From farmer@cse.ucsc.edu Tue Jul 25 22:56:42 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 WAA25060 for Message-Id: <200007252102.OAA02951@beta.cse.ucsc.edu> Subject: T0117(target 99 alignment) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0117.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-964558810.t99align.a2m' Content-Disposition: attachment; filename="t99-results-964558810.t99align.a2m" >T0117 MAEAASCARKGTKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNV NGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRR NGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYL QELHELHEDWLIHQRRPQSCKVLVLDADLNLENIGTEYQRSESSIFDAISSNQQPSPVLV SPSKRQRVAR >gi|4741228|emb|CAB41881.1|_1:250 (Y18048) deoxynucleoside kinase [Drosophila melanogaster]gi|5924308|gb|AAD56545.1|AF185268_1 (AF185268) deoxyribonucleoside kinase [Drosophila melanogaster]gi|7025919|gb|AAD47355.2|AF045610_1 (AF045610) deoxyribonucleoside kinase [Drosophila melanogaster]gi|7300459|gb|AAF55615.1| (AE003724) dnk gene product [Drosophila melanogaster] MAEAASCARKGTKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLL TEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKL KIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLI IYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSC KVLVLDADLNLENIGTEYQRSESSIFDAISSNQQPSPVLVSPSKRQRVAR >gi|6424683|gb|AAF08104.1|AF105217_1_34:271 (AF105217) thymidine kinase 2 [Mus musculus] mllrslrswaarslrsvgpgssrspgsldsgagPLWAPRRAWPPDKdrEN DKEKKAVVCIEGNIASGKTTCLEFFSNT-TDVEVLMEPVLKWRNVHGHNP LSLMYHDASRWGLTLQTYVQLTMLDQHTRPQMSPVRLMERSIYSARYIFV ENLYRSGKMPEVDYAILSEWFDWIVRNIDVSVDLIVYLRTTPEICYQRLK MRCREEEKVIPMEYLHAIHRLYEEWLVNGSLFPaAAPVLVIEADHNLEKM LELFEQNRARILT--PENWKHWTL------------glsdlqdsarnspa rarchgpra >gi|4456608|emb|CAA71523.2|_5:232 (Y10498) thymidine kinase [Homo sapiens] vqry-------AWPPDKEQEKEKKSVICVEGNIASGKTTCLEFFSNA-TD VEVLTEPVSKWRNVRGHNPLGLMYHDASRWGLTLQTYVQLTMLDRHTRPQ VSSVRLMERSIHSARYIFVENLYRSGKMPEVDYVVLSEWFDWILRNMDVS VDLIVYLRTNPETCYQRLKKRCREEEKVIPLEYLEAIHHLHEEWLIKGSL FPmAAPVLVIEADHHMERMLELFEQNRDRILT--PENRKHCP-------- ----- >gi|2497574|sp|O00142|KITM_HUMAN_10:234 THYMIDINE KINASE 2, MITOCHONDRIALgi|1905969|gb|AAC51167.1| (U77088) thymidine kinase 2 [Homo sapiens] mgafcqrps----------SDKEQEKEKKSVICVEGNIAGGKTTCLEFFS NA-TDVEVLTEPVSKWRNVRGHNPLGLMYHDASRWGLTLQTYVQLTMLDR HTRPQVSSVRLMERSIHSARYIFVENLYRSGKMPEVDYVVLSEWFDWILR NMDVSVDLIVYLRTNPETCYQRLKKRCREEEKVIPLEYLEAIHHLHEEWL IKGSLFPmAAPVLVIEADHHMERMLELFEQNRDRILT--PENRKHCP--- ---------- >gi|1905974|gb|AAC51168.1|_1:224 (U80628) thymidine kinase 2 isoform B [Homo sapiens] -----------DKEQEKEKKSVICVEGNIAGGKTTCLEFFSNA-TDVEVL TEPVSKWRNVRGHNPLGLMYHDASRWGLTLQTYVQLTMLDRHTRPQVSSV RLMERSIHSARYIFVENLYRSGKMPEVDYVVLSEWFDWILRNMDVSVDLI VYLRTNPETCYQRLKKRCREEEKVIPLEYLEAIHHLHEEWLIKGSLFPmA APVLVIEADHHMERMLELFEQNRDRILT--PENRKHCP------------ - >gi|2833282|sp|Q16854|DGK_HUMAN_35:276 DEOXYGUANOSINE KINASE PRECURSOR (DGUOK)gi|7434491|pir||JC6142 deoxyguanosine kinase (EC 2.7.1.113) precursor - humangi|1477482|gb|AAC50624.1| (U41668) deoxyguanosine kinase [Homo sapiens] maagrlflsrlrapfssmaksplegvsssrglha---------------- GRGPRRLSIEGNIAVGKSTFVKLLTKTYPEWHVATEPVATWQNIQAagnq kactaqslGNLLDMMYREPARWSYTFQTFSFLSRLKVQLEPFPekllqar KPVQIFERSVYSDRYIFAKNLFENGSLSDIEWHIYQDWHSFLLWEFASRi tLHGFIYLQASPQVCLKRLYQRAREEEKGIELAYLEQLHGQHEAWLIHkt tklhFEALMNIPVLVLDVNDDFSEEVTKQEDLMREVNTFVKN-------- -----------l >gi|4503269|ref|NP_000779.1|_1:257 deoxycytidine kinasegi|118447|sp|P27707|DCK_HUMAN DEOXYCYTIDINE KINASE (DCK)gi|105829|pir||A38585 deoxycytidine kinase (EC 2.7.1.74) - humangi|181510|gb|AAA35752.1| (M60527) deoxycytidine kinase [Homo sapiens] MATPPKRSCPSFSaSSEGTRIKKISIEGNIAAGKSTFVNILKQLCEDWEV VPEPVARWCNVqstqdefeeltmsqkNGGNVLQMMYEKPERWSFTFQTYA CLSRIRAQLASLNgklkdaeKPVLFFERSVYSDRYIFASNLYESECMNET EWTIYQDWHDWMNNqfGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGI PLEYLEKLHYKHESWLLHrtlktnFDYLQEVPILTLDVNEDFKDKY---E SLVEKVKEFL---------------------stl >gi|6681141|ref|NP_031858.1|_1:257 deoxycytidine kinasegi|1169273|sp|P43346|DCK_MOUSE DEOXYCYTIDINE KINASE (DCK)gi|1083283|pir||A55122 deoxycytidine kinase (EC 2.7.1.74) - mousegi|456677|emb|CAA54787.1| (X77731) deoxycytidine kinase [Mus musculus] MATPPKRFCPSPStSSEGTRIKKISIEGNIAAGKSTFVNILKQASEDWEV VPEPVARWCNVQStqeefeelttsqksgGNVLQMMYEKPERWSFTFQSYA CLSRIRAQLASLNgklkdaeKPVLFFERSVYSDRYIFASNLYESDCMNET EWTIYQDWHDWMNSqfGQSLELDGIIYLRATPEKCLNRIYLRGRNEEQGI PLEYLEKLHYKHESWLLHrtlktsFDYLQEVPVLTLDVNEDFKDKH---E SLVEKVKEFL---------------------stl >gi|4503319|ref|NP_001920.1|_18:259 deoxyguanosine kinasegi|1480198|emb|CAA66054.1| (X97386) deoxyguanosine kinase [Homo sapiens] maksplegvsssrglha----------------GRGPRRLSIEGNIAVGK STFVKLLTKTYPEWHVATEPVATWQNIQAagtqkactaqslGNLLDMMYR EPARWSYTFQTFSFLSRLKVQLEPFPekllqarKPVQIFERSVYSDRYIF AKNLFENDSLSDIEWHIYQDWHSFLLWEFASRitLHGFIYLQASPQVCLK RLYQRAREEEEGIELAYLEQLHGQHEAWLIHkttklhFEALMNIPVLVLD VNDDFSEEVTKQEDLMREVNTFVKN-------------------l >gi|6502515|gb|AAF14342.1|U90524_1_16:276 (U90524) deoxyguanosine kinase [Mus musculus] maagrfllrrlrasf-RSPLRNCFVDAPharaMHDGGGPRRLCIEGNIAV GKSTFVKLLMKTHPEWQVATEPIAEWQNIQAagaqkdgtskrlGNLLEMM YQEPARWSYTFQTLSFMSRLKVQLEPIPgrllqaeKSVRVFERSVYSDRY IFAKNLFENGSLSDIEWHIYQDWHSFLLQEFANRllLHGFIYLQASPQVC MERLYQRDREEEKGIELAYLQQLHSQHEDWFINkttklhFEALQHVPVLV LDVTEDFSENAARQEELMGQVNTFMRN-------------------l >gi|7434490|pir||S71315_20:259 deoxyguanosine kinase (EC 2.7.1.113) precursor - human maksplegvsssrglhagc------------------GPRRLSIEGNIAV GKSTFVKLLTKTYPEWHVATEPVATWQNIQAagtqkactaqslGNLLDMM YREPARWSYTFQTFSFLSRLKVQLEPFPekllqarKPVQIFERSVYSDRY IFAKNLFENDSLSDIEWHIYQDWHSFLLWEFASRitLHGFIYLQASPQVC LKRLYQRAREEEEGIELAYLEQLHGQHEAWLIHkttklhFEALMNIPVLV LDVNDDFSEEVTKQEDLMREVNTFVKN-------------------l >gi|1352235|sp|P48769|DCK_RAT_1:257 DEOXYCYTIDINE KINASE (DCK)gi|508570|gb|AAA65098.1| (L33894) deoxycytidine kinase [Rattus norvegicus] MATPPKRFCSSPStSSEGTRIKKISIEGNIAAGKSTFVNILKQVCEDWEV VPEPVARWCNVQStqdefeelttsqksgGNVLQMMYEKPERWSFIFQSYA CLSRIRAQLASLNgslrdaeKPVLFFERSVYSDRYIFASNLYESDCMNET EWTIYQDWHDWMNSqfGQSLELDGIIYLRATPEKCLNRIYIRGRDEEQGI PLEYLEKLHYKHESWLLHrtlktnFEYLQEVPILTLDVNLDFKDKE---E SLVEKVKEFL---------------------stt >gi|7304999|ref|NP_038792.1|_16:276 deoxyguanosine kinasegi|4877287|emb|CAB43121.1| (AJ133749) deoxyguanosine kinase 1 [Mus musculus] maagrfllrrlrasf-RSPLRNALVDAPharaMHDGGGPRRLCIEGNIAV GKSTFVKLLMKTHPEWQVATEPIAAWQNIQAagaqkdgtskrlGNLLEMM YQEPARWSYTFQTLSFMSRLKVQLEPIPgrllqaeKSVRVFERSVYSDRY IFAKNLFENGSLSDIEWHIYQDWHSFLLQEFANRllLHGFIYLQASPQVC MERLYQRDREEEKGIELAYLQQLHSQHEDWFINkttklhFEALQHVPVLV LDVTEDFSENAARQEELMGQVNTFMRN-------------------l >gi|4877289|emb|CAB43122.1|_1:245 (AJ133750) deoxyguanosine kinase 2 [Mus musculus] -------------MHDGGGPRRLCIEGNIAVGKSTFVKLLMKTHPEWQVA TEPIAAWQNIQAagaqkdgtskrlGNLLEMMYQEPARWSYTFQTLSFMSR LKVQLEPIPgrllqaeKSVRVFERSVYSDRYIFAKNLFENGSLSDIEWHI YQDWHSFLLQEFANRllLHGFIYLQASPQVCMERLYQRDREEEKGIELAY LQQLHSQHEDWFINkttklhFEALQHVPVLVLDVTEDFSENAARQEELMG QVNTFMRN-------------------l >gi|7330010|gb|AAF59999.1|AF210726_20_211:484 (AF210726) thymidine kinase [Macaca mulatta rhadinovirus 26-95] sgrrgaisgpsstkpshgagltrktktslsvslknllrikdddakvdvpr PVTVPVHLMQPHPMTEYRNAFLIYLEGVMGVGKTTLLNSMTGMVpqENVL SCPEPMKFWTCVYSNCLKEQrsIVKqgthgksITSARVYACQSKFALPFR ATAAGIGRnlqpwlvgngstkpANWIVFDRHLLSATVVFPLVHVKYNRLT PDHLFQILSLFSAH------DGDVVVLLTLNSSEAHRRIQSRGRKEEKGI TQNYLRQVawayHAVFCTWVMMQYLTPEQMVQLCVQTVSIEDICNMNSRL THRFLTLtklHEQSMIPMVAEMLVSVKEHV--tlmevclglfkelrklqi livdagehlddacglwgniygqvmsndaikpr >gi|4494925|gb|AAD21347.1|_211:484 (AF083501) thymidine kinase [Macaca mulatta rhadinovirus 17577] sgrrgaisgpsstkpshgagltrktktslsvslknllrikdddakvdvpr PVTVPVHLMQPHPMTEYRNAFLIYLEGVMGVGKTTLLNSMTGMVpqENVL SCPEPMKFWTCVYSNCLKEQrsIVKqgthgklITSARVYACQSKFALPFR ATAAGIGRnlqpwlvgngstkpANWIVFDRHLLSATVVFPLVHVKYNRLT PDHLFQILSLFSAH------DGDVVVLLTLNSSEAHRRIQSRGRKEEKGI TQNYLRQVawayHAVFCTWVMMQYLTPEQMVQLCVQTVSIEDICNMNSRL THRFLTLtklHEQSMIPMVAEMLVSVKEHV--tlmevclglfkelrklqi livdagehlddacglwgniygqvmsneaikpr >gi|66705|pir||KIBETE_266:540 thymidine kinase (EC 2.7.1.21) BXLF1 - human herpesvirus 4 (strain B95-8) fehlaahgrefsklskhaaqlkrlsgsvmnvlnlddaqdtrqakaqrkes MRVPIVTHLTNHVP-VIKPACSLFLEGAPGVGKTTMLNHLKAVFGDLtIV VPEPMRYWTHVY-ENAIKAMHKnvtrarhgreDTSAEVLACQMKFTTPFR VLASRKRSllvtesgarsvaplDCWILHDRHLLSASVVFPLMLLRSQLLS YSDFIQVLATFTAD------PGDTIVWMKLNVEENMRRLKKRGRKHESGL DAGYLKSVndayHAVYCAWLLTQYFAPEDIVKVCAGLTTITTVCHQSHTp iIRSGVAEKLYKNSIFSVLKevIQPFRADAVLLevclaftrtlaylqfvl vdlsefqddlpgcwteiymqalknpairsqffd >gi|1170666|sp|P03177|KITH_EBV_266:540 THYMIDINE KINASEgi|1334907|emb|CAA24799.1| (V01555) BXLF1 early reading frame, thymidine kinase (Littler et al, 1986). Weak homology to RF 36 VZV and HSV thymidine kinase. 4.0kb early RNA presumably encodes the TK. Also a 2.2kb late RNA here. [Human herpesvirus 4] fehlaahgrefsklskhaaqlkrlsgsvmnvlnlddaqdtrqakaqrkes MRVPIVTHLTNHVP-VIKPACSLFLEGAPGVGKTTMLNHLKAVFGDLtIV VPEPMRYWTHVY-ENAIKAMHKnvtrarhgreDTSAEVLACQMKFTTPFR VLASRKRSllvtesgarsvaplDCWILHDRHLLSASVVFPLMLLRSQLLS YSDFIQVLATFTAD------PGDTIVWMKLNVEENMRRLKKRGRKHESGL DAGYLKSVndayHAVYCAWLLTQYFAPEDIVKVCAGLTTITTVCHQSHTp iIRSGVAEKLYKNSIFSVLKevIQPFRADAVLLevclaftrtlaylqfvl vdlsefqddlpgcwteiymqalknpairsqffd >gi|1246355|gb|AAA93507.1|_266:540 (L37432) (thymidine kinase):(phleomycin/zeocin binding protein) fusion protein [Cloning vector pZEO-SG1] fehlaahgrefsklskhaaqlkrlsgsvmnvlnlddaqdtrqakaqrkes MRVPIVTHLTNHVP-VIKPACSLFLEGAPGVGKTTMLNHLKAVFGDLtIV VPEPMRYWTHVY-ENAIKAMHKnvtrarhgreDTSAEVLACQMKFTTPFR VLASRKRSllvtesgarsvaplDCWILHDRHLLSASVVFPLMLLRSQLLS YSDFIQVLATFTAD------PGDTIVWMKLNVEENMRRLKKRGRKHESGL DAGYLKSVndayHAVYCAWLLTQYFAPEDIVKVCAGLTTITTVCHQSHTp iIRSGVAEKLYKNSIFSVLKevIQPFRADAVLLevclaftrtlaylqfvl vdlsefqddlpgcwteiymqalknpairsqffd >gi|125448|sp|P21293|KITH_HSVSA_191:441 THYMIDINE KINASEgi|66706|pir||KIBEHS thymidine kinase (EC 2.7.1.21) - saimiriine herpesvirus 1 (strain 11[Onc])gi|60341|emb|CAA45643.1| (X64346) thymidine kinase [Saimiriine herpesvirus 2]gi|221856|dbj|BAA00432.1| (D00543) thymidine kinase [Saimiriine herpesvirus 2] tklegkqkmftrkkkgsfvkigsnmlefgeslksklhndskkspdepdgl -VHVPVHLLYPPKHQDPVPAFFIFLEGSIGVGKTTLLKSMNGILGGKNVl aFHEPIAYWTDVFS-NSLEEVYKltlpakvgrtSNSAKLLACQLKFASPL LALKTATDRlsspknsllssDMWVMFDRHPLSATVVFPYMHFQNGFLSFS HLIQLWSSFKAS------RGDNIILLNLNSQENLKRVKKRNRKEEKSVSI EHIRLLnncyHAVYCAWLLVQNFTPEEIVEVCFNAKHITD---------- ------LSSSKPSFLAKHVSTEDML--kssifntwiemtkahrdsctlme clltfckelekvqlihvnvspftddip >gi|118820|sp|P09250|KITH_VZVD_4:255 THYMIDINE KINASEgi|66707|pir||KIBE36 thymidine kinase (EC 2.7.1.21) - human herpesvirus 3gi|60025|emb|CAA27919.1| (X04370) ORF36 (AA1-341) [Human herpesvirus 3]gi|263540|gb|AAB24914.1| thymidine kinase, TK [varicella zoster virus VZV, Peptide, 341 aa] mst-----------DKTDVKMGVLRIYLDGAYGIGKTTAAEEFLHHFait pNRILLIGEPLSYWRNLAGEDAICGIYgtqtrrlngdvspEDAQRLTAHF QSLFCSPHAIMHAKIsalmdtstsdlvqvNKEPYKIMlsDRHPIASTICF PLSRYLVGDMSPAALPGLL-----FTLPAEPPGTNLVVCTVSLPSHLSRV SKRARPGE-TVNLPFVMVLRNVY------------IMLIntIIFLKTNNW HAGWNTLSFCNDVFKQKLQKSECIKLREVPGIED----tlfavlklpelc gefgnilplwawgmetlsncsrsmspfvlsleqtpqha >gi|1246358|gb|AAA93509.1|_1:256 (L37440) thymidine kinase:phleomycin/zeocin resistance fusion protein [Cloning vector pZEO-SG2] -------MASTDKTDVKMGVLRIYLDGAYGIGKTTAAEEFLHHFaitpNR ILLIGEPLSYWRNLAGEDAICGIYgtqtrrlngdvspEDAQRLTAHFQSL FCSPHAIMHAKIsalmdtstsdlvqvNKEPYKIMlsDRHPIASTICFPLS RYLVGDMSPAALPGLL-----FTLPAEPPGTNLVVCTVSLPSHLSRVSKR ARPGE-TVNLPFVMVLRNVY------------IMLIntIIFLKTNNWHAG WNTLSFCNDVFKQKLQKSECIKLREVPGIED----tlfavlklpelcgef gnilplwawgmetlsnclrsmspfvlsleqtpqha >gi|118822|sp|P14344|KITH_VZVW_4:255 THYMIDINE KINASEgi|66708|pir||KIBEEL thymidine kinase (EC 2.7.1.21) - human herpesvirus 3 (strains Ellen, Oka, ppIIa, and 5-1-1)gi|330327|gb|AAA45865.1| (M36160) thymidine kinase [Human herpesvirus 3]gi|5926722|dbj|BAA23727.2| (AB009252) thymidine kinase [Human herpesvirus 3]gi|5926724|dbj|BAA23728.2| (AB009253) thymidine kinase [Human herpesvirus 3] mst-----------DKTDVKMGVLRIYLDGAYGIGKTTAAEEFLHHFait pNRILLIGEPLSYWRNLAGEDAICGIYgtqtrrlngdvspEDAQRLTAHF QSLFCSPHAIMHAKIsalmdtstsdlvqvNKEPYKIMlsDRHPIASTICF PLSRYLVGDMSPAALPGLL-----FTLPAEPPGTNLVVCTVSLPSHLSRV SKRARPGE-TVNLPFVMVLRNVY------------IMLIntIIFLKTNNW HAGWNTLSFCNDVFKQKLQKSECIKLREVPGIED----tlfavlklpelc gefgnilplwawgmetlsnclrsmspfvlsleqtpqha >gi|118821|sp|P14343|KITH_VZVG_4:255 THYMIDINE KINASEgi|66711|pir||KIBEGK thymidine kinase (EC 2.7.1.21) - human herpesvirus 3 (strain GK) mst-----------DKTDVKMGVLRIYLDGAYGIGKTTAAEEFLHHFait pNRILLIGEPLSYWRNLAGEDAICGIYgtqtrrlngdvspEDAQRLTAHF QSLFCSPHAIMHAKIsalmdtstsdlvqvNKEPYKIMlsDRHPIASTICF PLSRYLVGDMSPAALPGLL-----FTLPAEPPGTNLVVCTVSLPSHLSRV SKRARPGE-TVNLPFVMVLRNVY------------IMLIntIIFLKTNNW HAGWNTLSFCNDVFKQKLQKSECIKLREVPGIED----tlfavlklpelc gefgnilplwawgmetlsnclrsmspfvlsleqtpqha >gi|118818|sp|P14341|KITH_VZV4_4:255 THYMIDINE KINASEgi|66710|pir||KIBE40 thymidine kinase (EC 2.7.1.21) - human herpesvirus 3 (strain 40a2) mst-----------DKTDVKMGVLRIYLDGAYGIGKTTAAEEFLHHFait pNRILLIGEPLSYWRNLAGEDAICGIYgtqtrrlngdvspEDAQRLTAHF QSLFCSPHAIMHAKIsalmdtstsdlvqvNKEPYKIMlsDRHPIASTICF PLSRYLVGDMSPAAPPGLL-----FTLPAEPPGTNLVVCTVSLPSHLSRV SKRARPGE-TVNLPFVMVLRNVY------------IMLIntIIFLKTNNW HAGWNTLSFCNDVFKQKLQKSECIKLREVPGIED----tlfavlklpelc gefgnilplwawgmetlsnclrsmspfvlsleqtpqha >gi|5732886|gb|AAD49322.1|_4:255 (AF162440) thymidine kinase [Human herpesvirus 3] mst-----------DKTDVKMGVLRIYLDGAYGIGKTTAAEEFLHHFait pNRILLIGEPLSYWRNLAGEDAICGIYgtqtrrlngdvspEDAQRLTAHF QSLFCSPHAIMHAKIsalmdtstsdlvqvNKEPYKIMlsDRHPIASTICF PLSGYLVGDMSPAALPGLL-----FTLPAEPPGTNLVVCTVSLPSHLSRV SKRARPGE-TVNLPFVMVLRNVY------------IMLIntIIFLKTNNW HAGWNTLSFCNDVFKQKLQKSECIKLREVPGIED----tlfavlklpelc gefgnilplwawgmetlsnclrsmspfvlsleqtpqha >gi|4019247|gb|AAC95545.1|_191:439 (AF083424) thymidine kinase [Ateline herpesvirus 3] trteekqkmftrkkkgsfvkigsnvlefggsiksklhnsckksvdspdgl -VHVPVHVLYPPLHQEPIPAFFIFLEGSIGVGKTTLLKSMRGILPGKNVl tFHEPMAFWKNVFS-NSLDEVYKltlpakvgsmTNSSKLLACQLKFAAPL LALKTSTDRlsisnrsnlssNMWVMFDRHPLSATVVFPYMHYQNGFLSFS HLVHLWGSFRAS------HGDNIILLNLNSQENLERVKRRNRKEEKCVSL EHIRMLnscyHAVYCAWLLVQNFTPEEIVEVCFNTKQITD---------- ------LRSSKPSFLEKHVSIED----vlkssifnawmdmtkayrdnctl meclltlckelekvqllhinassftdd >gi|2370245|emb|CAA73635.1|_191:441 (Y13183) thymidine kinase [Saimiriine herpesvirus 2] tklegkqkmftrkkkgsfvkigsnmlefgeslksklhndskkspdepdgl -VHVPVHLLYPPMHQELVPAFFIFLEGSIGVGKTTLLKSMNGILGGKNVl aFHEPIAYWTDVFS-NSLEEVYKltlpakvgrtSNSAKLLACQLKFASPL LALKTATDRlsshknsllssDMWVMFDRHPLSATVVFPYMHFQNGFLSFS HLIQLWSSFKAS------QGDNIILLNLNSQENLKRVRKRNRKEEKSVSI EHIRLLnncyHAVYCAWLLVQNFTPEEIVEVCFNAKHITD---------- ------LSSSKPSFLAKHVSTEDML--kssifntwiemtkahrdsctlme clltfckelekvqllhvnvssftddip >gi|118819|sp|P14342|KITH_VZV7_4:255 THYMIDINE KINASEgi|66709|pir||KIBE73 thymidine kinase (EC 2.7.1.21) - human herpesvirus 3 (strain 7-1-3) mst-----------DKTDVKMGVLRIYLDGAYGIGKTTAAEEFLHHFait pNRILLIGEPLSYWRNLAGEDAICGIYgtqtrrlngdvspEDAQRLTAHF QSLFCSPHAIMHAKIsalmdtstsdlvqvNKEPYKIMlsDQHPIASTICF PLSRYLVGDMSPAALPGLL-----FTLPAEPPGTNLVVCTVSLPSHLSRV SKRARPGE-TVNLPFVMVLRNVY------------IMLIntIIFLKTNNW HAGWNTLSFCNDVFKQKLQKSECIKLREVPGIED----tlfavlklpelc gefgnilplwawgmetlsnclrsmspfvlsleqtpqha >gi|5732882|gb|AAD49321.1|_4:255 (AF162437) thymidine kinase [Human herpesvirus 3] mst-----------DKTDVKMGVLRIYLDGAYGIGKTTAAEEFLHHFait pNRILLIGGPLSYWRNLAGEDAICGIYgtqtrrlngdvspEDAQRLTAHF QSLFCSPHAIMHAKIsalmdtstsdlvqvNKEPYKIMlsDRHPIASTICF PLSRYLVGDMSPAALPGLL-----FTLPAEPPGTNLVVCTVSLPSHLSRV SKRARPGE-TVNLPFVMVLRNVY------------IMLIntIIFLKTNNW HAGWNTLSFCNDVFKQKLQKSECIKLREVPGIED----tlfavlklpelc gefgnilplwawgmetlsnclrsmspfvlsleqtpqha >gi|7271649|gb|AAF44495.1|AF198100_142_24:232 (AF198100) ORF FPV151 Deoxycytidine kinase [Fowlpox virus] mafqelccsnllkfencslleth--------------------KKISIEG NISAGKSTLINILSD--NGYNVVQEPLEQWR---GNNLLDKLYKDPSRWA YTFQSHAFWTRTKTYIDALNKNkgNIILERSVFSDKYIFATALHDIGYID DTEWNIYNEYSKWMTEFMDIKIDGIIYLKTSPDICYKRMLNRARHEENTV KIDYLNLLHDKHEKWLSENNEHEfKVPVLEINGDGDFIDDSNRQSSILSN IYDFISE-------------------lyi >gi|7444320|pir||T03116_213:478 thymidine kinase (EC 2.7.1.21) - alcelaphine herpesvirus 1gi|2337984|gb|AAC58068.1| (AF005370) thymidine kinase [Alcelaphine herpesvirus 1] erhprqlsgavaqgairksprklkfkpakfkglsssllnpftasdsgrra RRQTPTCQPGFTPifqdlgEPHYVKACTVFFEGCMAAGKTTLLNFARQTL SDDeaLTIPEPMRFWTEVY-TNVLSQIVKinkecKPGKTSttaelVSCQL KFATPlktqslFLQRSVKKDSemqpvgplDKWVIVDRHQLSALVVFPLVL MRRGMLSFSDFFNLLGMFEAH------PGEVIALMSVNVEENFTRLKKRG RVCERHIDRDYIKEIkgsfNAAYCAWLFLQYFSIQTTMQ-ICMGLSSLDE ACATEGVCHTTASRIWNNSMLVTL------------sdiisqfsndytvq nvcynffsqlstlkfvvidlsafrhdvpgawgefym >gi|462450|sp|P33802|KITH_HSVBM_211:476 THYMIDINE KINASEgi|320275|pir||A60030 thymidine kinase (EC 2.7.1.21), BXLF1 homolog - alcelaphine herpesvirus 1 (strain WC11)gi|227948|prf||1714185A gene A [Bovine herpesvirus 3] erhprqlsgavaqgairksprklkfkpakfkglsssllnpftasdsgrra RRQTPTCQPGFTPifqdlgEPHYVKACTVFFEGCMAAGKTTLLNFARQTL SDDeaLTIPEPMRFWTEVY-TNVLSQIVKinkecKPGKTSttaelVSCQL KFATPlktqslFLQRSVKKDSemqpvgplDKWVIVDRHQLSALVVFPLVL MRRGMLSFSDFFNLLGMFEAH------PGEVIALMSVNVEENFTRLKKRG RVCERHIDRDYIKEIkgsfNAAYCAWLFLQYFSIQTTMQ-ICMGLSSLDE ACATEGVCHTTASRIWNNRMLVTL------------sdiisqfsndytvq nvcynffsqlstlkfvvidlsafrhdvpgawgefym >gi|2317936|gb|AAB66394.1|_307:574 (U97553) thymidine kinase [murid herpesvirus 4]gi|6625585|gb|AAF19286.1|AF105037_18 (AF105037) 21 [murid herpesvirus 4] mmtketgtksktafdklkgsfekfmsgntknegteehrsvvrrrgdgtgf RYSYMSKMSTDFPAGPTRCATVLYFDGGIAVGKTTALEAAAEFLHNILVI SEPIPYWTSTFDKNVCQQIYDvvktkekgkKHSKKVLQCQMAFAQPFHAT QHllrrtclgtkvsDGTCNNYVLIDRHMVSPTVIFPCLFFRLGVLRFCDL LSLLSVFSAQ------KFDNVVLFKLHPKVAATRVKERGRNPEGVINHTY LQLLNevldAIFCAWELLAIVPPEV---IVDAMLSQTSVKTVFQKagfva prarlmeqmFRDSIFNDLRENVRQLPL------------hgssiptllhk fcyelskphmvkldagqfpndvpglwthiytqiltdpai >gi|1246776|emb|CAA63755.1|_307:574 (X93468) thymidine kinase [murine herpesvirus 68] mmtketgtksksafdklkgsfekfmsgntknegteehrsvvrrrgdgtgf RYSYMSKMSTDFPAGPTRCATVLYFDGGIAVGKTTALEAAAEFLHNILVI SEPIPYWTSTFDKNVCQQIYDvvktkekgkKHSKKVLQCQMAFAQPFHAT QHllrrtclgtkvsDGTCNNYVLIDRHMVSPTVIFPCLFFRLGVLRFCDL LSLLSVFSAQ------KFDNVVLFKLHPKVAATRVKERGRNPEGVINHTY LQLLNevldAIFCAWELLAIVPPEV---IVDAMLSQTSVKTVFQKagfva prarlmeqmFRDSIFNDLRENVRQLPL------------hgssiptllhk fcyelskphmvkldagqfpndvpglwthiytqiltdpai >gi|586859|sp|P37529|YAAF_BACSU_2:216 HYPOTHETICAL 25.4 KD PROTEIN IN SERS-DNAZ INTERGENIC REGIONgi|2127021|pir||S66044 deoxypurine kinase (EC 2.7.1.-) yaaF - Bacillus subtilisgi|467404|dbj|BAA05250.1| (D26185) unknown [Bacillus subtilis]gi|2632281|emb|CAB11790.1| (Z99104) similar to deoxypurine kinase subunit [Bacillus subtilis] m------------KEHHIPKNSIITVAGTVGVGKSTLTKTLAKRLGFKTS LEEV-------DHNPYLEKFYHDFERWSFHLQIYFLAERFKEQKTIFEAG gGFVQDRSIYEDTGIFAKMHADKGTMSKVDYKTYTSLFEAMVMtPYFPHP DVLIYLEGDLENILNRIEQRGREMELQTSRSYWEEMHTRYENWISGFNAC PVLKLRIEDYDlLNDENSI---ENIVDQIASVIHDNQK------------ ----k >gi|1136820|gb|AAB08396.1|_234:510 (U40377) thymidine kinase [Kaposi's sarcoma-associated herpesvirus]gi|1718273|gb|AAC57102.1| (U75698) ORF 21; thymidine kinase TK homolog; EBV BXLF1 homolog [Kaposi's sarcoma-associated herpesvirus]gi|2246497|gb|AAB62622.1| (U93872) ORF 21, thymidine kinase (TK) homolog [Kaposi's sarcoma-associated herpesvirus] lkargrdvgdrlrdggfafsprgvksaigqnikswlgigessatavpvtt QLMVPVHLIRTPVTVDYRNVYLLYLEGVMGVGKSTLVNAVCGILPQERVt sFPEPMVYWTRAFTDCYKEISHLmksgkagDPLtsAKIYSCQNKFSLPFr tnataILRMMQPWNvgggsgrgTHWCVFDRHLLSPAVVFPLMHLKHGRLS FDHFFQLLSIFRAT------EGDVVAILTLSSAESLRRVRARGRKNDGTV EQNYIRELawayHAVYCSWIMLQYITVEQMVQLCVQTTNIPEICFRsvrl ahkeetlknlHEQSMLPMITGVLDPVRHHPVVI----------elcfcff telrklqfivadadkfhddvcglwteiyrqilsnpaikprain >gi|1360832|pir||S55615_275:521 thymidine kinase (EC 2.7.1.21) - equine herpesvirus 2gi|695193|gb|AAC13808.1| (U20824) thymidine kinase [Equine herpesvirus 2] wlrqpgvkskltsmkdlsgsfkslmhirsdgekhkqqqrpggsgapggat PRDVFNTFLGSGTCPSFKNAFFLYLEGSMGVGKTTLIRHMREINgDNVIS FVEPMFYWREVYSDCV-KLIYSackpfnlgkmSTSKKVLSAQMKFMTPMk clqtsVRRYVKANEplqektamDNWLLFDRHPLSATLVFPYLSLKNGYLA FEHFLALAANFTAH------EGDIIALLCMGEEDNLKMVKLRNRKGESGV TSAHLKDLgqafHACYCTWLLLKYLSPEDMVSVCCCDVTLNDICIMRSMS SSKV-------------------------tmakslfnksmfptlmdviqp frsnctiieicltlfmelkkvefivvnas >gi|125445|sp|P28855|KITH_HSVI1_6:211 THYMIDINE KINASEgi|66704|pir||KIBEIC thymidine kinase (EC 2.7.1.21) - ictalurid herpesvirus 1gi|331215|gb|AAA88108.1| (M75136) thymidine kinase [Ictalurid herpesvirus 1]gi|331292|gb|AAA88186.1| (M75136) thymidine kinase [Ictalurid herpesvirus 1] malre---------GPTPARFLPEGLVFCVEGNIGCGKSTLVKALMERVa gSGVNVVEEPVDQWVNHNGKNYLELSYTDPTGYAVPFQNLVFDSYVNVQR L---QNPDIMERSPMSATRVFCAVNGSRGVIPATALPGMAARGEAVMRTI ATRP-VFVYLELPPEECLRRMRRRDRTGEAGVGLDYLRLLHERYEAWLSS -----AEDVERVDASRSR-------EEIVDRVIEIL-------------- -------crrhprlrapltrksql >gi|464254|sp|P34942|NUDM_BOVIN_40:274 NADH-UBIQUINONE OXIDOREDUCTASE 42 KDA SUBUNIT, MITOCHONDRIAL PRECURSOR (COMPLEX I-42KD) (CI-42KD)gi|89675|pir||S17677 NADH dehydrogenase (ubiquinone) (EC 1.6.5.3) 42K chain precursor - bovinegi|230|emb|CAA42054.1| (X59419) NADH dehydrogenase (ubiquinone) 39 kDa subunit [Bos taurus] malrllrlvpprvggihtsvqfklqygplayilgekatk----------- ---KMTEKSKLITVDGNICSGKSKLAKEIAEKLGLKHFPEAGIHYVDSTT GdgkplpvqfsgNCSLEKFYDDPKsndGNSYRLQAWLYASRLLQYADALE hllstGQGVVLERSIYSD-FVFLEAMYRQGFIRKQCVDHYNQVKKVT-IC EYLPPHVVVYVDVPVPEVQSRIQKKGNPHEMKITSAYLQDIENAYKGTFL P-EMSEKCEVL-------------QYSAWEAQDAEKVVEDIEYLKYDKGP WLDQ----ndrnlhklrmlvqdklevlnytsipvflpevtvgahqsdqvf qeftelpg >gi|4758768|ref|NP_004535.1|_37:286 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10 (42kD)gi|6093592|sp|O95299|NUDM_HUMAN NADH-UBIQUINONE OXIDOREDUCTASE 42 KDA SUBUNIT, MITOCHONDRIAL PRECURSOR (COMPLEX I-42KD) (CI-42KD)gi|7513179|pir||JE0385 NADH dehydrogenase (ubiquinone) (EC 1.6.5.3) chain NDUFA10 - humangi|4191348|gb|AAD09755.1| (AF087661) NADH-ubiquinone oxidoreductase 42 kDa subunit [Homo sapiens] malrllklaatsasarvvaagaqrvrgihssvqckl-RYGMWHFLLGDKA skRLTERSRVITVDGNICTGKGKLAKEIAEKLGFKHFPEAGIHYPDSTTG dgkplatdyngNCSLEKFYDDPRsndGNSYRLQSWLYSSRLLQYSDALEh llttGQGVVLERSIFSD-FVFLEAMYNQGFIRKQCVDHYNEVKSVT-ICD YLPPHLVIYIDVPVPEVQRRIQKKGDPHEMKITSAYLQDIENAYKKTFLP -EMSEKCEVL-------------QYSAREAQDSKKVVEDIEYLKFDKGPW LKQ----dnrtlyhlrllvqdkfevlnytsipiflpevtigahqtdrvlh qfrelpg >gi|140631|sp|P21974|YF26_FOWP1_9:218 HYPOTHETICAL 25.9 KD PROTEINgi|93206|pir||D35216 FP26 protein - fowlpox virus (strain FP-1)gi|61227|emb|CAA35067.1| (X17202) ORF FP25.9 [Fowlpox virus]gi|7271557|gb|AAF44403.1|AF198100_50 (AF198100) ORF FPV059 Deoxycytidine kinase [Fowlpox virus] mdsineft-------------------SKKLSIEGNISSGKTDVLNILRN I-NNVVSFHDVEDRYTPIEKE-LIRKFHENPSRWSYALQTHYCMKRVRMH LECFvPSRVNILERSIFSDRYVFAEAATALGYMDDPEWALYCKQHDWYTD KLEIQFDGIIYLRTIPESCKERINEKSITEKNypNISIDYLKTLHEKHEL WLTQCK---KVPVLIIDGEEDFIFDPCAKKKLINEVTEFINS-------- -----------i >gi|1072623|pir||C56604_107:349 thymidine kinase (EC 2.7.1.21) - bovine herpesvirus 4gi|261090|gb|AAB24379.1| (S49773) thymidine kinase, TK [bovine herpesvirus type 4 BHV-4, Peptide, 445 aa] [Bovine herpesvirus 4]gi|449384|prf||1919221C thymidine kinase [Bovine herpesvirus 4] qqdiyerdnvyeatfftppreklpsitalsesfnnlsftdgtttspdwpa -KPAPAHLLYPRPPTGYTDAYFIFFEGVMGVGKTTLLKTLARnDMNNVII FEEAMNYWKTVFSDCH-KLIYDvmkmgkhgsfSVSSKLLACQMKFLTPlk slgrvtamfsgkeMQRSPGRSDVSHWVMFDRHALSACLVFPLVMLKSGML SFEHFISLVSTFRAN------EGDIIVLIALDHGEAIRRIKTRKRPEEET ISLTYVIRLHwcfvAVYNTWRLLQYFTAR-EATEVCLDIKTINGLCLSKD IC----------------------------yqkclefqtlwnesllavlr diifpyksdctilelclnvctqiqklkfvv >gi|7471796|pir||F75535_1:196 deoxyguanosine kinase/deoxyadenosine kinase subunit - Deinococcus radiodurans (strain R1)gi|6457974|gb|AAF09882.1|AE001891_1 (AE001891) deoxyguanosine kinase/deoxyadenosine kinase subunit [Deinococcus radiodurans] --------------------MYVAVSGNIGSGKSTLTRMLAER-YGLRPV YEPYAE------NPYLEDFYHDMRQYSFHSQVYFLSRRLEQHLGmVTGAR YVIQDRTVFEDANIFARNLYESGQMGERDWQTYRGLYEGV-LPALRVPDL LIHIDAGLPTLRRRIALRGRDYEQAIPDEYLAGLNRLYAGWIAAFDL--- CPVVRVDGDaLDFVHDPQAFEWVCGRV----------------------- --qahgyglpllr >gi|3023659|sp|Q59484|DGK2_LACAC_3:223 DEOXYGUANOSINE KINASE (DGUO KINASE) (DGK) (DEOXYNUCLEOSIDE KINASE COMPLEX I F-COMPONENT)gi|1361410|pir||B56168 deoxyguanosine kinase (EC 2.7.1.113) - Lactobacillus acidophilusgi|403984|gb|AAB09751.1| (U01881) deoxyguanosine kinase/deoxyadenosine kinase(I) subunit [Lactobacillus acidophilus] mt---------------------VIVLSGPIGAGKSSLTGILSKYLGTN- ------PFYESVDDNPVLPLFYENPKKYAFLLQVYFLNTRFRSIKSALTD DNNVLDRSIYED-ALFFQMNADIGRATPEEVDTYYELLHNMMSelDRMPK knPDLLVHIDVSYDTMLKRIQKRGRNYEQlsydpTLE-DYYKRLLRYYKP WYAKYDYSPKMT---IDGDKLD---FMASEEDRQEVLNQIVAKLKEMGKL EDDWKPNLV--k >gi|7428050|pir||G70129_5:203 deoxyguanosine/deoxyadenosine kinase I (EC 2.7.1.-) subunit 2 dck homolog - Lyme disease spirochetegi|2688138|gb|AAC66630.1| (AE001134) deoxyguanosine/deoxyadenosine kinase(I) subunit 2 (dck) [Borrelia burgdorferi] mevd--------------------LVIVIEGLIGVGKTTLGNILSKELE- -------VPFYSELNNDFtlaVLDKFYKDKSRWAFPVQINFLNERFKLIK GVFRTKGGILDRSIYGD-CVFASLLNCDGHISDEEYKIYIDLLDNM-LEH SQRPSLLVYLDCSIDEVERRIKNRNRSFEMNIPRDYLEGLNRKYLKWYDE YNLSSK-----IKFSYDNINIFS--EEDRNKVISLIRDKL---------- -------vl >gi|2496356|sp|P75396|Y268_MYCPN_7:222 HYPOTHETICAL PROTEIN MG268 HOMOLOGgi|2146291|pir||S73777 hypothetical protein yaaF - Mycoplasma pneumoniae (strain ATCC 29342)gi|1674139|gb|AAB96099.1| (AE000044) Mycoplasma pneumoniae, hypothetical protein (yaaF) homolog; similar to Swiss-Prot Accession Number P37529, from B. subtilis mktplk-----------PKFQPAKIANAVVVGGMIAFGKTTIAESLAKHL KGSKVIYELEEQDQLA--DLLLAKMYErnDELLYAPLFQLYFTLNRFNKY RKeCNNKTPTIFDRSIFED-WLFAK----QNIHRPSIFTYYNHLWNGIVK eliFKHGIPALYVILEGDWELFEQRLFQRNRKVEIdnfAKNKDYFKNLYK IYGEFIKNVCYDFGISHCIVNANQSV-------ESITKQVLEVLKSK--- ---------------nldweii >gi|4033719|gb|AAC97156.1|_1:185 (U49397) unknown [Streptococcus pyogenes] --------------------MLIVLAGTIGAGKSSLAAALGEHLGTD--- ----VFYEAVDNNPVLDFYYQDPKKYAFLLQIYFLNKRFKSIKEAYQADN NILDRSIFED-ELFLKLNYKNGNVTKTELDIYQELLANMLEELEGMpkkr PDLLIYIDVSFDKMLERIEKRGRSFE-QVDgnpslEQYYHQVHGEYPTWY EDYKVSPKMK---IDGN--------------------------------- ---------sldfvqnpqdlatvlkmidtklkelhll >gi|3023658|sp|Q59483|DGK1_LACAC_3:211 DEOXYADENOSINE KINASE (DADO KINASE) (DAK) (DEOXYNUCLEOSIDE KINASE COMPLEX I S-COMPONENT)gi|1361409|pir||A56168 deoxyadenosine kinase (EC 2.7.1.76) - Lactobacillus acidophilus (strain R-26)gi|403983|gb|AAB09750.1| (U01881) deoxyguanosine kinase/deoxyadenosine kinase(I) subunit [Lactobacillus acidophilus] mt---------------------VIVLSGPIGAGKSSLTSLLAEHLGTQ- ------AFYEGVDNNPILPLYYKDMAHYTFLLNTYLLNHRLAQINQAIRD HNSVSDRSIYED-ALFFKMNVDSGIADPTEFKIYDSLLENMMEqapgNPS KKPDLLIYIHVSLDTMLHRIQKRGRKFEQLSTdpslKDYYARLLSYYEPW YEKYNASPKMM---IDGDKYD---FVANEDARRKVINAIDQKLIDI---- ----------gnln >gi|6899038|gb|AAF30491.1|AE002108_4_11:225 (AE002108) deoxyguanosine kinase [Ureaplasma urealyticum] msdkkldflt-----------PSFKKNRVSNSIAIGGMIAFGKSTLAQAL HEKYQPSNVVYEMVEGDKLM--DLLLAKMYEreNNVLFGSLFQLYFVLNR FANYKNnCNRKSLTIFDRSIFED-WLFAHANIDK----PSVFSYYDGLWQ GVCKeliYEHGVPKLYVILDGDWELFKERIFKRNRKVEIdnfSINETYFK RLLEMYKNYMVNVCKDFGINYVVLDANNSV-------EQNVDEVTKILQK -------------------leneqdk >gi|833830|gb|AAB04138.1|_1:228 (U25806) thymidine kinase [Cercopithecine herpesvirus 9] -------MAQHGTCRDPVCITRVYLEGAFGIGKTTTALAFVNgsRVNPVF FIGEPMMYWRNMAGDDAINGIYGtqvrrkngeisdnDAQRLTAYFQGLFC SPHSMLHARIlhltvqnpnnlalkfFNNPVAIFDRHPVASNVCFPISRYV VGDMTPATLPGFL-----FAVSEEPEGTNLIVCTVSLTNHLTRITNRSRS GE-IIDVQFILVLRNVYimlintirylqakSDWLIDWFKLP--------- -------------------------------------------fcsnsfk qqlqekecitiqenpvientlfavfkipelcdsygelldlwkw >gi|1723139|sp|P47510|Y268_MYCGE_2:225 HYPOTHETICAL PROTEIN MG268gi|1361480|pir||F64229 deoxyguanosine/deoxyadenosine kinase(I) chain 2 homolog - Mycoplasma genitaliumgi|3844864|gb|AAC71490.1| (U39706) conserved hypothetical protein [Mycoplasma genitalium] m-------QLKKPHFQPNKIANCIVIGGMIALGKTTIANTLANHIQAAKV VCELETNDQLV--ELLLAKMYErsDELLYSPLFQLYFTLNRFgKYQNNCN TINPTIFDRSIFED-WLFAK----HNIIRPAVFSYYNQLWNRLAKelvNK HGVPNLYVILDGDWKLFEKRLFMRNRKVEIdnfTKNQLYFQNLHRVYTGF MEAVCNDFGINYCIIDAKLPIVTII-----------KMILEKLKLQKLDW ----------kfi >gi|586860|sp|P37530|YAAG_BACSU_4:206 HYPOTHETICAL 24.1 KD PROTEIN IN SERS-DNAZ INTERGENIC REGIONgi|2127022|pir||S66045 deoxypurine kinase (EC 2.7.1.-) yaaG - Bacillus subtilisgi|467405|dbj|BAA05251.1| (D26185) unknown [Bacillus subtilis]gi|2632282|emb|CAB11791.1| (Z99104) similar to deoxypurine kinase subunit [Bacillus subtilis] mnt-------------------APFIAIEGPIGAGKTTLATMLSQKFGFP MIneIVED---------NPYLDKFYDNIKEWSFQLEMFFLCHRYKQLEDT SDhflkkGQPVIADYHIYKN-VIFAE-----RTLSPHQLEKYKKIYHLLT DDL-PKPNFIIYIKASLPTLLHRIEKRGRPFEKKIETSYLEQLISDYEvA IKQLQEADPELTVLTVDGDsKDFVLNKSDFERIAAHVKELI--------- ------------v >gi|7461850|pir||T17919_1:188 kinase-like protein A416R - Chlorella virus PBCV-1gi|1620088|gb|AAC96784.1| (U42580) contains ATP/GTP-binding site motif A; similar to Bacillus subtilus 24.1 kDa protein, corresponds to Swiss-Prot Accession Number P37530 [Paramecium bursaria Chlorella virus 1] --------------------MIISVDGLMGSGKTTLLDRLEKR--GFKVF REPVGEWK------FLNKFYKNPKKYALALQLEILVSFTKY---TFTEDI VFTERCPQVSHYVFAKMLSAKGTLTDEEMATYKNFYDKMNLW---KPDVH IFLKCPIDVCEQRLKRRSDSY--TIDTEYMERLEKYY---SIFNKYTNST PIKFIDASKNEDEVE---EDFMNQVKDFVE-------------------- >gi|7461161|pir||T03086_3:191 probable thymidine kinase (EC 2.7.1.21) - Chilo iridescent virusgi|2738433|gb|AAB94460.1| (AF003534) putative thymidine kinase [Chilo iridescent virus] mt---------------------IICIDGIIGAGKSTVTHRLKK--NLYK CYEEPIDKWT------LLPNLYNDMKKYATPFQFQVLFSQYDQYLSfKDC KETVVVERCPWTSKNIFTSLMIENNLFDLSAIDTYNNLYERL----SYQV DHFIYIKVDSEMAFERIKKRDRFAEQNISFDYLKSLENKYATSLAT--LS PS-TVTIIDGSNTI-------EEVEFDVKTAINN---------------- ---flsh >gi|7471797|pir||G75535_1:192 deoxyguanosine kinase/deoxyadenosine kinase subunit - Deinococcus radiodurans (strain R1)gi|6457975|gb|AAF09883.1|AE001891_2 (AE001891) deoxyguanosine kinase/deoxyadenosine kinase subunit [Deinococcus radiodurans] --------------------MYVVVEGPIGVGKTSLAQRLAQRSGaelNL EVVEE----------NPFLAKFYEQPQAYAFQVQAFFLLSRFKQLSQLWQ PGlyrPEVVSDYLFDKDFIFAAMNLRD-----AEFDLYQDLYGHL-SPRL PTPDLVVYLRADPPELLRRIARRGRPFEHDMKAAYLADLTGRYDDYFRTY ----AHPHLILEAGNYD---FVANEADQQAIFDQI--------------- ------daalaqapagedr >gi|687841|gb|AAA62532.1|_60:274 (U21320) similar to NADH dehydrogenase [Caenorhabditis elegans] glatgllacsrsgalsnqvrgvvhksllrlpsehpepwdykhngfnyidg -------LKDDTRSHFHQNSKLIVVEGNIGSGKTTLAKQLADQLG---FV HFPEFRMDDIlvdrYGNDLrnyynkfparyrlpdISMFYKNPSgELSAAM QDRIFNCRFDQYLNAlahilNTGQGVVLERTPHSD-FVFANAMRDKNYIG HEYFKHYYFVRKNALPQLHFWPHLVVYLNTPTNKCLENIKRRGNTDEIaT VDERYLKTIEESYKDSLREYRNHSKI------------------------ --------------------------laydwtkpgdtdavvedierldld ffewhsgdvmeewntivdsvgwngwr >gi|7469438|pir||S76121_1:234 hypothetical protein - Synechocystis sp. (strain PCC 6803)gi|1001473|dbj|BAA10099.1| (D63999) hypothetical protein [Synechocystis sp.] MAIAKGNQGPSGKgrnslklGKTIMAALFIVLEGIDGSGKTTQGDLLLAH FQRQglaaVLSPEP-------TNGPVGRLIRQalqgdlftynDARQFEAQ MGYLFAADRHYHLYHPGDgveaklaqQCHVITTRYYFSS--------LAY NCHTEADWEFVQRLNQSF-----PQPDWVIYLDLPVDLALQRLGDRQQ-L EDQAPRECYEQreklisVHRNYDRIFAHY----QGQLCRLDASLPV---- ---EQLHQAIITKVEE-------------------ml >gi|3769437|gb|AAC64514.1|_3:218 (AF059316) thymidine kinase [macropodid herpesvirus type 2] ma------------------SVLRIYLDGPHGIGKTTLGSELTKVLahrA DVVFVPEPMAYWRAVGGVDTIASVYEtatrcDNKEISseeaslimANTQV LMNMPYmvLAQQMEPllgwgannhlpppLPGQTIIVDRHPIASLLCYPLA RYLRGSFTLQTAMSLL-----AFIPKIPHGTNLVLGKLSGGETTQRLYER GRPGE-VVDWHMIECIHNIYDRL--------QNTVTYIQQGNNWRDDWHK ---------------------------------ltpksamdiryepvsgs knprihetlfavfwapslaqpsgrlsnihasvf >gi|8247943|sp|Q55593|KTHY_SYNY3_1:210 THYMIDYLATE KINASE (DTMP KINASE) -----------------MAALFIVLEGIDGSGKTTQGDLLLAHFQRQgla aVLSPEP-------TNGPVGRLIRQalqgdlftynDARQFEAQMGYLFAA DRHYHLYHPGDgveaklaqQCHVITTRYYFSS--------LAYNCHTEAD WEFVQRLNQSF-----PQPDWVIYLDLPVDLALQRLGDRQQ-LEDQAPRE CYEQreklisVHRNYDRIFAHY----QGQLCRLDASLPV-------EQLH QAIITKVEE-------------------ml >gi|5926720|dbj|BAA23726.2|_4:167 (AB009251) thymidine kinase [Human herpesvirus 3] mst-----------DKTDVKMGVLRIYLDGAYGIGKTTAAEEFLHHFait pNRILLIGEPLSYWRNLAGEDAICGIYgtqtrrlngdvspEDAQRLTAHF QSLFCSPHAIMHAKIsalmdtstsdlvqvNKEPYKIMlsDRHPIASTICF PLSRYLVGDMSPAALPGLL-----FTLPADPPG----------------- -------------------------------------------------- ------------------------------------ptw >gi|1074411|pir||A64153_11:233 dTMP kinase (EC 2.7.4.9) - Haemophilus influenzae (strain Rd KW20) mnitkrckniYVGIAVRKMPNKSAEENMKGKFIVIEGLEGAGKSSAHQSV VRVLhelgiQDVVFTREP-------GGTPLAEKLRHlikheteepvtDKA ELLMLYAARIQLVENVIKPALMQGKWVVGDRHDMSS-------QAYQGGG RQLDPHFMLTLKETVLGNF--EPDLTIYLDIDPSVGLAR--ARGR-GELd rieQMDLDFFHRTRARYLELVKD-----NPKAVVINAEQSI-------EL VQADIESAVKNWWK----------------snek >gi|1730073|sp|P44719|KTHY_HAEIN_1:206 THYMIDYLATE KINASE (DTMP KINASE)gi|1573430|gb|AAC22114.1| (U32728) thymidylate kinase [Haemophilus influenzae Rd] -----------------MKGKFIVIEGLEGAGKSSAHQSVVRVLhelgiQ DVVFTREP-------GGTPLAEKLRHlikheteepvtDKAELLMLYAARI QLVENVIKPALMQGKWVVGDRHDMSS-------QAYQGGGRQLDPHFMLT LKETVLGNF--EPDLTIYLDIDPSVGLAR--ARGR-GELdrieQMDLDFF HRTRARYLELVKD-----NPKAVVINAEQSI-------ELVQADIESAVK NWWK----------------snek >gi|125440|sp|P22649|KITH_HSVBH_5:192 THYMIDINE KINASEgi|66696|pir||KIBEB2 thymidine kinase (EC 2.7.1.21) - bovine herpesvirus 2gi|221805|dbj|BAA00425.1| (D00537) thymidine kinase [Bovine herpesvirus 2] msrl--------------------LRVYVDGPHGLGKTTAASRLASERGD AIYLPEPMSYWSGAGEDDLVARVYtaqhrmdrgeidaREAAGVVLGAQLT MSTPYVALNGliaphigeEPSPGNatppdlILIFDRHPTASLLCYPLARY LTRCLPIESVLSLI-----ALIPPTPPGTNLILGTAPAEDHLSRLVARGP PGE-LPDARMLRAIRYVY-------------------------------- -------------------------------allantvkylqsggswrad lgsepprlplappeigdpnnpgghntllali >gi|6015696|emb|CAB57523.1|_3:188 (Y18930) thymidylate kinase [Sulfolobus solfataricus] mq--------------------KLIAIEGIDGSGKTTLANLLKEHLESKm klnvIVTREP-------FSEDIIKLIEKigwnDPILLVL----LFAADRe ihVNWLSKIKDADLIILDRYYFSS-------IAYQGALGVDE-----QWI KMV-NSYFPKPDMVILLDLPIEVAISRIKNDKFNFEEKI--KSLAKVREK YLKLAKEY------NFYVVDASKDK-------NEVLEQAIKIIQKNL--- --------------f >gi|7446649|pir||H75067_1:190 hypothetical protein PAB1012 - Pyrococcus abyssi (strain Orsay)gi|5458950|emb|CAB50437.1| (AJ248287) hypothetical protein [Pyrococcus abyssi] ---------------MGMEKMIVGIAGKIAAGKTTVAKFLEEFGFCRISC SEPLF------------------DILTGNTQGYSWVPEVEFKGEPTRENl ielGRILKEKYGEDILIRlavdklrnCENIAIDGVRSMGEVDAIKR---- -------MGGIVVYIEAKPEIRFERLRRRGSSKDRGI--KSLEDLL-KFD EWEEKLYETTKIK---EKADIVIVNEGTL-EELRDKIISAL--------- ------------glgkhvh >gi|7493480|pir||T41553_6:200 thymidylate kinase - fission yeast (Schizosaccharomyces pombe)gi|3192027|emb|CAA19357.1| (AL023794) thymidylate kinase [Schizosaccharomyces pombe] mskqn------------------RGRLIVIEGLDRSGKSTQCQLLVDKLI SQHEKAELFKFPDRTTAigkkiDDYLKESVQLNDQVIH---LLFSANRwe tIQYIYEQINKGvTCILDRYAFSG-IAFSAAKGLD-----------WEWC KSPDRGL-PRPDLVIFLNVDPRIAATR----GQYGE-----ERYEKIE-M QEKVLKNFQRLQKefreegLEFITLDASSSL-------EDVHSQIVDLVS N-------------------vnihetldvl >gi|7481957|pir||S77770_1:148 probable ATP-binding pyrimidine kinase - Mycoplasma capricolumgi|530420|emb|CAA83737.1| (Z33066) ATP-bind. pyrimidine kinases [Mycoplasma capricolum] -------------------------------------------------- -----------------------------MQIYMLTARSKQLKQAKNLEN IIFDRTLLED-PIFMKVNYDLNNVDQIDYNTYIEFYNNVVLenLKIPEnk lsFDIVIYLRVSTKTAISRIKKRGRSEEPLIGDEYWETLNKNYEEFYKQN VYNF--PFFVVDAELDV-------KAQIELIMNKLNS------------- ------iknpd >gi|8134528|sp|Q9YA48|KTHY_AERPE_2:201 PROBABLE THYMIDYLATE KINASE (DTMP KINASE)gi|7434643|pir||E72514 hypothetical protein APE2090 - Aeropyrum pernix (strain K1)gi|5105789|dbj|BAA81101.1| (AP000063) 208aa long hypothetical protein [Aeropyrum pernix] m--------------------RIVALEGIDGSGVSTHSRLLHARLAGAGV ksclWKEPTEGPV----GRLIRGFLRSTEgVDSDLMALLFAADRLWGLRl gvveRCGGSPeVLVVDRYKYSS-------LAYQGVGSGLEWV--DAVNRK A-----PEAEILVYIDVPTEVALRRITARER-REVFETPEFLERVKSMYE EVLRLARARG-VKVIRVEGVRGGVERGI--EDVQGEIAERVFE------- ------------alglara >gi|7463781|pir||H70198_61:256 thymidylate kinase (tmk) homolog - Lyme disease spirochetegi|2688733|gb|AAC67140.1| (AE001178) thymidylate kinase (tmk) [Borrelia burgdorferi] ngkinninvlllknnkfihsidnyyyiiiidnliidtkrkeekifvikil -------------------KNFYCIEGIDGSGKTSITNKLKALCNDEsry yftkepssGIIGEMIRK-QLMNFENPLEES---------TFAYLYAADRH DHLYKKGGileilntkSRKIITDRYLFSS-------IAYQGKLG------ -YELNKNF-----PLPEKVFFIETDPNIAYERIQK-NRTQSDLFELEKYK TFEQIALKYLKIFKKLEK-KINVIYINNSIKDNL---DKNAKKIFNLIK- -------------------f >gi|6016458|sp|O30175|KTHY_ARCFU_1:187 PROBABLE THYMIDYLATE KINASE (DTMP KINASE)gi|7434641|pir||E69257 thymidylate kinase (tmk) homolog - Archaeoglobus fulgidusgi|2650584|gb|AAB91163.1| (AE001102) thymidylate kinase (tmk) [Archaeoglobus fulgidus] --------------------MLIAVEGIDGAGKTTIAAYIAELLkekgYK VKVLKEP-------GDSKFGKKIKSSEERLSpeeele-----LFLKDREI DARENilpalQSGYAVVMDRYYFSN--------IAYQSARGIDARLIREM NEKI----APKPDLTILLDVEPEIALERVRKRGklSPFEKl----DYLRK VRKCF-------LENADETTVVVDASKPL-------EEVKEEVRKVIES- ------------------flnlkknsn >gi|7518683|pir||F71164_1:192 hypothetical protein PH0515 - Pyrococcus horikoshiigi|3256920|dbj|BAA29603.1| (AP000002) 195aa long hypothetical protein [Pyrococcus horikoshii] ---------------MGVEKTIVGIAGKIAAGKTTVAKFLEELGFCRISC SEP-----------LLDILTGNVSEYS-------WVPEVNFKGEPTRENl ielGRLLKEKYGEDILIRlaidklrrCKNIAIDGVRSLGEVEAIKR---- -------MGGIIIYIEARAEVRFERLRKRCSEKDRGI--KTLQDLL-RFD EWEERLYSTTNIK---EKADFVILNEGSL-EELKKKVREILRE------- ------------hsn >gi|547813|sp|P36590|KTHY_SCHPO_6:200 THYMIDYLATE KINASE (DTMP KINASE)gi|478751|pir||S28955 dTMP kinase (EC 2.7.4.9) - fission yeast (Schizosaccharomyces pombe)gi|4974|emb|CAA46698.1| (X65868) thymidylate kinase [Schizosaccharomyces pombe] mskqn------------------RGRLIVIEGLDRSGKSTQCQLLVDKLi lnmKRLKLFKFP-DRTTAIGKkiDDYLTESVQLNDQVIH---LLFSANRW epsIYYRANQQRCNCILDRYAFSG-IAFSAAKGLD-----------WEWC KSPDRGL-TRPDLVIFLNVDPRIAATR----GQYGE-----ERYEKIE-M QEKVLKNLQRLQKefreegLEFITLDASSYAL------EDVDSQIVDLVS N-------------------vnihetldvl >gi|6899310|gb|AAF30741.1|AE002130_8_2:202 (AE002130) uridine kinase [Ureaplasma urealyticum] m---------------NTKSPILILIAGASGSGKTTFANEIIARIP---- --------KNTTSVVICQDSY------------YISNSqlnkkerRLINY DHPSSFEWELM-REQLSDIkkrkkikvpiydykteir------LDKTIDI SDVDVIVLEGIYAIYDDVINQIADLKIFIETPKDECLIRrilrdVNERNR SFESVIT-QWRSTVSPMYDQFVEPSKKNANVSVLWNEHNRVALHLIHKW- -------------------------------innih >gi|7449169|pir||G70101_1:179 uridine kinase (udk) homolog - Lyme disease spirochetegi|2687881|gb|AAC66392.1| (AE001115) uridine kinase (udk) [Borrelia burgdorferi] -----------------MMAKIIGISGGSGSGKTTVVSKISEFIPEFVLI SQD-NYYKSVGDyehefskvnfdhpdafdNNL---FYEhlkNLKKNSpid MPLYDFINHKRQLKTVLVVPTPVVIVEG-----IMIFVEERVRN------ ------------------LIDLKIYIDTPNDIRFIRrlrrdISKRGRTVE SVID-QYLNTTRWGYYRFIEPTKEYADLII-------------------- ----------------------------pegghndkalyvlstflkslsk egldft >gi|2499090|sp|Q59190|URK_BORBU_2:178 URIDINE KINASE (URIDINE MONOPHOSPHOKINASE) (PYRIMIDINE RIBONUCLEOSIDE KINASE)gi|1405442|emb|CAA66081.1| (X97449) uridine kinase [Borrelia burgdorferi] m-------------------AKIIGISGGSGSGKTTVVSKISEFIPEFVL ISQD-NYYKSVGDyehefskvnfdhpdafdNNL---FYEhlkNLKKNSpi dMPLYDFINHKRQLKTVLVVPTPVVIVEG-----IMIFVEERVRN----- -------------------LIDLKIYIDTPNDIRFIRrlrrdISKRGRTV ESVID-QYLNTTRWGYYRFIEPTKEYADLII------------------- -----------------------------pegghndkalyvlstflksls kegldft >gi|3123135|sp|O28278|YK01_ARCFU_1:162 HYPOTHETICAL PROTEIN AF2001gi|7450209|pir||H69499 conserved hypothetical protein AF2001 - Archaeoglobus fulgidusgi|2648537|gb|AAB89254.1| (AE000964) conserved hypothetical protein [Archaeoglobus fulgidus] --------------------MLIALTGTPGTGKSSVAERLRERGYKVATV VELAE------------------------------------------KHG CIIDEEDGEI-VIDVESLAAR-----IDFEGIVEGHLSH----LLKPDVA IVLRCNPAVLRERLKGRNWSEE-----KLLENLEAEMLDVILVEALEHAS EVYEIDTTeMSL-------EEVIEAVEAIIRGDREARKRYKPGGID---- -wlseledrieefmrkv >gi|7450211|pir||H75093_1:156 thymidylate kinase related PAB0757 - Pyrococcus abyssi (strain Orsay)gi|5458565|emb|CAB50053.1| (AJ248286) THYMIDYLATE KINASE related (EC 2.7.4.9) [Pyrococcus abyssi] --------------------MLIAITGTPGVGKTTIAKLLAEKLGYEYVn lrdfalekgcgrevdgeveveidelayFVEKELKDRNV------------ ----------------------------------------------VLDG HLSHLM-----------------PVDLVVVLRAHPRIIGERLRERGYSKE KigeNVEAELVDAIlieaIDEHENVIEV-DTTNKTP-------------- ---EEIVEEIIGLIKSGVK----------------rrvgivdwsevydei ipylrlgge >gi|7483979|pir||C69413_57:237 thymidylate kinase homolog - Archaeoglobus fulgidusgi|2649268|gb|AAB89936.1| (AE001013) thymidylate kinase, putative [Archaeoglobus fulgidus] ggftllsrlcrstaassgsfrngcggcnsqgagqperfnfnrntilldgm --------------------RFIVIDGMDGAGKDTHAEFVRRRYaerGSV IVRTHP-------SDslfgrvakasllrrgkffHLMAAIFY--------F FDVIYSLLRYYGRAE----------------TVIFVRYLGGVLYLPERYA RVLYRFFRSV----LPTSPYMFYLEAEPEVCMERVARRSE-SEMFENIED FRRVRERAFRILKGW----KF----INTNRPI-------EETRREIERIL SE-------------------ldrrfp >gi|7939517|dbj|BAA95720.1|_23:59 (AB024028) uridine kinase-like protein [Arabidopsis thaliana] meklsngvrdhclisdyvspsa-------------PAPLKQPFVIGVAGG TASGKTTVCNMIMSQLHDQRVV---------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----------------------lvnqdsfyhsltkeklnkvheynfdhpd afntevllscmeklrsgqpvni >gi|7449772|pir||D70470_2:191 conserved hypothetical protein aq_1985 - Aquifex aeolicusgi|2984232|gb|AAC07761.1| (AE000766) hypothetical protein [Aquifex aeolicus] m--------------------KRIGLTGNIGCGKSTVAQMFREL--GAYV L----------DADKLIHSFYrkghpvyeevvktfgkgildeegnidrkk ladivfkdeeklRKLEEITH----RALYKEIEKITKNLSEDtLFILEASL LVE----------------------KGTYKNY--------DKLIVVYAPY EVCKERAIKRGMSEE-------------DFErRWKKQMPIEEKVKYAdyV IDNSGSI-------EETYKQVKKVYEE-------------------ltrd p >gi|2829455|sp|P56186|YACE_AERHY_2:24 HYPOTHETICAL 21.9 KD PROTEIN IN TAPD 3'REGION m--------------------YVVAITGGIGSGKTTIANQFAEL------ -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -gidvvdadviarevvepgapalaaiaahfgpdviaadgqldrrslrerv f --simple mime boundary-- From farmer@cse.ucsc.edu Thu Jul 27 02:55:21 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 CAA08172 for Message-Id: <200007270059.RAA17913@beta.cse.ucsc.edu> Subject: T0117(database hits) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0117.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-964558810.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 Jul 21 07:54:10 2000) Score method: average Summary of Database Hits: Average Target Template SeqID Reverse EValue Reverse EValue Reverse EValue SeqLabel 5tmp -72.24 3.498e-28 --------- --------- -72.24 3.5e-28 1qhiB -71.81 5.378e-28 -71.81 5.4e-28 --------- --------- : Chain B, Herpes Simplex Virus Type-I Thymidine Kinase Complexed With A Novel Non-Substrate Inhibitor, 9-(4-Hydroxybutyl)-N2- Phenylguaninegi|5822278|pdb|1QHI|A Chain A, Herpes Simplex Virus Type-I Thymidine Kinase Complexed With A Novel Non-Substrate Inhibitor, 9-(4-Hydroxybutyl)-N2- Phenylguanine 2ki5B -71.81 5.378e-28 -71.81 5.4e-28 --------- --------- : Chain B, Herpes Simplex Type-1 Thymidine Kinase In Complex With The Drug Aciclovir At 1.9a Resolutiongi|3212554|pdb|1KIM|B Chain B, Crystal Structure Of Thymidine Kinase From Herpes Simplex Virus Type I Complexed With Deoxythymidine 1vtk -71.71 5.943e-28 -71.71 5.9e-28 --------- --------- : Thymidine Kinase From Herpes Simplex Virus Type 1 In Complex With Adp And Deoxythymidine-Monophosphategi|2624651|pdb|2VTK| Thymidine Kinase From Herpes Simplex Virus Type 1 In Complex With Adp And Deoxythymidine 1ki6A -70.83 1.433e-27 -70.83 1.4e-27 --------- --------- : Chain A, Crystal Structure Of Thymidine Kinase From Herpes Simplex Virus Type I Complexed With A 5-Iodouracil Anhydrohexitol Nucleoside 1ki2B -70.71 1.616e-27 -70.71 1.6e-27 --------- --------- : Chain B, Crystal Structure Of Thymidine Kinase From Herpes Simplex Virus Type I Complexed With Ganciclovirgi|4139841|pdb|1KI7|B Chain B, Crystal Structure Of Thymidine Kinase From Herpes Simplex Virus Type I Complexed With 5-Iododeoxyuridine 4tmkA -67.41 4.38e-26 -67.41 4.4e-26 --------- --------- : Chain A, Complex Of E. Coli Thymidylate Kinase With The Bisubstrate Inhibitor Tp5agi|6729850|pdb|5TMP|A Chain A, Complex Of E. Coli Thymidylate Kinase With The Bisubstrate Inhibitor Aztp5a 5tmpA -48.55 6.797e-18 --------- --------- -48.55 6.8e-18 3tmkA -40.56 1.996e-14 -36.9 7.8e-13 -44.23 5.1e-16 : Chain A, Crystal Structure Of Yeast Thymidylate Kinase Complexed With The Bisubstrate Inhibitor Tp5a At 2.0 A Resolution: Implications For Catalysis And Azt Activationgi|4558231|pdb|3TMK|B Chain B, Crystal Structure Of Yeast Thymidylate Kinase Complexed With The Bisubstrate Inhibitor Tp5a At 2.0 A Resolution: Implications For Catalysis And Azt Activation 3vtk -39.91 3.842e-14 --------- --------- -39.91 3.9e-14 1kimA -39.89 3.92e-14 --------- --------- -39.89 3.9e-14 1qhiA -39.32 6.932e-14 --------- --------- -39.32 6.9e-14 2tmkA -33.43 2.505e-11 --------- --------- -33.43 2.5e-11 3adk -31.83 1.241e-10 -32.41 7e-11 -31.25 2.2e-10 : Adenylate Kinase (E.C.2.7.4.3) 1ukz -30.64 4.079e-10 -31.7 1.4e-10 -29.58 1.2e-09 : Uridylate Kinase (E.C.2.7.4.-) Complexed With Adp And Ampgi|999493|pdb|1UKY| Uridylate Kinase (E.C.2.7.4.-) Complexed With Two Adp Molecules 1qf9A -28.52 3.398e-09 -28.52 3.4e-09 --------- --------- : Chain A, Ph Influences Fluoride Coordination Number Of The Alfx Phosphoryl Transfer Transition State Analog In UmpCMP Kinasegi|5822578|pdb|5UKD|A Chain A, Ph Influences Fluoride Coordination Number Of The Alfx Phosphoryl Transfer Transition State Analog 5ukdA -27.6 8.526e-09 --------- --------- -27.6 8.5e-09 2cmkA -23.7 4.212e-07 -23.7 4.2e-07 --------- --------- : Chain A, Cytidine Monophosphate Kinase In Complex With Cytidine-Di- Phosphate 1zakA -23.07 7.909e-07 -23.07 7.9e-07 --------- --------- : Chain A, Adenylate Kinase From Maize In Complex With The Inhibitor P1,P5-Bis(Adenosine-5'-)pentaphosphate (Ap5a)gi|3114422|pdb|1ZAK|B Chain B, Adenylate Kinase From Maize In Complex With The Inhibitor P1,P5-Bis(Adenosine-5'-)pentaphosphate (Ap5a) 1ckeA -22.69 1.157e-06 -22.27 1.8e-06 -23.11 7.6e-07 : Chain A, Cmp Kinase From Escherichia Coli Free Enzyme Structure --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-964558810.t99pairwise.a2m' Content-Disposition: attachment; filename="t99-results-964558810.t99pairwise.a2m" >T0117 maeaascarkgtkyaegtQPFTVLIEGNIGSGKTTYLNHFEKYK-----N DICLLTEPV-----EKWRNVNG-VNLLELMYKDPKKWAMPFQSYVTLTML QSHTAPTNKK-LKIMERSIFSARYCFveNMRRNGSleQGMYNTLEEWYKF IEesihvQADLIIYLRTSPEVAYERIRQRARSEE-SCVPLKYLQELHELH EDWLIHQRrpqscKVLVLDADLNLENI---------------gteyqrse ssifdaissnqqpspvlvspskrqrvar >5tmp mRSKYIVIEGLEGAGKTTARNVVVETLEQLGIRDMVFTREPGGTQLAEKL RSLVLDIKSVGDEVITDKAEVLMFYAARVQLVETVIKPALANGTWVIGDR HDLSTQAYQGGGRGIDQHMLATLRDAVLGDFRPDLTLYLDVTPEVGLKRA RARGELDRIEQESFDFFNRTRARYLELAAQDKSIHTIDATQPLEAVMDAI RTTVTHWVKE-lda >T0117 MAEAASCARKGTKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLL TEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKL KIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLI IYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSC KVLVLDADLNLENIGTEYQRSESSIFDAISSNQQPSPVLVSPSKRQRVAR >1qhiB Chain B, Herpes Simplex Virus Type-I Thymidine Kinase Complexed With A Novel Non-Substrate Inhibitor, 9-(4-Hydroxybutyl)-N2- Phenylguaninegi|5822278|pdb|1QHI|A Chain A, Herpes Simplex Virus Type-I Thymidine Kinase Complexed With A Novel Non-Substrate Inhibitor, 9-(4-Hydroxybutyl)-N2- Phenylguanine safdqaarsrghnnrrtalrprrqqeatevr------------PEQKMPT LLRVYIDGPHGMGKTTTTQLLVALGsrDDIVYVPEPMTYWRVLGASETIA NIYTtqhrldqgeisagDAAVVMTSAQITMGMPYAVTDAvlaphiggEAG SSHapppalTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFV-----AL IPPTLPGTNIVLGALPEDRHIDRLAKRQRPGE-RLDLAMLAAIRRVY--- -------------------------------------------------- ----------gllantvrylqcggswredwgqlsgtavppqgaepqsnag prphigdtlftlfrapellapngdlynvfawaldvlakrlrsmhvfildy dqspagcrdallqltsgmvqthvttpgsipticdlartfaremgean >T0117 MAEAASCARKGTKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLL TEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKL KIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLI IYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSC KVLVLDADLNLENIGTEYQRSESSIFDAISSNQQPSPVLVSPSKRQRVAR >2ki5B Chain B, Herpes Simplex Type-1 Thymidine Kinase In Complex With The Drug Aciclovir At 1.9a Resolutiongi|3212554|pdb|1KIM|B Chain B, Crystal Structure Of Thymidine Kinase From Herpes Simplex Virus Type I Complexed With Deoxythymidine safdqaarsrghsnrrtalrprrqqeatevr------------PEQKMPT LLRVYIDGPHGMGKTTTTQLLVALGsrDDIVYVPEPMTYWRVLGASETIA NIYTtqhrldqgeisagDAAVVMTSAQITMGMPYAVTDAvlaphiggEAG SSHapppalTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFV-----AL IPPTLPGTNIVLGALPEDRHIDRLAKRQRPGE-RLDLAMLAAIRRVY--- -------------------------------------------------- ----------gllantvrylqcggswredwgqlsgtavppqgaepqsnag prphigdtlftlfrapellapngdlynvfawaldvlakrlrsmhvfildy dqspagcrdallqltsgmvqthvttpgsipticdlartfaremgean >T0117 MAEAASCARKGTKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLL TEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKL KIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLI IYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSC KVLVLDADLNLENIGTEYQRSESSIFDAISSNQQPSPVLVSPSKRQRVAR >1vtk Thymidine Kinase From Herpes Simplex Virus Type 1 In Complex With Adp And Deoxythymidine-Monophosphategi|2624651|pdb|2VTK| Thymidine Kinase From Herpes Simplex Virus Type 1 In Complex With Adp And Deoxythymidine qqeatevr------------PEQKMPTLLRVYIDGPHGMGKTTTTQLLVA LGsrDDIVYVPEPMTYWRVLGASETIANIYTtqhrldqgeisagDAAVVM TSAQITMGMPYAVTDAvlaphiggEAGSSHapppalTLIFDRHPIAALLC YPAARYLMGSMTPQAVLAFV-----ALIPPTLPGTNIVLGALPEDRHIDR LAKRQRPGE-RLDLAMLAAIRRVY-------------------------- -------------------------------------gllantvrylqcg gswredwgqlsgtavppqgaepqsnagprphigdtlftlfrapellapng dlynvfawaldvlakrlrsmhvfildydqspagcrdallqltsgmvqthv ttpgsipticdlartfaremgean >T0117 MAEAASCARKGTKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLL TEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKL KIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLI IYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSC KVLVLDADLNLENIGTEYQRSESSIFDAISSNQQPSPVLVSPSKRQRVAR >1ki6A Chain A, Crystal Structure Of Thymidine Kinase From Herpes Simplex Virus Type I Complexed With A 5-Iodouracil Anhydrohexitol Nucleoside mptl--------------------LRVYIDGPHGMGKTTTTQLLVALGsr DDIVYVPEPMTYWRVLGASETIANIYTtqhrldqgeisagDAAVVMTSAQ ITMGMPYAVTDAvlaphiggEAGSSHapppalTLIFDRHPIAALLCYPAA RYLMGSMTPQAVLAFV-----ALIPPTLPGTNIVLGALPEDRHIDRLAKR QRPGE-RLDLAMLAAIRRVY------------------------------ ---------------------------------gllantvrylqcggswr edwgqlsgtavppqgaepqsnagarphigdtlftlfrapellapngdlyn vfawaldvlakrlrsmhvfildydqspagcrdallqltsgmvqthvttpg sipticdlartfaremgean >T0117 MAEAASCARKGTKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLL TEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKL KIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLI IYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSC KVLVLDADLNLENIGTEYQRSESSIFDAISSNQQPSPVLVSPSKRQRVAR >1ki2B Chain B, Crystal Structure Of Thymidine Kinase From Herpes Simplex Virus Type I Complexed With Ganciclovirgi|4139841|pdb|1KI7|B Chain B, Crystal Structure Of Thymidine Kinase From Herpes Simplex Virus Type I Complexed With 5-Iododeoxyuridine mptl--------------------LRVYIDGPHGMGKTTTTQLLVALGsr DDIVYVPEPMTYWRVLGASETIANIYTtqhrldqgeisagDAAVVMTSAQ ITMGMPYAVTDAvlaphiggEAGSSHapppalTLIFDRHPIAALLCYPAA RYLMGSMTPQAVLAFV-----ALIPPTLPGTNIVLGALPEDRHIDRLAKR QRPGE-RLDLAMLAAIRRVY------------------------------ ---------------------------------gllantvrylqcggswr edwgqlsgtavppqgaepqsnagprphigdtlftlfrapellapngdlyn vfawaldvlakrlrsmhvfildydqspagcrdallqltsgmvqthvttpg sipticdlartfaremgean >T0117 MAEAASCARKGTKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLL TEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKL KIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLI IYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSC KVLVLDADLNLENIGTEYQRSESSIFDAISSNQQPSPVLVSPSKRQRVAR >4tmkA Chain A, Complex Of E. Coli Thymidylate Kinase With The Bisubstrate Inhibitor Tp5agi|6729850|pdb|5TMP|A Chain A, Complex Of E. Coli Thymidylate Kinase With The Bisubstrate Inhibitor Aztp5a -----------------MRSKYIVIEGLEGAGKTTARNVVVETLeqlgiR DMVFTREP-------GGTQLAEKLRSllldiksvgdevitDKAEVLMFYA ARVQLVETVIKPALANGTWVIGDRHDLST-------QAYQGGGRGIDQHM LATLRDAVLGDF--RPDLTLYLDVTPEVGLKRARARGE-LDRieQESFDF FNRTRARYLELAAQ-----DKSIHTIDATQPL-------EAVMDAIRTTV THWVKEL--------------da >T0117 maeaascarkgtkyaegtQPFTVLIEGNIGSGKTTYLNHFEKYK-----N DICLLTEPVEKWRN--VNGVNLLELMYKDPKKWAMPFQSYVT---LTMLQ SHTAPTNKKLK--IMERSIFSARYCFveNMRRNGSLeqgmyNTLEEWYKF IEESIhvQADLIIYLRTSPEVAYERIRQRARSE-ESCVPLKYLQELHELH EDWLihqrRPQScKVLVLDADLNLENI---------------gteyqrse ssifdaissnqqpspvlvspskrqrvar >5tmpA mRSKYIVIEGLEGAGKTTARNVVVETLEQLGIRDMVFTREPGGTQLAEKL RSLLLDIKSVGDEVITDKAEVLMFYAARVQLVETVIKPALANGTWVIGDR HDLSTQAYQGGGRGIDQHMLATLRDAVLGDFRPDLTLYLDVTPEVGLKRA RARGELDRIEQESFDFFNRTRARYLELAAQDKSIHTIDATQPLEAVMDAI RTTVTHWVK--elda >T0117 MAEAascarkgtkyaegtqPFTVLIEGNIGSGKTTYLNHFEKYKN-DICL LTEPVEKWRnvngVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKK LKIMERSIFSARYCFVENM----rRNGSLEQGMYNTLEEWYKFIEesihv qADLIIYLRTSPEVAYERirQRARSEESCVPLKYLQELHELHEDWLIHQR RPQSCKVLVLDAD-LNLENIGTEYQRSESSI-------------fdaiss nqqpspvlvspskrqrvar >3tmkA Chain A, Crystal Structure Of Yeast Thymidylate Kinase Complexed With The Bisubstrate Inhibitor Tp5a At 2.0 A Resolution: Implications For Catalysis And Azt Activationgi|4558231|pdb|3TMK|B Chain B, Crystal Structure Of Yeast Thymidylate Kinase Complexed With The Bisubstrate Inhibitor Tp5a At 2.0 A Resolution: Implications For Catalysis And Azt Activation MMGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLIN EYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGV AYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDER YETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIV EPVLSTHIDHDKFSFF >T0117 maeaascarkgtkyaegtqp----FTVLIEGNIGSGKTTYLNHFEKY--K NDICLLTEPVEKWRNVNGVNLLELMYKDPK-------------------- -KWAMPFQ---SYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRR NGSLEQGMYNTLEEWYKFIEESihvqaDLIIYLRTSPEVAYERIRQRARS EEScVPLKYLQELHE----------------------------------- -------------------------------------------------- ---------------------------------------lhedwlihqrr pqsckvlvldadlnlenigteyqrsessifdaissnqqpspvlvspskrq rvar >3vtk qqeatevrpeqkMPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPE PMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYA VTDAVLAPHIGGEAgssHAPPPALTLIFDRHPIAALLCYPAARYLMGSMT PQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLA AIRRVYGLLANTVRYLQCGGSWREDWGQLSGTavppqgaepqsnagpRPH IGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSP AGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEAN >T0117 maeaascarkgtkyaegtqp----FTVLIEGNIGSGKTTYLNHFekyknD ICLLTEPVEKWRNVNGVNLLELMYKDPK---------------------K WAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLE QGMYNTLEEWYkfieeSIHVQADLIIYLRTSPEVAYERIRQRARSEEScV PLKYLQELHE---------------------------------------- -------------------------------------------------- -------------------------------lhedwlihqrrpqsckvlv ldadlnlenigteyqrsessifdaissnqqpspvlvspskrqrvar >1kimA safdqaarsrghsnrrtalrprrqqeatevrpeqkMPTLLRVYIDGPHGM GKTTTTQLLvalgsrdDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQG EISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEagsshaPPPALTLI FDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPE DRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWG QLSgtavppqgaepqsnagPRPHIGDTLFTLFRAPELLAPNGDLYNVFAW ALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPT ICDLARTFAREMGEan >T0117 MAEAAScarkgtkyaegtqpftVLIEGNIGSGKTTYLNHFekyknDICLL TEPVEKWRNVNGVNLLELMYK-dpkk---------------WAMPFQSYV TLTMLQSHTAPTNKKL----kim--ERSIFSARYCFVE--NMRRNGSLEQ GMYNTLEEWYKFIEESIhVQADLIIYLRTSPEVAYERIRQRARSEEScVP LKYLQELHELHEDWLIHQRRPQ---------------------------- --------------------------SCKVLVLDADLNLENIGTEYQRSE SSI--FDAISSNQQPSPVLVSPSKRQRVAR >1qhiA -safdqaarsrghnnrrtalrprrqqeatevrpeqkmPTLLRVYIDGPHG MGKTTTTQLLvalgsrdDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQ GEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEagsshaPPPALTL IFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALP EDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDW GQLSgtavppqgaepqsnagPRPHIGDTLFTLFRAPELLAPNGDLYNVFA WALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIP TICDLARTFAREMGEan >T0117 maeaascarkgtkyaegt-QPFTVLIEGNIGSGKTTYLNHFEKYKNDICL -LTEPVekwRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNK KLKIMERSIFSARYCFVENMRRNGSLEQGMYntLEEWYKFIEESIhvQAD LIIYLRTSPEVAYERIRqrarseesCVPLKYLQELHELHEDWLIHQRrpq SCKVLVLDADLNLENI------------------------gteyqrsess ifdaissnqqpspvlvspskrqrvar >2tmkA mmGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLIN EYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGV AYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQdVDNNAEKSGfgder yetvKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIV EPVLSTHIDHDKFSFF >T0117 MAEAASCARKGTKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLL TEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKL KIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLI IYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSC KVLVLDADLNLENIGTEYQRSESSIFDAISSNQQPSPVLVSPSKRQRVAR >3adk Adenylate Kinase (E.C.2.7.4.3) xm-------------EEKLKKSKIIFVVGGPGSGKGTQCEKIVQKYGYTH LSTGDLLRAEVSSGSARGKMLSEIMEkGQLVPLETVLDMLRDAMVAKVDT SKGFLIDGYPREV-----------------------KQGEEF-ERKIGQP TLLLYVDAGPETMTKRLLKRGETSGRvdDNEETIKKRLETYYKATEPVIA FYEKRG---IVRKVNA-------EGSVDDVFSQV---------------- -----cthldtlk >T0117 MAEAASCARKGTKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLL TEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKL KIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLI IYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSC KVLVLDADLNLENIGTEYQRSESSIFDAISSNQQPSPVLVSPSKRQRVAR >1ukz Uridylate Kinase (E.C.2.7.4.-) Complexed With Adp And Ampgi|999493|pdb|1UKY| Uridylate Kinase (E.C.2.7.4.-) Complexed With Two Adp Molecules taattsqpafspdqvs---------------------VIFVLGGPGAGKG TQCEKLVKDYSFVhLSAGDLLRAEQGRAGSQYGELIKNCIKEGQIVPQEI TLALLRNAISDNVKankhkflidgfprkmDQAISFERDIVES-------- -----------------------------KFILFFDCPEDIMLERLLERG KTS--GRSDDNIESIKKRFNTFKETsmpviEYFETKSKVVRVRCDRSV-- -----EDVYKDVQDAIRDSL----------------- >T0117 MAEAASCARKGTKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLL TEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKL KIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLI IYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSC KVLVLDADLNLENIGTEYQRSESSIFDAISSNQQPSPVLVSPSKRQRVAR >1qf9A Chain A, Ph Influences Fluoride Coordination Number Of The Alfx Phosphoryl Transfer Transition State Analog In UmpCMP Kinasegi|5822578|pdb|5UKD|A Chain A, Ph Influences Fluoride Coordination Number Of The Alfx Phosphoryl Transfer Transition State Analog meks------------------KPNVVFVLGGPGSGKGTQCANIVRD--- --------FGWVHLSAGDLLRQEQQsgskdgemiaTMIKNGEIVPSIVTV KLLKNAIDANQGKNFLVDG--------FPRNEENN-----------NSWE ENMKDFV--DTKFVLFFDCPEEVMTQRLLKRGESS--GRSDDNIESIKKR FNTFNVQTKLVIDhynkfDKVKIIPANRDV-------NEVYNDVENLFKS -------------------mgf >T0117 maeaascarkgtkyaegt----QPFTVLIEGNIGSGKTTYLNHF-EKYkn DICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAP TNKKLKIMERSIfsarycfvenmrrngsLEQGMYNTLEEWYkfieeSIHV QADLIIYLRTSPEVAYERIRQRARSEescvplKYLQELHELHEDWLIHQR R---------PQSCKVLVLDADLNLENI-------------gteyqrses sifdaissnqqpspvlvspskrqrvar >5ukdA MEKSKPNVVFVLGGPGSGKGTQCANIVRDFGWVHLSAGDLLRQEQQSGSK DGEMIATMIKNGEIVPSIVTVKLLKNAIDANQGKNFLVDGFPRNEENNNS WEENMKDFVDTKFVLFFDCPEEVMTQRLLKRGESSGRSDDNIESIKKRFN TFNVQTKLVIDHYNKFDKVKIIPANRDVNEVYNDVENLFKSM--gf >T0117 MAEAASCARKGTKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLL TEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKL KIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLI IYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSC KVLVLDADLNLENIGTEYQRSESSIFDAISSNQQPSPVLVSPSKRQRVAR >2cmkA Chain A, Cytidine Monophosphate Kinase In Complex With Cytidine-Di- Phosphate ---------------MTAIAPVITIDGPSGAGKGTLCKAMAEALQ----- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- whlldsgaiyrvlalaalhhhvdvasedalvplashldvrfvstngnlev ilegedvsgeirtqevanaasqvaafprvreallrrqrafrelpgliadg rdmgtvvfpdapvkifldasseerahrrmlqlqekgfsvnferllaeike rddrdrnravaplvpaadalvldsttlsieqviekalqyarqklala >T0117 MAEAASCARKGTKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLL TEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKL KIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLI IYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSC KVLVLDADLNLENIGTEYQRSESSIFDAISSNQQPSPVLVSPSKRQRVAR >1zakA Chain A, Adenylate Kinase From Maize In Complex With The Inhibitor P1,P5-Bis(Adenosine-5'-)pentaphosphate (Ap5a)gi|3114422|pdb|1ZAK|B Chain B, Adenylate Kinase From Maize In Complex With The Inhibitor P1,P5-Bis(Adenosine-5'-)pentaphosphate (Ap5a) ala------------------DPLKVMISGAPASGKGTQCELIKTKYQLA HIS----------AGDLLRAEIAAgsengkrakEFMEKGQLVPDEIVVNM VKERLRQPDaqENGWLLDGYPRSYSQAMALETLEI--------------- ---------RPDTFILLDVPDELLVERVVGR------------------- -------------------------------------------------- --------------rldpvtgkiyhlkysppeneeiasrltqrfddteek vklrletyyqniesllstyeniivkvqgdatvdavfakidellgsilekk nemvsst >T0117 maeaascarkgtkyaegtq--PFTVLIEGNIGSGKTTYLNHFEKYKNdic lltepvekWRNVNGVNLLELMYK----------------------DPKKW AMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQ GMYNTLEEWYkfie--ESIHVQADLIIYLRTSPEVAYERIRQRARSEESC VPLK-YLQELHELHEDwlihqrrpqscKVLVLDAD-LNLENIGTEYQRSE SS-----ifdaissnqqpspvlvspskrqrvar >1ckeA Chain A, Cmp Kinase From Escherichia Coli Free Enzyme Structure mtAIAPVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHH HVDVASEDALVPLASHLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAA SQVAAFPRVREALLRRQRAFRELPGLIADGRDMGTVVFPDAPVKIFLDAS SEERAHRRMLQLQVKGFSVNFERLLAEIKerddrdrnravapLVPAADAL VLDSTTLSIEQVIEKALQYARQKLALA --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-964558810.t99pairwise.casp.al' Content-Disposition: attachment; filename="t99-results-964558810.t99pairwise.casp.al" Sorry, can't convert pairwise alignment for target T0117 and template 5tmp to CASP AL format PFRMAT AL TARGET T0117 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 1qhi_B K 13 P _ Y 14 E _ A 15 Q _ E 16 K _ G 17 M 46 T 18 P 47 Q 19 T 48 P 20 L 49 F 21 L 50 T 22 R 51 V 23 V 52 L 24 Y 53 I 25 I 54 E 26 D 55 G 27 G 56 N 28 P 57 I 29 H 58 G 30 G 59 S 31 M 60 G 32 G 61 K 33 K 62 T 34 T 63 T 35 T 64 Y 36 T 65 L 37 T 66 N 38 Q 67 H 39 L 68 F 40 L 69 E 41 V 70 K 42 A 71 Y 43 L 72 K 44 G 73 N 45 D _ D 46 D 77 I 47 I 78 C 48 V 79 L 49 Y 80 L 50 V 81 T 51 P 82 E 52 E 83 P 53 P 84 V 54 M 85 E 55 T 86 K 56 Y 87 W 57 W 88 R 58 R 89 N 59 V 90 V 60 L 91 N 61 G 92 G 62 A 93 V 63 S 94 N 64 E 95 L 65 T 96 L 66 I 97 E 67 A 98 L 68 N 99 M 69 I 100 Y 70 Y 101 K 71 T 102 D 72 D 116 P 73 A 117 K 74 A 118 K 75 V 119 W 76 V 120 A 77 M 121 M 78 T 122 P 79 S 123 F 80 A 124 Q 81 Q 125 S 82 I 126 Y 83 T 127 V 84 M 128 T 85 G 129 L 86 M 130 T 87 P 131 M 88 Y 132 L 89 A 133 Q 90 V 134 S 91 T 135 H 92 D 136 T 93 A 137 A 94 E 146 P 95 A 147 T 96 G 148 N 97 S _ K 98 S _ K 99 H _ L 100 T 158 K 101 L 159 I 102 I 160 M 103 F 161 E 104 D 162 R 105 R 163 S 106 H 164 I 107 P 165 F 108 I 166 S 109 A 167 A 110 A 168 R 111 L 169 Y 112 L 170 C 113 C 171 F 114 Y 172 V 115 P 173 E 116 A 174 N 117 A 175 M 118 R 176 R 119 Y 177 R 120 L 178 N 121 M 179 G 122 G 180 S 123 S 181 L 124 M 182 E 125 T 183 Q 126 P 184 G 127 Q 185 M 128 A 186 Y 129 V 187 N 130 L 188 T 131 A 189 L 132 F 190 E 133 V 191 I 139 A 192 E 140 L 193 E 141 I 194 S 142 P 195 I 143 P 196 H 144 T 197 V 145 L 198 Q 146 P 199 A 147 G 200 D 148 T 201 L 149 N 202 I 150 I 203 I 151 V 204 Y 152 L 205 L 153 G 206 R 154 A 207 T 155 L 208 S 156 P 209 P 157 E 210 E 158 D 211 V 159 R 212 A 160 H 213 Y 161 I 214 E 162 D 215 R 163 R 216 I 164 L 217 R 165 A 218 Q 166 K 219 R 167 R 220 A 168 Q 221 R 169 R 222 S 170 P 223 E 171 G 224 E 172 E 225 C 174 R 226 V 175 L 227 P 176 D 228 L 177 L 229 K 178 A 230 Y 179 M 231 L 180 L 232 Q 181 A 233 E 182 A 234 L 183 I 235 H 184 R 236 E 185 R 237 L 186 V 238 H 187 Y 239 TER END PFRMAT AL TARGET T0117 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 2ki5_B K 13 P _ Y 14 E _ A 15 Q _ E 16 K _ G 17 M 46 T 18 P 47 Q 19 T 48 P 20 L 49 F 21 L 50 T 22 R 51 V 23 V 52 L 24 Y 53 I 25 I 54 E 26 D 55 G 27 G 56 N 28 P 57 I 29 H 58 G 30 G 59 S 31 M 60 G 32 G 61 K 33 K 62 T 34 T 63 T 35 T 64 Y 36 T 65 L 37 T 66 N 38 Q 67 H 39 L 68 F 40 L 69 E 41 V 70 K 42 A 71 Y 43 L 72 K 44 G 73 N 45 D _ D 46 D 77 I 47 I 78 C 48 V 79 L 49 Y 80 L 50 V 81 T 51 P 82 E 52 E 83 P 53 P 84 V 54 M 85 E 55 T 86 K 56 Y 87 W 57 W 88 R 58 R 89 N 59 V 90 V 60 L 91 N 61 G 92 G 62 A 93 V 63 S 94 N 64 E 95 L 65 T 96 L 66 I 97 E 67 A 98 L 68 N 99 M 69 I 100 Y 70 Y 101 K 71 T 102 D 72 D 116 P 73 A 117 K 74 A 118 K 75 V 119 W 76 V 120 A 77 M 121 M 78 T 122 P 79 S 123 F 80 A 124 Q 81 Q 125 S 82 I 126 Y 83 T 127 V 84 M 128 T 85 G 129 L 86 M 130 T 87 P 131 M 88 Y 132 L 89 A 133 Q 90 V 134 S 91 T 135 H 92 D 136 T 93 A 137 A 94 E 146 P 95 A 147 T 96 G 148 N 97 S _ K 98 S _ K 99 H _ L 100 T 158 K 101 L 159 I 102 I 160 M 103 F 161 E 104 D 162 R 105 R 163 S 106 H 164 I 107 P 165 F 108 I 166 S 109 A 167 A 110 A 168 R 111 L 169 Y 112 L 170 C 113 C 171 F 114 Y 172 V 115 P 173 E 116 A 174 N 117 A 175 M 118 R 176 R 119 Y 177 R 120 L 178 N 121 M 179 G 122 G 180 S 123 S 181 L 124 M 182 E 125 T 183 Q 126 P 184 G 127 Q 185 M 128 A 186 Y 129 V 187 N 130 L 188 T 131 A 189 L 132 F 190 E 133 V 191 I 139 A 192 E 140 L 193 E 141 I 194 S 142 P 195 I 143 P 196 H 144 T 197 V 145 L 198 Q 146 P 199 A 147 G 200 D 148 T 201 L 149 N 202 I 150 I 203 I 151 V 204 Y 152 L 205 L 153 G 206 R 154 A 207 T 155 L 208 S 156 P 209 P 157 E 210 E 158 D 211 V 159 R 212 A 160 H 213 Y 161 I 214 E 162 D 215 R 163 R 216 I 164 L 217 R 165 A 218 Q 166 K 219 R 167 R 220 A 168 Q 221 R 169 R 222 S 170 P 223 E 171 G 224 E 172 E 225 C 174 R 226 V 175 L 227 P 176 D 228 L 177 L 229 K 178 A 230 Y 179 M 231 L 180 L 232 Q 181 A 233 E 182 A 234 L 183 I 235 H 184 R 236 E 185 R 237 L 186 V 238 H 187 Y 239 TER END PFRMAT AL TARGET T0117 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 1vtk K 13 P _ Y 14 E _ A 15 Q _ E 16 K _ G 17 M 46 T 18 P 47 Q 19 T 48 P 20 L 49 F 21 L 50 T 22 R 51 V 23 V 52 L 24 Y 53 I 25 I 54 E 26 D 55 G 27 G 56 N 28 P 57 I 29 H 58 G 30 G 59 S 31 M 60 G 32 G 61 K 33 K 62 T 34 T 63 T 35 T 64 Y 36 T 65 L 37 T 66 N 38 Q 67 H 39 L 68 F 40 L 69 E 41 V 70 K 42 A 71 Y 43 L 72 K 44 G 73 N 45 D 76 D 46 D 77 I 47 I 78 C 48 V 79 L 49 Y 80 L 50 V 81 T 51 P 82 E 52 E 83 P 53 P 84 V 54 M 85 E 55 T 86 K 56 Y 87 W 57 W 88 R 58 R 89 N 59 V 90 V 60 L 91 N 61 G 92 G 62 A 93 V 63 S 94 N 64 E 95 L 65 T 96 L 66 I 97 E 67 A 98 L 68 N 99 M 69 I 100 Y 70 Y 101 K 71 T 102 D 72 D 116 P 73 A 117 K 74 A 118 K 75 V 119 W 76 V 120 A 77 M 121 M 78 T 122 P 79 S 123 F 80 A 124 Q 81 Q 125 S 82 I 126 Y 83 T 127 V 84 M 128 T 85 G 129 L 86 M 130 T 87 P 131 M 88 Y 132 L 89 A 133 Q 90 V 134 S 91 T 135 H 92 D 136 T 93 A 137 A 94 E 146 P 95 A 147 T 96 G 148 N 97 S 149 K 98 S _ K 99 H _ L 100 T 158 K 101 L 159 I 102 I 160 M 103 F 161 E 104 D 162 R 105 R 163 S 106 H 164 I 107 P 165 F 108 I 166 S 109 A 167 A 110 A 168 R 111 L 169 Y 112 L 170 C 113 C 171 F 114 Y 172 V 115 P 173 E 116 A 174 N 117 A 175 M 118 R 176 R 119 Y 177 R 120 L 178 N 121 M 179 G 122 G 180 S 123 S 181 L 124 M 182 E 125 T 183 Q 126 P 184 G 127 Q 185 M 128 A 186 Y 129 V 187 N 130 L 188 T 131 A 189 L 132 F 190 E 133 V 191 I 139 A 192 E 140 L 193 E 141 I 194 S 142 P 195 I 143 P 196 H 144 T 197 V 145 L 198 Q 146 P 199 A 147 G 200 D 148 T 201 L 149 N 202 I 150 I 203 I 151 V 204 Y 152 L 205 L 153 G 206 R 154 A 207 T 155 L 208 S 156 P 209 P 157 E 210 E 158 D 211 V 159 R 212 A 160 H 213 Y 161 I 214 E 162 D 215 R 163 R 216 I 164 L 217 R 165 A 218 Q 166 K 219 R 167 R 220 A 168 Q 221 R 169 R 222 S 170 P 223 E 171 G 224 E 172 E 225 C 174 R 226 V 175 L 227 P 176 D 228 L 177 L 229 K 178 A 230 Y 179 M 231 L 180 L 232 Q 181 A 233 E 182 A 234 L 183 I 235 H 184 R 236 E 185 R 237 L 186 V 238 H 187 Y 239 TER END PFRMAT AL TARGET T0117 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 1ki6_A F 21 L 50 T 22 R 51 V 23 V 52 L 24 Y 53 I 25 I 54 E 26 D 55 G 27 G 56 N 28 P 57 I 29 H 58 G 30 G 59 S 31 M 60 G 32 G 61 K 33 K 62 T 34 T 63 T 35 T 64 Y 36 T 65 L 37 T 66 N 38 Q 67 H 39 L 68 F 40 L 69 E 41 V _ K 42 A _ Y 43 L _ K 44 G _ N 45 D _ D 46 D 77 I 47 I 78 C 48 V 79 L 49 Y 80 L 50 V 81 T 51 P 82 E 52 E 83 P 53 P 84 V 54 M 85 E 55 T 86 K 56 Y 87 W 57 W 88 R 58 R 89 N 59 V 90 V 60 L 91 N 61 G 92 G 62 A 93 V 63 S 94 N 64 E 95 L 65 T 96 L 66 I 97 E 67 A 98 L 68 N 99 M 69 I 100 Y 70 Y 101 K 71 T 102 D 72 D 116 P 73 A 117 K 74 A 118 K 75 V 119 W 76 V 120 A 77 M 121 M 78 T 122 P 79 S 123 F 80 A 124 Q 81 Q 125 S 82 I 126 Y 83 T 127 V 84 M 128 T 85 G 129 L 86 M 130 T 87 P 131 M 88 Y 132 L 89 A 133 Q 90 V 134 S 91 T 135 H 92 D 136 T 93 A 137 A 94 E 146 P 95 A 147 T 96 G _ N 97 S _ K 98 S _ K 99 H _ L 100 T 158 K 101 L 159 I 102 I 160 M 103 F 161 E 104 D 162 R 105 R 163 S 106 H 164 I 107 P 165 F 108 I 166 S 109 A 167 A 110 A 168 R 111 L 169 Y 112 L 170 C 113 C 171 F 114 Y 172 V 115 P 173 E 116 A 174 N 117 A 175 M 118 R 176 R 119 Y 177 R 120 L 178 N 121 M 179 G 122 G 180 S 123 S 181 L 124 M 182 E 125 T 183 Q 126 P 184 G 127 Q 185 M 128 A 186 Y 129 V 187 N 130 L 188 T 131 A 189 L 132 F 190 E 133 V 191 I 139 A 192 E 140 L 193 E 141 I 194 S 142 P 195 I 143 P 196 H 144 T 197 V 145 L 198 Q 146 P 199 A 147 G 200 D 148 T 201 L 149 N 202 I 150 I 203 I 151 V 204 Y 152 L 205 L 153 G 206 R 154 A 207 T 155 L 208 S 156 P 209 P 157 E 210 E 158 D 211 V 159 R 212 A 160 H 213 Y 161 I 214 E 162 D 215 R 163 R 216 I 164 L 217 R 165 A 218 Q 166 K 219 R 167 R 220 A 168 Q 221 R 169 R 222 S 170 P 223 E 171 G 224 E 172 E 225 C 174 R 226 V 175 L 227 P 176 D 228 L 177 L 229 K 178 A 230 Y 179 M 231 L 180 L 232 Q 181 A 233 E 182 A 234 L 183 I 235 H 184 R 236 E 185 R 237 L 186 V 238 H 187 Y 239 TER END PFRMAT AL TARGET T0117 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 1ki2_B F 21 L 50 T 22 R 51 V 23 V 52 L 24 Y 53 I 25 I 54 E 26 D 55 G 27 G 56 N 28 P 57 I 29 H 58 G 30 G 59 S 31 M 60 G 32 G 61 K 33 K 62 T 34 T 63 T 35 T 64 Y 36 T 65 L 37 T 66 N 38 Q 67 H 39 L 68 F 40 L 69 E 41 V 70 K 42 A 71 Y 43 L 72 K 44 G 73 N 45 D _ D 46 D 77 I 47 I 78 C 48 V 79 L 49 Y 80 L 50 V 81 T 51 P 82 E 52 E 83 P 53 P 84 V 54 M 85 E 55 T 86 K 56 Y 87 W 57 W 88 R 58 R 89 N 59 V 90 V 60 L 91 N 61 G 92 G 62 A 93 V 63 S 94 N 64 E 95 L 65 T 96 L 66 I 97 E 67 A 98 L 68 N 99 M 69 I 100 Y 70 Y 101 K 71 T 102 D 72 D 116 P 73 A 117 K 74 A 118 K 75 V 119 W 76 V 120 A 77 M 121 M 78 T 122 P 79 S 123 F 80 A 124 Q 81 Q 125 S 82 I 126 Y 83 T 127 V 84 M 128 T 85 G 129 L 86 M 130 T 87 P 131 M 88 Y 132 L 89 A 133 Q 90 V 134 S 91 T 135 H 92 D 136 T 93 A 137 A 94 E 146 P 95 A 147 T 96 G 148 N 97 S 149 K 98 S 150 K 99 H 151 L 100 T 158 K 101 L 159 I 102 I 160 M 103 F 161 E 104 D 162 R 105 R 163 S 106 H 164 I 107 P 165 F 108 I 166 S 109 A 167 A 110 A 168 R 111 L 169 Y 112 L 170 C 113 C 171 F 114 Y 172 V 115 P 173 E 116 A 174 N 117 A 175 M 118 R 176 R 119 Y 177 R 120 L 178 N 121 M 179 G 122 G 180 S 123 S 181 L 124 M 182 E 125 T 183 Q 126 P 184 G 127 Q 185 M 128 A 186 Y 129 V 187 N 130 L 188 T 131 A 189 L 132 F 190 E 133 V 191 I 139 A 192 E 140 L 193 E 141 I 194 S 142 P 195 I 143 P 196 H 144 T 197 V 145 L 198 Q 146 P 199 A 147 G 200 D 148 T 201 L 149 N 202 I 150 I 203 I 151 V 204 Y 152 L 205 L 153 G 206 R 154 A 207 T 155 L 208 S 156 P 209 P 157 E 210 E 158 D 211 V 159 R 212 A 160 H 213 Y 161 I 214 E 162 D 215 R 163 R 216 I 164 L 217 R 165 A 218 Q 166 K 219 R 167 R 220 A 168 Q 221 R 169 R 222 S 170 P 223 E 171 G 224 E 172 E 225 C 174 R 226 V 175 L 227 P 176 D 228 L 177 L 229 K 178 A 230 Y 179 M 231 L 180 L 232 Q 181 A 233 E 182 A 234 L 183 I 235 H 184 R 236 E 185 R 237 L 186 V 238 H 187 Y 239 TER END PFRMAT AL TARGET T0117 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 4tmk_A T 18 M _ Q 19 R 2 P 20 S 3 F 21 K 4 T 22 Y 5 V 23 I 6 L 24 V 7 I 25 I 8 E 26 E 9 G 27 G 10 N 28 L 11 I 29 E 12 G 30 G 13 S 31 A 14 G 32 G 15 K 33 K 16 T 34 T 17 T 35 T 18 Y 36 A 19 L 37 R 20 N 38 N 21 H 39 V 22 F 40 V 23 E 41 V 24 K 42 E 25 Y 43 T 26 K 44 L 27 N 45 R 33 D 46 D 34 I 47 M 35 C 48 V 36 L 49 F 37 L 50 T 38 T 51 R 39 E 52 E 40 P 53 P 41 N 61 G 42 G 62 G 43 V 63 T 44 N 64 Q 45 L 65 L 46 L 66 A 47 E 67 E 48 L 68 K 49 M 69 L 50 Y 70 R 51 K 71 S 52 D 72 D 67 P 73 K 68 K 74 A 69 K 75 E 70 W 76 V 71 A 77 L 72 M 78 M 73 P 79 F 74 F 80 Y 75 Q 81 A 76 S 82 A 77 Y 83 R 78 V 84 V 79 T 85 Q 80 L 86 L 81 T 87 V 82 M 88 E 83 L 89 T 84 Q 90 V 85 S 91 I 86 H 92 K 87 T 93 P 88 A 94 A 89 P 95 L 90 T 96 A 91 N 97 N 92 K 98 G 93 K 99 T 94 L 100 W 95 K 101 V 96 I 102 I 97 M 103 G 98 E 104 D 99 R 105 R 100 S 106 H 101 I 107 D 102 F 108 L 103 S 109 S 104 A 110 T 105 M 118 Q 106 R 119 A 107 R 120 Y 108 N 121 Q 109 G 122 G 110 S 123 G 111 L 124 G 112 E 125 R 113 Q 126 G 114 G 127 I 115 M 128 D 116 Y 129 Q 117 N 130 H 118 T 131 M 119 L 132 L 120 E 133 A 121 E 134 T 122 W 135 L 123 Y 136 R 124 K 137 D 125 F 138 A 126 I 139 V 127 E 140 L 128 E 141 G 129 S 142 D 130 I 143 F 131 Q 146 R 132 A 147 P 133 D 148 D 134 L 149 L 135 I 150 T 136 I 151 L 137 Y 152 Y 138 L 153 L 139 R 154 D 140 T 155 V 141 S 156 T 142 P 157 P 143 E 158 E 144 V 159 V 145 A 160 G 146 Y 161 L 147 E 162 K 148 R 163 R 149 I 164 A 150 R 165 R 151 Q 166 A 152 R 167 R 153 A 168 G 154 R 169 E 155 E 171 L 156 E 172 D 157 S 173 R 158 C 174 Q 161 V 175 E 162 P 176 S 163 L 177 F 164 K 178 D 165 Y 179 F 166 L 180 F 167 Q 181 N 168 E 182 R 169 L 183 T 170 H 184 R 171 E 185 A 172 L 186 R 173 H 187 Y 174 E 188 L 175 D 189 E 176 W 190 L 177 L 191 A 178 I 192 A 179 H 193 Q 180 S 199 D 181 C 200 K 182 K 201 S 183 V 202 I 184 L 203 H 185 V 204 T 186 L 205 I 187 D 206 D 188 A 207 A 189 D 208 T 190 L 209 Q 191 N 210 P 192 L 211 L 193 Q 219 E 194 R 220 A 195 S 221 V 196 E 222 M 197 S 223 D 198 S 224 A 199 I 225 I 200 F 226 R 201 D 227 T 202 A 228 T 203 I 229 V 204 S 230 T 205 S 231 H 206 N 232 W 207 Q 233 V 208 Q 234 K 209 P 235 E 210 S 236 L 211 TER END PFRMAT AL TARGET T0117 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 5tmp_A Q 19 R 2 P 20 S 3 F 21 K 4 T 22 Y 5 V 23 I 6 L 24 V 7 I 25 I 8 E 26 E 9 G 27 G 10 N 28 L 11 I 29 E 12 G 30 G 13 S 31 A 14 G 32 G 15 K 33 K 16 T 34 T 17 T 35 T 18 Y 36 A 19 L 37 R 20 N 38 N 21 H 39 V 22 F 40 V 23 E 41 V 24 K 42 E 25 Y 43 T 26 K 44 L 27 N 45 R 33 D 46 D 34 I 47 M 35 C 48 V 36 L 49 F 37 L 50 T 38 T 51 R 39 E 52 E 40 P 53 P 41 V 54 G 42 E 55 G 43 K 56 T 44 W 57 Q 45 R 58 L 46 N 59 A 47 V 60 L 50 N 61 R 51 G 62 S 52 V 63 L 53 N 64 L 54 L 65 L 55 L 66 D 56 E 67 I 57 L 68 K 58 M 69 S 59 Y 70 V 60 K 71 G 61 D 72 D 62 P 73 E 63 K 74 V 64 K 75 I 65 W 76 T 66 A 77 D 67 M 78 K 68 P 79 A 69 F 80 E 70 Q 81 V 71 S 82 L 72 Y 83 M 73 V 84 F 74 T 85 Y 75 L 86 V 79 T 87 Q 80 M 88 L 81 L 89 V 82 Q 90 E 83 S 91 T 84 H 92 V 85 T 93 I 86 A 94 K 87 P 95 P 88 T 96 A 89 N 97 L 90 K 98 A 91 K 99 N 92 L 100 G 93 K 101 T 94 I 102 I 97 M 103 G 98 E 104 D 99 R 105 R 100 S 106 H 101 I 107 D 102 F 108 L 103 S 109 S 104 A 110 T 105 R 111 Q 106 Y 112 A 107 C 113 Y 108 F 114 Q 109 N 117 G 110 M 118 G 111 R 119 G 112 R 120 R 113 N 121 G 114 G 122 I 115 S 123 D 116 L 124 Q 117 N 130 H 118 T 131 M 119 L 132 L 120 E 133 A 121 E 134 T 122 W 135 L 123 Y 136 R 124 K 137 D 125 F 138 A 126 I 139 V 127 E 140 L 128 E 141 G 129 S 142 D 130 I 143 F 131 Q 146 R 132 A 147 P 133 D 148 D 134 L 149 L 135 I 150 T 136 I 151 L 137 Y 152 Y 138 L 153 L 139 R 154 D 140 T 155 V 141 S 156 T 142 P 157 P 143 E 158 E 144 V 159 V 145 A 160 G 146 Y 161 L 147 E 162 K 148 R 163 R 149 I 164 A 150 R 165 R 151 Q 166 A 152 R 167 R 153 A 168 G 154 R 169 E 155 S 170 L 156 E 171 D 157 E 172 I 159 S 173 E 160 C 174 Q 161 V 175 E 162 P 176 S 163 L 177 F 164 K 178 D 165 Y 179 F 166 L 180 F 167 Q 181 N 168 E 182 R 169 L 183 T 170 H 184 R 171 E 185 A 172 L 186 R 173 H 187 Y 174 E 188 L 175 D 189 E 176 W 190 L 177 L 191 A 178 R 196 A 179 P 197 Q 180 Q 198 D 181 S 199 K 182 K 201 S 183 V 202 I 184 L 203 H 185 V 204 T 186 L 205 I 187 D 206 D 188 A 207 A 189 D 208 T 190 L 209 Q 191 N 210 P 192 L 211 L 193 E 212 E 194 N 213 A 195 I 214 V 196 TER END PFRMAT AL TARGET T0117 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 3tmk_A M 1 M 1 A 2 M 2 E 3 G 3 A 4 R 4 P 20 G 5 F 21 K 6 T 22 L 7 V 23 I 8 L 24 L 9 I 25 I 10 E 26 E 11 G 27 G 12 N 28 L 13 I 29 D 14 G 30 R 15 S 31 T 16 G 32 G 17 K 33 K 18 T 34 T 19 T 35 T 20 Y 36 Q 21 L 37 C 22 N 38 N 23 H 39 I 24 F 40 L 25 E 41 Y 26 K 42 K 27 Y 43 K 28 K 44 L 29 N 45 Q 30 D 46 N 32 I 47 C 33 C 48 K 34 L 49 L 35 L 50 L 36 T 51 K 37 E 52 F 38 P 53 P 39 V 54 E 40 E 55 R 41 K 56 S 42 W 57 T 43 R 58 R 44 V 63 I 45 N 64 G 46 L 65 G 47 L 66 L 48 E 67 I 49 L 68 N 50 M 69 E 51 Y 70 Y 52 K 71 L 53 D 72 T 54 P 73 D 55 K 74 D 56 K 75 S 57 W 76 F 58 A 77 Q 59 M 78 L 60 P 79 S 61 F 80 D 62 Q 81 Q 63 S 82 A 64 Y 83 I 65 V 84 H 66 T 85 L 67 L 86 L 68 T 87 F 69 M 88 S 70 L 89 A 71 Q 90 N 72 S 91 R 73 H 92 W 74 T 93 E 75 A 94 I 76 P 95 V 77 T 96 D 78 N 97 K 79 K 98 I 80 K 99 K 81 L 100 K 82 K 101 D 83 I 102 L 84 M 103 L 85 E 104 E 86 R 105 G 87 S 106 K 88 I 107 N 89 F 108 I 90 S 109 V 91 A 110 M 92 R 111 D 93 Y 112 R 94 C 113 Y 95 F 114 V 96 V 115 Y 97 E 116 S 98 N 117 G 99 M 118 V 100 R 120 A 105 N 121 K 106 G 122 G 107 S 123 T 108 L 124 N 109 E 125 G 110 Q 126 M 111 G 127 D 112 M 128 L 113 Y 129 D 114 N 130 W 115 T 131 C 116 L 132 L 117 E 133 Q 118 E 134 P 119 W 135 D 120 Y 136 V 121 K 137 G 122 F 138 L 123 I 139 L 124 E 140 K 125 A 147 P 126 D 148 D 127 L 149 L 128 I 150 T 129 I 151 L 130 Y 152 F 131 L 153 L 132 R 154 S 133 T 155 T 134 S 156 Q 135 P 157 D 136 E 158 V 137 V 159 D 138 A 160 N 139 Y 161 N 140 E 162 A 141 R 163 E 142 Q 166 K 143 R 167 S 144 A 168 G 145 R 169 F 146 S 170 G 147 E 171 D 148 E 172 E 149 S 173 R 150 C 174 Y 151 V 175 E 152 P 176 T 153 L 177 V 154 K 178 K 155 Y 179 F 156 L 180 Q 157 Q 181 E 158 E 182 K 159 L 183 V 160 H 184 K 161 E 185 Q 162 L 186 T 163 H 187 F 164 E 188 M 165 D 189 K 166 W 190 L 167 L 191 L 168 I 192 D 169 H 193 K 170 Q 194 E 171 R 195 I 172 R 196 R 173 P 197 K 174 Q 198 G 175 S 199 D 176 C 200 E 177 K 201 S 178 V 202 I 179 L 203 T 180 V 204 I 181 L 205 V 182 D 206 D 183 A 207 V 184 D 208 T 185 L 209 K 187 N 210 G 188 L 211 I 189 E 212 Q 190 N 213 E 191 I 214 V 192 G 215 E 193 T 216 A 194 E 217 L 195 Y 218 I 196 Q 219 W 197 R 220 Q 198 S 221 I 199 E 222 V 200 S 223 E 201 S 224 P 202 I 225 V 203 TER END PFRMAT AL TARGET T0117 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 3vtk F 21 L 50 T 22 R 51 V 23 V 52 L 24 Y 53 I 25 I 54 E 26 D 55 G 27 G 56 N 28 P 57 I 29 H 58 G 30 G 59 S 31 M 60 G 32 G 61 K 33 K 62 T 34 T 63 T 35 T 64 Y 36 T 65 L 37 T 66 N 38 Q 67 H 39 L 68 F 40 L 69 E 41 V 70 K 42 A 71 Y 43 L 72 K 44 R 75 N 45 D 76 D 46 D 77 I 47 I 78 C 48 V 79 L 49 Y 80 L 50 V 81 T 51 P 82 E 52 E 83 P 53 P 84 V 54 M 85 E 55 T 86 K 56 Y 87 W 57 W 88 R 58 R 89 N 59 V 90 V 60 L 91 N 61 G 92 G 62 A 93 V 63 S 94 N 64 E 95 L 65 T 96 L 66 I 97 E 67 A 98 L 68 N 99 M 69 I 100 Y 70 Y 101 K 71 T 102 D 72 T 103 P 73 Q 104 K 74 H 105 K 75 T 127 W 76 M 128 A 77 G 129 M 78 M 130 P 79 P 131 F 80 Y 132 Q 81 A 133 S 82 A 137 Y 83 V 138 V 84 L 139 T 85 A 140 L 86 P 141 T 87 H 142 M 88 I 143 L 89 G 144 Q 90 G 145 S 91 E 146 H 92 A 147 T 93 H _ A 94 A _ P 95 P 153 T 96 P 154 N 97 P 155 K 98 A 156 K 99 L 157 L 100 T 158 K 101 L 159 I 102 I 160 M 103 F 161 E 104 D 162 R 105 R 163 S 106 H 164 I 107 P 165 F 108 I 166 S 109 A 167 A 110 A 168 R 111 L 169 Y 112 L 170 C 113 C 171 F 114 Y 172 V 115 P 173 E 116 A 174 N 117 A 175 M 118 R 176 R 119 Y 177 R 120 L 178 N 121 M 179 G 122 G 180 S 123 S 181 L 124 M 182 E 125 T 183 Q 126 P 184 G 127 Q 185 M 128 A 186 Y 129 V 187 N 130 L 188 T 131 A 189 L 132 F 190 E 133 V 191 E 134 A 192 W 135 L 193 Y 136 I 194 K 137 P 195 F 138 P 196 I 139 T 197 E 140 L 198 E 141 P 199 S 142 G 200 D 148 T 201 L 149 N 202 I 150 I 203 I 151 V 204 Y 152 L 205 L 153 G 206 R 154 A 207 T 155 L 208 S 156 P 209 P 157 E 210 E 158 D 211 V 159 R 212 A 160 H 213 Y 161 I 214 E 162 D 215 R 163 R 216 I 164 L 217 R 165 A 218 Q 166 K 219 R 167 R 220 A 168 Q 221 R 169 R 222 S 170 P 223 E 171 G 224 E 172 E 225 S 173 R 226 V 175 L 227 P 176 D 228 L 177 L 229 K 178 A 230 Y 179 M 231 L 180 L 232 Q 181 A 233 E 182 A 234 L 183 I 235 H 184 R 236 E 185 R 237 TER END PFRMAT AL TARGET T0117 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 1kim_A F 21 L 50 T 22 R 51 V 23 V 52 L 24 Y 53 I 25 I 54 E 26 D 55 G 27 G 56 N 28 P 57 I 29 H 58 G 30 G 59 S 31 M 60 G 32 G 61 K 33 K 62 T 34 T 63 T 35 T 64 Y 36 T 65 L 37 T 66 N 38 Q 67 H 39 L 68 F 40 L 69 D 46 D 77 I 47 I 78 C 48 V 79 L 49 Y 80 L 50 V 81 T 51 P 82 E 52 E 83 P 53 P 84 V 54 M 85 E 55 T 86 K 56 Y 87 W 57 W 88 R 58 R 89 N 59 V 90 V 60 L 91 N 61 G 92 G 62 A 93 V 63 S 94 N 64 E 95 L 65 T 96 L 66 I 97 E 67 A 98 L 68 N 99 M 69 I 100 Y 70 Y 101 K 71 T 102 D 72 T 103 P 73 Q 104 K 74 H 105 K 75 T 127 W 76 M 128 A 77 G 129 M 78 M 130 P 79 P 131 F 80 Y 132 Q 81 A 133 S 82 V 134 Y 83 T 135 V 84 D 136 T 85 A 137 L 86 V 138 T 87 L 139 M 88 A 140 L 89 P 141 Q 90 H 142 S 91 I 143 H 92 G 144 T 93 G 145 A 94 E 146 P 95 P _ T 96 P 154 N 97 P 155 K 98 A 156 K 99 L 157 L 100 T 158 K 101 L 159 I 102 I 160 M 103 F 161 E 104 D 162 R 105 R 163 S 106 H 164 I 107 P 165 F 108 I 166 S 109 A 167 A 110 A 168 R 111 L 169 Y 112 L 170 C 113 C 171 F 114 Y 172 V 115 P 173 E 116 A 174 N 117 A 175 M 118 R 176 R 119 Y 177 R 120 L 178 N 121 M 179 G 122 G 180 S 123 S 181 L 124 M 182 E 125 T 183 Q 126 P 184 G 127 Q 185 M 128 A 186 Y 129 V 187 N 130 L 188 T 131 A 189 L 132 F 190 E 133 V 191 E 134 A 192 W 135 L 193 Y 136 I 194 S 142 P 195 I 143 P 196 H 144 T 197 V 145 L 198 Q 146 P 199 A 147 G 200 D 148 T 201 L 149 N 202 I 150 I 203 I 151 V 204 Y 152 L 205 L 153 G 206 R 154 A 207 T 155 L 208 S 156 P 209 P 157 E 210 E 158 D 211 V 159 R 212 A 160 H 213 Y 161 I 214 E 162 D 215 R 163 R 216 I 164 L 217 R 165 A 218 Q 166 K 219 R 167 R 220 A 168 Q 221 R 169 R 222 S 170 P 223 E 171 G 224 E 172 E 225 S 173 R 226 V 175 L 227 P 176 D 228 L 177 L 229 K 178 A 230 Y 179 M 231 L 180 L 232 Q 181 A 233 E 182 A 234 L 183 I 235 H 184 R 236 E 185 R 237 TER END PFRMAT AL TARGET T0117 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 1qhi_A A 2 P 47 E 3 T 48 A 4 L 49 A 5 L 50 S 6 R 51 V 23 V 52 L 24 Y 53 I 25 I 54 E 26 D 55 G 27 G 56 N 28 P 57 I 29 H 58 G 30 G 59 S 31 M 60 G 32 G 61 K 33 K 62 T 34 T 63 T 35 T 64 Y 36 T 65 L 37 T 66 N 38 Q 67 H 39 L 68 F 40 L 69 D 46 D 77 I 47 I 78 C 48 V 79 L 49 Y 80 L 50 V 81 T 51 P 82 E 52 E 83 P 53 P 84 V 54 M 85 E 55 T 86 K 56 Y 87 W 57 W 88 R 58 R 89 N 59 V 90 V 60 L 91 N 61 G 92 G 62 A 93 V 63 S 94 N 64 E 95 L 65 T 96 L 66 I 97 E 67 A 98 L 68 N 99 M 69 I 100 Y 70 Y 101 K 71 T 102 W 76 V 119 A 77 V 120 M 78 M 121 P 79 T 122 F 80 S 123 Q 81 A 124 S 82 Q 125 Y 83 I 126 V 84 T 127 T 85 M 128 L 86 G 129 T 87 M 130 M 88 P 131 L 89 Y 132 Q 90 A 133 S 91 V 134 H 92 T 135 T 93 D 136 A 94 A 137 P 95 V 138 T 96 L 139 N 97 A 140 K 98 P 141 K 99 H 142 L 100 I 143 E 104 A 156 R 105 L 157 S 106 T 158 I 107 L 159 F 108 I 160 S 109 F 161 A 110 D 162 R 111 R 163 Y 112 H 164 C 113 P 165 F 114 I 166 V 115 A 167 E 116 A 168 N 117 C 171 M 118 Y 172 R 119 P 173 R 120 A 174 N 121 A 175 G 122 R 176 S 123 Y 177 L 124 L 178 E 125 M 179 Q 126 G 180 G 127 S 181 M 128 M 182 Y 129 T 183 N 130 P 184 T 131 Q 185 L 132 A 186 E 133 V 187 E 134 L 188 W 135 A 189 Y 136 F 190 K 137 V 191 F 138 A 192 I 139 L 193 E 140 I 194 E 141 P 195 S 142 P 196 I 143 T 197 V 145 L 198 Q 146 P 199 A 147 G 200 D 148 T 201 L 149 N 202 I 150 I 203 I 151 V 204 Y 152 L 205 L 153 G 206 R 154 A 207 T 155 L 208 S 156 P 209 P 157 E 210 E 158 D 211 V 159 R 212 A 160 H 213 Y 161 I 214 E 162 D 215 R 163 R 216 I 164 L 217 R 165 A 218 Q 166 K 219 R 167 R 220 A 168 Q 221 R 169 R 222 S 170 P 223 E 171 G 224 E 172 E 225 S 173 R 226 V 175 L 227 P 176 D 228 L 177 L 229 K 178 A 230 Y 179 M 231 L 180 L 232 Q 181 A 233 E 182 A 234 L 183 I 235 H 184 R 236 E 185 R 237 L 186 V 238 H 187 Y 239 E 188 G 240 D 189 L 241 W 190 L 242 L 191 A 243 I 192 N 244 H 193 T 245 Q 194 V 246 R 195 R 247 R 196 Y 248 P 197 L 249 Q 198 Q 250 S 199 S 321 C 200 M 322 K 201 H 323 V 202 V 324 L 203 F 325 V 204 I 326 L 205 L 327 D 206 D 328 A 207 Y 329 D 208 D 330 L 209 Q 331 N 210 S 332 L 211 P 333 E 212 A 334 N 213 G 335 I 214 C 336 G 215 R 337 T 216 D 338 E 217 A 339 Y 218 L 340 Q 219 L 341 R 220 Q 342 S 221 L 343 E 222 T 344 S 223 S 345 S 224 G 346 I 225 M 347 F 226 T 350 D 227 H 351 A 228 V 352 I 229 T 353 S 230 T 354 S 231 P 355 N 232 G 356 Q 233 S 357 Q 234 I 358 P 235 P 359 S 236 T 360 P 237 I 361 V 238 C 362 L 239 D 363 V 240 L 364 S 241 A 365 P 242 R 366 S 243 T 367 K 244 F 368 R 245 A 369 Q 246 R 370 R 247 E 371 V 248 M 372 A 249 G 373 R 250 E 374 TER END PFRMAT AL TARGET T0117 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 2tmk_A Q 19 R 4 P 20 G 5 F 21 K 6 T 22 L 7 V 23 I 8 L 24 L 9 I 25 I 10 E 26 E 11 G 27 G 12 N 28 L 13 I 29 D 14 G 30 R 15 S 31 T 16 G 32 G 17 K 33 K 18 T 34 T 19 T 35 T 20 Y 36 Q 21 L 37 C 22 N 38 N 23 H 39 I 24 F 40 L 25 E 41 Y 26 K 42 K 27 Y 43 K 28 K 44 L 29 N 45 Q 30 D 46 P 31 I 47 N 32 C 48 C 33 L 49 K 34 L 50 L 36 T 51 K 37 E 52 F 38 P 53 P 39 V 54 E 40 R 58 R 41 N 59 S 42 V 60 T 43 N 61 R 44 G 62 I 45 V 63 G 46 N 64 G 47 L 65 L 48 L 66 I 49 E 67 N 50 L 68 E 51 M 69 Y 52 Y 70 L 53 K 71 T 54 D 72 D 55 P 73 D 56 K 74 S 57 K 75 F 58 W 76 Q 59 A 77 L 60 M 78 S 61 P 79 D 62 F 80 Q 63 Q 81 A 64 S 82 I 65 Y 83 H 66 V 84 L 67 T 85 L 68 L 86 F 69 T 87 S 70 M 88 A 71 L 89 N 72 Q 90 R 73 S 91 W 74 H 92 E 75 T 93 I 76 A 94 V 77 P 95 D 78 T 96 K 79 N 97 I 80 K 98 K 81 K 99 K 82 L 100 D 83 K 101 L 84 I 102 L 85 M 103 E 86 E 104 G 87 R 105 K 88 S 106 N 89 I 107 I 90 F 108 V 91 S 109 M 92 A 110 D 93 R 111 R 94 Y 112 Y 95 C 113 V 96 F 114 Y 97 V 115 S 98 E 116 G 99 N 117 V 100 M 118 A 101 R 119 Y 102 R 120 S 103 N 121 A 104 G 122 A 105 S 123 K 106 L 124 G 107 E 125 T 108 Q 126 N 109 G 127 G 110 M 128 M 111 Y 129 D 112 L 132 L 113 E 133 D 114 E 134 W 115 W 135 C 116 Y 136 L 117 K 137 Q 118 F 138 P 119 I 139 D 120 E 140 V 121 E 141 G 122 S 142 L 123 I 143 L 124 Q 146 K 125 A 147 P 126 D 148 D 127 L 149 L 128 I 150 T 129 I 151 L 130 Y 152 F 131 L 153 L 132 R 154 S 133 T 155 T 134 S 156 Q 135 P 157 V _ E 158 D _ V 159 N _ A 160 N _ Y 161 A _ E 162 E _ R 163 K _ I 164 S _ R 165 G _ C 174 K 155 V 175 F 156 P 176 Q 157 L 177 E 158 K 178 K 159 Y 179 V 160 L 180 K 161 Q 181 Q 162 E 182 T 163 L 183 F 164 H 184 M 165 E 185 K 166 L 186 L 167 H 187 L 168 E 188 D 169 D 189 K 170 W 190 E 171 L 191 I 172 I 192 R 173 H 193 K 174 Q 194 G 175 R 195 D 176 S 199 E 177 C 200 S 178 K 201 I 179 V 202 T 180 L 203 I 181 V 204 V 182 L 205 D 183 D 206 V 184 A 207 T 185 D 208 N 186 L 209 K 187 N 210 G 188 L 211 I 189 E 212 Q 190 N 213 E 191 I 214 V 192 TER END PFRMAT AL TARGET T0117 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 3adk Y 14 E 2 A 15 E 3 E 16 K 4 G 17 L 5 T 18 K 6 Q 19 K 7 P 20 S 8 F 21 K 9 T 22 I 10 V 23 I 11 L 24 F 12 I 25 V 13 E 26 V 14 G 27 G 15 N 28 G 16 I 29 P 17 G 30 G 18 S 31 S 19 G 32 G 20 K 33 K 21 T 34 G 22 T 35 T 23 Y 36 Q 24 L 37 C 25 N 38 E 26 H 39 K 27 F 40 I 28 E 41 V 29 K 42 Q 30 Y 43 K 31 K 44 Y 32 N 45 G 33 D 46 Y 34 I 47 T 35 C 48 H 36 L 49 L 37 L 50 S 38 T 51 T 39 E 52 G 40 P 53 D 41 V 54 L 42 E 55 L 43 K 56 R 44 W 57 A 45 R 58 E 46 N 59 V 47 V 60 S 48 N 61 S 49 G 62 G 50 V 63 S 51 N 64 A 52 L 65 R 53 L 66 G 54 E 67 K 55 L 68 M 56 M 69 L 57 Y 70 S 58 K 71 E 59 D 72 I 60 P 73 M 61 K 74 E 62 K 75 G 64 W 76 Q 65 A 77 L 66 M 78 V 67 P 79 P 68 F 80 L 69 Q 81 E 70 S 82 T 71 Y 83 V 72 V 84 L 73 T 85 D 74 L 86 M 75 T 87 L 76 M 88 R 77 L 89 D 78 Q 90 A 79 S 91 M 80 H 92 V 81 T 93 A 82 A 94 K 83 P 95 V 84 T 96 D 85 N 97 T 86 K 98 S 87 K 99 K 88 L 100 G 89 K 101 F 90 I 102 L 91 M 103 I 92 E 104 D 93 R 105 G 94 S 106 Y 95 I 107 P 96 F 108 R 97 S 109 E 98 A 110 V 99 E 134 K 100 W 135 Q 101 Y 136 G 102 K 137 E 103 F 138 E 104 I 139 F 105 E 141 E 106 S 142 R 107 I 143 K 108 H 144 I 109 V 145 G 110 Q 146 Q 111 A 147 P 112 D 148 T 113 L 149 L 114 I 150 L 115 I 151 L 116 Y 152 Y 117 L 153 V 118 R 154 D 119 T 155 A 120 S 156 G 121 P 157 P 122 E 158 E 123 V 159 T 124 A 160 M 125 Y 161 T 126 E 162 K 127 R 163 R 128 I 164 L 129 R 165 L 130 Q 166 K 131 R 167 R 132 A 168 G 133 R 169 E 134 S 170 T 135 E 171 S 136 E 172 G 137 S 173 R 138 C 174 D 141 V 175 N 142 P 176 E 143 L 177 E 144 K 178 T 145 Y 179 I 146 L 180 K 147 Q 181 K 148 E 182 R 149 L 183 L 150 H 184 E 151 E 185 T 152 L 186 Y 153 H 187 Y 154 E 188 K 155 D 189 A 156 W 190 T 157 L 191 E 158 I 192 P 159 H 193 V 160 Q 194 I 161 R 195 A 162 R 196 F 163 P 197 Y 164 Q 198 E 165 S 199 K 166 C 200 R 167 K 201 G 168 L 205 I 169 D 206 V 170 A 207 R 171 D 208 K 172 L 209 V 173 N 210 N 174 L 211 A 175 Q 219 E 176 R 220 G 177 S 221 S 178 E 222 V 179 S 223 D 180 S 224 D 181 I 225 V 182 F 226 F 183 D 227 S 184 A 228 Q 185 I 229 V 186 TER END PFRMAT AL TARGET T0117 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 1ukz T 22 V 18 V 23 I 19 L 24 F 20 I 25 V 21 E 26 L 22 G 27 G 23 N 28 G 24 I 29 P 25 G 30 G 26 S 31 A 27 G 32 G 28 K 33 K 29 T 34 G 30 T 35 T 31 Y 36 Q 32 L 37 C 33 N 38 E 34 H 39 K 35 F 40 L 36 E 41 V 37 K 42 K 38 Y 43 D 39 K 44 Y 40 N 45 S 41 D 46 F 42 I 47 V 43 C 48 L 45 L 49 S 46 L 50 A 47 T 51 G 48 E 52 D 49 P 53 L 50 V 54 L 51 E 55 R 52 K 56 A 53 W 57 E 54 R 58 Q 55 N 59 G 56 V 60 R 57 N 61 A 58 G 62 G 59 V 63 S 60 N 64 Q 61 L 65 Y 62 L 66 G 63 E 67 E 64 L 68 L 65 M 69 I 66 Y 70 K 67 K 71 N 68 D 72 C 69 P 73 I 70 K 74 K 71 K 75 E 72 W 76 G 73 A 77 Q 74 M 78 I 75 P 79 V 76 F 80 P 77 Q 81 Q 78 S 82 E 79 Y 83 I 80 V 84 T 81 T 85 L 82 L 86 A 83 T 87 L 84 M 88 L 85 L 89 R 86 Q 90 N 87 S 91 A 88 H 92 I 89 T 93 S 90 A 94 D 91 P 95 N 92 T 96 V 93 N 97 K 94 K 98 D 110 K 99 Q 111 L 100 A 112 K 101 I 113 I 102 S 114 M 103 F 115 E 104 E 116 R 105 R 117 S 106 D 118 I 107 I 119 F 108 V 120 S 109 E 121 A 110 S 122 D 148 K 123 L 149 F 124 I 150 I 125 I 151 L 126 Y 152 F 127 L 153 F 128 R 154 D 129 T 155 C 130 S 156 P 131 P 157 E 132 E 158 D 133 V 159 I 134 A 160 M 135 Y 161 L 136 E 162 E 137 R 163 R 138 I 164 L 139 R 165 L 140 Q 166 E 141 R 167 R 142 A 168 G 143 R 169 K 144 S 170 T 145 E 171 S 146 C 174 G 147 V 175 R 148 P 176 S 149 L 177 D 150 K 178 D 151 Y 179 N 152 L 180 I 153 Q 181 E 154 E 182 S 155 L 183 I 156 H 184 K 157 E 185 K 158 L 186 R 159 H 187 F 160 E 188 N 161 D 189 T 162 W 190 F 163 L 191 K 164 I 192 E 165 H 193 T 166 Q 194 E 172 R 195 Y 173 R 196 F 174 P 197 E 175 Q 198 T 176 S 199 K 177 C 200 S 178 K 201 K 179 V 202 V 180 L 203 V 181 V 204 R 182 L 205 V 183 D 206 R 184 A 207 C 185 D 208 D 186 L 209 R 187 N 210 S 188 L 211 V 189 Q 219 E 190 R 220 D 191 S 221 V 192 E 222 Y 193 S 223 K 194 S 224 D 195 I 225 V 196 F 226 Q 197 D 227 D 198 A 228 A 199 I 229 I 200 S 230 R 201 S 231 D 202 N 232 S 203 Q 233 L 204 TER END PFRMAT AL TARGET T0117 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 1qf9_A Q 19 K 5 P 20 P 6 F 21 N 7 T 22 V 8 V 23 V 9 L 24 F 10 I 25 V 11 E 26 L 12 G 27 G 13 N 28 G 14 I 29 P 15 G 30 G 16 S 31 S 17 G 32 G 18 K 33 K 19 T 34 G 20 T 35 T 21 Y 36 Q 22 L 37 C 23 N 38 A 24 H 39 N 25 F 40 I 26 E 41 V 27 K 42 R 28 Y 43 D 29 E 55 F 30 K 56 G 31 W 57 W 32 R 58 V 33 N 59 H 34 V 60 L 35 N 61 S 36 G 62 A 37 V 63 G 38 N 64 D 39 L 65 L 40 L 66 L 41 E 67 R 42 L 68 Q 43 M 69 E 44 Y 70 Q 45 K 71 Q 46 D 72 T 57 P 73 M 58 K 74 I 59 K 75 K 60 W 76 N 61 A 77 G 62 M 78 E 63 P 79 I 64 F 80 V 65 Q 81 P 66 S 82 S 67 Y 83 I 68 V 84 V 69 T 85 T 70 L 86 V 71 T 87 K 72 M 88 L 73 L 89 L 74 Q 90 K 75 S 91 N 76 H 92 A 77 T 93 I 78 A 94 D 79 P 95 A 80 T 96 N 81 N 97 Q 82 K 98 G 83 K 99 K 84 L 100 N 85 K 101 F 86 I 102 L 87 M 103 V 88 E 104 D 89 R 105 G 90 F 114 F 91 V 115 P 92 E 116 R 93 N 117 N 94 M 118 E 95 R 119 E 96 R 120 N 97 N 121 N 98 E 133 N 99 E 134 S 100 W 135 W 101 Y 136 E 102 K 137 E 103 F 138 N 104 I 139 M 105 E 140 K 106 E 141 D 107 S 142 F 108 I 143 V 109 Q 146 D 110 A 147 T 111 D 148 K 112 L 149 F 113 I 150 V 114 I 151 L 115 Y 152 F 116 L 153 F 117 R 154 D 118 T 155 C 119 S 156 P 120 P 157 E 121 E 158 E 122 V 159 V 123 A 160 M 124 Y 161 T 125 E 162 Q 126 R 163 R 127 I 164 L 128 R 165 L 129 Q 166 K 130 R 167 R 131 A 168 G 132 R 169 E 133 S 170 S 134 E 171 S 135 C 174 G 136 V 175 R 137 P 176 S 138 L 177 D 139 K 178 D 140 Y 179 N 141 L 180 I 142 Q 181 E 143 E 182 S 144 L 183 I 145 H 184 K 146 E 185 K 147 L 186 R 148 H 187 F 149 E 188 N 150 D 189 T 151 W 190 F 152 L 191 N 153 I 192 V 154 H 193 Q 155 Q 194 T 156 R 195 K 157 R 196 L 158 P 197 V 159 Q 198 I 160 S 199 D 161 C 200 D 167 K 201 K 168 V 202 V 169 L 203 K 170 V 204 I 171 L 205 I 172 D 206 P 173 A 207 A 174 D 208 N 175 L 209 R 176 N 210 D 177 L 211 V 178 Q 219 N 179 R 220 E 180 S 221 V 181 E 222 Y 182 S 223 N 183 S 224 D 184 I 225 V 185 F 226 E 186 D 227 N 187 A 228 L 188 I 229 F 189 S 230 K 190 S 231 S 191 TER END PFRMAT AL TARGET T0117 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 5ukd_A Q 19 K 5 P 20 P 6 F 21 N 7 T 22 V 8 V 23 V 9 L 24 F 10 I 25 V 11 E 26 L 12 G 27 G 13 N 28 G 14 I 29 P 15 G 30 G 16 S 31 S 17 G 32 G 18 K 33 K 19 T 34 G 20 T 35 T 21 Y 36 Q 22 L 37 C 23 N 38 A 24 H 39 N 25 F 40 I 26 E 41 R 28 K 42 D 29 Y 43 F 30 D 46 G 31 I 47 W 32 C 48 V 33 L 49 H 34 L 50 L 35 T 51 S 36 E 52 A 37 P 53 G 38 V 54 D 39 E 55 L 40 K 56 L 41 W 57 R 42 R 58 Q 43 N 59 E 44 V 60 Q 45 N 61 Q 46 G 62 S 47 V 63 G 48 N 64 S 49 L 65 K 50 L 66 D 51 E 67 G 52 L 68 E 53 M 69 M 54 Y 70 I 55 K 71 A 56 D 72 T 57 P 73 M 58 K 74 I 59 K 75 K 60 W 76 N 61 A 77 G 62 M 78 E 63 P 79 I 64 F 80 V 65 Q 81 P 66 S 82 S 67 Y 83 I 68 V 84 V 69 T 85 T 70 L 86 V 71 T 87 K 72 M 88 L 73 L 89 L 74 Q 90 K 75 S 91 N 76 H 92 A 77 T 93 I 78 A 94 D 79 P 95 A 80 T 96 N 81 N 97 Q 82 K 98 G 83 K 99 K 84 L 100 N 85 K 101 F 86 I 102 L 87 M 103 V 88 E 104 D 89 R 105 G 90 S 106 F 91 I 107 P 92 L 124 R 93 E 125 N 94 Q 126 E 95 G 127 E 96 M 128 N 97 Y 129 N 98 N 130 N 99 T 131 S 100 L 132 W 101 E 133 E 102 E 134 E 103 W 135 N 104 Y 136 M 105 S 142 K 106 I 143 D 107 H 144 F 108 V 145 V 109 Q 146 D 110 A 147 T 111 D 148 K 112 L 149 F 113 I 150 V 114 I 151 L 115 Y 152 F 116 L 153 F 117 R 154 D 118 T 155 C 119 S 156 P 120 P 157 E 121 E 158 E 122 V 159 V 123 A 160 M 124 Y 161 T 125 E 162 Q 126 R 163 R 127 I 164 L 128 R 165 L 129 Q 166 K 130 R 167 R 131 A 168 G 132 R 169 E 133 S 170 S 134 E 171 S 135 K 178 G 136 Y 179 R 137 L 180 S 138 Q 181 D 139 E 182 D 140 L 183 N 141 H 184 I 142 E 185 E 143 L 186 S 144 H 187 I 145 E 188 K 146 D 189 K 147 W 190 R 148 L 191 F 149 I 192 N 150 H 193 T 151 Q 194 F 152 R 195 N 153 R 196 V 154 P 197 N 164 Q 198 K 165 S 199 F 166 C 200 D 167 K 201 K 168 V 202 V 169 L 203 K 170 V 204 I 171 L 205 I 172 D 206 P 173 A 207 A 174 D 208 N 175 L 209 R 176 N 210 D 177 L 211 V 178 E 212 N 179 N 213 E 180 I 214 V 181 TER END PFRMAT AL TARGET T0117 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 2cmk_A E 16 M _ G 17 T _ T 18 A 3 Q 19 I 4 P 20 A 5 F 21 P 6 T 22 V 7 V 23 I 8 L 24 T 9 I 25 I 10 E 26 D 11 G 27 G 12 N 28 P 13 I 29 S 14 G 30 G 15 S 31 A 16 G 32 G 17 K 33 K 18 T 34 G 19 T 35 T 20 Y 36 L 21 L 37 C 22 N 38 K 23 H 39 A 24 F 40 M 25 E 41 A 26 K 42 E 27 Y 43 A 28 K 44 L 29 N 45 Q 30 TER END PFRMAT AL TARGET T0117 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 1zak_A Q 19 D 4 P 20 P 5 F 21 L 6 T 22 K 7 V 23 V 8 L 24 M 9 I 25 I 10 E 26 S 11 G 27 G 12 N 28 A 13 I 29 P 14 G 30 A 15 S 31 S 16 G 32 G 17 K 33 K 18 T 34 G 19 T 35 T 20 Y 36 Q 21 L 37 C 22 N 38 E 23 H 39 L 24 F 40 I 25 E 41 K 26 K 42 T 27 Y 43 K 28 K 44 Y 29 N 45 Q 30 D 46 L 31 I 47 A 32 C 48 H 33 L 49 I 34 L 50 S 35 N 61 A 36 G 62 G 37 V 63 D 38 N 64 L 39 L 65 L 40 L 66 R 41 E 67 A 42 L 68 E 43 M 69 I 44 Y 70 A 45 K 71 A 46 D 72 E 56 P 73 F 57 K 74 M 58 K 75 E 59 W 76 K 60 A 77 G 61 M 78 Q 62 P 79 L 63 F 80 V 64 Q 81 P 65 S 82 D 66 Y 83 E 67 V 84 I 68 T 85 V 69 L 86 V 70 T 87 N 71 M 88 M 72 L 89 V 73 Q 90 K 74 S 91 E 75 H 92 R 76 T 93 L 77 A 94 R 78 P 95 Q 79 T 96 P 80 N 97 D 81 K 98 E 84 K 99 N 85 L 100 G 86 K 101 W 87 I 102 L 88 M 103 L 89 E 104 D 90 R 105 G 91 S 106 Y 92 I 107 P 93 F 108 R 94 S 109 S 95 A 110 Y 96 R 111 S 97 Y 112 Q 98 C 113 A 99 F 114 M 100 V 115 A 101 E 116 L 102 N 117 E 103 M 118 T 104 R 119 L 105 R 120 E 106 N 121 I 107 Q 146 R 108 A 147 P 109 D 148 D 110 L 149 T 111 I 150 F 112 I 151 I 113 Y 152 L 114 L 153 L 115 R 154 D 116 T 155 V 117 S 156 P 118 P 157 D 119 E 158 E 120 V 159 L 121 A 160 L 122 Y 161 V 123 E 162 E 124 R 163 R 125 I 164 V 126 R 165 V 127 Q 166 G 128 R 167 R 129 TER END PFRMAT AL TARGET T0117 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 1cke_A P 20 A 5 F 21 P 6 T 22 V 7 V 23 I 8 L 24 T 9 I 25 I 10 E 26 D 11 G 27 G 12 N 28 P 13 I 29 S 14 G 30 G 15 S 31 A 16 G 32 G 17 K 33 K 18 T 34 G 19 T 35 T 20 Y 36 L 21 L 37 C 22 N 38 K 23 H 39 A 24 F 40 M 25 E 41 A 26 K 42 E 27 Y 43 A 28 K 44 L 29 N 45 Q 30 W 57 W 31 R 58 H 32 N 59 L 33 V 60 L 34 N 61 D 35 G 62 S 36 V 63 G 37 N 64 A 38 L 65 I 39 L 66 Y 40 E 67 R 41 L 68 V 42 M 69 L 43 Y 70 A 44 K 71 L 45 D 72 D 68 P 73 V 69 K 74 R 70 K 75 F 71 W 76 V 72 A 77 S 73 M 78 T 74 P 79 N 75 F 80 G 76 Q 81 N 77 S 82 L 78 Y 83 E 79 V 84 V 80 T 85 I 81 L 86 L 82 T 87 E 83 M 88 G 84 L 89 E 85 Q 90 D 86 S 91 V 87 H 92 S 88 T 93 G 89 A 94 E 90 P 95 I 91 T 96 R 92 N 97 T 93 K 98 Q 94 K 99 E 95 L 100 V 96 K 101 A 97 I 102 N 98 M 103 A 99 E 104 A 100 R 105 S 101 S 106 Q 102 I 107 V 103 F 108 A 104 S 109 A 105 A 110 F 106 R 111 P 107 Y 112 R 108 C 113 V 109 F 114 R 110 V 115 E 111 E 116 A 112 N 117 L 113 M 118 L 114 R 119 R 115 R 120 R 116 N 121 Q 117 G 122 R 118 S 123 A 119 L 124 F 120 E 125 R 121 Q 126 E 122 G 127 L 123 M 128 P 124 Y 129 G 125 N 130 L 126 T 131 I 127 L 132 A 128 E 133 D 129 E 134 G 130 W 135 R 131 Y 136 D 132 E 141 T 135 S 142 V 136 I 143 V 137 H 144 F 138 V 145 P 139 Q 146 D 140 A 147 A 141 D 148 P 142 L 149 V 143 I 150 K 144 I 151 I 145 Y 152 F 146 L 153 L 147 R 154 D 148 T 155 A 149 S 156 S 150 P 157 S 151 E 158 E 152 V 159 E 153 A 160 R 154 Y 161 A 155 E 162 H 156 R 163 R 157 I 164 R 158 R 165 M 159 Q 166 L 160 R 167 Q 161 A 168 L 162 R 169 Q 163 S 170 V 164 E 171 K 165 E 172 G 166 S 173 F 167 C 174 S 168 V 175 V 169 P 176 N 170 L 177 F 171 K 178 E 172 Y 179 L 174 L 180 L 175 Q 181 A 176 E 182 E 177 L 183 I 178 H 184 K 179 E 185 L 193 L 186 V 194 H 187 P 195 E 188 A 196 D 189 A 197 K 201 D 198 V 202 A 199 L 203 L 200 V 204 V 201 L 205 L 202 D 206 D 203 A 207 S 204 D 208 T 205 L 209 L 207 N 210 S 208 L 211 I 209 E 212 E 210 N 213 Q 211 I 214 V 212 G 215 I 213 T 216 E 214 E 217 K 215 Y 218 A 216 Q 219 L 217 R 220 Q 218 S 221 Y 219 E 222 A 220 S 223 R 221 S 224 Q 222 TER END --simple mime boundary-- From farmer@cse.ucsc.edu Thu Jul 27 03:10:10 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 DAA08292 for Message-Id: <200007270115.SAA09472@beta.cse.ucsc.edu> Subject: T0117(target 99 secondary structure prediction) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0117.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-964558810.t99secstr.fasta' Content-Disposition: attachment; filename="t99-results-964558810.t99secstr.fasta" >T0117 LLLLLLLLLLLLLLLLLLLLEEEEEELLLLLLHHHHHHHHHHHHLLLEEELLLLHHHHLLLLLHHHHHHHHLHHHHHHHHHHHHHHHHHHHHHLLLLLLEEEEELLLLHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHLLLLLLLEEEEEELLHHHHHHHHHHHLLLLLLLLLHHHHHHHHHHHHHHHHHHHHLLLLEEEEEELLLLHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLHHHHHHL --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-964558810.t99secstr.casp.ss' Content-Disposition: attachment; filename="t99-results-964558810.t99secstr.casp.ss" PFRMAT SS TARGET T0117 AUTHOR UCSC Target99 server METHOD This prediction was derived from the following methods METHOD by averaging the corresponding probabilities: METHOD Method 0: METHOD TARGET T0117 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-20228/target-align-20228.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 53.3544 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: T0117 METHOD model_file: /projects/compbio/tmp/sam-nn-tmp.beta.24422/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: Wed Jul 26 18:07:34 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-20228/target-align-20228.a2m METHOD METHOD guide seq name: T0117 METHOD ###end 0 MODEL 1 M C 0.632 A C 0.54 E C 0.488 A C 0.506 A C 0.449 S C 0.403 C C 0.397 A C 0.446 R C 0.539 K C 0.639 G C 0.699 T C 0.697 K C 0.651 Y C 0.624 A C 0.599 E C 0.572 G C 0.561 T C 0.578 Q C 0.57 P C 0.483 F E 0.481 T E 0.693 V E 0.748 L E 0.732 I E 0.687 E E 0.521 G C 0.602 N C 0.58 I C 0.495 G C 0.5 S C 0.511 G C 0.545 K H 0.506 T H 0.567 T H 0.624 Y H 0.674 L H 0.714 N H 0.728 H H 0.732 F H 0.733 E H 0.726 K H 0.698 Y H 0.644 K H 0.478 N C 0.627 D C 0.614 I C 0.468 C E 0.475 L E 0.54 L E 0.474 T C 0.466 E C 0.546 P C 0.542 V C 0.397 E H 0.414 K H 0.423 W H 0.416 R H 0.389 N C 0.367 V C 0.441 N C 0.574 G C 0.579 V C 0.493 N H 0.451 L H 0.543 L H 0.599 E H 0.614 L H 0.609 M H 0.571 Y H 0.515 K H 0.465 D C 0.562 P H 0.532 K H 0.55 K H 0.586 W H 0.549 A H 0.573 M H 0.591 P H 0.607 F H 0.63 Q H 0.627 S H 0.622 Y H 0.619 V H 0.595 T H 0.572 L H 0.526 T H 0.57 M H 0.618 L H 0.633 Q H 0.623 S H 0.599 H H 0.575 T H 0.494 A C 0.453 P C 0.506 T C 0.584 N C 0.625 K C 0.64 K C 0.593 L E 0.44 K E 0.594 I E 0.625 M E 0.559 E E 0.426 R C 0.416 S C 0.486 I C 0.425 F C 0.409 S H 0.454 A H 0.516 R H 0.543 Y H 0.576 C H 0.586 F H 0.6 V H 0.632 E H 0.651 N H 0.646 M H 0.627 R H 0.604 R H 0.589 N H 0.52 G C 0.61 S C 0.604 L C 0.578 E C 0.624 Q H 0.615 G H 0.638 M H 0.648 Y H 0.685 N H 0.688 T H 0.69 L H 0.705 E H 0.698 E H 0.707 W H 0.703 Y H 0.686 K H 0.669 F H 0.628 I H 0.558 E H 0.532 E H 0.472 S C 0.468 I C 0.479 H C 0.564 V C 0.628 Q C 0.681 A C 0.652 D C 0.604 L E 0.56 I E 0.677 I E 0.723 Y E 0.705 L E 0.657 R E 0.517 T C 0.557 S C 0.713 P H 0.621 E H 0.708 V H 0.74 A H 0.744 Y H 0.77 E H 0.769 R H 0.765 I H 0.749 R H 0.735 Q H 0.719 R H 0.618 A C 0.615 R C 0.647 S C 0.616 E C 0.489 E C 0.466 S C 0.458 C C 0.484 V C 0.509 P C 0.576 L H 0.73 K H 0.754 Y H 0.762 L H 0.785 Q H 0.801 E H 0.795 L H 0.781 H H 0.765 E H 0.763 L H 0.752 H H 0.75 E H 0.754 D H 0.761 W H 0.748 L H 0.736 I H 0.703 H H 0.669 Q H 0.568 R H 0.486 R H 0.429 P C 0.555 Q C 0.559 S C 0.561 C C 0.483 K E 0.403 V E 0.581 L E 0.618 V E 0.624 L E 0.573 D E 0.431 A C 0.512 D C 0.597 L C 0.558 N C 0.549 L H 0.402 E H 0.394 N H 0.458 I H 0.471 G H 0.456 T H 0.471 E H 0.517 Y H 0.554 Q H 0.708 R H 0.722 S H 0.717 E H 0.737 S H 0.759 S H 0.765 I H 0.76 F H 0.764 D H 0.759 A H 0.76 I H 0.74 S H 0.688 S H 0.622 N C 0.494 Q C 0.483 Q C 0.425 P C 0.362 S C 0.358 P C 0.373 V C 0.362 L C 0.392 V C 0.447 S C 0.573 P C 0.578 S C 0.57 K H 0.521 R H 0.566 Q H 0.564 R H 0.524 V H 0.474 A H 0.394 R C 0.529 END --simple mime boundary--