(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)

Sequence numbers correspond to the following labels:

    • T0281 1whz, Thermus thermophilus
              10        20              30                 40         5
              |         |               |                  |          
   1 MWMPPRPEEVARKLRRLGFVER.MA....K.GGHRLYT.....HP...D.GRIVVVP.FHSGELP
   2 -LLPVSGRDMCKILEMLGFQKV.HQ....V.GSHVRYV.....HP...D.GRKTVVPvHGNEDLG
   3 -LLPVSGRDMCKILEMLGFQKV.YQ....V.GSHVRYV.....HP...D.GRKTVVPvHGNEDLG
   4 -LPSVQAKDFIRVIKKLGFFLE.RQ....K.GSHAIYK.....NTq..G.NRVVVPI.HPGKDLK
   5 -LPVISGMQAIKAFSKAGWLPH.RQ....V.GSHVVLR.....KE...G.SKVTLTV.PKHKELK
   6 -LPIISGMQAIKAFSKAGWLPH.RQ....V.GSHVVLR.....KE...G.SKVTLTV.PKHKELK
   7 -LPGLTGKKVINTLEKLGFQVV.RQ....R.GSHVQME.....HD...D.GRLVTVPvHAGKTIG
   8 --VPLPSKKVIKALESMGFEQI.RQ....K.GSHLFLR.....HP...D.GRTTIIPvHPTNKIG
   9 -LPNISGKQCIEVLKKIGFYQK.RR....Q.SSHIILR.....RD...N.PFLQVVV.PDHQTLP
  10 -LPVISGMQAIEAFSKAGWLPH.RQ....V.GSHVVLR.....KE...G.SKITLTV.PKHKELK
  11 -LPTPSALEVIKALNSQGFQVI.SQ....K.GNHIKMK.....KKap.D.KILVVIV.PDHPEIP
  12 --LPLPAKKVVKALENIGFEQI.RQ....K.GSHLFLR.....HP...D.GRTTIVPmHPTEKIG
  13 ----MKSGDIIAALQKDGWYEV.AT....K.GSHVQFK.....HPk..K.HGRVTVP.HPKRDLP
  14 ----MKVREVIKHLEADGWYLV.AT....K.GSHRQYK.....HPak.P.GRVTIAG.HSGDDLA
  15 ----MNSREVIAALEADGWVEV.AR....R.GSHAQFK.....HPt..K.SGRVTVP.HPKRDLP
  16 -LPVISGMQAIKAFYKAGWLPH.RQ....V.GSHVVLR.....KE...G.SKVTLTV.PKHKELK
  17 -LIPITGQELVRLLQEEGFQVV.WV....R.GSHVRLR.....HP...D.GRVTTVPvHPGETLR
  18 -LIPITGQELVRLLQEEGFQVV.WV....R.GSHVRLR.....HP...D.GRVTTVPvHPGETLR
  19 -----SSREIVKIITKDGWYEV.NC....V.GDHHQYK.....HPt..K.KGRLTIP.HPKKDLP
  20 ----MKVKEVLKRLKADGWYQV.RM....R.GSHRILA.....HPdk.S.GIVVVPG.KLSNDIP
  21 ----MNSAEIIRQLQADGWFEV.AR....K.GSHAQFK.....HRd..K.QGRVTVP.HPKRDIP
  22 ----MTAKEIEKILKADGWYFV.TA....K.GSHNQYK.....HTv..K.SGKVTVP.NHKGDIP
  23 ----MQSRQLVKELEADGWVLD.RV....T.GSHHMFK.....HPe..K.SQTVPVP.HPKKDLP
  24 ----MDSKELIKQLERSGWTLR.GV....K.GSHHVFT.....HPd..R.PGHISVP.HPKKDLG
  25 ----MDGKELIKQLERSGWTLR.SV....K.GSHHVFA.....HPd..R.PGHISVP.HPKKDLG
  26 ----MKIREVIKLIENDGWYLV.RT....R.GSHRQFK.....HPsk.S.GLVTIPG.KLSDDIA
  27 ---RVKSSELIKLLETNGWKLM.RV....K.GSHHQFK.....HP...DfAAVITVP.HPKKDVK
  28 ---GFRYREIIKRLKAFGFVFD.RQa...A.GSHEIWY.....NPd..K.DKYTTIP.NHAGDMP
  29 -----TSREVIKILQNDGWYEV.AV....V.GSHHQFK.....HSi..K.KGRVTVK.HPDKDIP
  30 --AGFSYRQIIKILKTFGFVFH.RQa...A.GSHEIWF.....NPe..T.NRYTTIP.NHSGDMP
  31 ----MKVSEVIKRLETDGWYLA.RT....K.GSHRQFK.....HPdk.T.GTVTVSG.KPSVDVP
  32 -LPIVDPKTMEKVLLKLGFQRV.RQ....K.GSHVFYR.....HS...N.GKYTTIPfHAKETCP
  33 ----MNSTDLIQQPKADGWYRV.HT....V.GSHHQYK.....HPt..K.PGKVTVP.HPRKGLP
  34 ----VDSKTAIKMIEEDGWYLD.RV....K.GSHHQYK.....HPt..K.KGTVTIP.HPRKDLG
  35 ----MKSKDLIDELLAAGCEFV.RHg...K.GSHQIWK.....SPi..S.GKKFPVP.HPKGSLP
  36 ----------------------.--....K.GGHRLYT.....HP...D.GRIVVVP.FHIGELP
  37 -LRPVSRRELVARLKALGFSGP.YT....G.GRHQFMV.....RG...S.IRLVLPN.PHRGEIG
  38 ----MKVKVILKILERDGWYVA.RI....R.GSHRQLK.....HPhk.A.GLVTVLG.KPSDELA
  39 --PRLTAKEAEKLLLQNGFVFS.RQ....K.GSHRIYV.....KD...K.IRQVLPF.HFGETLH
  40 -LPRMTAKEAEKLLLQNNFLID.RQ....K.GSHRIYK.....KG...L.YRMVIPH.HIGEILH
  41 ----VSGEDVIKALRKLGYVPA.RQ....K.GSHVVLT.....GP...S.GKIIVIP.L-HKRIK
  42 ----MKVRDAIERVEADGWYLD.RT....K.DSHQQFK.....HPdk.P.GLVTVPG.KFSDDLA
  43 ------SKQIIKRIEADGWKFH.HA....T.GSHHHFT.....HPt..K.KGIVTVQ.HPEKDLK
  44 ----MKCSEFRRWLQAQGAEFK.AA....K.GSHFKVY.....LN...G.KATIFAD.HGSKEMH
  45 --TNISSRKAIKAFRKLGFEKD.RH....T.GDHFILK.....KTet.S.TITFPIP.HPRQELN
  46 ----ISGKKLCKIVEKKGWTLK.KI....T.GSHHIYE.....KTde.N.KILSIPV.HRNQNLK
  47 ----MKRRQLLKHLAAHGVVLA.RE....G.ANHSIYR.....DP...R.TGATVPV.PRHAEIS
  48 -LPRMTAKEAEKLLLQNDFSID.RQ....K.GSHRIYK.....KG...L.YRMVIPH.HSGEILH
  49 ----MKRRELIRHLEENGCLFL.RE....G.GKHTIYY.....NP...I.NNRTSAV.PRHTEIV
  50 ----MKSADLLKELIAAGCELK.RH....KaSSHQIWW.....SPi..T.GKTFPVP.HPKKDLP
  51 ----VKRKELIKYLEQNGFYLL.RE....G.GNHSIYT.....NE...-.-IKTLPV.KRHRTID
  52 --MPMTQKEMVKLLTAHGWIKT.RGg...K.GSHIKME.....KQ...G.ERPITIL.H--GELN
  53 ----MESGELIKRLEDAGWQIR.GGrktnS.GSHVTLC.....KP...GvRKIITLP.YPRKDIS
  54 --PRLTAKEAEKLLLQNGFVFS.RQ....K.GSHRIYV.....KD...K.IRQVLPF.HSGEILH
  55 ----MKTTELVKRLKGLGFQEV.GG....K.-KHIKYR.....HP...D.GRWTVIS.KGSHEIS
  56 --MPMTQKEMVKLLTAHGWIKT.RGg...K.GSHIKME.....KQ...G.ERPITIL.H--GKLN
  57 ----QKIRELKAILQKAGFNYR.PA....K.GSHTFWT.....HPlilD.EPVTIAG.KDGDDAP
  58 --PRLTAKEAEKLLLQNGFVFS.RQ....K.GSHRIYV.....KD...K.IRQVLPF.HSGEILH
  59 --PRLTAKEAEKLLLQNGFVFS.RQ....K.GTHRIYV.....KD...K.IRQVLPF.HSGEILH
  60 --PRLTAKEAEKLLLQNGFILS.RQ....K.GSHRIYV.....KD...K.IRQVLPF.HSGEILH
  61 --SPFSGRDVVKAMVNSGIYEWdRT....N.GDHAILVwn6esHD...S.PRRTVPV.PLHDELR
  62 --PRLTAKEAEKLLLQNGFVFS.RQ....K.GSHRIYV.....KD...K.IRQVLPF.HSGEILH
  63 ----MTERELKKIAKKQGFSKT.NFg...K.GSHEVWK.....HP...D.GRTVTIPkPKEKDYR
  64 ---PMTPKQMIKLLKKNGFYEV.SQ....N.GSHKKFR.....DN...N.GHQTIVP.MHNKDLG
  65 --------------EEDGWYLD.RV....K.GSHHQYK.....HPt..K.KGTVTIP.HPRKDLG
  66 --PEVRSQEVYYLLEAFGFEEK.KS....K.GSHHSFR.....DSq..G.KTITVPK.TGGQKVK


      0        60        70
     |         |         |
   1 KGTFKRILRDAGLTEEEFHNL
   2 TGLIKEILKQTRISRETYEEL
   3 TGLIKEILKQSRISREMYEEL
   4 QGTLMGMIKDIGLEKEKFFDL
   5 PGLLRNLIKVSGLTVEEFEAL
   6 PGLLRNLIKASGLTVEEFEAL
   7 RGWLSKILRDAELTREEFIAL
   8 KGMINKIIKDVKITRDEWIEL
   9 KGTLRAIIRDADTSVEDFINL
  10 PSLLRNLIKVSGLTVEEFETL
  11 SGTLKSIIRQAGMTDDEFVKL
  12 SGMINKIIKDAKITRNEWIEL
  13 IGTLRSIEKQSGL--------
  14 PGTLNSILKQAQLK-------
  15 LGTLRSIERQADL--------
  16 PGLLRNLIKASGLTIEEFEV-
  17 PGTLLAILKDVGWSKETY---
  18 PGTLLAILKDVGWSKETY---
  19 IGTVRSIFKQAGI--------
  20 IGTLSAIWKQAKLG-------
  21 IGTLRSIEKQSGL--------
  22 IGTVKAILKQAG---------
  23 LGTVKAIRKLAG---------
  24 IGLLNSILKAAG---------
  25 IGLLNSILKAAG---------
  26 IGTLKNILKQAQL--------
  27 PGTLRQILKDAN---------
  28 EGTLRAILKQAEIDPEDFL--
  29 IATLKTIEKQSGI--------
  30 EGTLRAILKQTAIEPEDFL--
  31 IGTLKNIWRQAQLE-------
  32 SHLIRKIIREAGISVEEFKK-
  33 TATQRSILKQAG---------
  34 -HLEKSIKKQAG---------
  35 IGTVRSIKKDAG---------
  36 KGTFKRILRDAGLTEEEFHNL
  37 VDLLKRILRQAGIEEEEW---
  38 PGTLASILKQS----------
  39 PKIVKEIME------------
  40 PKIIKQLFEIIE---------
  41 TGLLRAIIREVGVSVKIFIKL
  42 PGTLSSIWRQA----------
  43 KGTEHSILKQAG---------
  44 EGLRKSIIKQLGL--------
  45 PLTLKNILIQTNTTLEDFL--
  46 IGTLKSIMKIANLT-------
  47 DALVRRICKEIGI--------
  48 PKIIKQLFEIIE---------
  49 DVLVVKICKDLE---------
  50 LGTVRSIKKMAG---------
  51 RITANEICKQAGL--------
  52 KYTERGIRKQAG---------
  53 KGLLRQAQKIAGI--------
  54 PKIVKEIME------------
  55 VDLLKNMEKQI----------
  56 KYTERGIRKQAG---------
  57 KYLEKQIKKVLN---------
  58 PKIVKEIME------------
  59 PKIVKEIME------------
  60 PKIVKEIME------------
  61 EGTLKEIGEQAGM--------
  62 PKIVKEIM-------------
  63 PGTLNNILK------------
  64 KGLEDTILKQAG---------
  65 -HLEKSIKKQAG---------
  66 GVYVQQIVELLNL--EEW---