; SAM: /projects/compbio/bin/i686/prettyalign v3.3.2 (February, 2001) compiled 06/24/02_10:51:09 ; (c) 1992-2001 Regents of the University of California, Santa Cruz ; ; Sequence Alignment and Modeling Software System ; http://www.cse.ucsc.edu/research/compbio/sam.html ; ; ----------------- 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, 1998. ; A. Krogh et al., Hidden Markov models in computational biology: ; Applications to protein modeling, JMB 235:1501-1531, Feb 1994. ; --------------------------------------------------------------------- ; Sequences correspond to the following labels: ; 1 T0147_twice ; 2 1a4mA ; 3 1add ; 4 1ejrC ; 5 1eywA ; 6 1ezwA ; 7 1fwcC ; 8 1gdeA ; 9 1gox ; 10 1hw6A ; 11 1hzyA ; 12 1i0dA ; 13 1i60A ; 14 1korA ; 15 1pta ; 16 1qfeA ; 17 1ubpC ; 18 2mnr ; 19 4ubpC 10 20 30 40 | | | | 1 ........MYPVDLHMHTVASTHAYSTLSDYIAQAKQKGIKLFAITDH...GPD........MED 2 tpafnk..-PKVELHVH----LDGAIKPETILYFGKKRGIA-------...LPA........DTV 3 tpafnk..-PKVELHVH----LDGAIKPETILYFGKKRGIA-------...LPA........DTV 4 xsn50gkv----------------------------------------...---........--- 5 dri69vst----------------------------------------...---........--- 6 xae17kpt------------------KIAHLIKVAEDNGFEYAWICDH...YNN........YSY 7 xsn44evk----------------------------------------...---........--- 8 xal10elv----------------------------------------...---........--- 9 xm137rnv-------------------VAQLVRRAERAGFKAIALTVD...TPR........LGR 10 xtv31tqr----------------------AVEEALEVGYRHI-----...DTAaiy36xxx--D 11 xdr70vst----------------------------------------...---........--- 12 xdr70vst----------------------------------------...---........--- 13 mkl13len-----------------SNLKLDLELCEKHGYDYIEI---...RTM........DKL 14 mki.....----------------------------------------...---........--- 15 rin68vst----------------------------------------...---........--- 16 mkt11lii----------------------------------------...---........--- 17 mk132tag--GIDTHVHFINPD--------QVDVALANGITTL-----fg.GGT........GPA 18 ev137yds------H-----SLDGVKLATERAVTAAELGFRAVKT---...--K........IGY 19 mk132tag--GIDTHVHFINPD--------QVDVALANGITTL-----fgg-GT........GPA 50 60 70 80 90 100 | | | | | | 1 APHH........WHFINMRIW.PRVVDGVGILR.GIEANIKNVDGEIDCSGKMFDSLDLIIAGFH 2 EELRnii12slp---------.-----------.----------------GFLA----------- 3 EELR........N------II.-----------.-------GMDKPLSLPGFLAK---------- 4 ----........---------.-----------.------------------------------- 5 ----........---------.-----------.------------------------------- 6 MGVL........T------LA.AVITSKIKLGP.GI---TNP----------------------- 7 ----........---------.-----------.------------------------------- 8 ----........---------.-----------.------------------------------- 9 READ........I--------.---KNRF----.-----VLP----PFLTLKNFEGIDLXXXXXX 10 EPAA........AIAESLAKL.-----------.------------------ALDQVDLYL--VH 11 ----........---------.-----------.------------------------------- 12 ----........---------.-----------.------------------------------- 13 PEYL........K--------.-----------.---------DHSLDDLAEYFQTHHIKPLALN 14 ----........---------.-----------.------------------------------- 15 ----........---------.-----------.------------------------------- 16 ----........---------.-----------.-------------------GEGMPKIIVSLM 17 EGSKattvtp..-GPWNIEKM.LKSTEGLPINV.G------------------------------ 18 PALD........QDLAVVRSIrQAVGDDFGIMVd------Y--N--------------------- 19 EGSKattvtp..-GPWNIEKM.LKSTEGLPINV.G------------------------------ 110 120 130 140 | | | | 1 EPVFAPHDK........ATNTQAMIATIASGNVHIISHPGNPK........YEIDVKAVAEAAA. 2 ---------kfd12agcREAIKRI-------------------........---AYEFVEMKAK. 3 ----FDY--ympviagcREAIKRI-------------------........---AYEFVEMKAK. 4 ---------ir123tpgPWYISRMLQAADSLPVNI-GLLGKGNvsq.....----PDALREQVA. 5 --FDIGRDV........----SLLAEVSRAADVHIVAATGLWFdpp10lrsVEELTQFFLREIQ. 6 ---------yt133npk--------------------------d.......FEVAVPKIEEGAK. 7 ---------fg129tpgPWYISRMLQAADSLPVNI-GLLGKGNvsq.....----PDALREQVA. 8 ---------........--------------------------........SASEIRKLFDIAA. 9 XXXGLSSY-vag29vkgVITAEDARLAVQHGAAGIIVSNHGARqldyvp..ATIMALEEVVKAA. 10 WPTPAADNY........VHAWEKMIELRAAGLTRSIGVSNHLV........-----PHLERIVA. 11 --FDIGRDV........----SLLAEVSRAADVHIVAATGLWFdpp10lrsVEELTQFFLREIQy 12 --FDIGRDV........----SLLAEVSRAADVHIVAATGLWFdpp10lrsVEELTQFFLREIQy 13 ALVFFNNRDekghnei.ITEFKGMMETCKTLGVKYVVAVPLVTe.......QKIVKEEIKK---. 14 ---------........-----------------VLAYSGGLD........TSIILKWLKET--. 15 --FDIGRDV........----SLLAEVSRAADVHIVAATGLWFdpp10lrsVEELTQFFLREIQy 16 G------RD........INSVKAEALAYREATFDILEWRVDHFmdiastqsVLTAARVIRDAMP. 17 ---------........-----------------ILGKGHGSS........----IAPIMEQID. 18 ----QSLDV........PAAIKRS-QALQQEGVTWIEEPTLQH........---DYEGHQRIQS. 19 ---------........-----------------ILGKGHGSS........----IAPIMEQID. 150 160 170 180 | | | | 1 ...K.......HQ........V...ALEINNSSFL..HSRKGSEDNCR....EVAAAVRDAGGWV 2 ...E.......GV........V...YVEVRYSPHLlaNSKV---DPMPwnqt------------- 3 ...E.......GV........V...YVEVRYSPHLlaNSKV---DPMPwnqt------------- 4 ...A.......GV........I...GLKIHEAW--..---GATPAAID....CALTVADEMDIQV 5 ...YgiedtgiRA........G...IIKVATTG--..KATPFQELVLK....AAARASLATGVPV 6 ...E.......AGrsl11aayT...CFSIDKDE--..----DKAIEAT....KIVVAFIVMGSP- 7 ...A.......GV........I...GLKIHEDW--..---GATPAAID....CALTVADEMDIQV 8 ...G.......MK........D...VISLGIGE--..-PDFDTPQHIK....EYAKEALDKGLT- 9 ...Q.......GR........I...PVFLDGGV--..--------RRG....TDVFKALALGAAG 10 ...A.......TG........VvpaVNQIELHP--..------AYQQR....EITDWAAAHDVKI 11 gieD.......TG........IragIIKVATTG--..KATPFQELVLK....AAARASLATGVPV 12 gieD.......TG........IragIIKVATTG--..KATPFQELVLK....AAARASLATGVPV 13 ...-.......--........-...----------..----SSVDVLT....ELSDIAEPYGVKI 14 ...Y.......RA........E...VIAFTADI--..----GQGEEVE....EAREKALRTGASK 15 gieD.......TG........IragIIKVATTG--..KATPFQELVLK....AAARASLATGVPV 16 ...D.......IP........L...LFTFRSAKEG..GEQTITTQHYL....TLNRAAIDSGLVD 17 ...A.......GA........A...GLKIHEDW--..---GATPASID....RSLTVADEADVQV 18 ...K.......LN........V...PVQMGENW--..--------LGP....EEMFKALSIGACR 19 ...A.......GA........A...GLKIHEDW--..---GATPASID....RSLTVADEADVQV 190 200 210 220 230 240 250 | | | | | | | 1 .ALGSDSHTAFTMGEFEECLKILDAVDFPPERILNVSPRRLLNFLESRGMAPIAEFADLMYPVDL 2 .-----------------------EGDVTPDDVVDLVNQGLQEGEQAFGIKVR------------ 3 .-----------------------EGDVTPDDVVDLVNQGLQEGEQAFGIKVR------------ 4 .ALHSDTLNESGFV----------------EDTLAAIGGRTIHTFHTEG---------------- 5 .TT----HTAASQRDGEQQAAIFESEGLSPSRV-------------------------------- 6 .------------------DVVLERHGIDTEK--------------------------------- 7 .ALHSDTLNESGFV----------------EDTLAAIGGRTIHTFHTEG---------------- 8 .------HYGPNIGLLELREAIAEKLKK----Q-------------------------------- 9 .VF----------IGRPVVFSLAAEGEAGVKKVLQMMRDEFELTMALSGCRSLKEISRS------ 10 eSWGPLGQGKYDLFGAEPVTAAAAAHGKTPAQA-------------VLRWHLQKGFVVFPKSV-- 11 .TT----HTAASQRDGEQQAAIFESEGLSPSRV-------------------------------- 12 .TT----HTAASQRDGEQQAAIFESEGLSPSRV-------------------------------- 13 .ALEFVGHPQCTVNTFEQAYEIVNTV--------------------------------NRDNVGL 14 .AIALDL----------------------KEEF----VRDFVFPMMRAGAVYEGYYLLGTSIA-- 15 .TT----HTAASQRDGEQQAAIFESEGLSPSRV-------------------------------- 16 .MI------------------------------------------------------------DL 17 .AIHSDTLNEAGF----------------LEDTLRAINGRVIHSFHVEG---------------- 18 .LAMPDAMKIGGVTGWIRASALAQQFGIPM----------------------------------- 19 .AIHSDTLNEAGF----------------LEDTLRAINGRVIHSFHVEG---------------- 260 270 280 290 300 310 | | | | | | 1 HMHTVASTHAYSTLSDYIAQAKQKGIKLFAITDHGPDMEDAPHHWHFINMRIWPRVVDGVGILRG 2 ----------------------------------------------------------------- 3 ----------------------------------------------------------------- 4 -----------------------------AGGGHAPDIITACAHPNILPSSTNPT---------- 5 ----------------------------------------------------------------- 6 -AEQIAEAIGKGDFGTAIGLVDEDMIEAFSIAGD------------------------------- 7 -----------------------------AGGGHAPDIITACAHPNILPSSTNPTLPYTLN---- 8 ---------------------------------N------------------------------G 9 ----------------------------------------------------------------- 10 --------------------RRERLEENLDVF--------------------------------- 11 ----------------------------------------------------------------- 12 ----------------------------------------------------------------- 13 VLDSFHFHAMGSNIESLKQADGKKI---------------------FIY---------------- 14 ----------------------------------------------------------------- 15 ----------------------------------------------------------------- 16 ELFTGD----------------------------------------------------------- 17 -----------------------------AGGGHAPDIMAMAGHPNVLPSSTNPTRPFTVN---- 18 ----------------------------------------------------------------- 19 -----------------------------AGGGHAPDIMAMAGHPNVLPSSTNPTRPFTVN---- 320 330 340 350 360 370 3 | | | | | | 1 IEANIKNVDGEIDCSGKMFDSLDLIIAGFHEPVFAPHDKATNTQAMIATIASGNVHIIS...HPG 2 -------------------------------------------------------SILCcmrHQP 3 -------------------------------------------------------SILCcmrHQP 4 -----------------------------------------------------------...--- 5 --------------------------------CIGHSDDTDDLSYLTALAARGYLIGLD...HIP 6 -----------------------------------------------------------...--- 7 ----------------------------------------TIDEHLDMLMVAH------...--- 8 IEADPKTEIMVLLGANQAFLMGLSAFLKDGEEVLIPTPAF--VSYAPAVILAGGKPVEV...PTY 9 -----------------------------------------------------------...--- 10 -----------------------------------------------------------...--- 11 --------------------------------CIGHSDDTDDLSYLTALAARGYLIGLD...HIP 12 --------------------------------CIGHSDDTDDLSYLTALAARGYLIGLD...HIP 13 --------HI------DDTEDFPIGFLTDEDRVWPGQGAIDLDAHLSALKEIGFSDVVS...--- 14 -----------------------RPL---------------IAKHLVRIAEEEGAEAIA...HGA 15 --------------------------------------------------------CIG...HSD 16 ---------------------------------------ADVKATVDYAHAHNVYVVMSn..HDF 17 -----------------------------------------------------------...--- 18 -----------------------------------------------------------...--- 19 -----------------------------------------------------------...--- 80 390 400 410 420 430 | | | | | | 1 NPKY..EIDVKAVAEAAAKHQVALEI...NNSSFLHSRKGSE........DNCREVAAAVRDAGG 2 SW--s.LEVLELCKKYNQKTVVAMDL...AGDETI-EGSSLF........PGHVEAYEGAVKNGI 3 SW--s.LEVLELCKKYNQKTVVAMDL...AGDETI-EGSSLF........PGHVEAYEGAVKNGI 4 LPYT..LNTIDEHLDMLMXXXXXXXX...XXXXXAFAESRIR........RETIAAEDVLHDLGA 5 HSAI..GLEDNASASAL---------...-------LGIRSW........QTRALLIKALIDQGY 6 ---P..DTVVDKIEELLKAGVTQVVV...G------SPIGPD........KEKAIEL-------- 7 --HL..DPDIAEDVAFAESRI-----...------------R........RETIAAEDVLHDLGA 8 EEDEf.RLNVDELKKYVTDKTRALII...NSPCNPTGAVLTK........KDLEEIADFVVEHDL 9 ----..--------------------...-------------........--------------- 10 ----..--------------------...-------------........--------------- 11 HSAI..GLEDNASASAL---------...-------LGIRSW........QTRALLIKALIDQGY 12 HSAI..GLEDNASASAL---------...-------LGIRSW........QTRALLIKALIDQGY 13 ----..--------------------...-------------........--------------- 14 TGKGndQVRFELTAYALKPDIKVI--...-------------........--------------- 15 DTD-..---DLSYLTALAARGYLIGLdhiPHSAIALLGIRSW........QTRALLIKALIDQGY 16 HQTPsaEEMVSRLRKMQALGADIPKI...A------VMPQSK........HDVLTLLTATLEM-- 17 ----..TIDEHLDMLMVCHHL-----...---------KQNIped12rirPETIAAEDILHDLGI 18 ----..--------------------...-------------........--------------- 19 ----..TIDEHLDMLMVCHH------...-------------........--------------- 440 450 460 470 480 4 | | | | | 1 ..WVALGSDSHTAFTMGE.....FEECLKILDAVDFPPERILNVSPRRLLNFLESRGMAPIAEFA 2 ..HRTV------------.....------------------------------------------ 3 ..HRTV------------.....------------------------------------------ 4 ..FSLTSSDSQAMGRVGEvilrtWQVAHRMKVQRGALAEETGDNDNFRVKRYIAKYT-------- 5 mkQILVSND---------.....------------------------------------------ 6 ..----------------.....------------------------------------------ 7 ..FSLTSSDSQAMGRVGEvi...------------------------------------------ 8 ..IVIS------------.....------------------------------------------ 9 ..----------------.....------------------------------------------ 10 ..----------------.....------------------------------------------ 11 mkQILVSND---------.....------------------------------------------ 12 mkQILVSND---------.....------------------------------------------ 13 ..----------------.....----------VELFRPEYYKLTAEEAIQTAKKT--------- 14 ..----------------.....------------APWREWSFQGRKEMIAYAEAHGIPV----- 15 mkQILVSNDW----LFGF.....SSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVP------ 16 ..----------------.....------------------------------------------ 17 ..ISMMSTDALAMGRAGE.....------------------------------------------ 18 ..----------------.....------------------------------------------ 19 ..----------------.....------------------------------------------ 90 | 1 DL......... 2 --ha139eyq. 3 --ha139eyq. 4 --in159flf. 5 --wlf64rax. 6 --vgq11fkx. 7 --lr196flf. 8 --de191klv. 9 --hia17xxx. 10 --dfd32xxx. 11 --wlf64ras. 12 --wlf64ras. 13 --tvd11fsm. 14 --px236xxx. 15 --qet20ptl. 16 --qqh61hna. 17 --mv198flf. 18 --ssh65ylv. 19 --lk246flf.