; SAM: prettyalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:15 ; (c) 1992-1999 Regents of the University of California, Santa Cruz ; ; Sequence Alignment and Modeling Software System ; http://www.cse.ucsc.edu/research/compbio/sam.html ; ; ------ Citations (HMMs, SAM) ------ ; A. Krogh et al., Hidden Markov models in computational biology: ; ------------- Citations (SAM, SAM-T99, HMMs) ----------------- ; R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: ; Extension and analysis of the basic method, CABIOS 12:95-107, 1996. ; K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting ; remote protein homologies, Bioinformatics 14(10):846-856, 1999. ; A. Krogh et al., Hidden Markov models in computational biology: ; Applications to protein modeling, JMB 235:1501-1531, Feb 1994. ; -------------------------------------------------------------- ; Sequence numbers correspond to the following labels: ; 1 gi|2828193|sp|P30621|MOXR_METEX_14:84 ; 2 gi|2589001|dbj|BAA23276.1|_23:93 ; 3 gi|266551|sp|P29901|MOXR_PARDE_8:78 ; 4 gi|1147800|gb|AAA85134.1|_183:256 ; 5 gi|6324833|ref|NP_014902.1|_183:256 ; 6 gi|6226340|sp|O51204|Y186_BORBU_4:128 ; 7 gi|7463982|pir||D64609_6:124 ; 8 gi|7464783|pir||H71905_6:123 ; 9 gi|6968130|emb|CAB72945.1|_16:130 ; 10 gi|7450024|pir||B72052_1:131 ; 11 gi|7190852|gb|AAF39625.1|_1:142 ; 12 gi|7450025|pir||H71502_1:145 ; 13 gi|6226431|sp|O05515|YDIB_BACSU_1:152 ; 14 gi|6226350|sp|P74415|Y257_SYNY3_4:143 ; 15 gi|6226476|sp|O52749|YJEE_ANASP_12:151 ; 16 gi|6226308|sp|Q9ZED0|Y013_RICPR_4:136 ; 17 gi|6226401|sp|O67011|Y843_AQUAE_7:127 ; 18 gi|2801652|gb|AAB97417.1|_6:123 ; 19 gi|6226403|sp|O83845|Y875_TREPA_2:130 ; 20 gi|401636|sp|P31805|YJEE_ECOLI_1:151 ; 21 gi|1176349|sp|P44492|YJEE_HAEIN_1:157 ; 22 T0104 ; 23 gi|7225682|gb|AAF40894.1|_4:149 ; 24 gi|7380656|emb|CAB85246.1|_4:149 ; 25 gi|7450019|pir||H72229_1:152 ; 26 gi|6226477|sp|O86788|YJEE_STRCO_2:138 ; 27 gi|2496467|sp|Q50706|YY22_MYCTU_18:165 ; 28 gi|2496468|sp|Q49864|YY22_MYCLE_6:154 ; 29 gi|7471517|pir||E75283_10:143 10 20 30 40 50 60 | | | | | | 1 WRDAAARFEREIAKAVVGQDRAIRLLTIAIFARGHVMLEGDVGVGKTTLLRAVARGLGGA...YE 2 WRARALEFEGEVGRAIVGQERAIRLLVIAVFARGHVLLEGDVGVGKTTLLRAVAHALGGS...YE 3 WHARFRDAEAALNGVVLGQARTIRLLLISALCRGHVLLAGDVGTGKTTLLRAMARALGGP...YG 4 IGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIG-A...NF 5 IGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIG-A...NF 6 ------EFKSEKKMINFSKSFFYPL-----PIGKIFVLSGDMGSGKTSFLKGLALNLGIS...-Y 7 --------------DELDKVAAAIL---KDDFKGVVLLKGVVGSGKTTLVQACLKHLGLD...IQ 8 --------------DELDKVAAAIL---KDDFKGVVLLKGVVGSGKTTLVQACLKHLGLD...IQ 9 ----------------------QIM-----PKEGVVLLQGDLASGKTSLVQAWVKFLGLD...VR 10 MGRYRRVSHSSQETLLLGTELGQVL-----VPGAVLLLFGDYGAGKTEFVRGIVSGYLGDtiaEE 11 MGRYRRVTDSCEETIDLAAKLGHLL-----IPGMVVLLSGDYGAGKTEFVRGIVQGFLGEtavGQ 12 MGRYRRVTHSCEETIDLATRVGRDL-----TLGMVVLLSGDYGSGKTEFVRGIVQGFLGEaavDQ 13 MKQLKWRTVNPEETKAIAKLTAAFA-----KPGDVLTLEGDLGAGKTTFTKGFAEGLGIT...RI 14 -NSMEFFLPDLNATDQWGQQLAQQL-----PLGTIILLQGDLGAGKTSLVQGLGRGLGIT...GE 15 ---TKIFLADKESTLNLGILLGETL-----TAGSVILLEGDLGAGKTTLVQGLGKGLSIT...EP 16 -------LNSKKETKNFAKLFAQNL-----KPNDIVLLNGDLGAGKTFFCREIIKHFCGKn..TN 17 -----VILESEEDTYKLAEEIAQLL-----KGSEVICLRGTLGAGKTTFVKALAKALKVKnp.SA 18 --TFSVALHNETATAQLMADLALLV-----GPGDVITLTGDLGAGKTAAARAMIRYLADDea.LE 19 ----RCVSRSAQDTARWGTVVGRLL-----EEGSVVVLQGALAAGKTCFVKGLALGLGIQ...EE 20 MMNRVIPLPDEQATLDLGERVAKAC-----DGATVIYLYGDLGAGKTTFSRGFLQALGHQ...GN 21 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQ...GN 22 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQ...GN 23 LPSISRFLADEAATLDLGAAWSSRL-----NAPLVIYLEGDLGAGKTTLTRGILRGLGHQ...GA 24 LPSISRFLADEAATLDLGAAWSSRL-----NAPLVIYLEGDLGAGKTTLTRGILRGLGHQ...GA 25 MRHLRFENLTEEQLKRLAKILTENL-----KGGEVVILSGNLGAGKTTFVKGMIRAIGLDe..KM 26 --------------RELGRRLAKLL-----RAGDLVMLSGELGAGKTTLTRGLGEGLGVR...GA 27 -GGGTATLPRVEDTLTLGSRLGEQL-----CAGDVVVLSGPLGAGKTVLAKGIAMAMDVE...GP 28 LRSGAVICERVEDTVALGSRLGEQL-----RAGDVVVLSGPLGAGKTVLAKGIAVAMDVD...GP 29 --GERRLLRGVDEQRALGAALARAL-----APGSVLFLEGELGAGKTTLTQGLLAALGFD...GH 70 80 90 100 110 | | | | | 1 RVEGTVDMM---...-..-----------------------------.---.....--------. 2 RVEGTIDLM---...-..-----------------------------.---.....--------. 3 RVEGTVDLL---...-..-----------------------------.---.....--------. 4 IFSPASGIVDKY...I..-----------------------------.---.....--------. 5 IFSPASGIVDKY...I..-----------------------------.---.....--------. 6 FTSPTYNIVNVY...D..FINFKFYHIDLYRVSSLEEFELVGGLEILmDLD.....SIIAIEWP. 7 ATSPTFSLMHAY...-..--SESVFHYDFY-MHDLKACLELGMLECL.LEK.....GIHFVEWGd 8 ATSPTFSLMHAY...-..--SESVFHYDFY-MRDLETCLELGMLECL.LEK.....GIHFVEWGd 9 VDSPTFSTMQKY...E..NHDICIYHYDIY-QEGLEGLLANGLFENF.FEK.....GLHLVEWGg 10 VASPSFSILHVY...G..NEPKRLCHYDLYRIDQKNQEY---IFQDA.EED.....DVLCIEWA. 11 VASPSFSLLHVY...E..AMGRRVCHYDLYRLETMHVKSGEGLFQDA.EEE.....DLICVEWP. 12 VASPSFALLHVY...E..AGGRRVCHYDLYRLETMDIKNGADLFQDA.EEE.....DLICVEWP. 13 VNSPTFTIIKEY...N..DGVLPLYHMDVYRMED--ESEDLGLDEYF.HGQ.....GVCLVEWA. 14 IVSPTFTIVNEY...R..EGKMPLYHLDLYRLNTLEVEYLYPEQYWQ.GEDfpl..GITAVEWP. 15 IVSPTFTLINEY...T..EGRIPLYHLDLYRLEPQEVLSLNLEIYWE.GIEiip..GIVAIEWS. 16 IISPTFNLLQIY...K..TPKFNIYHYDMYRIKSPEEIYELGFEEAL.NGN.....-LILIEWS. 17 VRSPTFTLVNEY...E..TDKGKLIHIDLYRVPDFDYSEFIG-----.--E.....GILAVEWE. 18 VPSPTFTLVQGY...E..LPPFPVMHADLYRVEDESELEEIGCRRCS.DAT.....-LVLIEWP. 19 ITSPTFTLLAVY...-..HGRLTLYHMDVYRLASLEDFFDIGAQECV.YGT.....GVCVIEWG. 20 VKSPTYTLVEPY...T..LDNLMVYHFDLYRLADPEELEFMGIRDYF.AND.....AICLVEWP. 21 VKSPTYTLVEEY...N..IAGKMIYHFDLYRLADPEELEFMGIRDYF.NTD.....SICLIEWS. 22 VKSPTYTLVEEY...N..IAGKMIYHFDLYRLADPEELEFMGIRDYF.NTD.....SICLIEWS. 23 VKSPTYAIVESY...P..LERFTLHHFDLYRFSFPEEWEDAGLDELF.AAN.....SVCLIEWP. 24 VKSPTYAIVESY...P..LERFTLHHFDLYRFSFPEEWEDAGLDELF.AAN.....SVCLIEWP. 25 VKSPTFTLMNVY...-..PGLKTIYHLDLYRLQDTDFLSLDVEDILE.DED.....GIMVVEWG. 26 VTSPTFVIARVH...PslGDGPPLVHVDAYRLSGGLDEMEDLDLDVS.LSD.....SVIVVEWG. 27 ITSPTFVLARMHrprR..PGTPAMVHVDVYRLLDHNSADLLSELDSL.DLDtdledAVVVVEWG. 28 VISPTYVLARVHlprR..LGTPAMIHVDVYRLLDHRDADLVGELDSL.DLDtdlaeAVVVMEWG. 29 VTSPTYALMQLY...P..ASAGQVLHVDAYRVRDVAELYEMDLDELI.AGS.....RLSVIEWG. 120 130 140 150 | | | | 1 -----------...--------..------------------------ 2 -----------...--------..------------------------ 3 -----------...--------..------------------------ 4 -----------...--------..------------------------ 5 -----------...--------..------------------------ 6 QIALSIVPKDRl..FSLTFKIV..G----------------------- 7 EKLEKILKKYD...LAIKVVEV..KTEST------------------- 8 EKLEKILKKYD...LAIKVVEI..KTES-------------------- 9 ENLKKTLMKFGistIQIKISIK..DDKRK------------------- 10 DRL----PKPR...FCDTI---..----NIYITMQTN----------- 11 EVV-NLLPQFRks.VCVHMCLL..ADSQREVVI--------------- 12 EAV-NLLPQFRks.VCVQMRSL..TDAQREVSIGVT------------ 13 HLIEEQLPQER...LQIVIKRAg.DDEREITFTAVGNRYEMLCEELSR 14 ERL-PQLPSQY...LQIQLCHQ..GEGRSIALTA-------------- 15 ERM-PYKPSTY...INVLLTYG..DEGSRQAEITPF------------ 16 EIIKHLLTPPL...IEVNLKVL..DNNKRLCSIHK------------- 17 ERD----KPCD...IILEIEIL..DENKRK------------------ 18 ERARRRCPR--...--------..------------------------ 19 ERVASELPEYT...VTISLRVL..ADGNR------------------- 20 QQGTGVLPDPD...VEIHIDYQ..AQGREARVSAVSSAGELLLARL-- 21 EKGQGILPEAD...ILVNIDYY..DDARNIELIAQTNLGKNIISAFS- 22 EKGQGILPEAD...ILVNIDYY..DDARNIELIAQTNLGKNIISAFSN 23 QQGGEFTPPAD...ITATLTHD..GDGRKCLLTAHTERGRE------- 24 QQGGEFTPPAD...ITATLTHD..GGGRKCLLTAHTERGRE------- 25 DLFDGFWPEDS...IKVKIEIA..DESHRNVEILIPEEVNFLVEKIE- 26 EGKVEELTEDR...LRLRIDRAvgDTADEVRHVTVTGLGERW------ 27 EGLAERLSQRH...LDVRLERV..SHSDTRIATWSW------------ 28 AGLAECLAARH...LDIRLERV..RYSDVRIATWQW------------ 29 EGLYADYPQAP...IYLFEHVE..GDPETRR-----------------