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