gi|2340117|gb|AAC53506.1|_378:471 (U83629) Sp100 [Mus caroli]gi|2340152|gb|AAC12948.1| (U83654) Sp100 [Mus caroli] tgrkkrerlgsylirnikipmktswktavlarsantssqrrrkrgpripr EENADFGGAELPVVCGNVQGFLNKEKFKQGIYSRSIRSETGRLFTPMDFE IEGNCEKAKNWRQTIRCKGWTLRELIQQGVLQDPPRKKKETPRNprqmkr qvnal >gi|2340121|gb|AAC53508.1|_378:471 (U83632) alternatively spliced; lacks nucleotides 1 to 91 [Mus caroli] tgrkkrerlgsylirnikipmktswktavlarsantssqrrrkrgpripr EENADFGGAELPAVCGNVQGFLNKEKFKQGIYVRSIRSETGRLFTPMDFE IEGNCEKAKNWRQTIRCKGWTLRELIQKGVLQDPPRKKKENPRNprqmkr qvnal >gi|2340131|gb|AAC53513.1|_360:453 (U83636) alternatively spliced; lacks exon 11 [Mus musculus] gggkkrerlgsylirnikipmkpswktaflarsanpssqrrrkrgpripr EENADFGGAELPVVCGNAQGFLDKEKFKQGIYVRSIRGKTGRLFTPMDFE IEGNCEKAKNWRQTIRCKGWTLRELIQKGVLQDPPRKKKETPRNprqtrr qvnal >gi|7305513|ref|NP_038701.1|_378:471 nuclear antigen Sp100gi|2340129|gb|AAC53512.1| (U83630) Sp100 [Mus musculus] tgrkkrerlgsylirnikipmkpswktaflarsanpssqrrrkrgpripr EENADFGGAELPVVCGNAQGFLDKEKFKQGIYVRSIRGKTGRLFTPMDFE IEGNCEKAKNWRQTIRCKGWTLRELIQKGVLQDPPRKKKETPRNprqtrr qvnal >gi|1362890|pir||B49515_214:312 phosphoprotein 75 - human wnsevmmrvqkartkcarksrskekkkekdicssskrrfqknihrrgkpk SDTVDFHCSKLPVTCGEAKGILYKKKMKHGSSVKCIRNEDGTWLTPNEFE VEGKGRNAKNWKRNIRCEGMTLGELLKRKNSDECEVCCqggqlLCCGTCp rvfhedchippveakrmlwsctfcrmkrssgsqqchhvsktlerqmqpq >gi|4758588|ref|NP_004501.1|_251:349 interferon-induced protein 75, 52kDgi|4239654|gb|AAD13402.1| (L22343) nuclear phosphoprotein [Homo sapiens] wnsevmmrvqkartkcarksrskekkkekdicssskrrfqknihrrgkpk SDTVDFHCSKLPVTCGEAKGILYKKKMKHGSSVKCIRNEDGTWLTPNEFE VEGKGRNAKNWKRNIRCEGMTLGELLKRKNSDECEVCCqggqlLCCGTCp rvfhedchippveakrmlwsctfcrmkrssgsqqchhvsktlerqmqpq >gi|4758586|ref|NP_004500.1|_153:246 interferon-induced protein 41, 30kDgi|1362889|pir||A49515 phosphoprotein 41 - humangi|402205|gb|AAA18806.1| (L22342) phosphoprotein [Homo sapiens] wnsevmmrvqkartkcarksrskekkkekdicssskrrfqknihrrgkpk SDTVDFHCSKSPVTCGEAKGILYKKKMKHGSSVKCIRNEDGTWLTPNEFE VEGKGRNAKNWKRNIRCEGMTLGELLKSGLLLCPPRINLKRELNsk >gi|3293448|gb|AAC25718.1|_125:217 (AF068896) suppressin [Homo sapiens] tekatlivvhtdgsivettglkgpaapltpgpqspptplapgqekggtky NWDPSVYDSELPVRCRNISGTLYKNRLgSAAGDGASSRGRTG--TCPTEF EAMAGRASSKDWKRSIRYAGRPLQCLIQDGILNPHAASCTCAACCddmtl sgpvxlfvpykrrkkenelpttpvkkdspknitllpataattftv >gi|3293450|gb|AAC25719.1|_125:217 (AF068897) suppressin [Homo sapiens] tekatlivvhtdgsivettglkgpaapltpgpqspptplapgqekggtky NWDPSVYDSELPVRCRNISGTLYKNRLgSAAGDGASSRGRTG--TCPTEF EAMAGRASSKDWKRSIRYAGRPLQCLIQDGILNPHAASCTCAACCddmtl sgpvrlfvpykrrkkenelpttpvkkdspknitllpataattftv >gi|2133648|pir||S69214_210:303 deformed epidermal autoregulatory factor-1 - fruit fly (Drosophila melanogaster)gi|1209883|gb|AAC47040.1| (U46686) DEAF-1 [Drosophila melanogaster]gi|7293736|gb|AAF49105.1| (AE003515) Deaf1 gene product [Drosophila melanogaster]gi|1589475|prf||2211283A DEAF-1 protein [Drosophila melanogaster] ttatntiglnhdgsgsnnshdslatlehaaggasgvggggggtgggssgw SENPSTQHNEVfQIRCKTTCAELYRSKLGSGGRGRCVKYKD-KWHTPSEF EHVCGRGSSKDWKRSIKYGGKSLQSLIDEGTLTPHATNCSCTVCCddeag esasgpvrlftpykrrkrnqtdldmesgpkrkrnthhsnnnnsnt >gi|7496508|pir||T19470_71:162 hypothetical protein C25G4.4 - Caenorhabditis elegansgi|3874418|emb|CAA94573.1| (Z70680) similar to SAND domain [Caenorhabditis elegans] cdgfqaegsdhhhstmtpfqesqrnvyqilyghpanddfprpitplqiti --PEGDASPTVPVSCGVVNGKMHLNLFmCPGIHQPCIEVGN-DLLSPKQF TIRGDKERQKDWKASIRVGRSSLRTHMEAMTIDFYEHMNRCSGKCqsrny vnapseevlqarkskrtseagqlkyeienemagkeadnddnrksa >gi|7497426|pir||T19932_73:163 hypothetical protein C44F1.2 - Caenorhabditis elegansgi|3874918|emb|CAA88849.1| (Z49067) weak similarity to the human high mobility group protein I-C (PIR accession number S43153) [Caenorhabditis elegans] neemlvpsdpnfeidgrrvqenmydvswdqaselsytyldtpsehiwtpi ---VPLNATTVPVTCGYVKGIMHLKLFrCPGIRQACIEYES-QYLTPKQF TELGGKGRQKDWKACIRVENVSLRTLLENKTIDFYNHKSICHGQCqsrny mnstgrapvnkrhledvlasgddasepteqssgqiseepikkrgr >gi|7108552|gb|AAF36470.1|AF128125_1_193:276 (AF128125) autoimmune regulator [Mus musculus] ppatlasksvsspgshlktkppkkpdgnlesqhlplgngiqtmaasvqra ---VTVASGDVPGTRGAVEGILIQQVFESGRSKKCIQVGG-EFYTPNKFE --DPSGNLKNKARS----GSSLKPVVRAKGAQGRDEQKVGQQCGvpplps lpsepqvnqnedecavchdggeliccdgcprafhlaclspplqe >gi|7108550|gb|AAF36469.1|AF128124_1_193:276 (AF128124) autoimmune regulator [Mus musculus] ppatlasksvsspgshlktkppkkpdgnlesqhlplgngiqtmaasvqra ---VTVASGDVPGTRGAVEGILIQQVFESGRSKKCIQVGG-EFYTPNKFE --DPSGNLKNKARS----GSSLKPVVRAKGAQGRDEQKVGQQCGvpplps lpsepqvnqknedecavchdggeliccdgcprafhlaclspplq >gi|7108544|gb|AAF36466.1|AF128121_1_193:276 (AF128121) autoimmune regulator [Mus musculus] ppatlasksvsspgshlktkppkkpdgnlesqhlplgngiqtmaasvqra ---VTVASGDVPGTRGAVEGILIQQVFESGRSKKCIQVGG-EFYTPNKFE --DPSGNLKNKARS----GSSLKPVVRAKGAQGRDEQKVGQQCGvpplps lpsepqvnqnedecavchdggeliccdgcprafhlaclspplqe >gi|7108542|gb|AAF36465.1|AF128120_1_193:276 (AF128120) autoimmune regulator [Mus musculus] ppatlasksvsspgshlktkppkkpdgnlesqhlplgngiqtmaasvqra ---VTVASGDVPGTRGAVEGILIQQVFESGRSKKCIQVGG-EFYTPNKFE --DPSGNLKNKARS----GSSLKPVVRAKGAQGRDEQKVGQQCGvpplps lpsepqvnqknedecavchdggeliccdgcprafhlaclspplq >gi|7108536|gb|AAF36462.1|AF128117_1_193:276 (AF128117) autoimmune regulator [Mus musculus] ppatlasksvsspgshlktkppkkpdgnlesqhlplgngiqtmaasvqra ---VTVASGDVPGTRGAVEGILIQQVFESGRSKKCIQVGG-EFYTPNKFE --DPSGNLKNKARS----GSSLKPVVRAKGAQGRDEQKVGQQCGvpplps lpsepqvnqnedecavchdggeliccdgcprafhlaclspplqe >gi|7108534|gb|AAF36461.1|AF128116_1_193:276 (AF128116) autoimmune regulator [Mus musculus] ppatlasksvsspgshlktkppkkpdgnlesqhlplgngiqtmaasvqra ---VTVASGDVPGTRGAVEGILIQQVFESGRSKKCIQVGG-EFYTPNKFE --DPSGNLKNKARS----GSSLKPVVRAKGAQGRDEQKVGQQCGvpplps lpsepqvnqknedecavchdggeliccdgcprafhlaclspplq >gi|7504108|pir||T22598_6:96 hypothetical protein F53H4.5 - Caenorhabditis elegansgi|3877542|emb|CAB03138.1| (Z81089) similar to SAND domain [Caenorhabditis elegans] mifdq-----LLKIIFQVKCGTLTAKMVTKLFtCPGIHQNCILIDGeTEY ISPKEFTVRANKDKQKDWKGSIRIGKSNLRTLMEMRSLDFHDHPNQCSAK Cqsrnyitpkdptsdpsgrrrssttklipqnmfshipsafpnastslftv p >gi|7108532|gb|AAF36460.1|AF128115_1_193:264 (AF128115) autoimmune regulator [Mus musculus] ppatlasksvsspgshlktkppkkpdgnlesqhlplgngiqtmaasvqra ---VTVASGDVPGTRGAVEGILIQQVFESGRSKKCIQVGG-EFYTPNKFE --DPSGNLKNKARS----GSSLKPVVRAKGAQ------------vtipgr deqkvgqqcgvpplpslpsepqvnqnedecavchdggeliccdg >gi|7108548|gb|AAF36468.1|AF128123_1_193:264 (AF128123) autoimmune regulator [Mus musculus] ppatlasksvsspgshlktkppkkpdgnlesqhlplgngiqtmaasvqra ---VTVASGDVPGTRGAVEGILIQQVFESGRSKKCIQVGG-EFYTPNKFE --DPSGNLKNKARS----GSSLKPVVRAKGAQ------------vtipgr deqkvgqqcgvpplpslpsepqvnqnedecavchdggeliccdg >gi|7108546|gb|AAF36467.1|AF128122_1_193:264 (AF128122) autoimmune regulator [Mus musculus] ppatlasksvsspgshlktkppkkpdgnlesqhlplgngiqtmaasvqra ---VTVASGDVPGTRGAVEGILIQQVFESGRSKKCIQVGG-EFYTPNKFE --DPSGNLKNKARS----GSSLKPVVRAKGAQ------------vtipgr deqkvgqqcgvpplpslpsepqvnqknedecavchdggeliccd >gi|7108540|gb|AAF36464.1|AF128119_1_193:264 (AF128119) autoimmune regulator [Mus musculus] ppatlasksvsspgshlktkppkkpdgnlesqhlplgngiqtmaasvqra ---VTVASGDVPGTRGAVEGILIQQVFESGRSKKCIQVGG-EFYTPNKFE --DPSGNLKNKARS----GSSLKPVVRAKGAQ------------vtipgr deqkvgqqcgvpplpslpsepqvnqnedecavchdggeliccdg >gi|7108538|gb|AAF36463.1|AF128118_1_193:264 (AF128118) autoimmune regulator [Mus musculus] ppatlasksvsspgshlktkppkkpdgnlesqhlplgngiqtmaasvqra ---VTVASGDVPGTRGAVEGILIQQVFESGRSKKCIQVGG-EFYTPNKFE --DPSGNLKNKARS----GSSLKPVVRAKGAQ------------vtipgr deqkvgqqcgvpplpslpsepqvnqknedecavchdggeliccd >gi|6753020|ref|NP_033776.1|_193:264 autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)gi|3550508|emb|CAA07620.1| (AJ007715) autoimmune regulator [Mus musculus]gi|4426599|gb|AAD20444.1| (AF079536) autoimmune regulator [Mus musculus]gi|4456675|emb|CAB36909.1| (AJ132243) Aire protein [Mus musculus]gi|5669676|gb|AAD46421.1|AF105002_1 (AF105002) autoimmune regulator [Mus musculus]gi|6706793|emb|CAB66141.1| (AJ243821) APECED protein [Mus musculus]gi|7108573|gb|AAF36481.1|AF128772_1 (AF128772) autoimmune regulator [Mus musculus]gi|7108575|gb|AAF36482.1|AF128773_1 (AF128773) autoimmune regulator [Mus musculus] ppatlasksvsspgshlktkppkkpdgnlesqhlplgngiqtmaasvqra ---VTVASGDVPGTRGAVEGILIQQVFESGRSKKCIQVGG-EFYTPNKFE --DPSGNLKNKARS----GSSLKPVVRAKGAQ------------vtipgr deqkvgqqcgvpplpslpsepqvnqknedecavchdggeliccd >gi|7495061|pir||T32370_82:195 hypothetical protein C01B12.2 - Caenorhabditis elegansgi|2429436|gb|AAB70975.1| (AF025458) C01B12.2 gene product [Caenorhabditis elegans] vnepklckfikeesphkvkqepyddedlvhlgsesipsptsstsppfpte ---PAVQTIKLPkymeLKCGALVARLHTELFiCPGIREKCIEVLDcpGEL LTPVEFTIKAEKSKQKDWKGAIKHNGRMLRyascsfqllkteqfnrTLME FKQLDFYNHHEMCSFKChsrnyitknggsvpklppknvqrrhssasttsn vsqtainqllqgelikn >gi|7239187|gb|AAF43110.1|AF169948_1_1:61 (AF169948) SP100-HMG nuclear autoantigen [Hylobates lar] --------------------------------KKCIQSEDKKWFTPREFE IEGDRRASKNWKLSIRCGGYTLKFLMENKLLPEPPSTRKKRIL-kshnnt lvdpcavhkkknpdasvnlseflkkcsemwktifakekgkfedm >gi|3392940|emb|CAA08759.1|_192:265 (AJ009610) AIRE [Homo sapiens] apaaltprgtaspgsqlkakppkkpessaeqqrlplgngiqtmsasvqra ---VAMSSGDVPGARGAVEGILIQQVFESGGSKKCIQVGG-EFYTPSKFE ---DSGSGKNKARS----SSGPKPLVRAKGAQGAA---------pgggea rlgqqgsvpaplalpsdpqlhqknedecavcrdggeliccdgcp >gi|4557291|ref|NP_000374.1|_192:265 autoimmune regulator AIRE isoform 1gi|3334119|sp|O43918|AIRE_HUMAN AUTOIMMUNE REGULATOR (APECED PROTEIN)gi|2665371|emb|CAB10790.1| (Z97990) AIRE protein [Homo sapiens]gi|2696615|dbj|BAA23988.1| (AB006682) AIRE-1 [Homo sapiens]gi|2696619|dbj|BAA23990.1| (AB006684) AIRE-1 [Homo sapiens]gi|7768776|dbj|BAA95560.1| (AP001754) autoimmune regulator (APECED protein) [Homo sapiens] apaaltprgtaspgsqlkakppkkpessaeqqrlplgngiqtmsasvqra ---VAMSSGDVPGARGAVEGILIQQVFESGGSKKCIQVGG-EFYTPSKFE ---DSGSGKNKARS----SSGPKPLVRAKGAQGAA---------pgggea rlgqqgsvpaplalpsdpqlhqknedecavcrdggeliccdgcp >gi|7239183|gb|AAF43108.1|AF169946_1_1:42 (AF169946) SP100-HMG nuclear autoantigen [Pan troglodytes] -------------------------------------------------- -EGDRGASKNWKLSIRCGGYTLKVLTENKFLPEPPSTRKKRIL-eshnnt lvdpceehkkknpdasvkfseflkkrsemwktifakekgkfedm >gi|7239185|gb|AAF43109.1|AF169947_1_1:36 (AF169947) SP100-HMG nuclear autoantigen [Gorilla gorilla] -------------------------------------------------- -------SKNWKLSIRCGGYTLKVLMENKLLPEPPSTRKKRIL-eshnnt lvdpceehkkknpdasvkfseflkkcsemwktifakekgkfedm --simple mime boundary-- From farmer@cse.ucsc.edu Thu Jul 6 09:34:02 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 JAA01820 for Message-Id: <200007060738.AAA14065@beta.cse.ucsc.edu> Subject: t0105(database hits) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: t0105.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-962822209.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 Mon Jul 3 11:52:44 2000) Score method: average Summary of Database Hits: Average Target Template SeqID Reverse EValue Reverse EValue Reverse EValue SeqLabel 1scmA -6.55 32.43 --------- --------- -6.55 32 1a3s -6.29 42.05 -6.29 42 --------- --------- : mol:protein length:160 Ubc9 1u9aA -6.29 42.05 -6.29 42 --------- --------- : mol:protein length:160 Ubc9 1u9b -6.29 42.05 -6.29 42 --------- --------- : mol:protein length:160 Ubiquitin-Conjugating Enzyme E9 1tie -6.17 47.4 -6.17 47 --------- --------- : mol:protein length:172 Erythrina Trypsin Inhibitor (Kunitz) De-3 - --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-962822209.t99pairwise.a2m' Content-Disposition: attachment; filename="t99-results-962822209.t99pairwise.a2m" >t0105 deninfkqselpvtcgevkgtl---------------------YKERFKQ GTSKKCIQSEDKKWFTPREFE-----------iegdrgasknwklsircg gytlkvlmenkflpeppstrkkvtik >1scmA mol:protein length:60 Myosin (Regulatory Domain) - Chain A RLSKIISMFQAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRKWLVLRNWQW WKLYSKVKPL >t0105 DENINFKQSELPVTCGEVKGTLYKERFKQGTSKKCIQSEDKKWFTPREFE IEGDRGASKNWKLSIRCGGYTLKVLMENKFLPEPPSTRK-----kvtik >1a3s mol:protein length:160 Ubc9 gsmsgialsrlaqerkawrkdhpfgfvavptknpdgtmnlmnwecaipgk kgtpwegglfklrmlfkddypss-----------PPKCKFEPPLFHPNVY PSGTVCLSILEED------------------KDWRPAITIKQILLGiqEL LNEPNIQDPAQAEAYTIYCqnrveyekrvraqakkfaps >t0105 DENINFKQSELPVTCGEVKGTLYKERFKQGTSKKCIQSEDKKWFTPREFE IEGDRGASKNWKLSIRCGGYTLKVLMENKFLPEPPSTRK-----kvtik >1u9aA mol:protein length:160 Ubc9 lnmsgialsrlaqerkawrkdhpfgfvavptknpdgtmnlmnwecaipgk kgtpwegglfklrmlfkddypss-----------PPKCKFEPPLFHPNVY PSGTVCLSILEED------------------KDWRPAITIKQILLGiqEL LNEPNIQDPAQAEAYTIYCqnrveyekrvraqakkfaps >t0105 DENINFKQSELPVTCGEVKGTLYKERFKQGTSKKCIQSEDKKWFTPREFE IEGDRGASKNWKLSIRCGGYTLKVLMENKFLPEPPSTRK-----kvtik >1u9b mol:protein length:160 Ubiquitin-Conjugating Enzyme E9 lnmsgialsrlaqerkawrkdhpfgfvavptknpdgtmnlmnwecaipgk kgtpwegglfklrmlfkddypss-----------PPKCKFEPPLFHPNVY PSGTVCLSILEED------------------KDWRPAITIKQILLGiqEL LNEPNIQDPAQAEAYTIYCqnrveyekrvraqakkfaps >t0105 DENINFKQSELPVTCGEVKGTLYKERFKQGTSKKCIQSEDKKWFTPREFE IEGDRGASKNWKLSIRCGGYTLKVLMENKFLPEPPSTRK-----kvtik >1tie mol:protein length:172 Erythrina Trypsin Inhibitor (Kunitz) De-3 - vlldgngevvqnggtyyllpqvwaqgggvqlaktgeetcpltvvqspnel sdgkpiriesrlrsafipdddkvrigfayapkcapspwwtvvedeqegls vklsedestqf---------DYPFKFEQVSDQLHSYKLlyCEGKHEKCAS IGI--------------NRDQKGYRRLVVTEDYPLTVVLKK--------- -------dess --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-962822209.t99pairwise.casp.al' Content-Disposition: attachment; filename="t99-results-962822209.t99pairwise.casp.al" PFRMAT AL TARGET t0105 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 1scm_A Y 23 Y 798 K 24 K 799 E 25 K 800 R 26 L 801 F 27 Q 802 K 28 D 803 Q 29 Q 804 G 30 R 805 T 31 I 806 S 32 G 807 K 33 L 808 K 34 S 809 C 35 V 810 I 36 I 811 Q 37 Q 812 S 38 R 813 E 39 N 814 D 40 I 815 K 41 R 816 K 42 K 817 W 43 W 818 F 44 L 819 T 45 V 820 P 46 L 821 R 47 R 822 E 48 N 823 F 49 W 824 E 50 Q 825 TER END PFRMAT AL TARGET t0105 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 1a3s P 12 P 72 V 13 P 73 T 14 K 74 C 15 C 75 G 16 K 76 E 17 F 77 V 18 E 78 K 19 P 79 G 20 P 80 T 21 L 81 L 22 F 82 Y 23 H 83 K 24 P 84 E 25 N 85 R 26 V 86 F 27 Y 87 K 28 P 88 Q 29 S 89 G 30 G 90 T 31 T 91 S 32 V 92 K 33 C 93 K 34 L 94 C 35 S 95 I 36 I 96 Q 37 L 97 S 38 E 98 E 39 E 99 D 40 D 100 K 59 K 101 N 60 D 102 W 61 W 103 K 62 R 104 L 63 P 105 S 64 A 106 I 65 I 107 R 66 T 108 C 67 I 109 G 68 K 110 G 69 Q 111 Y 70 I 112 T 71 L 113 L 72 L 114 K 73 G 115 V 74 E 118 L 75 L 119 M 76 L 120 E 77 N 121 N 78 E 122 K 79 P 123 F 80 N 124 L 81 I 125 P 82 Q 126 E 83 D 127 P 84 P 128 P 85 A 129 S 86 Q 130 T 87 A 131 R 88 E 132 K 89 A 133 TER END PFRMAT AL TARGET t0105 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 1u9a_A P 12 P 72 V 13 P 73 T 14 K 74 C 15 C 75 G 16 K 76 E 17 F 77 V 18 E 78 K 19 P 79 G 20 P 80 T 21 L 81 L 22 F 82 Y 23 H 83 K 24 P 84 E 25 N 85 R 26 V 86 F 27 Y 87 K 28 P 88 Q 29 S 89 G 30 G 90 T 31 T 91 S 32 V 92 K 33 C 93 K 34 L 94 C 35 S 95 I 36 I 96 Q 37 L 97 S 38 E 98 E 39 E 99 D 40 D 100 K 59 K 101 N 60 D 102 W 61 W 103 K 62 R 104 L 63 P 105 S 64 A 106 I 65 I 107 R 66 T 108 C 67 I 109 G 68 K 110 G 69 Q 111 Y 70 I 112 T 71 L 113 L 72 L 114 K 73 G 115 V 74 E 118 L 75 L 119 M 76 L 120 E 77 N 121 N 78 E 122 K 79 P 123 F 80 N 124 L 81 I 125 P 82 Q 126 E 83 D 127 P 84 P 128 P 85 A 129 S 86 Q 130 T 87 A 131 R 88 E 132 K 89 A 133 TER END PFRMAT AL TARGET t0105 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 1u9b P 12 P 72 V 13 P 73 T 14 K 74 C 15 C 75 G 16 K 76 E 17 F 77 V 18 E 78 K 19 P 79 G 20 P 80 T 21 L 81 L 22 F 82 Y 23 H 83 K 24 P 84 E 25 N 85 R 26 V 86 F 27 Y 87 K 28 P 88 Q 29 S 89 G 30 G 90 T 31 T 91 S 32 V 92 K 33 C 93 K 34 L 94 C 35 S 95 I 36 I 96 Q 37 L 97 S 38 E 98 E 39 E 99 D 40 D 100 K 59 K 101 N 60 D 102 W 61 W 103 K 62 R 104 L 63 P 105 S 64 A 106 I 65 I 107 R 66 T 108 C 67 I 109 G 68 K 110 G 69 Q 111 Y 70 I 112 T 71 L 113 L 72 L 114 K 73 G 115 V 74 E 118 L 75 L 119 M 76 L 120 E 77 N 121 N 78 E 122 K 79 P 123 F 80 N 124 L 81 I 125 P 82 Q 126 E 83 D 127 P 84 P 128 P 85 A 129 S 86 Q 130 T 87 A 131 R 88 E 132 K 89 A 133 TER END PFRMAT AL TARGET t0105 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 1tie E 10 D 112 L 11 Y 113 P 12 P 114 V 13 F 115 T 14 K 116 C 15 F 117 G 16 E 118 E 17 Q 119 V 18 V 120 K 19 S 121 G 20 D 122 T 21 Q 123 L 22 L 124 Y 23 H 125 K 24 S 126 E 25 Y 127 R 26 K 128 F 27 L 129 K 28 C 132 Q 29 E 133 G 30 G 134 T 31 K 135 S 32 H 136 K 33 E 137 K 34 K 138 C 35 C 139 I 36 A 140 Q 37 S 141 S 38 I 142 E 39 G 143 D 40 I 144 R 55 N 145 G 56 R 146 A 57 D 147 S 58 Q 148 K 59 K 149 N 60 G 150 W 61 Y 151 K 62 R 152 L 63 R 153 S 64 L 154 I 65 V 155 R 66 V 156 C 67 T 157 G 68 E 158 G 69 D 159 Y 70 Y 160 T 71 P 161 L 72 L 162 K 73 T 163 V 74 V 164 L 75 V 165 M 76 L 166 E 77 K 167 N 78 K 168 TER END --simple mime boundary-- From farmer@cse.ucsc.edu Thu Jul 6 09:37:10 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 JAA01842 for Message-Id: <200007060741.AAA15563@beta.cse.ucsc.edu> Subject: t0105(target 99 secondary structure prediction) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: t0105.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-962822209.t99secstr.fasta' Content-Disposition: attachment; filename="t99-results-962822209.t99secstr.fasta" >t0105 LLLLLLLLLLLLEELLLEEEEEEEEELLLLLLEEEEEELLLLEELLLEEEELLLLLLLHHHHHHHHHLLLLHHHHHHHLLLLLLLLLLLLLLLL --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-962822209.t99secstr.casp.ss' Content-Disposition: attachment; filename="t99-results-962822209.t99secstr.casp.ss" PFRMAT SS TARGET t0105 AUTHOR UCSC Target99 server METHOD This prediction was derived from the following methods METHOD by averaging the corresponding probabilities: METHOD Method 0: METHOD TARGET t0105 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-10803/target-align-10803.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 13.7462 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: t0105 METHOD model_file: /projects/compbio/tmp/sam-nn-tmp.beta.26928/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: Thu Jul 6 00:40:14 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-10803/target-align-10803.a2m METHOD METHOD guide seq name: t0105 METHOD ###end 0 MODEL 1 D C 0.657 E C 0.636 N C 0.659 I C 0.546 N C 0.532 F C 0.462 K C 0.514 Q C 0.547 S C 0.578 E C 0.543 L C 0.534 P C 0.575 V E 0.457 T E 0.423 C C 0.516 G C 0.549 E C 0.503 V E 0.384 K E 0.441 G E 0.48 T E 0.545 L E 0.58 Y E 0.551 K E 0.513 E E 0.466 R E 0.46 F C 0.392 K C 0.592 Q C 0.65 G C 0.699 T C 0.658 S C 0.564 K E 0.422 K E 0.517 C E 0.631 I E 0.647 Q E 0.593 S E 0.465 E C 0.617 D C 0.678 K C 0.657 K C 0.494 W E 0.517 F E 0.462 T C 0.639 P C 0.67 R C 0.597 E E 0.384 F E 0.486 E E 0.498 I E 0.45 E C 0.474 G C 0.618 D C 0.686 R C 0.635 G C 0.562 A C 0.544 S C 0.502 K H 0.499 N H 0.521 W H 0.632 K H 0.645 L H 0.647 S H 0.615 I H 0.615 R H 0.603 C H 0.553 G C 0.461 G C 0.615 Y C 0.548 T C 0.466 L H 0.632 K H 0.653 V H 0.665 L H 0.666 M H 0.657 E H 0.646 N H 0.612 K C 0.555 F C 0.559 L C 0.576 P C 0.634 E C 0.622 P C 0.612 P C 0.579 S C 0.646 T C 0.611 R C 0.549 K C 0.495 K C 0.504 V C 0.582 T C 0.625 I C 0.661 K C 0.808 END --simple mime boundary--