; SAM: prettyalign v3.2 (July 31, 2000) compiled 08/11/00_16:27:51 ; (c) 1992-2000 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, 1999. ; 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 RECJ_ECOLI/382-451 ; 2 RECJ_ERWCH/381-449 ; 3 RECJ_HAEIN/376-445 ; 4 P73518/390-455 ; 5 O32044/370-436 ; 6 O83702/514-575 ; 7 Q9Z7Z0/390-454 ; 8 P94659/317-381 ; 9 O84453/389-453 ; 10 Q9ZD22/386-452 ; 11 Q9ZMA0/338-403 ; 12 O67909/370-434 ; 13 Y371_MYCGE/252-315 ; 14 O51269/507-572 ; 15 Q9ZM41/283-342 ; 16 O67552/249-312 ; 17 O51564/262-322 ; 18 O83450/285-343 ; 19 P71615/275-333 ; 20 MGPA_MYCPN/261-317 ; 21 MGPA_MYCGE/296-360 ; 22 O31824/247-305 ; 23 YG33_METJA/394-461 ; 24 O58017/401-472 ; 25 O28250/387-458 ; 26 Y988_METJA/239-310 ; 27 O73979/249-318 ; 28 Y977_METJA/396-466 ; 29 O26266/371-441 ; 30 O57804/392-465 ; 31 O29523/379-449 ; 32 O27473/379-449 ; 33 O29559/362-431 ; 34 Y831_METJA/355-424 ; 35 YYBT_BACSU/588-647 ; 36 O66728/230-290 ; 37 O58035/847-912 ; 38 SYA_ARCFU/831-899 ; 39 O67323/793-863 ; 40 SYA_THIFE/800-870 ; 41 SYA_ECOLI/799-869 ; 42 SYA_BACSU/801-872 ; 43 SYA_HAEIN/798-868 ; 44 SYA_BARBA/810-882 ; 45 SYA_SYNY3/797-870 ; 46 Q9ZCA4/802-873 ; 47 SYA_METJA/829-887 ; 48 Q9Z714/793-865 ; 49 O84754/846-917 ; 50 O57734/333-400 ; 51 SYAC_SCHPO/881-951 ; 52 SYAC_YEAST/877-950 ; 53 SYA_METTH/817-891 ; 54 SYA_THETH/808-882 ; 55 SYA_MYCTU/821-895 ; 56 O01541/890-961 ; 57 SYA_HUMAN/886-957 ; 58 SYA_BOMMO/889-960 ; 59 SYA_HELPY/772-839 ; 60 SYA_ARATH/923-996 10 20 30 40 50 60 | | | | | | 1 HRPVIAFA---PAGDGTLKGSGRS--IQGLHMRD---ALERLDTLYPGMML-KFG-GHAMAAGLS 2 HRPVIAFA---PAGDGILKGSGRS--IAGLHLH----ALERLDTCHPGLML-KFG-GHAMAAGLS 3 HRPVIAFA---QDSEGILKGSARS--IEGLHMRD---VLERIHSQHPNMIL-KFG-GHAMAAGLS 4 GRPAILLN---TQDGKIAKGSARS--VANIDLY------ALLHSQRHLML--GFG-GHPFAAGLS 5 YRPAIVLGI--DEEKGIAKGSARS--IRGFNLF------ESLSECRDILP--HFG-GHPMAAGMT 6 ---VIICI----MADGHAVGSLRS--ARGYHLF------SLLDPLADLFS--DYG-GHAFAAGFS 7 NKPVVIIA----IQRGIGKGSART--IGSFPLLG------VLKKCSSLLL--SYG-GHDFAAGVI 8 NKPVAIIS----NQGGVGKGSLRT--IGSFPLLG------ILQKCSSLFI--SYG-GHDFAAGII 9 NKPVAIIA----LQDGIGKGSLRT--IGSFPLLG------VLRKC-ESFFL-SYG-GHDFAAGLM 10 DKPVVVVA----LNNGIGKASCRS--ILGIDFS-----AEIINAKSKDLII-SGG-GHAMAAGFT 11 QKPSLVFT----FKEGVYKGSARS--SPNIDLID---ALNGVSSL----LL-GYG-GHRQACGLS 12 NKPVAVFS----KGKTKAVGSIRS--IESIDVY------DKVSTMRDMFL--KWG-GHDKAMGLT 13 KGVKIWTTVYFNESIKKWIGSIRS---RNIPIN------NFAQMF-------NGG-GHKYAAAFV 14 QKVAIFLT----KQDNIIKGSIRS--NNKINSK-------TLISIIPSHLVINSG-GHKAAAGFT 15 ----FYID-----VNSKGNVSLRA--NGNCDVC----------ELSQMCF--NGG-GHRNASGGK 16 EGVKVAYALIEKPEEGVWKVSLRA--KGNVNVG------KIAERL-------GGG-GHKYASGAK 17 NEILGILK---EMEDGSIIVGLRS--KDSFDVG----------KLAEDFG---GG-GHKNASGFR 18 EAIVVVRQ----ESPTHCSVGFRS--RGSIDVS------VIAARF-------GGG-GHRCAAGLR 19 AEVAAVFK---EVEPHRWSVSMRA---KTVNLA----------AVASGFG---GG-GHRLAAG-Y 20 HIWLFFIE----EGKNHYRVEFRS---NGINVR----------EVALKYG---GG-GHIQASGAV 21 YKIWLFFI---EQANNEIRIDLRS---NGINVR------DIAIKY-------GGG-GHNNASGAI 22 LDYIAILS------MGSKRVSLRT--IHDYIDV---------SEIAGRYG---GG-GHAKASGCS 23 ISTTFVFG----IVGDEIHISART--KDLRLNLG-----EILNKA---FG---GG-GHQTAAAAK 24 ITTVLVFG----IVDDRIEISART--RDVRVNIG-----NVMKEAFGEIG--SGG-GHPQAGGAR 25 ISTVVVFG----VIKDTVYVSARN--KDVRIHMG-----EVLRRAFGDVG--SAG-GHAHAAGAQ 26 ADVAFVVAV--RKKEKEIRVSARC--RKHVSKY--VHLGNLMEKIGKELGG-SGG-GHSEAGGLN 27 ADVAIVGS-----EKDGVRISARA--KDYLVKQG-LHLGKIMEKVGPIIKG-SGG-GHAGAAGAN 28 MKPIFAIT----EDENGYKVSARC--PKLLCFAEDVNLAKAIKYASEKVNG-SGG-GHKFACGAY 29 RRPMIGLG----ETADGLKVSLRC--SRLLAFDG-IHFGSIMRRVAEKVGG-SGG-GHATACGAY 30 EKPVIVFAD-TDEDPNLIKGSART--TEKALERG-YHLGEALRKAAEIIGG-EGG-GHAIAAGIR 31 EKPIIAFA----ESDKGVKVSARA--TYRLVERG-VHLAKALKRAAEAVGG-VGG-GHSVAAGAT 32 DIPLLGLS----RMDQHVKVSART--TRPAVERG-VNLGVALRDAAASFGG-TGG-GHDIAAGAM 33 DKPLIVVN----IKNEYAKVSART--NEALAER--VDLAEVMRLAAEKVGG-RGG-GHRVAAGAN 34 DKPVIGYH----IEGDIAKFSARG--NRDLVNRG-LNLSVAM-AVAKEFGG-NGG-GHDVASGAV 35 EASFAVAR----RDEQTVCISARS--LGEVNVQ------IIMEAL-------EGG-GHLTNAATQ 36 SDAFFVII----EAEGKTYVFGRS--QSEDVDVG-----EILSHF-------GGG-GHREAGAVK 37 KRVVVLIS-----RDGYFAVSVGS-------EVG-VEANELAKKITLIAGG-GGG-GRRDIAQGK 38 EKGAVGCLM--AKGEGKVFVVTFS--GQKYDAR------ELLREIGRVAKG-SGG-GRKDVAQGA 39 KDVVFIAS----RKGDKINFVIGV--SKEISDK--VNAKEVIREVGKVLKG-GGG-GRADLAQGG 40 DGVIVLAG----VEREKVALIAGV--GKGLTGR--VHAGELVNTVAQPLGG-KGG-GRPELAQAG 41 STIIVLAT----VVEGKVSLIAGV--SKDVTDR--VKAGELIGMVAQQVGG-KGG-GRPDMAQAG 42 SAVIVLGA----VQNDKVNISAGV--TKDLIEKG-LHAGKLVKQAAEVCGG-GGG-GRPDMAQAG 43 SGVIAFAS----ILDEKVNLVVGV--TNDLTAK--IKAGELVNLMAQQVGG-KGG-GRPDMAMAG 44 SGVVAFIS---VSEDGKGSAVVGV--TDDLTDT--LNAVDLVRIISVTLGGQGGG-GRRDMAQAG 45 ESAVVLAS---IPEEGKVSLVAAF--SPQLVKTKQLKAGQFIGAIAKICGG-GGG-GRPNLAQAG 46 NLIVVYIA----HGVDKLSITVAV--SKAITDK--FNAGIIAKELSLFLGGSGGG-GQASIAQAG 47 NAIVVLLN-------DKGNILCKR--GENVDIK----MNELIRYIAK------GG-GREHLAQ-- 48 EKLISLWT---TEKNGKYIVLSRV--SDDLITQG-VHAQDLLKAVLTPCGG-RWG-GKDQSAQGS 49 NFISLWIT----EKNGRYIVLSRV--SDDLTKRG-VQAHTLLAELLAPYGG-RCG-GKAISAQGS 50 SNTILLLA------NEKYVLFAKN---EGVPVS----MRELLKEVIDELGG-KGG-GTDNLARGR 51 DKSIYLLA----SDDTKVAHACLV--SPEAMKK--LTPQEWSQKVCHSIGG-RSG-GKGDTCQGV 52 DKSIYLLA----GNDPEGRVAHGCYISNAALAKG-IDGSALAKKVSSIIGG-KAG-GKGNVFQGM 53 LELSATVDA-VVLANPEGKIVGAA--SEDAVKAG-LRINEVISQAAAVLGG-GGG-GRPHLAQGA 54 DDLVARGAD-VALVLSGGQAVLKL--SPKAQGMG-LEAGALFRALAEKAGG-RGG-GKGALAQGG 55 SEPAVVALI-AEGESQTVPYAVAA--NPAAQDLG-IRANDLVKQLAVAVEG-RGG-GKADLAQGS 56 AVMAFSVN----EDSGKVLCLAKV--DKSLVSNG-LKANEWVNEVCTVLGG-KGG-GKDANAQLT 57 SAMLFTVD----NEAGKITCLCQV--PQNAANRG-LKASEWVQQVSGLMDG-KGG-GKDVSAQAT 58 AAMFFSVD----KDADKIYCLAAV--PKSDVEKG-LLASEWVQSVVDIIGG-KGG-GKAESAQAS 59 RLLAMVFK----KENERITLACGV---KNAPIK----ANVWANEVAQILGG-KGG-GRGDFASAG 60 SIMVFSTD----ESTNKAVVCAGV--PEKSDQFKPLDVTEWLTTALGPLKG-RCGKGKGGLASGQ 70 80 | | 1 LEEDK------FKLFQQRFGE 2 LVEDR------FDEFRQRFAD 3 IREEH------FADFQHIFNQ 4 LPLDK------LPLFTEAVNQ 5 LKAED------VPDLRSRLNE 6 IPSER------IPQLLHRMEL 7 MKEDK------VEDFKKKFVH 8 INEDQ------VEAFRKKFIH 9 IKEDQ------VEGFRKKFIH 10 ATASK------LQELQDFLND 11 VGKNNI-----VSLFETLENF 12 LPSNR------LEEFREKVNQ 13 LDEKNQ-----FMKLVQIMDD 14 LHENL------LEDFIKELEY 15 IDGFKES--FNYKDIKEQVEE 16 IKTNS------YEEALKKLLE 17 IKQGS------LEIVKNRMLA 18 I-EGT------VDELLPRFVA 19 TTTGS------IDDAVASLRA 20 LKSKRD--------IIRVVQD 21 ITNKKQIS-DVVSDCVKKIVY 22 ITDEV------YELFVAEAFR 23 IPLGIFKAVSDKEALRKLVEE 24 IPLGIFKLARDKTSLLRLVEE 25 IPLGIFGETNEKDLLAKLITE 26 APYDKS------KSKEKVIKE 27 GKENLD------EAIKFLVKE 28 IPDNK-------REFIKYLEI 29 IPSERE------REFLELLDR 30 VPKAR------FAEFRKLIDK 31 IPEGRE------DEFLKLLDR 32 VPYRDM------ESFLQLVDE 33 ITPDK------VEEFLKEVDR 34 VSKDK------VQEFLKRVDE 35 LSGIS------VSEALERLKH 36 LENVS------AERIKELIKA 37 VKDISK-----AKDVIESIKS 38 VQQLLD-----REEMLDVIFR 39 GKAPDK-----FPEAVKLLKE 40 AGNPAA-----LDAALNAARD 41 GTDAAA-----LPAALASVKG 42 GKQPEK-----LEEALASVED 43 GSQLEN-----VTQAIKVAQD 44 GSEGGK-----ADEALVALKD 45 GRDASK-----LPEALATAKQ 46 GNDIIN-----LTNINKKLWS 47 GKYEGD-----VEEIKKKVIE 48 APALPA-----TEVLNETLWQ 49 SAELPQ-----IEFLNKTLRQ 50 VEAKPEE---IFDVALEKLRS 51 GDKPLS-----IDVAVEEAIE 52 GDKPAA-----IKDAVDDLES 53 GPATDK-----VDEALEEARA 54 GLDPRK-----AREALPGLLP 55 GKNPTG-----IDAALDAVRS 56 GENVDK-----LDAAVELAQK 57 GKNVGC-----LQEALQLATS 58 GNNPNS-----LNEAIQIANE 59 GKDIEN-----LQAALNLAKN 60 GTDASQ-----VQAALDMASS