; 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 T0101 ; 2 gi|6175856|gb|AAF05308.1|AF171228_1_26:425 ; 3 gi|2121035|pir||S69796_26:425 ; 4 gi|3914287|sp|Q47473|PELL_ERWCH_26:425 ; 5 gi|5256971|dbj|BAA81753.1|_286:663 ; 6 gi|4499931|emb|CAB39324.1|_385:730 ; 7 gi|7465555|pir||S77623_18:328 ; 8 gi|129764|sp|P22751|PELX_ERWCH_384:688 ; 9 gi|3873279|gb|AAD04920.1|_19:328 ; 10 gi|3873281|gb|AAD04921.1|_18:328 ; 11 gi|3873283|gb|AAD04922.1|_19:327 ; 12 gi|7482933|pir||A69511_127:387 ; 13 gi|7475519|pir||A70065_34:329 10 20 30 40 50 60 | | | | | | 1 ADCSSDLTSGISTKRIYYVAPNGNSSNNGSSFNAPMSFSAAMAAVN..PGELILLKPGTYTIPYT 2 ADCSSDLTSGIITKRIYYVAPNGTSSNNGSSFNAPMSFSAAMAAVN..PGELILLKPGTYTIPYT 3 ADCSSDLTSGISTKRIYYVAPNGNSSNNGSSFNAPMSFSAAMAAVN..PGELILLKPGTYTIPYT 4 ADCSSDLTSGISTKRIYYVAPNGSSSNNGNSFNSPMSFTAAMAAAN..PGELILLKPGTYTIPYT 5 ---------------DLIVAPNGQEGNPGT-LNQPTTLTSAITRIQ..PGRTIYMRGGTYAFSET 6 ---------KLADAKNLYVSPEGKADNNGS-KNAPLDIKTAINALQ..AGGTLRLMDGDYS---- 7 ---------------------------------DRASIQAAIDAAYaaGGGTVYLPAGEYRVSAA 8 ---------TLADARNLYVSPEGKAGNDGS-KNAPLDIKTAINALP..GGGTLWLMDGDYS---- 9 ----------------------------------RVAIQAAIDAAHaaGGGTVYLPPGEYRVSAA 10 ---------------------------------DTDAIQAAIDAAHkaGGGTVYLPSGEYRVSGG 11 ----------------------------------RAAIQAAIDAAHaaGGGTVHLPAGEYRVSGG 12 ----------------------------------------------..----------------- 13 --------------DYLYVSPNGSDQNEGTKEKPFRTLAHASEKAA..AGTTVMIREGTYH---- 70 80 90 100 110 120 | | | | | | 1 QGKGNTITFNKSGKDGAPIYVAAANCGRAVFD.......FSFPDSQWVQASYGFYVTGDYWYFKG 2 QGKGNTITFNKSGKEGAPIYVAAANCGRAVFD.......FSFPDSQWVQASYGFYVTGDYWYFKS 3 QGKGNTITFNKSGKDGAPIYVAAANCGRAVFD.......FSFPDSQWVQASYGFYVTGDYWYFKG 4 QGKGNTITFNKSGKEGSPIYVAAANCGRAVFD.......FSFPDSQWVQASYGFYVTGDYWYFKG 5 ----VLIERGNNGLEGARKRIVGYNGEKPVLD.......FSA--QAFDPMNRGLQINGHYWHVQG 6 ---ATVIPVSASG-NANGIKTLMPAGKKAIF-.......------------HGLQLNASYWKVKG 7 GEPGDGCLMLKDG-----VYLAGAGMGETVIK.......LIDGSDQ--------KITGMVRSAYG 8 ---ATVIPVSATQRKG--MKTLMPVGKKAVF-.......------------HGLQLNASYWKVKG 9 GEPSDGCLTLRDN-----VYLAGAGMGQTVIK.......LVDGSAQ--------KITGIVRSPFG 10 DEASDGALIIKSN-----VYIVGAGMGETVIK.......LVDGWDE--------KLTGIIRSANG 11 ERGVDGALMMKSN-----VYLAGAGMGETVVK.......LLDGWNG--------HVNGMIRSSGT 12 --------------NG--------------IE.......VYGDDSQLDKVFAGLRADGSDPSDSG 13 ----ETLDVKHSGTDGKPITFRNYENENVVISgesvanaEYETPLIRIHDKHDIAISGLTIQDLS 130 140 150 160 170 1 | | | | | 1 VEVTRAGYQGAYVIGSHNTFENTAFHHNRNTGLEINN........GGSYNTVINSDAYRNYDPKK 2 VEVTQAGYQGAYVIGSHNTFENTAFHHNRNTGLEINN........GGSYNTVINSDAYRNYDPKK 3 VEVTRAGYQGAYVIGSHNTFENTAFHHNRNTGLEINN........GGSYNTVINSDAYRNYDPKK 4 IEVTRAGYQGAYVTGSHNTFENTAFHHNRNTGLEINN........GGSYNTVINSDAYRNYDPKK 5 IEVKEAGDNGIFIGGNYNRIENVETHHNKDTGLQISRyss9trdeWPSYNEIINVYSHNNYDPD- 6 VEITEKSFR---IEGSYNQIERVLAHHCDNTGIQVSSndsvgrplWASHNLILNSESHSNQDPSK 7 EETSNFGMRDLTLDGNRD-----------NTSGKVDG........W-----------FNGYIPGG 8 IEITEKSFR---IEGSHNQIERLLAHHCDNTGIQVSSsdnvgrplWASHNLILNSESHSNQHPSK 9 EETSNFGMRDLTLDGNRA-----------NTVDKVDG........W-----------FNGYAPGQ 10 EKTHDYGISDLTIDGNQD-----------NTEGEVDG........F-----------YTGYIPGK 11 EETHDFGVRDLTLDGNRD----------NNPEGTVFG........F-----------YTGYKFG- 12 F--PRISSHGIRILSNNTTVNSSIAAYNGGLGIRFEGs.......GVNSGKAVNSIAYYNAL--- 13 VSSEEATAIGIYVSGSSSHIA-IKDNHIRGIKTTADE........GNAHGIAVYG---------- 80 190 200 210 220 230 2 | | | | | | 1 NGSMADGFGPKQKQGPGNRFVGCRAWENSDDGFDLFDS.....PQKVVIENSWAFRNGINYWNDS 2 NGSMADGFGPKQKQGPGNRFISCRAWENSDDGFDLFDS.....PQKVVIENSWAFRNGINYWNDS 3 NGSMADGFGPKQKQGPGNRFVGCRAWENSDDGFDLFDS.....PQKVVIENSWAFRNGINYWNDS 4 NGSMADGFGPKQKQGQGNRFGGCRAWENSDDGFDLFDS.....PQKVVIENSWAFRNGINYWSDS 5 DGEDADGFAAKLTSGPGNVFDGCIAAYNVDDGWDLYTKsdtgaIYPVIIRNSIAYNNGSTEGGHS 6 --KDADGFAIKMRVGEGNVIRGAFSHDNVDDGFDLFNK.....-----IEDG---PNGVVVIGNS 7 DGADRDV-----------TIERVEVREMSGYGFDPHEQ.....TINLTIRDSVAHDNGLD----- 8 --KDADGFAVKMRVGEGNVIRGAFSHDNVDDGFDLFNK.....-----IEDG---PNGAVMIENS 9 PGADRNV-----------TIERVEVREMSGYGFDPHEQ.....TINLVLRDSVAHHNGLD----- 10 NGADYNV-----------TVERVEIREVSRYAFDPHEQ.....TINLTIRDSVAHDNGKD----- 11 DGADRNV-----------IVERVEAREMSGYGFDPHAR.....TVNLVIRDSVAHDNGFV----- 12 SGSNLDGFIA-VNGASNVIFENCVAANNSGSGIDNYNG.....-GRITIRNCSVVKNGWGNAEPS 13 TGSMKDI----------------RIEDNTVEKLTLGAS.....-EAVVLNGN---IDGFTVAGNV 40 250 260 270 280 | | | | | 1 AFAGN.GNGFKLGG.......NQAVGNHRITRSVAFGNVSKGFD........QNNNAGGVTVINN 2 AFAGN.GNGFKLGG.......NQAVGNHRITRSVAFGNVSKGFD........QNNNAGGVTVINN 3 AFAGN.GNGFKLGG.......NQAVGNHRITRSVAFGNVSKGFD........QNNNAGGVTVINN 4 SFAGN.GNGFKLGG.......NQAVGNHRITRSVAFGNVSKGFD........QNNNAGGVTVINN 5 TSNSD.GNGFKLGG.......SNIPVNHIVENNMAFGNKKHGFT........YNSNPGSITMTNN 6 ISVNNtSNGFKLGG.......EGQPVAHQVKNSIAIGNHMDGFS........DNFNPGALQVTNN 7 -----.--GFVA--.......-DYLVDSVFENNVAYANDRHGFN........VVTSTHDFVMTNN 8 ISLNNtSNGFKLGG.......EGQPVAHQVKNSIAIGNHMDGFS........DNFNPGALQVSNN 9 -----.--GFVA--.......-DYQIGGTFENNVAYANDRHGFN........IVTSTNDFVMRNN 10 -----.--GFVA--.......-DFQIGAVFENNVSYNNGRHGFN........IVTSSHDIVFTNN 11 -----.--GFVA--.......-DHQIDGAFENNVAYNNDLHGFN........VVTSSHDFTLSDN 12 -----.--GIRVSG.......S----GSEIVNNLVAENVGDGIL........-------VTPTGS 13 VRNNN.NIGIDLIGyegtadkNDYVRNGVVENNTVYQNSTYGNPayg11ggiYVDGGHDIEIKNN 290 300 310 320 330 340 | | | | | | 1 TSYKNG........INYGFGS....NVQSGQKHYFRNNVSLSASVTVSNADAKSNSWDTGPAASA 2 TSYKNG........INYGFGS....NVQSGQKHYFRNNVFLSASVTVNNADAKSNSWDTGPAASA 3 TSYKNG........INYGFGS....NVQSGQKHYFRNNVSLSASVTVSNADAKSNSWDTGPAASA 4 TSYKNG........INYGFGS....NVKSGQKHYFRNNVSLSGSATVNNADAKSNSWDTGPVASA 5 TSWNNG........TRSGSNF....AFDRG-THLFANNLSFEASS--SDKYATSTDIDGSNLWWH 6 IALDN-........VRFNFIFrpspYYGPEKQGIFKNNVSLRTQPG-KYDDAVVGRVDASNYFIK 7 VAYGNGssg18psnILIDGGA....YYDNAREGVL---LKMTSDITLQNADIHGNGSSGVRVYGA 8 IALDN-........VRFNFIFrpspYYGYEKQGIFKNNVSLRTQPG-KYDDAVVGRLDASNYFI- 9 VAYGNGgng18penILIDGGS....YYDNGLEGVL---VKMSNNVTVQNADIHGNGSSGVRVYGA 10 VAYGNGang18vynVEIEGGS....FHDNGQEGVL---IKMSTDVTLQGAEIYGNGYAGVRVQGV 11 VAYGNGaag18aynIRIDGGS....YHDNALEGVL---IKLSHDVTLQNAHIYDNGTAGVRIAGA 12 TSTPTG........IKISRNS....IFKNGYVGIDLNVEDTSNNMG------------------- 13 TVYDND........IGIEATS....EH----KGKYANAIQITDNKVYNNAYTG------------ 350 360 370 380 390 400 | | | | | | 1 SDFVSLD.TSLATVSRDNDGTLPETSLFRLSANSKLINAGTKESNISYSGSAPDLGAFERN 2 SDFVSLD.TSLATTSRDNDGTLPETSLFRLSASSKLINAGTKESNISYSGSAPDLGAFERN 3 SDFVSLD.TSLATVSRDNDGTLPETSLFRLSANSKLINAGTKESNISYSGSAPDLGAFERN 4 SDFVSLD.TSLATISRDNDGTLPETALFRLSTNSKLINAGTKESNISYSGSAPDLGAFERN 5 NTKGSQNaKNLKVTASDFISLIPTVS---RDANGAPVIGGF----LQLTGSSSLKGA---- 6 NN-RALN.SQGKEITTANYKSVTVPAVFNRDEKGNLQLGDF-------------------- 7 QDVQILD.NQIHDNAQA--AAVPEVLLQSFDDTAGASGTYYTTLNTRIEGN---------- 8 -------.----------------------------------------------------- 9 QGVQILG.NQIHDNAKT--AVAPEVLLQSYDDTLGVSGNYYTTLNTRVEGN---------- 10 EDVRILD.NYIHDNAQS--KANAEVIVESYDDRDGPSDDYYETQNVTVKGN---------- 11 QDVQLLD.NRIHDNVQN--GTYPEVLLQAFDDSG-ITGNVYETLNTLIEGN---------- 12 -DNVTLN.DGQLDCSQPNCGIDYPVITAAQLIGSSLHIEGFINDENAGSGSSSFAGA---- 13 -------.-----------------------------------------------------