; SAM: prettyalign v2.1.1 (Apr 24, 1998) compiled 04/27/98_12:32:27. ; SAM: Sequence Alignment and Modeling Software System ; (c) 1992-1998 Regents of the University of California, Santa Cruz ; http://www.cse.ucsc.edu/research/compbio/sam.html ; ; ------ Citations (HMMs, SAM) ------ ; A. Krogh et al., Hidden Markov models in computational biology: ; Applications to protein modeling, JMB 235:1501-1531, Feb 1994. ; R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: ; Extension and analysis of the basic method, CABIOS 12:95-107, 1996. ; ----------------------- ; Sequence numbers correspond to the following labels: ; 1 PIR2:C69673_69:372 ; 2 T0049_1:392 ; 3 T0049_1:392 ; 4 GP:AB002150_7_12:284 ; 5 PIR2:E65017_90:271 ; 6 GP:MTV008_19_28:193 ; 7 PIR2:A44832_55:199 ; 8 SW:PBP4_NOCLA_6:203 ; 9 GP:MTCY4C12_15_60:301 ; 10 GP:CEY45F10D_5_62:244 ; 11 GP:CEC40H5_5_12:194 ; 12 GP:MTCY9F9_42_42:227 ; 13 GP:MTCY4D9_11_79:225 ; 14 PIR2:S76446_78:225 ; 15 GP:D86380_1_39:307 ; 16 GP:MTCY02B10_31_2:191 ; 17 SW:Y07V_MYCTU_2:359 ; 18 PIR2:S75832_1:289 ; 19 SW:PBPE_BACSU_2:226 ; 20 GP:BSZ94043_42_7:231 ; 21 SW:DAC_STRSQ_56:233 ; 22 GP:STMSDDP_1_56:233 ; 23 3D:3PTE_25:202 ; 24 GP:AB008454_1_33:230 ; 25 GP:AB008455_1_33:230 10 20 30 40 50 60 70 80 | | | | | | | | 1 evkkk---.....-----TAKKSEEQIKTVDRNQKISNYLKEIGFSG-TAMIVR..N.GEIVTNKGFGYAD.....RKHY.....IQ..NN.PLTSFYVGSSQKAL.IATAILQL 2 .....MTA.....ASLDPTAFSLDAASLAARLDAVFDQALRERRLVGAVAIVAR..H.GEILYRRAQGLAD.....REAG.....RP..MR.EDTLFRLASVTKPI.VALAVLRL 3 .....MTA.....ASLDPTAFSLDAASLAARLDAVFDQALRERRLVGAVAIVAR..H.GEILYRRAQGLAD.....REAG.....RP..MR.EDTLFRLASVTKPI.VALAVLRL 4 aagfp---.....---------------------------------GAVLVVVK..D.GRIIKKAAYGYSK.....KYEGsellrRPakMK.TRTMFDLASNTKMYaTNFALQRL 5 psvnl---.....-------------------------------------LIIK..D.NQIVYRKAWGAAKky7vlMEQP.....VK..AT.TGTLYDLASNTKMYaTNFALQKL 6 rnfvl---.....-----------------------------RNEVGAAVAVWV..D.GDLVVNLWGGSAD.....AGGT.....RP..WQ.HDTLATVLSGTKAL.TATCVHQL 7 vdlwa---.....-----------------------------------------..-.---------GTAD.....KDGA.....EA..WH.SDTIVNLFSCTKTF.TAVTALQL 8 mpfdh---.....----------------AHWQERFDALRTEHHVPGAALAVFV..D.GD-LHELASGVLH.....RGTG.....VA..VT.TDSVFQSGSVAKVY.TATLVMQL 9 aafde---.....------------------LDAKINAGMKAYAIPGVAVAVWA..G.GQ-EYVKGYGVTN.....VDHP.....MP..VD.GDTVFRIGSTTKTF.TGTVMMRL 10 glsia---.....--------------------------------------VSL..D.GKMVWKSGFGYAN.....LESF.....AK..CT.GDSVMRIASISKPI.TATLAAQC 11 rvehf---.....--------------------------MKDLNIPGLSIAIAK..K.EQLKFAAGFGYTD.....IRQQ.....EP..VT.PNHQFRVGSVSKPV.TAAAIMLL 12 ttytp---.....-------------HIKASSQDVLDGAINA-DEPGCSAAVGV..E.GKVIWSGVRGIAD.....LASG.....AK..IT.TDTVFDIASVSKQF.TATAILLL 13 gdsmt---.....-----------------------------------------..-.-------------.....---G.....VP..AT.TAMHFRNGAVAISY.VATLLLKL 14 apnsp---.....-----------------------------------------..-.-------------.....----.....-P..ID.AKSLFQIGSITKSF.TSVLLLQA 15 ptqsv---.....--------SSSVQTSTQRDRNSVKQAVRDTLQLGFPGILAKtsE.GGKTWSYAAGVAN.....LSSK.....KP..MK.TDFRFRIGSVTKTF.TATVVLQL 16 i....---.....-----------------------------------------..-.-------------.....----.....--..--.--------------.-------- 17 m....---.....--------------------------------------VWQ..R.EKLLQVNEIGYRD.....IDAG.....VP..MQ.RDTLFRIASMTKPV.TVAAAMSL 18 .....MGAvl7siWFSHPPLRPGDRASLNQYLIDRLNQ--GEGKELGSAALALI..HnGKVDTIHTVGVEN.....VDSG.....SP..VDpENTLYQMASVSKLV.TAWGVMKL 19 m....---.....------------KQNKRKHLQTLFETLGEKHQFNGTVLAAE..G.GDILYHHSFGYAE.....MTEK.....RP..LK.TNSLFELASLSKPF.TALGIILL 20 ggggm---.....------------KQNKRKHLQTLFETLGEKHQFNGTVLAAE..G.GDILYHHSFGYAE.....MTEK.....RP..LK.TNSLFELASLSKPF.TALGIILL 21 sqgap---.....---------------------------------GAMVRVDD..N.GTIHQLSE-GVAD.....RATG.....RA..IT.TTDRFRVGSVTKSF.SAVVLLQL 22 sqgap---.....---------------------------------GAMVRVDD..N.GTIHQLSE-GVAD.....RATG.....RA..IT.TTDRFRVGSVTKSF.SAVVLLQL 23 sqgap---.....---------------------------------GAMVRVDD..N.GTIHQLSE-GVAD.....RATG.....RA..IT.TTDRFRVGSVTKSF.SAVVLLQL 24 idavi---.....------------------------QPLMKKYGVPGMAIAVS..V.DGKQQIYPYGVAS.....KQTG.....KP..IT.EQTLFEVGSLSKTF.TATLAVYA 25 idavi---.....------------------------QPLMKKYGVPGMAIAVS..V.DGKQQIYPYGVAS.....KQTG.....KP..IT.EQTLFEVGSLSKTF.TATLAVYA 90 100 110 120 130 140 150 160 | | | | | | | | 1 EEKGKLQTSDPV.....STYLPHFP--..---..-NGQT.....ITLKNLLTHT..SGIN....GH.....IEG..NGAITPD.....-----------DLI.....K....D.I 2 VARGELALDAPV.....TRWLPEFRPR..LAD..GSEPL.....VTIHHLLTHT..SGLG....YW.....LLE..GAGSVYD.....RLGISDGIDLRDFD.....L....D.E 3 VARGELALDAPV.....TRWLPEFRPR..LAD..GSEPL.....VTIHHLLTHT..SGLG....YW.....LLE..GAGSVYD.....RLGISDGIDLRDFD.....L....D.E 4 VSQGKLDVYEKV.....SAYLPGFKDQ..PGD..LIKGK.....TRYVSLMSSStnSGLPssfyFY.....TPE..KAGKYYS.....Q------------E.....R....D.K 5 MSEGKLHPDDRI.....AKYIPGFADS..PNDtiKGKNT.....LRISDLLHHS..GGF-....--.....---..PADPQYP.....NKAVAG--ALYSQD.....K....G.Q 6 VDRGELDLHAPV.....ARYWPEF---..-GQ..AGKQA.....ITLAMVMSHR..SG--....--.....---..-AIGPRG.....RLGWEQVAD-----.....W....D.F 7 VAEGKLQLDAPV.....AKYWPEF---..-AA..AGKES.....ITLRQLLCHQ..AGL-....--.....---..-------.....-------PAIREML.....P....T.E 8 VDAGELRLDTRV.....ADVLPGF-AV..ADA..EVART.....VTIGRLLSHT..SGIA....GD.....FTL..DTGRG--.....-----------DDC.....L....A.R 9 VERGKVDLDSPV.....RRYIPDF-AV..ADE..SASAT.....VTVRQLLNHT..AGWD....GR.....NGQ..DFGRGDD.....AVAL----------.....-....-.- 10 VENGTLDLDEDI.....RKYLPEFPAK..KFK..NEDVK.....ITMRQLLSHS..AGIR....HY.....ATE..KKKSETH.....EDPSNNNTETPEFL.....S....N.K 11 IDKGHFTLDSKLf17qyPRYVTE----..---..-----.....ITVRHLLEHT..AGGW....DN.....LQS..DAAWVQP.....EMTTKELIEYV---.....-....-.- 12 VEAGKLTLDDPI.....SQYVPELPDW..A--..---QT.....VTVEQLMHQT..SGIP....DY.....VAL..LAARGYQ.....---------VSDRT.....I....EaE 13 VDEKKLRLDDKL.....SRWLPDFPH-..---..--ADR.....VTLGQLAQMT..SGYP....DY.....VLG..N--EAFD.....AELYAN--PFRQWT.....T....Q.E 14 EAENKVNLGDDF.....TTYLPEYDHW..NG-..-----.....VTITQLLNMT..SGLP....NYsdsptLNY..GFVQSPE.....R--IWQDKELVDVV.....Y....P.Q 15 AEENRLNLDDSI.....EKWLPGVI-Q..GNG..YDDKQ.....ITIRQLLNHT..SGIA....EY.....---..-------.....--TRSKSFDLMDTK.....KsyraE.E 16 ------------.....----------..---..-----.....----------..----....--.....---..-------.....--------------.....-....-.- 17 VDEGKLALRDPI.....TRWAPELCKVavLDD..AAGPLdr9raILIEDLLTHT..SGLA....YG.....FSVsgPISRAYQ.....RLPFGQGPDV----.....-....-.- 18 VEMGQINLDDPV.....LSHLRRWQFP..ADS..PYRGE.....VTIAQLLSHT..GGQN....DH.....LGY..G------.....--GFLPGQPLQTLEqs6ltK....D.V 19 EEKGILGYEDKV.....DRWLPGFPY-..---..---QG.....VTIRHLLNHT..SGLP....DY.....MGW..FFAN-WD.....SHKIAVNQDIVDML.....M....N.E 20 EEKGILGYEDKV.....DRWLPGFPY-..---..---QG.....VTIRHLLNHT..SGLP....DY.....MGW..FFAN-WD.....SHKIAVNQDIVDML.....M....N.E 21 VDEGKLDLDASV.....NTYLPGLLP-..---..--DDR.....ITVRQVMSHR..SGLY....DY.....TND..MFAQTVPgfesvRNKVFSYQDLITLS.....L....K.H 22 VDEGKLDLDASV.....NTYLPGLLP-..---..--DDR.....ITVRQVMSHR..SGLY....DY.....TND..MFAQTVPgfesvRNKVFSYQDLITLS.....L....K.H 23 VDEGKLDLDASV.....NTYLPGLLP-..---..--DDR.....ITVRQVMSHR..SGLY....DY.....TND..MFAQTVPgfesvRNKVFSYQDLITLS.....L....K.H 24 QQQGKLSFNDPA.....SRYLPELRGS..AFD..G----.....VSLLNLATHT..SGLP....LF.....VPD..-------.....-----------DVT.....N....D.A 25 QQQGKLSFNDPA.....SRYLPELRGS..AFD..G----.....VSLLNLATHT..SGLP....LF.....VPD..DV-----.....------------TD.....N....A.Q 170 180 190 200 210 220 230 | | | | | | | 1 E.....L.....QGIKRQP.GV---....-..--WDY.K.D.SNYs.V.L.AYIIAEVSGEPYEQYIKNHIFKPAGMTHA.....GF.Y-.....--..-----..-KTYEKEPY 2 N.....L.....RRLASAP.LSFAP....G..SGWQY.S.L.ALD..V.L.GAVVERATGQPLAAAVDALVAQPLGMRDC.....GF.VS.....AE..PERFA..VPYHDGQPE 3 N.....L.....RRLASAP.LSFAP....G..SGWQY.S.L.ALD..V.L.GAVVERATGQPLAAAVDALVAQPLGMRDC.....GF.VS.....AE..PERFA..VPYHDGQPE 4 T.....I.....EYLTKIP.LDYQT....G..TKHVY.S.DiGYM..L.L.GCIVEKLTGKPLDVYTEQELYKPL-----.....--.--.....--..-----..--------- 5 T.....L.....EMIKRTP.LEYQP....G..SKHIY.S.DvDYM..L.L.GFIVESVTGQPLDRYVEESIYRPLGLTHT.....VF.--.....--..-----..--------- 6 V.....C.....EQLAAAE.PWWQP....GaaQGYHM.T.T.FGF..I.L.GEVFRRVTGRTVGQYLRTEIAEPLG----.....--.--.....--..-----..--------- 7 A.....Lyd7mvDTLAAEA.PWWTP....G..QGHGY.E.A.ITYgwL.V.GELLRRADGRGPGESIVARVARPLGL---.....--.--.....--..-----..--------- 8 F.....V.....DACADVG.QDCPP....D..TVISYcS.T.GYA..I.L.GRIVEVLTGQSWDDALRDRLFTPLGLHQS.....MT.LP.....EE..ALRFR..VAM------ 9 Y.....V.....KAMTRLP.QLTPP....G..TAFAY.N.N.SGL..V.VaGRIIELVAGTTYESTVQRLLLDPLQLAHT.....RY.FSd14svVD..GKPIA..VTDFWTFPR 10 Pyn7daL.....AIFKNDD.LVEKP....G..SKFSY.TtY.GLT..L.A.GAVLEKCSGKTYRQLANQL-FSDLGMRNT.....--.--.....--..-----..--------- 11 -.....-.....--LTNVP.LEYKP....G..TMWIY.S.NfGYQ..L.L.GYLIETTTGMSYEAFVKKNIFAPSGVYD-.....--.--.....--..-----..--------- 12 A.....R.....QALAAAPeLQFKP....G..TRFDY.S.N.SNY..LlL.GEIVHRASGQPLPEFLSAEIFQPLGL---.....--.--.....--..-----..--------- 13 L.....L.....DQISSRP.LLYDP....G..TNWNY.A.H.TNY..LlL.GLALEKAAGQDMPTLLQRKVLSPLGLTAT.....--.--.....--..-----..--------- 14 P.....-.....-NLPAPP.L----....N..TGYAY.T.N.TAY..T.LgGLVLEKVYGQSYAELIDKKLLQPLELNNT.....FY.--.....--..-----..--------- 15 L.....V.....KMGISMP.PDFAP....G..KSWSY.S.N.TGY..VlL.GILIETVTGNSYAEEIENRIIEPLELSNTf16arGY.IQ.....LDgaSEPKD..VTYYN---- 16 -.....-.....-------.-----....-..-----.-.-.---..-.-.---------------IDERVLGPAGMTDT.....GFyVS.....AD..AQRRA..ATMY-RLDE 17 W.....L.....AALATLP.LVHQP....G..DRVTY.S.H.AID..V.L.GVIVSRIEDAPLYQIIDERVLGPAGMTDT.....GFyVS.....AD..AQRRA..ATMY-RLDE 18 A.....F.....GEPRGVE.AVYPP....G..EEFSY.S.G.GGYt.V.L.QLLVEEVTGQSFAEFMQEQILHPLGMTGA.....NF.--.....--..-----..--------- 19 G.....L.....SG-----.-YFEP....N..EGWMY.S.N.TGY..VlL.AVIIEKASGMSYADFIKTSIFLPAGMNET.....--.--.....--..-----..-RVYNRRLS 20 G.....L.....SG-----.-YFEP....N..EGWMY.S.N.TGY..VlL.AVIIEKASGMSYADFIKTSIFLPAGMNET.....--.--.....--..-----..-RVYNRRLS 21 G.....V.....TN-----.---AP....G..AAYSY.S.N.TNF..V.VaGMLIEKLTGHSVATEYQNRIFTPLNLTDT.....FY.VH.....PD..-----..--------- 22 G.....V.....TN-----.---AP....G..AAYSY.S.N.TNF..V.VaGMLIEKLTGHSVATEYQNRIFTPLNLTDT.....FY.VH.....PD..-----..--------- 23 G.....V.....TN-----.---AP....G..AAYSY.S.N.TNF..V.VaGMLIEKLTGHSVATEYQNRIFTPLNLTDT.....FY.VH.....PD..-----..--------- 24 Q.....L.....MAYYRA-.--WQPkhpaG..SYRVY.SnL.GIV..M.L.GMIAAKSLDQPFIQAMEQGMLPALGMSHT.....-Y.VQ.....VP..AAQMAnyAQGYSKDDK 25 L.....M.....AYYRAWQ.PKHPA....G..SYRVY.SnL.GIG..M.L.GMIAAKSLDQPFTQAMEQGMLPALGMRHT.....-Y.VQ.....VP..AAQMAnyAQGYNKDDK 240 250 260 270 280 290 300 310 320 | | | | | | | | | 1 P-----------.....----AVGYKME.....GSK.....TVTP--Y.....IPDLSQLYGAGDIYMSAIDM.YKFDQ.....ALIDGKLYSQKSYEKMFTPGSSSTYGMGFYV 2 PVRMRDGIEVPL.....PEGHGAAVRFA.....PSR.....VFEPGAY.....PSGGAGMYGSADDVLRALEA.IRANP.....GFLPETLADAARRDQAGVGAETRGPGWGFGY 3 PVRMRDGIEVPL.....PEGHGAAVRFA.....PSR.....VFEPGAY.....PSGGAGMYGSADDVLRALEA.IRANP.....GFLPETLADAARRDQAGVGAETRGPGWGFGY 4 --RLKHTLYNPLqkgfkPKQFAATERMG.....NTRd17geVHDEKAFysmdgVSGHAGLFSNADDMAILLQV.MLNKG.....SYRNISLFDQE-------------------- 5 ------------.....-----------.....---.....-------.....--------------------.-----.....------------------------------- 6 ------------.....-----------.....---.....-------.....--------------------.-----.....------------------------------- 7 ------------.....-----------.....---.....-------.....--------------------.-----.....------------------------------- 8 ------------.....-----------.....---.....-------.....--------------------.-----.....------------------------------- 9 S-----------.....-----------.....---.....-------.....CNPTGGLMSTARDQLRYAQF.HLGDG.....------------------------------- 10 ------------.....-----------.....---.....-------.....--------------------.-----.....------------------------------- 11 ------------.....-----------.....---.....-------.....--------------------.-----.....------------------------------- 12 ------------.....-----------.....---.....-------.....--------------------.-----.....------------------------------- 13 ------------.....-----------.....---.....-------.....--------------------.-----.....------------------------------- 14 ------------.....-----------.....---.....-------.....--------------------.-----.....------------------------------- 15 ------------.....-----------.....---.....----PSM.....GSSAGDMISTADDLNKFFSY.LLGGK.....LLKEQQL------------------------ 16 QDRLRHDV----.....---------MG.....PPH.....VT-PPSF.....CNAGGGLWSTADDYLRFVRM.LLGDGt14vrLMRTDRLTDEQKRH-SFLGAP-FWVGRGFGL 17 QDRLRHDV----.....---------MG.....PPH.....VT-PPSF.....CNAGGGLWSTADDYLRFVRM.LLGDGt14vrLMRTDRLTDEQKRH-SFLGAP-FWVGRGFGL 18 --------DWPT.....IVDQGRANNLAt10psPPR.....HFT----.....ATGAASLYASLADMVKFAQAhLQPNS.....VLKADTL------------------------ 19 PERIDHYA----.....-----------.....---.....-------.....-------YG-------YVYD.VHSET.....YVLPDELEE---------------------- 20 PERIDHYA----.....-----------.....---.....-------.....-------YG-------YVYD.VHSET.....YVLPDELEE---------------------- 21 ------------.....-----------.....---.....-------.....--------------------.-----.....------------------------------- 22 ------------.....-----------.....---.....-------.....--------------------.-----.....------------------------------- 23 ------------.....-----------.....---.....-------.....--------------------.-----.....------------------------------- 24 PVRVNPG-----.....-----------.....---.....-------.....--------------------.-----.....------------------------------- 25 PVRVNPG-----.....-----------.....---.....-------.....--------------------.-----.....------------------------------- 330 340 350 360 370 380 390 | | | | | | | 1 -------------...--APGSYSNHGVMPGFNILNsfsKSGQTIVILFSNIQ-------------------nnakl. 2 LSAVLDDPAAAGT...PQHAGTLQWGGVYGHSWFVD...RALGLSVLLLTNTAYEGMSGPLTIALRDAVYAR...... 3 LSAVLDDPAAAGT...PQHAGTLQWGGVYGHSWFVD...RALGLSVLLLTNTAYEGMSGPLTIALRDAVYAR...... 4 -------------...--------------------...---------------------------------nsrpv. 5 -------------...--------------------...---------------------------------npllk. 6 -------------...--------------------...---------------------------------advhi. 7 -------------...--------------------...---------------------------------dfhvg. 8 -------------...--------------------...---------------------------------shlge. 9 -------------...--------------------...---------------------------------rapng. 10 -------------...--------------------...---------------------------------qldtk. 11 -------------...--------------------...---------------------------------iqvar. 12 -------------...--------------------...---------------------------------amvvd. 13 -------------...--------------------...---------------------------------ansdt. 14 -------------...--------------------...---------------------------------pipsy. 15 -------------...--------------------...---------------------------------kqmlt. 16 NLSVVTDPAKSRPlfgPGGLGTFSWPGAYGTWWQAD...PSADLILLYLIQHCPDLSVDAAAAVAGNPSLAKlrtaq. 17 NLSVVTDPAKSRPlfgPGGLGTFSWPGAYGTWWQAD...PSADLILLYLIQHCPDLSVDAAAAVAGNPSLAKlrtaq. 18 -------------...--------------------...---------------------------------qrmat. 19 -------------...--------------------...---------------------------------tnyvv. 20 -------------...--------------------...---------------------------------tnyvv. 21 -------------...--------------------...---------------------------------tvipg. 22 -------------...--------------------...---------------------------------tvipg. 23 -------------...--------------------...---------------------------------tvipg. 24 -------------...--------------------...---------------------------------pldak. 25 -------------...--------------------...---------------------------------pldae.