; SAM: prettyalign v3.2 (June, 2000) compiled 07/10/00_09:40:44 ; (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 (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|4336092|gb|AAD17623.1|_2:170 ; 2 gi|1794167|dbj|BAA11217.1|_42:210 ; 3 gi|7483286|pir||D69371_3:174 ; 4 gi|7468910|pir||G71502_6:174 ; 5 gi|8163328|gb|AAF73606.1|_6:174 ; 6 gi|7468223|pir||H72051_5:173 ; 7 gi|1706437|sp|P54394|DING_BACSU_3:162 ; 8 gi|6014995|sp|O67074|DP3E_AQUAE_13:178 ; 9 gi|6225287|sp|Q9ZHF6|DPO3_THEMA_352:518 ; 10 gi|6014996|sp|O83649|DP3E_TREPA_15:175 ; 11 gi|6685391|sp|Q9ZCJ9|DP3E_RICPR_7:164 ; 12 gi|7477983|pir||H70794_10:171 ; 13 gi|7468222|pir||A72083_2:165 ; 14 gi|7468909|pir||B71536_3:159 ; 15 gi|8163241|gb|AAF73567.1|_2:159 ; 16 gi|6822230|emb|CAB70936.1|_2:186 ; 17 gi|7227909|sp|Q9ZVE0|ORN_ARATH_21:200 ; 18 gi|7227907|sp|Q17819|ORN_CAEEL_8:186 ; 19 gi|7227120|gb|AAF42197.1|_4:178 ; 20 gi|7379329|emb|CAB83884.1|_4:178 ; 21 T0109 ; 22 gi|1176352|sp|P45340|ORN_HAEIN_1:181 ; 23 gi|1361151|pir||S56390_24:202 ; 24 gi|1730261|sp|P39287|ORN_ECOLI_1:179 ; 25 gi|7227908|sp|Q9Y3B8|ORN_HUMAN_5:184 ; 26 gi|7661646|ref|NP_056338.1|_37:216 ; 27 gi|7227905|sp|O07708|ORN_MYCLE_2:181 ; 28 gi|7227904|sp|O06174|ORN_MYCTU_2:181 ; 29 gi|6277197|dbj|BAA86266.1|_2:180 ; 30 gi|7301049|gb|AAF56185.1|_32:209 ; 31 gi|7227906|sp|O94626|ORN_SCHPO_1:177 ; 32 gi|6323088|ref|NP_013160.1|_50:238 ; 33 gi|1019712|gb|AAA98633.1|_49:221 10 20 30 40 50 | | | | | 1 ----TRQLVVVDCETTGL-HDG.AAILEVAAVNIDTG---AE.......LHFVPFVTREQLAQAQ 2 -DARELDTLVLDFETTGFNPEV.DRVISIGWVEIRNSNIRLN.......SARHVFINHAIDI--- 3 GSLRKVQFLSIDLETTGLNQKK.DEIIAIGAVPIIGTRILAG.......ESYYRLLRPEKFK--- 4 ----DVEFVCLDCETTGLDVKK.DRVIEFAAIRF--TFDEII.......DSVEFLIHPERAV--- 5 ----DIEFVCLDCETTGLDVKK.DRVIEFAAIRF--TFDEVI.......DSVEFLIHPERAV--- 6 ---KDTVFTCLDCEMTGLDVKK.DRIIEIAAVRF--TFDSVI.......SSIEFLINPERVV--- 7 ----KQRFVVIDVETTGNSPKKgDKIIQIAAVVIENG--QIT.......ERFSKYINPNKSI--- 8 -NLLDGTFVVIDLEATGFDVEK.SEVIDLAAVRVEGG--IIT.......EKFSTLVYPGYFI--- 9 -TFGDATFVVLDFETTGLDPQV.DEIIEIGAVKIQGG--QIV.......DEYHTLIKPSREI--- 10 -------FTAFDTETTGLKAEE.DRIIEIGAVTFDRK--GII.......ARFSTLIFPDRAI--- 11 --------IILDTETTGLDPQQgHRIVEIGAIEMVNKV-LTG.......KHFHFYINPERDM--- 12 -SHQDRGWAVIDVETSGFRPGQ.ARIISLAVLGLDAA-GRLE.......QSVVSLLNPKVDP--- 13 SSQTMDVLIFYDTETTGTQIER.DRIIEIAAYNS-----VTD.......ESFLTYVNPEIPI--- 14 ------ALIFYDTETTGTQIDK.DRIVELAAYNG-----TTS.......ESFQTLVNPEIPI--- 15 -----PDLIFYDTETTGTQIDK.DRIVEIAAYNG-----TTG.......ESFQTLVNPEIPI--- 16 TSWFEGPLAAFDTETTGVDTET.DRIVSAALVVQDAP-GLRP.......RVTRWLVNPGVPV--- 17 -GDYKQPLVWIDLEMTGLNVEV.DRILEIACIITNGDLTQSV.......EGPDLVVRQTKDCLDK 18 CDKIEQRIIWIDCEMTGLDVEK.QTLCEIALIVTDSELNTIA.......TGPDIVIHQPKEVLDN 19 ----KNNLCWLDMEMTGLNPET.DRIIEVAMIITDSDLNVLA.......QSEVYAVHQSDDVLNK 20 ----KNNLCWLDMEMTGLNPET.DRIIEVAMIITDSDLNVLA.......QSEVYAIHQSDELLDN 21 MSFDKQNLIWIDLEMTGLDPEK.ERIIEIATIVTDKNLNILA.......EGPVLAVHQSDELLNK 22 MSFDKQNLIWIDLEMTGLDPEK.ERIIEIATIVTDKNLNILA.......EGPVLAVHQSDELLNK 23 MSANENNLIWIDLEMTGLDPER.DRIIEIATLVTDANLNILA.......EGPTIAVHQSDEQLAL 24 MSANENNLIWIDLEMTGLDPER.DRIIEIATLVTDANLNILA.......EGPTIAVHQSDEQLAL 25 -ESMAQRMVWVDLEMTGLDIEK.DQIIEMACLITDSDLNILA.......EGPNLIIKQPDELLDS 26 -ESMAQRMVWVDLEMTGLDIEK.DQIIEMACLITDSDLNILA.......EGPNLIIKQPDELLDS 27 ----HDELVWIDCEMTGLDLGS.DQLIEIAALVTDADLNILG.......DGVDVVIHIDSTALSS 28 ----QDELVWIDCEMTGLDLGS.DKLIEIAALVTDADLNILG.......DGVDVVMHADDAALSG 29 ----NDRMVWIDCEMTGLSLAD.DALIEVAALVTDSELNVLG.......EGVDIVIRPPDAALET 30 -CGLDTDIVWMDLEMTGLDIEK.DKILEVACIITDQDLNVKS.......EGPCFAINHPQEVYDS 31 MSNLKQPLVWIDCEMTGLEVGK.HVLMEVAAIITDGNLRPVE.......EKFDAVIKLDEKQLSE 32 --KLFKPLVWIDCEMTGLDHVN.DRIIEICCIITDGHLAPVKaadgqgdSHYESVIHYGPEVMNK 33 -TKLFKPLVWIDCEMTGLDHVN.DRIIEICCIITDGHLAPVKaadgqgdSHYETVIHYGPEVMNK 60 70 80 90 100 110 12 | | | | | | 1 PMAMQMNRYYERGIWQRRL.SPDST-DA.AYWKLANMLAG---.---NTFGGSNPAFDSRLLAAA 2 ----CHESVKVHHIRPETLhVSGISEQA.AFTQLLDVIAG---.---KILVAHGCIMEQRFLEQY 3 -----HESMKFHGLDPARL.KTAHDFSE.IAEEVADLLRG---.---KVLVGYAIELDYGFLKRA 4 ----SAESQKIHKISDAML.RDKPKFGE.VFSRIKGFFKE---.--RDHIVGHHVGFDLQVLSQE 5 ----SAESQKIHKISDAML.KDKPKFSE.VFSTIKGFFKE---.--RDYIVGHHVGFDLQVLSQE 6 ----SAESQRVHHISNAML.RDQPKIAE.VFPQIKAFFKE---.--GDYIVGHSVGFDLQVLAQE 7 ----PAFIEQLTGISNQMV.ENEQPFEA.VAEEVFQLLDG---.---AYFVAHNIHFDLGFVKYE 8 ----PERIKKLTGITNAML.VGQPTIEE.VLPEFLEFVGD---.---NIVVGHFVEQDIKFINKY 9 ----SRKSSEITGITQEML.ENKRSIEE.VLPEFLGFLED---.---SIIVAHNANFDYRFLRLW 10 ----PPDVSKINHITDDML.VNKPRFCE.IVSDFSRFIKG---.---TVLVAHNANFDVEFLNAE 11 ----PFEAYKIHGISGEFL.KDKPLFKT.IANDFLKFIAD---.---STLIIHNAPFDIKFLNHE 12 ------GPTHVHGLTAAML.DGQPQFAD.IAGEVVDVLRG---.---RTLVAHNVAFDYAFLAAE 13 ----PDEASKIHGITTDAV.LSAPKFPE.AYEGFRKFCGE---.-DSILVAHNNDGFDFPLLGKE 14 ----PAEATKIHGITTAEV.ADAPRFPE.AYQKFIEFCGT---.-DNILVAHNNNAFDYPLLVRE 15 ----PAEATKIHGITTSEV.ANAPKFPE.AYQQFSDFCGT---.-DNILVAHNNNAFDYPLLLRE 16 ----PESATAVHGLTEEYV.QRHGRWPApVMYEMAEALTEQAR.AG-RPLVVMNAPFDLTLLDRE 17 MDDWCQTHHGASGLTKKVL.LSAITERE.AEQKVIEFVKKHVG.SGNPLLAGNSVYVDFLFLKKY 18 MEEWPRNTFHENGLMEKII.ASKYSMAD.AENEVIDFLKLHAL.PGKSPIAGNSIYMDRLFIKKY 19 MDEWNTATHGRTGLTQRVR.ESSHTEAE.VEQKLLDFMSEWVP.GRATPMCGNSIHQDRRFMVKY 20 MDEWNTATHGRTGLTQRVR.ESSHTEAE.VEQKLLDFMSEWVP.RRATPMCGNSIHQDRRFMVKY 21 MNDWCQKTHSENGLIERIK.ASKLTERA.AELQTLDFLKKWVP.KGASPICGNSIAQDKRFLVKY 22 MNDWCQKTHSENGLIERIK.ASKLTERA.AELQTLDFLKKWVP.KGASPICGNSIAQDKRFLVKY 23 MDDWNVRTHTASGLVERVK.ASTMGDRE.AELATLEFLKQWVP.AGKSPICGNSIGQDRRFLFKY 24 MDDWNVRTHTASGLVERVK.ASTMGDRE.AELATLEFLKQWVP.AGKSPICGNSIGQDRRFLFKY 25 MSDWCKEHHGKSGLTKAVK.ESTITLQQ.AEYEFLSFVRQQTP.PGLCPLAGNSVHEDKKFLDKY 26 MSDWCKEHHGRSGLTKAVK.ESTITLQQ.AEYEFLSFVRQQTP.PGLCPLAGNSVHEDKKFLDKY 27 MIDVVAEMHSRSGLINEVE.SSIVDLVT.AESIVLDYINNHVKqPKTAPLAGNSIATDRSFIARD 28 MIDVVAEMHSRSGLIDEVK.ASTVDLAT.AEAMVLDYINEHVKqPKTAPLAGNSIATDRAFIARD 29 MPEVVRQMHTASGLLDE-L.AGGTTLAD.AEEQVLAYVREHVKePGKAPLCGNSVGTDRGFLARD 30 MNEWCMKHHYNSGLIDRCK.SSDVNLEE.ASNLVLSYLEKNIP.KRACPLGGNSVYTDRLFIMKF 31 MNDWCIEQHGKSGLTERCR.QSNLTVKD.VENQLLAYIKKYIPkKREALIAGNSVHADVRFLSVE 32 MNEWCIEHHGNSGLTAKVL.ASEKTLAQ.VEDELLEYIQRYIPdKNVGVLAGNSVHMDRLFMVRE 33 MNEWCIEHHGNSESHPKVL.ASEKTLAQ.VEDELLEYIQRYIPdKNVGVLAGNSVHMDRLFMVRE 0 130 140 150 160 170 | | | | | | 1 MPDGAPE...WHHRLADLAAFT--AGKLNLDPvel11vceRLG.VTVSDRHSALADAHATATCFT 2 IKMKYQN...LKLPLIWLDTLK--IEQYRTQLrpt14irkELN.LPTYQAHNALNDAIATAEL-- 3 LKREGYK...VENKRIDVIDFEKAVCYILGERpvg12lakKYR.VEVSYRHNALADAFITAQIFQ 4 SERLGET...LLPKHHYVIDTLRLAKGYGDSPnns9alarHFN.VPHQGNHRAMKDVEMNVKVFK 5 SERLGET...LLPKQHYVIDTLRLAKEYGDSPnns9alarHFN.VPHQGNHRAMKDVEMNVKVFK 6 MERIGET...FLSKYTIIDTLR-LAKEYGDSPnns9slavHFN.VPYDGNHRAMKDVEININIFK 7 LHKA-GF...QLPDCEVLDTVE-LSRIVFPGFegy10lseELQ.LRHDQPHRADSDAEVTGLI-- 8 TKQY-RG...KKFRNPSLCTLK-LARKVFPGLkky10iaeNFG.FETNGVHRALKDATLTAEIFI 9 IKKVMG-...LDWERPYIDTLA-LAKSLLKLRsys9svveKLG.LGPFRHHRALDDARVTAQVFL 10 LSLC-KK...QPLSHKVVDTYA-MAQAVFPGLgrh12lalQFG.LTVHAAHRAEDDARVCMELFT 11 LSLLKRTeikFLELTNTIDTLV-MARNMFPGArys11krfKVD.NSGRQLHGALKDAAL------ 12 AEIAEAE...LPVDF--VMCTVELARRLQLGVdnl10laaHWG.VPQQRPHDAFDDVRVLTGIL- 13 CRRH-SL...EPLTNRTIDSLK-WAQKYRPDLpkh10lrqVYG.FAENQAHRALDDVVILHKVFT 14 CRRH-GL...SEPQLRTIDSLK-WAKKYRTDLpqh10lrqVYG.FEENQAHRALDDVITLYRVF- 15 CRRH-GL...PEPQLRTIDSLK-WAKKYRTDLpqh10lrqVYG.FEENNAHRALDDVITLHRVF- 16 LRRHRAS...SLGRWLERTPLHVLDPHVLDKHldr16lcaHYG.VELAGAHDAAADAQAALEVVR 17 MPELAAL...FPHILVDVSSVKALCARWFPIEr.......RKA.PAKKNNHRAMDDIRESIKELK 18 MPKLDKF...AHYRCIDVSTIKGLVQRWYPDY........-KH.PKKQCTHRAFDDIMESIAELK 19 MPKLENY...FHYRNLDVSTLKELAKRWNPPV........AKS.VVKRGSHKALDDILESIEEMR 20 MPKLENY...FHYRNLDVSTLKELAKRWNPPV........AKS.VVKRGSHKALDDILESIEEMR 21 MPDLADY...FHYRHLDVSTLKELAARWKPEI........LEG.FKKENTHLALDDIRESIKELA 22 MPDLADY...FHYRHLDVSTLKELAARWKPEI........LEG.FKKENTHLALDDIRESIKELA 23 MPELEAY...FHYRYLDVSTLKELARRWKPEI........LDG.FTKQGTHQAMDDIRESVAELA 24 MPELEAY...FHYRYLDVSTLKELARRWKPEI........LDG.FTKQGTHQAMDDIRESVAELA 25 MPQFMKH...LHYRIIDVSTVKELCRRWYPEEy.......EFA.PKKAASHRALDDISESIKELQ 26 MPQFMKH...LHYRIIDVSTVKELCRRWYPEEy.......EFA.PKKAASHRALDDISESIKELQ 27 MPTLDSF...LHYRMIDVSSIKELCRRWYPRI........YFGqPAKGLTHRALADIHESIRELR 28 MPTLDSF...LHYRMIDVSSIKELCRRWYPRI........YFGqPPKGLTHRALADIHESIRELR 29 MRELEGY...LHYRIVDVSSVKELARRWYPRA........YFNsPAKNGNHRALADIRDSITELR 30 MPLVDAY...LHYRIVDVSTIKELAKRWHPAIl.......DSA.PKKSFTHRSLDDIRESIKELA 31 MPKIIEH...LHYRIIDVSTIKELAKRWCPDI........-PA.YDKKGDHRALSDILESIGELQ 32 FPKVIDH...LFYRIVDVSSIMEVARRHNPALq.......ARN.PKKEAAHTAYSDIKESIAQLQ 33 FPKVIDH...LFYRIVDVSSIMEVARRHNPALq.......ARN.PKKEAAHTAYSDIK------- 180 | 1 ILR------- 2 ---------- 3 VQ-------- 4 HLTKRF---- 5 HLTKRF---- 6 HLCKRF---- 7 ---------- 8 KI-------- 9 RFVE------ 10 T--------- 11 ---------- 12 ---------- 13 ---------- 14 ---------- 15 ---------- 16 AVGRR----- 17 YYKKTIFK-- 18 NYRESIFV-- 19 HYREHFL--- 20 HYREHFL--- 21 YYREHFMKLD 22 YYREHFMKL- 23 YYREHFI--- 24 YYREHFI--- 25 FYRNNIFK-- 26 FYRNNIFK-- 27 FYRRTAFVPP 28 FYRRTAFVPQ 29 YYREAVFVPQ 30 YYKANL---- 31 HYRSY----- 32 WYMDNYLKPP 33 ----------