From farmer@cse.ucsc.edu Tue Jun 27 21:12:36 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 VAA04419 for Message-Id: <200006271916.MAA30587@beta.cse.ucsc.edu> Subject: T0104(target 99 alignment) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0104.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-962133418.t99align.a2m' Content-Disposition: attachment; filename="t99-results-962133418.t99align.a2m" >T0104 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQ GNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGIRDYFNTDSICLIEWSEKGQG ILPEADILVNIDYYDDARNIELIAQTNLGKNIISAFSN >gi|1176349|sp|P44492|YJEE_HAEIN_1:158 HYPOTHETICAL PROTEIN HI0065gi|1074243|pir||H64141 hypothetical protein HI0065 - Haemophilus influenzae (strain Rd KW20)gi|1573014|gb|AAC21743.1| (U32692) conserved hypothetical protein [Haemophilus influenzae Rd] MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLT RGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGI RDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGK NIISAFSN >gi|7225682|gb|AAF40894.1|_4:149 (AE002401) conserved hypothetical protein [Neisseria meningitidis MC58] msdLPSISRFLADEAATLDLGAAWSSRL-----NAPLVIYLEGDLGAGKT TLTRGILRGLGHQGAVKSPTYAIVESYPLERFTLHHFDLYRFSFPEEWED AGLDELFAANSVCLIEWPQQGGEFTPPADITATLTHDGDGRKCLLTAHTE RGRE-------slpl >gi|7380656|emb|CAB85246.1|_4:149 (AL162757) conserved hypothetical protein [Neisseria meningitidis] msdLPSISRFLADEAATLDLGAAWSSRL-----NAPLVIYLEGDLGAGKT TLTRGILRGLGHQGAVKSPTYAIVESYPLERFTLHHFDLYRFSFPEEWED AGLDELFAANSVCLIEWPQQGGEFTPPADITATLTHDGGGRKCLLTAHTE RGRE-------slpl >gi|401636|sp|P31805|YJEE_ECOLI_1:145 HYPOTHETICAL 16.9 KDA PROTEIN IN PSD-AMIB INTERGENIC REGION (URF2)gi|1361143|pir||S56393 hypothetical 16.9K protein (psd-amiB intergenic region) - Escherichia coligi|304913|gb|AAA20096.1| (L19346) urf2 [Escherichia coli]gi|537009|gb|AAA97064.1| (U14003) urf2 of GenBank Accession Number L19346 [Escherichia coli]gi|1790610|gb|AAC77125.1| (AE000489) orf, hypothetical protein [Escherichia coli] MMNRVIPLPDEQATLDLGERVAKAC-----DGATVIYLYGDLGAGKTTFS RGFLQALGHQGNVKSPTYTLVEPYTLDNLMVYHFDLYRLADPEELEFMGI RDYFANDAICLVEWPQQGTGVLPDPDVEIHIDYQAQGREARVSAVSSAGE --------lllarlag >gi|7190852|gb|AAF39625.1|_1:154 (AE002349) conserved hypothetical protein [Chlamydia muridarum] MGRYRRVTDSCEETIDLAAKLGHLL-----IPGMVVLLSGDYGAGKTEFV RGIVQGFLGETavgQVASPSFSLLHVYEAMGRRVCHYDLYRLETMHVKSG EGLFQDAEEEDLICVEWPEV-VNLLPQFRKSVCVHMcllADSQREVVI-- --EVAEDCDLGFFMgkd >gi|6226431|sp|O05515|YDIB_BACSU_1:151 HYPOTHETICAL 17.9 KDA PROTEIN IN PHOB-GROES INTERGENIC REGIONgi|7450018|pir||C69786 conserved hypothetical protein ydiB - Bacillus subtilisgi|1945107|dbj|BAA19715.1| (D88802) E. coli hypothetical protein; P31805 (267) [Bacillus subtilis]gi|2632904|emb|CAB12410.1| (Z99107) similar to hypothetical proteins [Bacillus subtilis] MKQLKWRTVNPEETKAIAKLTAAFA-----KPGDVLTLEGDLGAGKTTFT KGFAEGLGITRIVNSPTFTIIKEYNDGVLPLYHMDVYRMED--ESEDLGL DEYFHGQGVCLVEWAHLIEEQLPQERLQIVIKRaGDDEREITFTAVGNRY EMLCEELS-rhdnisn >gi|7450025|pir||H71502_1:154 probable (ATPase or kinase) - Chlamydia trachomatis (serotype D, strain UW3/Cx)gi|3328975|gb|AAC68139.1| (AE001324) (ATPase or Kinase) [Chlamydia trachomatis] MGRYRRVTHSCEETIDLATRVGRDL-----TLGMVVLLSGDYGSGKTEFV RGIVQGFLGEAavdQVASPSFALLHVYEAGGRRVCHYDLYRLETMDIKNG ADLFQDAEEEDLICVEWPEA-VNLLPQFRKSVCVQMrslTDAQREVSI-- --GVTDSCDLSFFMend >gi|6226350|sp|P74415|Y257_SYNY3_4:149 HYPOTHETICAL 17.7 KDA PROTEIN SLL0257gi|7450017|pir||S76256 hypothetical protein - Synechocystis sp. (strain PCC 6803)gi|1653602|dbj|BAA18515.1| (D90914) hypothetical protein [Synechocystis sp.] mne-NSMEFFLPDLNATDQWGQQLAQQL-----PLGTIILLQGDLGAGKT SLVQGLGRGLGITGEIVSPTFTIVNEYREGKMPLYHLDLYRLNTL-EVEY LYPEQYWQGEdfplGITAVEWPER-LPQLPSQYLQIQLCHQGEGRSIALT AQDWAMD--------lkellpps >gi|6226403|sp|O83845|Y875_TREPA_1:134 HYPOTHETICAL PROTEIN TP0875gi|7450022|pir||A71271 conserved hypothetical protein TP0875 - syphilis spirochetegi|3323187|gb|AAC65838.1| (AE001257) conserved hypothetical protein [Treponema pallidum] ---MRCVSRSAQDTARWGTVVGRLL-----EEGSVVVLQGALAAGKTCFV KGLALGLGIQEEITSPTFTLLAVYH-GRLTLYHMDVYRLASLEDFFDIGA QECVYGTGVCVIEWGERVASELPEYTVTISLRVlADGNREITV------- ---------a >gi|7450019|pir||H72229_1:138 conserved hypothetical protein - Thermotoga maritima (strain MSB8)gi|4982205|gb|AAD36699.1|AE001806_9 (AE001806) conserved hypothetical protein [Thermotoga maritima] MRHLRFENLTEEQLKRLAKILTENL-----KGGEVVILSGNLGAGKTTFV KGMIRAIGLDEkMVKSPTFTLMNVYP-GLKTIYHLDLYRLQDTDFLSLDV EDILEDEDGIMVVEWGDLFDGFWPEDSIKVKIEIaDESHRNVEI------ ----------lipeevnflvekieryrkelqnt >gi|6226308|sp|Q9ZED0|Y013_RICPR_4:142 HYPOTHETICAL PROTEIN RP013gi|7450020|pir||F71708 hypothetical protein RP013 - Rickettsia prowazekiigi|3860584|emb|CAA14485.1| (AJ235270) unknown [Rickettsia prowazekii] mht-------LNSKKETKNFAKLFAQNL-----KPNDIVLLNGDLGAGKT FFCREIIKHFCGKNtNIISPTFNLLQIYKTPKFNIYHYDMYRIKSPEEIY ELGFEEALNGN-LILIEWSEIIKHLLTPPLIEVNLKVlDNNKRLCSIHKE NFLFD--------fl >gi|7471517|pir||E75283_10:145 conserved hypothetical protein - Deinococcus radiodurans (strain R1)gi|6460164|gb|AAF11897.1|AE002066_1 (AE002066) conserved hypothetical protein [Deinococcus radiodurans] maaqallsv--GERRLLRGVDEQRALGAALARAL-----APGSVLFLEGE LGAGKTTLTQGLLAALGFDGHVTSPTYALMQLYPASAGQVLHVDAYRVRD VAELYEMDLDELIAGSRLSVIEWGEGLYADYPQAPIYlfEHVEGDPETRR VT-----------------rrr >gi|6226476|sp|O52749|YJEE_ANASP_13:160 HYPOTHETICAL 17.9 KDA PROTEINgi|2896025|gb|AAC03104.1| (AF046871) unknown [Anabaena PCC7120] mtidqmtidqmt----KIFLADKESTLNLGILLGETL-----TAGSVILL EGDLGAGKTTLVQGLGKGLSITEPIVSPTFTLINEYTEGRIPLYHLDLYR LE-PQEVLSLNLEIYWEGIeiipGIVAIEWSER-MPYKPSTYINVLLTYg DEGSRQAEITPFNCTISDLIA----tk >gi|2496468|sp|Q49864|YY22_MYCLE_6:160 HYPOTHETICAL 17.6 KDA PROTEIN U229Fgi|2145802|pir||S72986 hypothetical protein B229_C2_205 - Mycobacterium lepraegi|467118|gb|AAA17300.1| (U00020) u229f; match to 16.9 kd E.coli protein in amiB region (yjeE); B229_C2_205 [Mycobacterium leprae] maeysLRSGAVICERVEDTVALGSRLGEQL-----RAGDVVVLSGPLGAG KTVLAKGIAVAMDVDGPVISPTYVLARVHlprRLGTPAMIHVDVYRLLDH RDADLVGELDSLDLDtdlaeAVVVMEWGAGLAECLAARHLDIRLERvrYS DVRIATWQWVCSRDR--------p >gi|6226477|sp|O86788|YJEE_STRCO_1:144 HYPOTHETICAL 15.8 KDA PROTEIN SC6G4.25gi|7480504|pir||T35576 probable ATP/GTP binding protein - Streptomyces coelicolorgi|3449259|emb|CAA20403.1| (AL031317) putative ATP /GTP binding protein [Streptomyces coelicolor A3(2)] -------------MRELGRRLAKLL-----RAGDLVMLSGELGAGKTTLT RGLGEGLGVRGAVTSPTFVIARVHPslGDGPPLVHVDAYRLSGGLDEMED LDLDVSLSDSVIVVEWGEGKVEELTEDRLRLRIDRavGDTADEVRHVTVT GLGERWATADVSvlag >gi|2496467|sp|Q50706|YY22_MYCTU_18:168 HYPOTHETICAL 18.2 KDA PROTEIN RV3422Cgi|7477616|pir||C70738 hypothetical protein Rv3422c - Mycobacterium tuberculosis (strain H37RV)gi|1449365|emb|CAB01034.1| (Z77165) hypothetical protein Rv3422c [Mycobacterium tuberculosis] msregirrrpkaraglt-GGGTATLPRVEDTLTLGSRLGEQL-----CAG DVVVLSGPLGAGKTVLAKGIAMAMDVEGPITSPTFVLARMHrprRPGTPA MVHVDVYRLLDHNSADLLSELDSLDLDtdledAVVVVEWGEGLAERLSQR HLDVRLERvsHSDTRIATW----SWGRS------- >gi|7450024|pir||B72052_1:138 yjee hypothetical protein - Chlamydia pneumoniae (strain CWL029)gi|4376956|gb|AAD18796.1| (AE001648) YjeE hypothetical protein [Chlamydophila pneumoniae]gi|7189025|gb|AAF37975.1| (AE002172) conserved hypothetical protein [Chlamydophila pneumoniae AR39] MGRYRRVSHSSQETLLLGTELGQVL-----VPGAVLLLFGDYGAGKTEFV RGIVSGYLGDTiaeEVASPSFSILHVYGNEPKRLCHYDLYRID---QKNQ EYIFQDAEEDDVLCIEWADR----LPKPRFCDTI-------NIYITMQTN MEREIII----ekr >gi|2801652|gb|AAB97417.1|_9:141 (AF042096) unknown [Bradyrhizobium japonicum] msapttfs-----VALHNETATAQLMADLALLV-----GPGDVITLTGDL GAGKTAAARAMIRYLADDEalEVPSPTFTLVQGYELPPFPVMHADLYRVE DESELEEIGCRRCSDAT-LVLIEWPERARRRCPR------IASTSHSPIV RLWARTHV----------pptspvtaraqprsrv >gi|6226340|sp|O51204|Y186_BORBU_1:135 HYPOTHETICAL PROTEIN BB0186gi|7450023|pir||B70123 conserved hypothetical protein BB0186 - Lyme disease spirochetegi|2688077|gb|AAC66574.1| (AE001129) conserved hypothetical protein [Borrelia burgdorferi] ---MILEFKSEKKMINFSKSFFYPL-----PIGKIFVLSGDMGSGKTSFL KGLALNLGISY-FTSPTYNIVNVYDFINFKFYHIDLYRVSSLEEFELVGG LEILmDLDSIIAIEWPQIALSIVPKDRLFsLTFKIVGSGRVVEL------ ----------ng >gi|6226401|sp|O67011|Y843_AQUAE_5:131 HYPOTHETICAL PROTEIN AQ_843gi|7450021|pir||H70372 conserved hypothetical protein aq_843 - Aquifex aeolicusgi|2983396|gb|AAC06981.1| (AE000710) hypothetical protein [Aquifex aeolicus] mell---KEVILESEEDTYKLAEEIAQLL-----KGSEVICLRGTLGAGK TTFVKALAKALKVKNpsAVRSPTFTLVNEYETDKGKLIHIDLYRVPDFDY SEFIG-------EGILAVEWEER----DKPCDIILEIEIlDENKRKVRIY ---------------rk >gi|7464783|pir||H71905_7:130 hypothetical protein jhp0654 - Helicobacter pylori (strain J99)gi|4155206|gb|AAD06230.1| (AE001497) putative [Helicobacter pylori J99] mranld---------------ELDKVAAAILKD---DFKGVVLLKGVVGS GKTTLVQACLKHLGLDIQATSPTFSLMHAYS---ESVFHYDFY-MRDLET CLELGMLECLLEKGIHFVEWGdEKLEKILKKYDLAIKVVEiktESTSRFY TI----------------kia >gi|6968130|emb|CAB72945.1|_4:134 (AL139076) putative ATP /GTP-binding protein [Campylobacter jejuni] mke----FILAKNEIKTML------QIM-----PKEGVVLLQGDLASGKT SLVQAWVKFLGLDVRVDSPTFSTMQKYENHDICIYHYDIY-QEGLEGLLA NGLFENFFEKGLHLVEWGgENLKKTLMKFGIStiqIKISIKDDKRKYEIY ---------------e >gi|7463982|pir||D64609_7:130 conserved hypothetical protein HP0716 - Helicobacter pylori (strain 26695)gi|2313840|gb|AAD07766.1| (AE000584) conserved hypothetical protein [Helicobacter pylori 26695] mranld---------------ELDKVAAAILKD---DFKGVVLLKGVVGS GKTTLVQACLKHLGLDIQATSPTFSLMHAYS---ESVFHYDFY-MHDLKA CLELGMLECLLEKGIHFVEWGdEKLEKILKKYDLAIKVVEvktESTSRFY TI----------------kia >gi|2828193|sp|P30621|MOXR_METEX_14:120 MOXR PROTEIN (MXAR PROTEIN)gi|1771259|emb|CAA69191.1| (Y07864) mxaR [Methylobacterium extorquens] mntlrpgdamltdWRDAAARFEREIAKAVVGQDRAIRLLTIAIFARGHVM LEGDVGVGKTTLLRAVARGLGGAY-------------------------- -------------------------ERVEGTVDMMPTDLIYHTYLGEDGR PRVEPGPVLRRAEDLSVFFFNeinrarpqvhalllrimaersvsafnrey rfpnlqvfadrnrvereetfe >gi|2589001|dbj|BAA23276.1|_23:129 (AB004097) ORF4 [Hyphomicrobium methylovorum] mnrpvvgreqdaaesdrmdlkdWRARALEFEGEVGRAIVGQERAIRLLVI AVFARGHVLLEGDVGVGKTTLLRAVAHALGGSY----------------- ----------------------------------ERVEGTIDLMPSDMIY YTFLNEDGKPRVEPGPVLRHGSDLSVFFFNeinrarpqvhslllrlmaer sitafntehffphvlvfadrnriereetfe >gi|266551|sp|P29901|MOXR_PARDE_8:114 MOXR PROTEINgi|94691|pir||D41377 moxR protein - Paracoccus denitrificans mdsnisdWHARFRDAEAALNGVVLGQARTIRLLLISALCRGHVLLAGDVG TGKTTLLRAMARALGGPY-------------------------------- -------------------GRVEGTVDLLPTDLIYSTHIAEDGRPRIEPG PVLEQGEDMAVFFFNeinrarpqvhalllrlmaerslsafrreyrfphlq vfadrnqierdetfe >gi|2370245|emb|CAA73635.1|_204:237 (Y13183) thymidine kinase [Saimiriine herpesvirus 2] kkgsfvkigsnmlefgeslksklhndskkspdepdglvhvpvhllyppmh ----------------------QEL-----VPAFFIFLEGSIGVGKTTLL KSMNGILGGKN--------------------------------------- -------------------------------------------------- --------vlafhepiaywtdvfsnsleevykltlpakvgrtsnsaklla cqlkfasp >gi|4019247|gb|AAC95545.1|_207:237 (AF083424) thymidine kinase [Ateline herpesvirus 3] sfvkigsnvlefggsiksklhnsckksvdspdglvhvpvhvlypplhqep ------------------------------IPAFFIFLEGSIGVGKTTLL KSMRGILPGKN--------------------------------------- -------------------------------------------------- --------vltfhepmafwknvfsnsldevykltlpakvgsmtnssklla cqlkfaap >gi|1147800|gb|AAA85134.1|_210:255 (U43720) Sug2p [Saccharomyces cerevisiae] pretdplvynmtsfeqgeitfdgigglteqirelrevielplknpeifqr ---------------------------VGIKPPKGVLLYGPPGTGKTLLA KAVAATIGANF-IFSPASGIVDKY-------------------------- -------------------------------------------------- --------igesariiremfayakehepciifmdevdaiggrrfsegtsa dreiqrtl >gi|6324833|ref|NP_014902.1|_210:255 ATPase; component of the 26S proteasome cap subunit; Rpt4pgi|2506090|sp|P53549|SUG2_YEAST PROBABLE 26S PROTEASE SUBUNIT SUG2 (PROTEASOMAL CAP SUBUNIT)gi|2133163|pir||S67156 26S proteasome regulatory particle chain RPT4 - yeast (Saccharomyces cerevisiae)gi|1420585|emb|CAA99481.1| (Z75167) ORF YOR259c [Saccharomyces cerevisiae]gi|1931623|gb|AAB51594.1| (U93262) proteasome cap subunit [Saccharomyces cerevisiae] pretdplvynmtsfeqgeitfdgigglteqirelrevielplknpeifqr ---------------------------VGIKPPKGVLLYGPPGTGKTLLA KAVAATIGANF-IFSPASGIVDKY-------------------------- -------------------------------------------------- --------igesariiremfayakehepciifmdevdaiggrrfsegtsa dreiqrtl --simple mime boundary-- From farmer@cse.ucsc.edu Tue Jun 27 22:19:41 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 WAA04967 for Message-Id: <200006272024.NAA10345@beta.cse.ucsc.edu> Subject: T0104(database hits) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0104.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-962133418.t99dbhits.txt" The E-value is an estimate of approximately how many sequences would score this well by chance in the database searched. For SAM-T99, E-values less than about 0.01 are roughly equivalent, as sequences that score that well have most likely already been included in the SAM-T99 multiple alignment. Database: PDB Score method: average Summary of Database Hits: Average Target Template SeqID Reverse EValue Reverse EValue Reverse EValue SeqLabel 5p21 -16.36 0.001775 --------- --------- -16.36 0.0018 1ctqA -16.32 0.001847 --------- --------- -16.32 0.0018 2cmkA -14.47 0.01175 -14.47 0.012 --------- --------- : mol:protein length:227 Cytidine Monophosphate Kinase 1kao -14.22 0.01508 --------- --------- -14.22 0.015 3rabA -13.71 0.02512 --------- --------- -13.71 0.025 3tmkA -13.56 0.02918 --------- --------- -13.56 0.029 1ek0A -13.04 0.04909 --------- --------- -13.04 0.049 1hurA -12.67 0.07107 --------- --------- -12.67 0.071 1mh1 -12.45 0.08856 --------- --------- -12.45 0.089 1ckeA -12.44 0.08989 -14.49 0.012 -10.38 0.7 : mol:protein length:227 Cytidine Monophosphate Kinase 5tmp -12.42 0.09125 --------- --------- -12.42 0.091 1skyE -12.22 0.1115 -12.22 0.11 --------- --------- : mol:protein length:473 F1-Atpase 1do0A -12.16 0.1183 -12.16 0.12 --------- --------- : mol:protein length:442 Heat Shock Locus U 1do0B -12.16 0.1183 -12.16 0.12 --------- --------- : mol:protein length:442 Heat Shock Locus U 1do0C -12.16 0.1183 -12.16 0.12 --------- --------- : mol:protein length:442 Heat Shock Locus U 1do0D -12.16 0.1183 -12.16 0.12 --------- --------- : mol:protein length:442 Heat Shock Locus U 1do0E -12.16 0.1183 -12.16 0.12 --------- --------- : mol:protein length:442 Heat Shock Locus U 1do0F -12.16 0.1183 -12.16 0.12 --------- --------- : mol:protein length:442 Heat Shock Locus U 1do2A -12.16 0.1183 -12.16 0.12 --------- --------- : mol:protein length:442 Heat Shock Locus U 1do2B -12.16 0.1183 -12.16 0.12 --------- --------- : mol:protein length:442 Heat Shock Locus U --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-962133418.t99pairwise.a2m' Content-Disposition: attachment; filename="t99-results-962133418.t99pairwise.a2m" >T0104 mesltqyipdefsmlrfgkkfaeillklhtEKAIMVYLNGDLGAGKTTLT RGMLQGIGHQGNVKSPTYTLVEEyNIAGKMIYHFDLYRLADPEELEFMGI RDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTN--- -----------------------------------------------lgk niisafsn >5p21 mol:protein length:166 c-H-Ras p21 Protein (Amino Acids 1 - 166) Co MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGET CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQI KRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQ GVEDAFYTLVREIRQH >T0104 mesltqyipdefsmlrfgkkfaeillklhtek--AIMVYLNGDLGAGKTT LTRGMLQ-gighqgnvksptyt-LVEEYNIAGKMIYHFDL--------YR LADPE-ELEFMGIRDYFnt-----------------DSICLIEWSEKGQG ILPE-ADILVNID---y------YDDARNIELIAQTNLGKNIISA----F SN------------- >1ctqA mol:protein length:166 Transforming Protein P21/H-Ras-1 MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGET CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQI KRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQ GVEDAFYTLVREIRQH >T0104 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLT RGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGI RDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGK NIISAFSN >2cmkA mol:protein length:227 Cytidine Monophosphate Kinase mtaiap----------------------------------VITIDGPSGA GKGTLCKAMAEALQW----------------------------------- -------------------------------------------------- --------------hlldsgaiyrvlalaalhhhvdvasedalvplashl dvrfvstngnlevilegedvsgeirtqevanaasqvaafprvreallrrq rafrelpgliadgrdmgtvvfpdapvkifldasseerahrrmlqlqekgf svnferllaeikerddrdrnravaplvpaadalvldsttlsieqviekal qyarqklala >T0104 mesltqyipdefsmlrfgkkfaeillklhte-KAIMVYLNGDLGAGKTTL TRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMiYHFDLYRLADPEELEFMG IRDYFNTDSICLI------------------------------------- -------------------------------------------------e wsekgqgilpeadilvnidyyddarnieliaqtnlgkniisafsn >1kao mol:protein length:167 Rap2A MREYKVVVLGSGGVGKSALTVQFVTGTFIEKYDPTIEDFYRKEIEVDSSP SVLEILDTAGTEQFASMRDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQI IRVKRYEKVPVILVGNKVDLESEREVSSSEGRALAEEWGCPFMETSAKSK TMVDELFAEIVRQM---nya >T0104 mesltqyipdefsmlrfgkkfaeillklhtekaim-------VYLNGDLG AGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPE ELEFMGIRDYFNTDSICLI------------------------------- -------------------------------------------------- ----ewsekgqgilpeadilvnidyyddarnieliaqtnlgkniisafsn >3rabA mol:protein length:169 Rab3A NFDYMFKILIIGNSSVGKTSFLFRYADDSFTPAFVSTVGIDFKVKTIYRN DKRIKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWS TQIKTYSWDNAQVLLVGNKCDMEDERVVSSERGRQLADHLGFEFFEASAK DNINVKQTFERLVDVICEK >T0104 MESLtqyipdefsmlrfgkkfaeillklhtekAIMVYLNGDLGAGKTTLT RGMLQGIG-HQGNVKSPTYTLV------EEYNIAGKMIYHFDLYRLADPE ELEFM-GIRDYFNTDSICLIEWSEKGQG----i----------------- -LPEADILVNIDYYDDa--------RNIELIAQTNLGKNIISAF------ -sn--------------------------------------------- >3tmkA mol:protein length:216 Thymidylate Kinase MMGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLIN EYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGV AYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDER YETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIV EPVLSTHIDHDKFSFF >T0104 mesltqyipdefsmlrfgkkfaeillklhtekaim-----VYLNGDLGAG KTTLTRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEEL EFMGIRDYFNTDSICLI--------------------------------- -------------------------------------------------- -----ewsekgqgilpeadilvnidyyddarnieliaqtnlgkniisafs n >1ek0A mol:protein-het length:170 Gtp-Binding Protein Ypt51 vts---IKLVLLGEAAVGKSSIVLRFVSNDFAENKEPTIGAAFLTQRVTI NEHTVKFEIWDTAGQERFASLAPXYYRNAQAALVVYDVTKPQSFIKARHW VKELHEQASKDIIIALVGNKIDXLQEGGERKVAREEGEKLAEEKGLLFFE TSAKTGENVNDVFLGIGEKI---plk >T0104 mesltqyipdefsmlrfGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLT RGMLQGighQGNVKSPTYTLVEEYNIAGkmiyHFDLYRLADPEELEFMGI RDYFNTDSICLIEWSE-----KGQGILPEADILVNIDYYDDAR------- -------NIELIAQTN-LGKN--------IISAFSN-------------- ---- >1hurA mol:protein length:180 Molecule: Human Adp-Ribosylation Factor 1; S GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGF NVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVN EAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHR NWYIQATCATSGDGLYEGLDWLSNQLRNQK >T0104 mesltqyipdefsmlrfgkkfaeillklhte---KAIMVYLNGDLGAGKT TLTRGMLQGighqgnvksptyt-LVEEYNIAGKMIYHFDL--------YR LADPEELE--FMGIRDYF-------------NTDSICL-I-EWSEKGQGI LPEADILVNI-----d----------------------YYDDARNIEL-- --------IAQTNLGKNIISAFSN---- >1mh1 mol:protein length:186 Rac1 GSPQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDG KPVNLGLWDTAGQEDYDRLRPLSYPQTDVSLICFSLVSPASFENVRAKWY PEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKE IGAVKYLECSALTQRGLKTVFDEAIRAVLCPPPvkk >T0104 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLT RGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGI RDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGK NIISAFSN >1ckeA mol:protein length:227 Cytidine Monophosphate Kinase mtaiap----------------------------------VITIDGPSGA GKGTLCKAMAEALQW----------------------------------- -------------------------------------------------- --------------hlldsgaiyrvlalaalhhhvdvasedalvplashl dvrfvstngnlevilegedvsgeirtqevanaasqvaafprvreallrrq rafrelpgliadgrdmgtvvfpdapvkifldasseerahrrmlqlqvkgf svnferllaeikerddrdrnravaplvpaadalvldsttlsieqviekal qyarqklala >T0104 mesltqyipdefsmlrfgkkfaeillklhteKAIMVYLNGDLGAGKTTLT RGMLQGIGHQGN---------VKSPTYTLVEEYNIAGkmIYHFDLYRLAD PEELEFMGIR---------------------------------------- -------------------------------------------------- -------------------------------------------dyfntds icliewsekgqgilpeadilvnidyyddarnieliaqtnlgkniisafsn >5tmp mRSKYIVIEGLEGAGKTTARNVVVETLEQLGIRDMVFTREPGGTQLAEKL RSLVLDIKSVGDEVITDKAEVLMFYAARVQLVETVIKPALANGTWVIGDR HDLSTQAYQGGGRGIDQHMLATLRDAVLGDFRPDLTLYLDVTPEVGLKRA RARGELDRIEQESFDFFNRTRARYLELAAQDKSIHTIDATQPLEAVMDAI RTTVTHWVKELda >T0104 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLT RGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGI RDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGK NIISAFSN >1skyE mol:protein length:473 F1-Atpase mtrgrviqvmgpvvdvkfenghlpaiynalkiqhkarnenevdidltlev alhlgddtvrtiamastdglirgmevidtgapisvpvgqvtlgrvfnvlg epidlegdipadarrdpihrpapkfe------ELATEVEILETGIKVVDL L--APYIKGGKIGLFGGAGVGKTVLIQELIHNIAQEHGGIS--------- -------------------------------------------------- ----------------------------------vfagvgertregndly hemkdsgvisktamvfgqmneppgarmrvaltgltmaeyfrdeqgqdgll fidnifrftqagsevsallgrmpsaigyqptlatemgqlqeritstakgs itsiqaiyvpaddytdpapattfshldattnlerklaemgiypavdplvs tsralapeivgeehyqvarkvqqtlerykelqdiiailgmdelsdedklv vhrarriqfflsqnfhvaeqftgqpgsyvpvketvrgfkeilegkydhlp edrfrlvgrieevvekakamgvev >T0104 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLT RGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGI RDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGK NIISAFSN >1do0A mol:protein length:442 Heat Shock Locus U semtpreivseldkhiigqdnak-RSVAIALRNRWRRMQLNEELRHEV-- ----TPKNILMIGPTGVGKTEIARRLAK---------------------- -------------------------------------------------- -------------------------------lanapfikveatkftevgy vgkevdsiirdltdaavkmvrvqaieknryraeelaeerildvlippakn nwgqteqqqepsaarqafrkklregqlddkeieidlaaapmgveimappg meemtsqlqsmfqnlggqkqkarklkikdamkllieeeaaklvnpeelkq daidaveqhgivfideidkickrgessgpdvsregvqrdllplvegctvs tkhgmvktdhilfiasgafqiakpsdlipelqgrlpirvelqalttsdfe riltepnasitvqykalmategvnieftdsgikriaeaawqvnestenig arrlhtvlerlmeeisydasdlsgqnitidadyvskhldalvadedlsrf il >T0104 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLT RGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGI RDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGK NIISAFSN >1do0B mol:protein length:442 Heat Shock Locus U semtpreivseldkhiigqdnak-RSVAIALRNRWRRMQLNEELRHEV-- ----TPKNILMIGPTGVGKTEIARRLAK---------------------- -------------------------------------------------- -------------------------------lanapfikveatkftevgy vgkevdsiirdltdaavkmvrvqaieknryraeelaeerildvlippakn nwgqteqqqepsaarqafrkklregqlddkeieidlaaapmgveimappg meemtsqlqsmfqnlggqkqkarklkikdamkllieeeaaklvnpeelkq daidaveqhgivfideidkickrgessgpdvsregvqrdllplvegctvs tkhgmvktdhilfiasgafqiakpsdlipelqgrlpirvelqalttsdfe riltepnasitvqykalmategvnieftdsgikriaeaawqvnestenig arrlhtvlerlmeeisydasdlsgqnitidadyvskhldalvadedlsrf il >T0104 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLT RGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGI RDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGK NIISAFSN >1do0C mol:protein length:442 Heat Shock Locus U semtpreivseldkhiigqdnak-RSVAIALRNRWRRMQLNEELRHEV-- ----TPKNILMIGPTGVGKTEIARRLAK---------------------- -------------------------------------------------- -------------------------------lanapfikveatkftevgy vgkevdsiirdltdaavkmvrvqaieknryraeelaeerildvlippakn nwgqteqqqepsaarqafrkklregqlddkeieidlaaapmgveimappg meemtsqlqsmfqnlggqkqkarklkikdamkllieeeaaklvnpeelkq daidaveqhgivfideidkickrgessgpdvsregvqrdllplvegctvs tkhgmvktdhilfiasgafqiakpsdlipelqgrlpirvelqalttsdfe riltepnasitvqykalmategvnieftdsgikriaeaawqvnestenig arrlhtvlerlmeeisydasdlsgqnitidadyvskhldalvadedlsrf il >T0104 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLT RGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGI RDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGK NIISAFSN >1do0D mol:protein length:442 Heat Shock Locus U semtpreivseldkhiigqdnak-RSVAIALRNRWRRMQLNEELRHEV-- ----TPKNILMIGPTGVGKTEIARRLAK---------------------- -------------------------------------------------- -------------------------------lanapfikveatkftevgy vgkevdsiirdltdaavkmvrvqaieknryraeelaeerildvlippakn nwgqteqqqepsaarqafrkklregqlddkeieidlaaapmgveimappg meemtsqlqsmfqnlggqkqkarklkikdamkllieeeaaklvnpeelkq daidaveqhgivfideidkickrgessgpdvsregvqrdllplvegctvs tkhgmvktdhilfiasgafqiakpsdlipelqgrlpirvelqalttsdfe riltepnasitvqykalmategvnieftdsgikriaeaawqvnestenig arrlhtvlerlmeeisydasdlsgqnitidadyvskhldalvadedlsrf il >T0104 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLT RGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGI RDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGK NIISAFSN >1do0E mol:protein length:442 Heat Shock Locus U semtpreivseldkhiigqdnak-RSVAIALRNRWRRMQLNEELRHEV-- ----TPKNILMIGPTGVGKTEIARRLAK---------------------- -------------------------------------------------- -------------------------------lanapfikveatkftevgy vgkevdsiirdltdaavkmvrvqaieknryraeelaeerildvlippakn nwgqteqqqepsaarqafrkklregqlddkeieidlaaapmgveimappg meemtsqlqsmfqnlggqkqkarklkikdamkllieeeaaklvnpeelkq daidaveqhgivfideidkickrgessgpdvsregvqrdllplvegctvs tkhgmvktdhilfiasgafqiakpsdlipelqgrlpirvelqalttsdfe riltepnasitvqykalmategvnieftdsgikriaeaawqvnestenig arrlhtvlerlmeeisydasdlsgqnitidadyvskhldalvadedlsrf il >T0104 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLT RGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGI RDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGK NIISAFSN >1do0F mol:protein length:442 Heat Shock Locus U semtpreivseldkhiigqdnak-RSVAIALRNRWRRMQLNEELRHEV-- ----TPKNILMIGPTGVGKTEIARRLAK---------------------- -------------------------------------------------- -------------------------------lanapfikveatkftevgy vgkevdsiirdltdaavkmvrvqaieknryraeelaeerildvlippakn nwgqteqqqepsaarqafrkklregqlddkeieidlaaapmgveimappg meemtsqlqsmfqnlggqkqkarklkikdamkllieeeaaklvnpeelkq daidaveqhgivfideidkickrgessgpdvsregvqrdllplvegctvs tkhgmvktdhilfiasgafqiakpsdlipelqgrlpirvelqalttsdfe riltepnasitvqykalmategvnieftdsgikriaeaawqvnestenig arrlhtvlerlmeeisydasdlsgqnitidadyvskhldalvadedlsrf il >T0104 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLT RGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGI RDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGK NIISAFSN >1do2A mol:protein length:442 Heat Shock Locus U semtpreivseldkhiigqdnak-RSVAIALRNRWRRMQLNEELRHEV-- ----TPKNILMIGPTGVGKTEIARRLAK---------------------- -------------------------------------------------- -------------------------------lanapfikveatkftevgy vgkevdsiirdltdaavkmvrvqaieknryraeelaeerildvlippakn nwgqteqqqepsaarqafrkklregqlddkeieidlaaapmgveimappg meemtsqlqsmfqnlggqkqkarklkikdamkllieeeaaklvnpeelkq daidaveqhgivfideidkickrgessgpdvsregvqrdllplvegctvs tkhgmvktdhilfiasgafqiakpsdlipelqgrlpirvelqalttsdfe riltepnasitvqykalmategvnieftdsgikriaeaawqvnestenig arrlhtvlerlmeeisydasdlsgqnitidadyvskhldalvadedlsrf il >T0104 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLT RGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGI RDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGK NIISAFSN >1do2B mol:protein length:442 Heat Shock Locus U semtpreivseldkhiigqdnak-RSVAIALRNRWRRMQLNEELRHEV-- ----TPKNILMIGPTGVGKTEIARRLAK---------------------- -------------------------------------------------- -------------------------------lanapfikveatkftevgy vgkevdsiirdltdaavkmvrvqaieknryraeelaeerildvlippakn nwgqteqqqepsaarqafrkklregqlddkeieidlaaapmgveimappg meemtsqlqsmfqnlggqkqkarklkikdamkllieeeaaklvnpeelkq daidaveqhgivfideidkickrgessgpdvsregvqrdllplvegctvs tkhgmvktdhilfiasgafqiakpsdlipelqgrlpirvelqalttsdfe riltepnasitvqykalmategvnieftdsgikriaeaawqvnestenig arrlhtvlerlmeeisydasdlsgqnitidadyvskhldalvadedlsrf il --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-962133418.t99pairwise.casp.al' Content-Disposition: attachment; filename="t99-results-962133418.t99pairwise.casp.al" PFRMAT AL TARGET T0104 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 5p21 E 31 M 1 K 32 T 2 A 33 E 3 I 34 Y 4 M 35 K 5 V 36 L 6 Y 37 V 7 L 38 V 8 N 39 V 9 G 40 G 10 D 41 A 11 L 42 G 12 G 43 G 13 A 44 V 14 G 45 G 15 K 46 K 16 T 47 S 17 T 48 A 18 L 49 L 19 T 50 T 20 R 51 I 21 G 52 Q 22 M 53 L 23 L 54 I 24 Q 55 Q 25 G 56 N 26 I 57 H 27 G 58 F 28 H 59 V 29 Q 60 D 30 G 61 E 31 N 62 Y 32 V 63 D 33 K 64 P 34 S 65 T 35 P 66 I 36 T 67 E 37 Y 68 D 38 T 69 S 39 L 70 Y 40 V 71 R 41 E 72 K 42 E 73 Q 43 N 75 V 44 I 76 V 45 A 77 I 46 G 78 D 47 K 79 G 48 M 80 E 49 I 81 T 50 Y 82 C 51 H 83 L 52 F 84 L 53 D 85 D 54 L 86 I 55 Y 87 L 56 R 88 D 57 L 89 T 58 A 90 A 59 D 91 G 60 P 92 Q 61 E 93 E 62 E 94 E 63 L 95 Y 64 E 96 S 65 F 97 A 66 M 98 M 67 G 99 R 68 I 100 D 69 R 101 Q 70 D 102 Y 71 Y 103 M 72 F 104 R 73 N 105 T 74 T 106 G 75 D 107 E 76 S 108 G 77 I 109 F 78 C 110 L 79 L 111 C 80 I 112 V 81 E 113 F 82 W 114 A 83 S 115 I 84 E 116 N 85 K 117 N 86 G 118 T 87 Q 119 K 88 G 120 S 89 I 121 F 90 L 122 E 91 P 123 D 92 E 124 I 93 A 125 H 94 D 126 Q 95 I 127 Y 96 L 128 R 97 V 129 E 98 N 130 Q 99 I 131 I 100 D 132 K 101 Y 133 R 102 Y 134 V 103 D 135 K 104 D 136 D 105 A 137 S 106 R 138 D 107 N 139 D 108 I 140 V 109 E 141 P 110 L 142 M 111 I 143 V 112 A 144 L 113 Q 145 V 114 T 146 G 115 N 147 N 116 TER END PFRMAT AL TARGET T0104 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 1ctq_A A 33 E 3 I 34 Y 4 M 35 K 5 V 36 L 6 Y 37 V 7 L 38 V 8 N 39 V 9 G 40 G 10 D 41 A 11 L 42 G 12 G 43 G 13 A 44 V 14 G 45 G 15 K 46 K 16 T 47 S 17 T 48 A 18 L 49 L 19 T 50 T 20 R 51 I 21 G 52 Q 22 M 53 L 23 L 54 I 24 Q 55 Q 25 L 70 F 28 V 71 V 29 E 72 D 30 E 73 E 31 Y 74 Y 32 N 75 D 33 I 76 P 34 A 77 T 35 G 78 I 36 K 79 E 37 M 80 D 38 I 81 S 39 Y 82 Y 40 H 83 R 41 F 84 K 42 D 85 Q 43 L 86 V 44 Y 87 L 53 R 88 D 54 L 89 I 55 A 90 L 56 D 91 D 57 P 92 T 58 E 93 A 59 E 94 Q 61 L 95 E 62 E 96 E 63 F 97 Y 64 M 98 S 65 G 99 A 66 I 100 M 67 R 101 R 68 D 102 D 69 Y 103 Q 70 F 104 Y 71 D 107 S 89 S 108 F 90 I 109 E 91 C 110 D 92 L 111 I 93 I 112 H 94 E 113 Q 95 W 114 Y 96 S 115 R 97 E 116 E 98 K 117 Q 99 G 118 I 100 Q 119 K 101 G 120 R 102 I 121 V 103 L 122 K 104 P 123 D 105 E 124 S 106 A 125 D 108 D 126 V 109 I 127 P 110 L 128 M 111 V 129 V 112 N 130 L 113 I 131 V 114 D 132 G 115 Y 134 V 125 D 135 E 126 D 136 S 127 A 137 R 128 R 138 Q 129 N 139 A 130 I 140 Q 131 E 141 D 132 L 142 L 133 I 143 A 134 A 144 R 135 Q 145 S 136 T 146 Y 137 N 147 G 138 L 148 I 139 G 149 P 140 K 150 Y 141 N 151 I 142 I 152 E 143 I 153 T 144 S 154 S 145 A 155 A 146 F 156 G 151 S 157 V 152 N 158 E 153 TER END PFRMAT AL TARGET T0104 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 M 35 V 7 V 36 I 8 Y 37 T 9 L 38 I 10 N 39 D 11 G 40 G 12 D 41 P 13 L 42 S 14 G 43 G 15 A 44 A 16 G 45 G 17 K 46 K 18 T 47 G 19 T 48 T 20 L 49 L 21 T 50 C 22 R 51 K 23 G 52 A 24 M 53 M 25 L 54 A 26 Q 55 E 27 G 56 A 28 I 57 L 29 G 58 Q 30 H 59 W 31 TER END PFRMAT AL TARGET T0104 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 1kao K 32 R 2 A 33 E 3 I 34 Y 4 M 35 K 5 V 36 V 6 Y 37 V 7 L 38 V 8 N 39 L 9 G 40 G 10 D 41 S 11 L 42 G 12 G 43 G 13 A 44 V 14 G 45 G 15 K 46 K 16 T 47 S 17 T 48 A 18 L 49 L 19 T 50 T 20 R 51 V 21 G 52 Q 22 M 53 F 23 L 54 V 24 Q 55 T 25 G 56 G 26 I 57 T 27 G 58 F 28 H 59 I 29 Q 60 E 30 G 61 K 31 N 62 Y 32 V 63 D 33 K 64 P 34 S 65 T 35 P 66 I 36 T 67 E 37 Y 68 D 38 T 69 F 39 L 70 Y 40 V 71 R 41 E 72 K 42 E 73 E 43 Y 74 I 44 N 75 E 45 I 76 V 46 A 77 D 47 G 78 S 48 K 79 S 49 M 80 P 50 Y 82 S 51 H 83 V 52 F 84 L 53 D 85 E 54 L 86 I 55 Y 87 L 56 R 88 D 57 L 89 T 58 A 90 A 59 D 91 G 60 P 92 T 61 E 93 E 62 E 94 Q 63 L 95 F 64 E 96 A 65 F 97 S 66 M 98 M 67 G 99 R 68 I 100 D 69 R 101 L 70 D 102 Y 71 Y 103 I 72 F 104 K 73 N 105 N 74 T 106 G 75 D 107 Q 76 S 108 G 77 I 109 F 78 C 110 I 79 L 111 L 80 I 112 V 81 TER END PFRMAT AL TARGET T0104 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 3rab_A V 36 I 25 Y 37 L 26 L 38 I 27 N 39 I 28 G 40 G 29 D 41 N 30 L 42 S 31 G 43 S 32 A 44 V 33 G 45 G 34 K 46 K 35 T 47 T 36 T 48 S 37 L 49 F 38 T 50 L 39 R 51 F 40 G 52 R 41 M 53 Y 42 L 54 A 43 Q 55 D 44 G 56 D 45 I 57 S 46 G 58 F 47 H 59 T 48 Q 60 P 49 G 61 A 50 N 62 F 51 V 63 V 52 K 64 S 53 S 65 T 54 P 66 V 55 T 67 G 56 Y 68 I 57 T 69 D 58 L 70 F 59 V 71 K 60 E 72 V 61 E 73 K 62 Y 74 T 63 N 75 I 64 I 76 Y 65 A 77 R 66 G 78 N 67 K 79 D 68 M 80 K 69 I 81 R 70 Y 82 I 71 H 83 K 72 F 84 L 73 D 85 Q 74 L 86 I 75 Y 87 W 76 R 88 D 77 L 89 T 78 A 90 A 79 D 91 G 80 P 92 Q 81 E 93 E 82 E 94 R 83 L 95 Y 84 E 96 R 85 F 97 T 86 M 98 I 87 G 99 T 88 I 100 T 89 R 101 A 90 D 102 Y 91 Y 103 Y 92 F 104 R 93 N 105 G 94 T 106 A 95 D 107 M 96 S 108 G 97 I 109 F 98 C 110 I 99 L 111 L 100 I 112 M 101 TER END PFRMAT AL TARGET T0104 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 E 2 M 2 S 3 G 3 L 4 R 4 A 33 G 5 I 34 K 6 M 35 L 7 V 36 I 8 Y 37 L 9 L 38 I 10 N 39 E 11 G 40 G 12 D 41 L 13 L 42 D 14 G 43 R 15 A 44 T 16 G 45 G 17 K 46 K 18 T 47 T 19 T 48 T 20 L 49 Q 21 T 50 C 22 R 51 N 23 G 52 I 24 M 53 L 25 L 54 Y 26 Q 55 K 27 G 56 K 28 I 57 L 29 G 58 Q 30 H 59 N 32 Q 60 C 33 G 61 K 34 N 62 L 35 V 63 L 36 K 64 K 37 S 65 F 38 P 66 P 39 T 67 E 40 Y 68 R 41 T 69 S 42 L 70 T 43 V 71 R 44 E 72 E 51 E 73 Y 52 Y 74 L 53 N 75 T 54 I 76 D 55 A 77 D 56 G 78 S 57 K 79 F 58 M 80 Q 59 I 81 L 60 Y 82 S 61 H 83 D 62 F 84 Q 63 D 85 A 64 L 86 I 65 Y 87 H 66 R 88 L 67 L 89 L 68 A 90 F 69 D 91 S 70 P 92 A 71 E 93 N 72 E 94 R 73 L 95 W 74 E 96 E 75 F 97 I 76 M 98 V 77 G 99 K 79 I 100 I 80 R 101 K 81 D 102 K 82 Y 103 D 83 F 104 L 84 N 105 L 85 T 106 E 86 D 107 G 87 S 108 K 88 I 109 N 89 C 110 I 90 L 111 V 91 I 112 M 92 E 113 D 93 W 114 R 94 S 115 Y 95 E 116 V 96 K 117 Y 97 G 118 S 98 Q 119 G 99 G 120 V 100 L 122 L 123 P 123 L 124 E 124 K 125 A 125 P 126 D 126 D 127 I 127 L 128 L 128 T 129 V 129 L 130 N 130 F 131 I 131 L 132 D 132 S 133 Y 133 T 134 Y 134 Q 135 D 135 D 136 D 136 V 137 R 138 F 146 N 139 G 147 I 140 D 148 E 141 E 149 L 142 R 150 I 143 Y 151 A 144 E 152 Q 145 T 153 T 146 V 154 N 147 K 155 L 148 F 156 G 149 Q 157 K 150 E 158 N 151 K 159 I 152 V 160 I 153 K 161 S 154 Q 162 A 155 T 163 F 156 F 164 TER END PFRMAT AL TARGET T0104 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 1ek0_A V 36 L 10 Y 37 V 11 L 38 L 12 N 39 L 13 G 40 G 14 D 41 E 15 L 42 A 16 G 43 A 17 A 44 V 18 G 45 G 19 K 46 K 20 T 47 S 21 T 48 S 22 L 49 I 23 T 50 V 24 R 51 L 25 G 52 R 26 M 53 F 27 L 54 V 28 Q 55 S 29 G 56 N 30 I 57 D 31 G 58 F 32 H 59 A 33 Q 60 E 34 G 61 N 35 N 62 K 36 V 63 E 37 K 64 P 38 S 65 T 39 P 66 I 40 T 67 G 41 Y 68 A 42 T 69 A 43 L 70 F 44 V 71 L 45 E 72 T 46 E 73 Q 47 Y 74 R 48 N 75 V 49 I 76 T 50 A 77 I 51 G 78 N 52 K 79 E 53 M 80 H 54 I 81 T 55 Y 82 V 56 H 83 K 57 F 84 F 58 D 85 E 59 L 86 I 60 Y 87 W 61 R 88 D 62 L 89 T 63 A 90 A 64 D 91 G 65 P 92 Q 66 E 93 E 67 E 94 R 68 L 95 F 69 E 96 A 70 F 97 S 71 M 98 L 72 G 99 A 73 I 100 P 74 R 101 X 75 D 102 Y 76 Y 103 Y 77 F 104 R 78 N 105 N 79 T 106 A 80 D 107 Q 81 S 108 A 82 I 109 A 83 C 110 L 84 L 111 V 85 I 112 V 86 TER END PFRMAT AL TARGET T0104 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 1hur_A G 18 G 2 K 19 N 3 K 20 I 4 F 21 F 5 A 22 A 6 E 23 N 7 I 24 L 8 L 25 F 9 L 26 K 10 K 27 G 11 L 28 L 12 H 29 F 13 T 30 G 14 E 31 K 15 K 32 K 16 A 33 E 17 I 34 M 18 M 35 R 19 V 36 I 20 Y 37 L 21 L 38 M 22 N 39 V 23 G 40 G 24 D 41 L 25 L 42 D 26 G 43 A 27 A 44 A 28 G 45 G 29 K 46 K 30 T 47 T 31 T 48 T 32 L 49 I 33 T 50 L 34 R 51 Y 35 G 52 K 36 M 53 L 37 L 54 K 38 Q 55 L 39 G 56 G 40 Q 60 E 41 G 61 I 42 N 62 V 43 V 63 T 44 K 64 T 45 S 65 I 46 P 66 P 47 T 67 T 48 Y 68 I 49 T 69 G 50 L 70 F 51 V 71 N 52 E 72 V 53 E 73 E 54 Y 74 T 55 N 75 V 56 I 76 E 57 A 77 Y 58 G 78 K 59 H 83 N 60 F 84 I 61 D 85 S 62 L 86 F 63 Y 87 T 64 R 88 V 65 L 89 W 66 A 90 D 67 D 91 V 68 P 92 G 69 E 93 G 70 E 94 Q 71 L 95 D 72 E 96 K 73 F 97 I 74 M 98 R 75 G 99 P 76 I 100 L 77 R 101 W 78 D 102 R 79 Y 103 H 80 F 104 Y 81 N 105 F 82 T 106 Q 83 D 107 N 84 S 108 T 85 I 109 Q 86 C 110 G 87 L 111 L 88 I 112 I 89 E 113 F 90 W 114 V 91 S 115 V 92 E 116 D 93 K 117 R 99 G 118 V 100 Q 119 N 101 G 120 E 102 I 121 A 103 L 122 R 104 P 123 E 105 E 124 E 106 A 125 L 107 D 126 M 108 I 127 R 109 L 128 M 110 V 129 L 111 N 130 A 112 I 131 E 113 D 132 D 114 Y 133 E 115 Y 134 L 116 D 135 R 117 D 136 D 118 A 137 A 119 R 138 V 120 N 139 N 135 I 140 A 136 E 141 A 137 L 142 E 138 I 143 I 139 A 144 T 140 Q 145 D 141 T 146 K 142 N 147 L 143 L 148 L 145 G 149 H 146 K 150 S 147 N 151 L 148 I 152 A 157 I 153 T 158 S 154 C 159 A 155 A 160 F 156 T 161 S 157 S 162 N 158 G 163 TER END PFRMAT AL TARGET T0104 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 1mh1 K 32 Q 2 A 33 A 3 I 34 I 4 M 35 K 5 V 36 C 6 Y 37 V 7 L 38 V 8 N 39 V 9 G 40 G 10 D 41 D 11 L 42 G 12 G 43 A 13 A 44 V 14 G 45 G 15 K 46 K 16 T 47 T 17 T 48 C 18 L 49 L 19 T 50 L 20 R 51 I 21 G 52 S 22 M 53 Y 23 L 54 T 24 Q 55 T 25 G 56 N 26 L 70 F 28 V 71 P 29 E 72 G 30 E 73 E 31 Y 74 Y 32 N 75 I 33 I 76 P 34 A 77 T 35 G 78 V 36 K 79 F 37 M 80 D 38 I 81 N 39 Y 82 Y 40 H 83 S 41 F 84 A 42 D 85 N 43 L 86 V 44 Y 87 L 53 R 88 G 54 L 89 L 55 A 90 W 56 D 91 D 57 P 92 T 58 E 93 A 59 E 94 G 60 L 95 Q 61 E 96 E 62 F 97 D 65 M 98 R 66 G 99 L 67 I 100 R 68 R 101 P 69 D 102 L 70 Y 103 S 71 F 104 Y 72 N 105 S 86 T 106 P 87 D 107 A 88 S 108 S 89 I 109 F 90 C 110 E 91 L 111 N 92 I 112 R 94 E 113 K 96 W 114 W 97 S 115 Y 98 E 116 P 99 K 117 E 100 G 118 V 101 Q 119 R 102 G 120 H 103 I 121 H 104 L 122 C 105 P 123 P 106 E 124 N 107 A 125 T 108 D 126 P 109 I 127 I 110 L 128 I 111 V 129 L 112 N 130 V 113 I 131 G 114 Y 133 G 142 Y 134 L 143 D 135 A 144 D 136 M 145 A 137 A 146 R 138 K 147 N 139 E 148 I 140 I 149 E 141 G 150 L 142 A 151 I 143 Q 162 A 144 R 163 Q 145 G 164 T 146 L 165 N 147 K 166 L 148 T 167 G 149 V 168 K 150 F 169 N 151 D 170 I 152 E 171 I 153 A 172 S 154 I 173 A 155 R 174 F 156 A 175 S 157 V 176 N 158 L 177 TER END PFRMAT AL TARGET T0104 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 M 35 V 7 V 36 I 8 Y 37 T 9 L 38 I 10 N 39 D 11 G 40 G 12 D 41 P 13 L 42 S 14 G 43 G 15 A 44 A 16 G 45 G 17 K 46 K 18 T 47 G 19 T 48 T 20 L 49 L 21 T 50 C 22 R 51 K 23 G 52 A 24 M 53 M 25 L 54 A 26 Q 55 E 27 G 56 A 28 I 57 L 29 G 58 Q 30 H 59 W 31 TER END Sorry, can't convert pairwise alignment for target T0104 and template 5tmp to CASP AL format PFRMAT AL TARGET T0104 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 1sky_E Y 7 E 127 I 8 L 128 P 9 A 129 D 10 T 130 E 11 E 131 F 12 V 132 S 13 E 133 M 14 I 134 L 15 L 135 R 16 E 136 F 17 T 137 G 18 G 138 K 19 I 139 K 20 K 140 F 21 V 141 A 22 V 142 E 23 D 143 I 24 L 144 L 25 L 145 L 28 A 146 H 29 P 147 T 30 Y 148 E 31 I 149 K 32 K 150 A 33 G 151 I 34 G 152 M 35 K 153 V 36 I 154 Y 37 G 155 L 38 L 156 N 39 F 157 G 40 G 158 D 41 G 159 L 42 A 160 G 43 G 161 A 44 V 162 G 45 G 163 K 46 K 164 T 47 T 165 T 48 V 166 L 49 L 167 T 50 I 168 R 51 Q 169 G 52 E 170 M 53 L 171 L 54 I 172 Q 55 H 173 G 56 N 174 I 57 I 175 G 58 A 176 H 59 Q 177 Q 60 E 178 G 61 H 179 N 62 G 180 V 63 G 181 K 64 I 182 S 65 S 183 TER END PFRMAT AL TARGET T0104 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 1do0_A E 2 R 25 S 3 S 26 L 4 V 27 T 5 A 28 Q 6 I 29 Y 7 A 30 I 8 L 31 P 9 R 32 D 10 N 33 E 11 R 34 F 12 W 35 S 13 R 36 M 14 R 37 L 15 M 38 R 16 Q 39 F 17 L 40 G 18 N 41 K 19 E 42 K 20 E 43 F 21 L 44 A 22 R 45 E 23 H 46 I 24 E 47 L 25 V 48 K 32 T 49 A 33 P 50 I 34 K 51 M 35 N 52 V 36 I 53 Y 37 L 54 L 38 M 55 N 39 I 56 G 40 G 57 D 41 P 58 L 42 T 59 G 43 G 60 A 44 V 61 G 45 G 62 K 46 K 63 T 47 T 64 T 48 E 65 L 49 I 66 T 50 A 67 R 51 R 68 G 52 R 69 M 53 L 70 L 54 A 71 Q 55 K 72 TER END PFRMAT AL TARGET T0104 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 1do0_B E 2 R 25 S 3 S 26 L 4 V 27 T 5 A 28 Q 6 I 29 Y 7 A 30 I 8 L 31 P 9 R 32 D 10 N 33 E 11 R 34 F 12 W 35 S 13 R 36 M 14 R 37 L 15 M 38 R 16 Q 39 F 17 L 40 G 18 N 41 K 19 E 42 K 20 E 43 F 21 L 44 A 22 R 45 E 23 H 46 I 24 E 47 L 25 V 48 K 32 T 49 A 33 P 50 I 34 K 51 M 35 N 52 V 36 I 53 Y 37 L 54 L 38 M 55 N 39 I 56 G 40 G 57 D 41 P 58 L 42 T 59 G 43 G 60 A 44 V 61 G 45 G 62 K 46 K 63 T 47 T 64 T 48 E 65 L 49 I 66 T 50 A 67 R 51 R 68 G 52 R 69 M 53 L 70 L 54 A 71 Q 55 K 72 TER END PFRMAT AL TARGET T0104 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 1do0_C E 2 R 25 S 3 S 26 L 4 V 27 T 5 A 28 Q 6 I 29 Y 7 A 30 I 8 L 31 P 9 R 32 D 10 N 33 E 11 R 34 F 12 W 35 S 13 R 36 M 14 R 37 L 15 M 38 R 16 Q 39 F 17 L 40 G 18 N 41 K 19 E 42 K 20 E 43 F 21 L 44 A 22 R 45 E 23 H 46 I 24 E 47 L 25 V 48 K 32 T 49 A 33 P 50 I 34 K 51 M 35 N 52 V 36 I 53 Y 37 L 54 L 38 M 55 N 39 I 56 G 40 G 57 D 41 P 58 L 42 T 59 G 43 G 60 A 44 V 61 G 45 G 62 K 46 K 63 T 47 T 64 T 48 E 65 L 49 I 66 T 50 A 67 R 51 R 68 G 52 R 69 M 53 L 70 L 54 A 71 Q 55 K 72 TER END PFRMAT AL TARGET T0104 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 1do0_D E 2 R 25 S 3 S 26 L 4 V 27 T 5 A 28 Q 6 I 29 Y 7 A 30 I 8 L 31 P 9 R 32 D 10 N 33 E 11 R 34 F 12 W 35 S 13 R 36 M 14 R 37 L 15 M 38 R 16 Q 39 F 17 L 40 G 18 N 41 K 19 E 42 K 20 E 43 F 21 L 44 A 22 R 45 E 23 H 46 I 24 E 47 L 25 V 48 K 32 T 49 A 33 P 50 I 34 K 51 M 35 N 52 V 36 I 53 Y 37 L 54 L 38 M 55 N 39 I 56 G 40 G 57 D 41 P 58 L 42 T 59 G 43 G 60 A 44 V 61 G 45 G 62 K 46 K 63 T 47 T 64 T 48 E 65 L 49 I 66 T 50 A 67 R 51 R 68 G 52 R 69 M 53 L 70 L 54 A 71 Q 55 K 72 TER END PFRMAT AL TARGET T0104 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 1do0_E E 2 R 25 S 3 S 26 L 4 V 27 T 5 A 28 Q 6 I 29 Y 7 A 30 I 8 L 31 P 9 R 32 D 10 N 33 E 11 R 34 F 12 W 35 S 13 R 36 M 14 R 37 L 15 M 38 R 16 Q 39 F 17 L 40 G 18 N 41 K 19 E 42 K 20 E 43 F 21 L 44 A 22 R 45 E 23 H 46 I 24 E 47 L 25 V 48 K 32 T 49 A 33 P 50 I 34 K 51 M 35 N 52 V 36 I 53 Y 37 L 54 L 38 M 55 N 39 I 56 G 40 G 57 D 41 P 58 L 42 T 59 G 43 G 60 A 44 V 61 G 45 G 62 K 46 K 63 T 47 T 64 T 48 E 65 L 49 I 66 T 50 A 67 R 51 R 68 G 52 R 69 M 53 L 70 L 54 A 71 Q 55 K 72 TER END PFRMAT AL TARGET T0104 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 1do0_F E 2 R 25 S 3 S 26 L 4 V 27 T 5 A 28 Q 6 I 29 Y 7 A 30 I 8 L 31 P 9 R 32 D 10 N 33 E 11 R 34 F 12 W 35 S 13 R 36 M 14 R 37 L 15 M 38 R 16 Q 39 F 17 L 40 G 18 N 41 K 19 E 42 K 20 E 43 F 21 L 44 A 22 R 45 E 23 H 46 I 24 E 47 L 25 V 48 K 32 T 49 A 33 P 50 I 34 K 51 M 35 N 52 V 36 I 53 Y 37 L 54 L 38 M 55 N 39 I 56 G 40 G 57 D 41 P 58 L 42 T 59 G 43 G 60 A 44 V 61 G 45 G 62 K 46 K 63 T 47 T 64 T 48 E 65 L 49 I 66 T 50 A 67 R 51 R 68 G 52 R 69 M 53 L 70 L 54 A 71 Q 55 K 72 TER END PFRMAT AL TARGET T0104 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 1do2_A E 2 R 25 S 3 S 26 L 4 V 27 T 5 A 28 Q 6 I 29 Y 7 A 30 I 8 L 31 P 9 R 32 D 10 N 33 E 11 R 34 F 12 W 35 S 13 R 36 M 14 R 37 L 15 M 38 R 16 Q 39 F 17 L 40 G 18 N 41 K 19 E 42 K 20 E 43 F 21 L 44 A 22 R 45 E 23 H 46 I 24 E 47 L 25 V 48 K 32 T 49 A 33 P 50 I 34 K 51 M 35 N 52 V 36 I 53 Y 37 L 54 L 38 M 55 N 39 I 56 G 40 G 57 D 41 P 58 L 42 T 59 G 43 G 60 A 44 V 61 G 45 G 62 K 46 K 63 T 47 T 64 T 48 E 65 L 49 I 66 T 50 A 67 R 51 R 68 G 52 R 69 M 53 L 70 L 54 A 71 Q 55 K 72 TER END PFRMAT AL TARGET T0104 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 1do2_B E 2 R 25 S 3 S 26 L 4 V 27 T 5 A 28 Q 6 I 29 Y 7 A 30 I 8 L 31 P 9 R 32 D 10 N 33 E 11 R 34 F 12 W 35 S 13 R 36 M 14 R 37 L 15 M 38 R 16 Q 39 F 17 L 40 G 18 N 41 K 19 E 42 K 20 E 43 F 21 L 44 A 22 R 45 E 23 H 46 I 24 E 47 L 25 V 48 K 32 T 49 A 33 P 50 I 34 K 51 M 35 N 52 V 36 I 53 Y 37 L 54 L 38 M 55 N 39 I 56 G 40 G 57 D 41 P 58 L 42 T 59 G 43 G 60 A 44 V 61 G 45 G 62 K 46 K 63 T 47 T 64 T 48 E 65 L 49 I 66 T 50 A 67 R 51 R 68 G 52 R 69 M 53 L 70 L 54 A 71 Q 55 K 72 TER END --simple mime boundary-- From farmer@cse.ucsc.edu Tue Jun 27 22:24:53 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 WAA05013 for Message-Id: <200006272029.NAA14891@beta.cse.ucsc.edu> Subject: T0104(target 99 secondary structure prediction) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0104.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-962133418.t99secstr.fasta' Content-Disposition: attachment; filename="t99-results-962133418.t99secstr.fasta" >T0104 LLLLHHHLLLHHHHHHHHHHHHHHHHHHLLLLLLEEEEELLLLLLHHHHHHHHHHHHLLLLLELLLLHEEEEELLLLLLEEEEEEEEELLLHHHHHHHLHHHHHLLLLEEEEELLHHHHLLLLLLLEEEEEEELLLLLEEEEEEELLLHHHHHHHHHL --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-962133418.t99secstr.casp.ss' Content-Disposition: attachment; filename="t99-results-962133418.t99secstr.casp.ss" PFRMAT SS TARGET T0104 AUTHOR UCSC Target99 server METHOD This prediction was derived from the following methods METHOD by averaging the corresponding probabilities: METHOD Method 0: METHOD TARGET T0104 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-861/target-align-861.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 21.99 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: T0104 METHOD model_file: /projects/compbio/tmp/sam-nn-tmp.beta.7877/model.mod METHOD database_files: /projects/compbio/bin/scripts/hmm-target99-dir/pcc/data/overrep-2260.verify.mixed.seq /projects/compbio/bin/scripts/hmm-target99-dir/pcc/data/overrep-2260.verify.mixed.2d METHOD scoring_mode: local METHOD null_model: reverse METHOD scoring_algorithm: EM METHOD adjust_score: 2 METHOD date: Tue Jun 27 13:27:27 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-861/target-align-861.a2m METHOD METHOD guide seq name: T0104 METHOD ###end 0 MODEL 1 M C 0.614 E C 0.556 S C 0.5 L C 0.415 T H 0.384 Q H 0.386 Y H 0.373 I C 0.418 P C 0.473 D C 0.484 E H 0.639 F H 0.673 S H 0.688 M H 0.691 L H 0.723 R H 0.73 F H 0.734 G H 0.723 K H 0.744 K H 0.749 F H 0.744 A H 0.733 E H 0.717 I H 0.691 L H 0.658 L H 0.747 K H 0.709 L H 0.626 H C 0.442 T C 0.47 E C 0.599 K C 0.614 A C 0.616 I C 0.439 M E 0.647 V E 0.71 Y E 0.702 L E 0.636 N E 0.448 G C 0.593 D C 0.59 L C 0.548 G C 0.608 A C 0.565 G C 0.5 K H 0.515 T H 0.565 T H 0.617 L H 0.648 T H 0.664 R H 0.678 G H 0.68 M H 0.67 L H 0.675 Q H 0.649 G H 0.607 I H 0.498 G C 0.617 H C 0.649 Q C 0.592 G C 0.528 N C 0.494 V E 0.452 K C 0.471 S C 0.651 P C 0.551 T C 0.426 Y H 0.383 T E 0.436 L E 0.491 V E 0.493 E E 0.435 E E 0.384 Y C 0.416 N C 0.547 I C 0.583 A C 0.636 G C 0.612 K C 0.526 M E 0.413 I E 0.57 Y E 0.587 H E 0.572 F E 0.55 D E 0.488 L E 0.53 Y E 0.524 R E 0.464 L C 0.379 A C 0.535 D C 0.608 P H 0.552 E H 0.603 E H 0.605 L H 0.589 E H 0.585 F H 0.57 M H 0.509 G C 0.459 I H 0.533 R H 0.571 D H 0.574 Y H 0.541 F H 0.481 N C 0.447 T C 0.567 D C 0.6 S C 0.516 I E 0.551 C E 0.652 L E 0.667 I E 0.633 E E 0.508 W C 0.418 S C 0.534 E H 0.44 K H 0.48 G H 0.494 Q H 0.476 G C 0.421 I C 0.466 L C 0.611 P C 0.634 E C 0.545 A C 0.527 D C 0.411 I E 0.53 L E 0.592 V E 0.617 N E 0.621 I E 0.618 D E 0.587 Y E 0.506 Y C 0.514 D C 0.671 D C 0.692 A C 0.622 R C 0.451 N E 0.511 I E 0.575 E E 0.579 L E 0.57 I E 0.504 A E 0.452 Q E 0.372 T C 0.414 N C 0.469 L C 0.438 G H 0.429 K H 0.5 N H 0.517 I H 0.54 I H 0.53 S H 0.535 A H 0.541 F H 0.477 S H 0.405 N C 0.555 END --simple mime boundary--