(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             
                             |          |               |             
   1 .....M..W..MP..P..R..PEEVARKLRRLG.FV.ERMA.K....GGHRLY.TH....P....
   2 .....M..Sr.LL..Pv.S..GRDMCKILEMLG.FQ.KVHQ.V....GSHVRY.VH....P....
   3 .....M..G..RL..SgfR..YREIIKRLKAFG.FV.FDRQaA....GSHEIW.YN....P....
   4 .....M..Sr.LL..Pv.S..GRDMCKILEMLG.FQ.KVYQ.V....GSHVRY.VH....P....
   5 .....M..K..SY..-..S..SREIVKIITKDG.WY.EVNC.V....GDHHQY.KH....P....
   6 .....M..-..--..-..K..SGDIIAALQKDG.WY.EVAT.K....GSHVQF.KH....P....
   7 .....M..S..GL..PiiS..GMQAIKAFSKAG.WL.PHRQ.V....GSHVVL.RK....E....
   8 .....M..Sk.IL..Pl.P..AKKVVKALENIG.FE.QIRQ.K....GSHLFL.RH....P....
   9 .....M..S..GL..PviS..GMQAIKAFYKAG.WL.PHRQ.V....GSHVVL.RK....E....
  10 .....M..S..GL..PviS..GMQAIKAFSKAG.WL.PHRQ.V....GSHVVL.RK....E....
  11 .....M..-..--..-..N..SREVIAALEADG.WV.EVAR.R....GSHAQF.KH....P....
  12 .....M..Dk.IV..Pl.P..SKKVIKALESMG.FE.QIRQ.K....GSHLFL.RH....P....
  13 .....M..S..GL..PviS..GMQAIEAFSKAG.WL.PHRQ.V....GSHVVL.RK....E....
  14 sksq.-..G..VR..V..K..SSELIKLLETNG.WK.LMRV.K....GSHHQF.KH....P....
  15 .....M..K..V-..-..-..-REVIKHLEADG.WY.LVAT.K....GSHRQY.KH....Pa...
  16 .....M..P..KL..PglT..GKKVINTLEKLG.FQ.VVRQ.R....GSHVQM.EH....D....
  17 .....M..SprLI..Pi.T..GQELVRLLQEEG.FQ.VVWV.R....GSHVRL.RH....P....
  18 .....M..SprLI..Pi.T..GQELVRLLQEEG.FQ.VVWV.R....GSHVRL.RH....P....
  19 .....M..S..YL..PivD..PKTMEKVLLKLG.FQ.RVRQ.K....GSHVFY.RH....S....
  20 .....M..K..V-..-..-..-KEVLKRLKADG.WY.QVRM.R....GSHRIL.AH....P....
  21 slf..M..G..RL..AgfS..YRQIIKILKTFG.FV.FHRQaA....GSHEIW.FN....P....
  22 .....M..P..KL..PtpS..ALEVIKALNSQG.FQ.VISQ.K....GNHIKM.KKka..P....
  23 .....M..-..--..-..Q..SRQLVKELEADG.WV.LDRV.T....GSHHMF.KH....P....
  24 .....M..K..I-..-..-..-REVIKLIENDG.WY.LVRT.R....GSHRQF.KH....P....
  25 .....M..P..MT..P..-..-KQMIKLLKKNG.FY.EVSQ.N....GSHKKF.RD....N....
  26 .....M..K..V-..-..-..-SEVIKRLETDG.WY.LART.K....GSHRQF.KH....P....
  27 .....M..-..--..-..N..SAEIIRQLQADG.WF.EVAR.K....GSHAQF.KH....R....
  28 .....Mi.G..YK..M..T..AKEIEKILKADG.WY.FVTA.K....GSHNQY.KH....Tv...
  29 .....M..S..KL..PniS..GKQCIEVLKKIG.FY.QKRR.Q....SSHIIL.RR....D....
  30 .....M..-..--..-..D..GKELIKQLERSG.WT.LRSV.K....GSHHVF.AH....P....
  31 .....M..S..--..-..S..SKQIIKRIEADG.WK.FHHA.T....GSHHHF.TH....P....
  32 .....M..S..NL..P..SvqAKDFIRVIKKLG.FF.LERQ.K....GSHAIY.KN....T....
  33 .....M..-..--..-..D..SKELIKQLERSG.WT.LRGV.K....GSHHVF.TH....P....
  34 .....M..K..SY..-..T..SREVIKILQNDG.WY.EVAV.V....GSHHQF.KH....Si...
  35 .....M..S..YS..Pf.S..GRDVVKAMVNSGiYE.WDRT.N....GDHAILvWN....Ppesh
  36 .....M..-..--..-..N..STDLIQQPKADG.WY.RVHT.V....GSHHQY.KH....P....
  37 rqe..-..G..ET..V..D..SKTAIKMIEEDG.WY.LDRV.K....GSHHQY.KH....P....
  38 .....M..K..LPrdV..S..GEDVIKALRKLG.YV.PARQ.K....GSHVVL.TG....P....
  39 .....M..K..V-..-..-..-RDAIERVEADG.WY.LDRT.K....DSHQQF.KH....P....
  40 pt...-..S..NLtnI..S..SRKAIKAFRKLG.FE.KDRH.T....GDHFIL.KK....T....
  41 .....MarR..LR..Pv.S..RRELVARLKALG.FS.GPYT.G....GRHQFM.VR....-....
  42 .....M..P..SA..I..S..RRNLIKKFKSLG.YTgPYSG.K....KKHQFM.TK....G....
  43 .....M..-..--..-..K..SKDLIDELLAAG.CE.FVRHgK....GSHQIW.KS....Pi...
  44 .....-..-..--..-..-..------MIEEDG.WY.LDRV.K....GSHHQY.KH....P....
  45 .....M..K..SI..-..S..GKKLCKIVEKKG.WT.LKKI.T....GSHHIY.EK....T....
  46 .....M..S..V-..-..K..RKELIKYLEQNG.FY.LLRE.G....GNHSIY.TN....E....
  47 .....M..K..V-..-..-..-KVILKILERDG.WY.VARI.R....GSHRQL.KH....P....
  48 .....M..-..--..-..E..SGELIKRLEDAG.WQ.IRGG.RktnsGSHVTL.CK....P....
  49 .....M..-..--..-..T..ERELKKIAKKQG.FS.KTNFgK....GSHEVW.KH....P....
  50 .....M..-..--..-..K..SADLLKELIAAG.CE.LKRH.Ka...SSHQIW.WS....Pi...
  51 .....-..-..--..-..-..------------.--.--MA.K....GGHRLY.TH....P....
  52 .....M..P..RL..-..T..AKEAEKLLLQNG.FV.FSRQ.K....GSHRIY.VK....-....
  53 .....M..P..KL..PrvS..TQKTVKTLEKLG.FV.QIRQ.K....GSHLIL.KKqlksE....
  54 .....M..P..KL..PnvT..GNQLIQVLNKVG.FQ.FVRQ.K....GSHMRL.RH....E....
  55 .....M..P..RL..-..T..AKEAEKLLLQNG.FV.FSRQ.K....GSHRIY.VK....-....
  56 .....M..P..RL..-..T..AKEAEKLLLQNG.FV.FSRQ.K....GSHRIY.VK....-....
  57 dqf..L..K..QP..PevR..SQEVYYLLEAFG.FE.EKKS.K....GSHHSF.RD....S....
  58 .....M..P..RL..-..T..AKEAEKLLLQNG.FV.FSRQ.K....GSHRIY.VK....-....
  59 .....M..-..--..-..K..RRQLLKHLAAHG.VV.LARE.G....ANHSIY.RD....P....
  60 ggksaM..P..M-..-..T..QKEMVKLLTAHG.WI.KTRGgK....GSHIKM.EK....Q....
  61 .....-..-..--..-..-..------ALK---.--.LVKV.K....GSHHKF.KK....-....


                 40                50         60                70    
                 |                 |          |                 |    
   1 D.G.RI.V....V..V.PFH.S.G..E.LPKG.TFKRILRDAGL....TEEEF...HN.L....
   2 D.G.RK.T....V..V.PVH.G.Ne.D.LGTG.LIKEILKQTRI....SRETY...EE.Lrkk.
   3 DkD.KY.T....T..I.PNH.A.G..D.MPEG.TLRAILKQAEI....DPEDF...LK.Tgk..
   4 D.G.RK.T....V..V.PVH.G.Ne.D.LGTG.LIKEILKQSRI....SREMY...EE.Lrkk.
   5 TkK.GR.L....T..I.PHP.K.K..D.LPIG.TVRSIFKQAGI....KIL--...--.-....
   6 K.KhGR.V....T..V.PHP.K.R..D.LPIG.TLRSIEKQSGL....KLR--...--.-....
   7 G.S.KV.Tl...T..V.PKH.K.-..E.LKPG.LLRNLIKASGL....TVEEF...EA.Llk..
   8 D.G.RT.T....I..V.PMH.P.T..EkIGSG.MINKIIKDAKI....TRNEW...IE.Linr.
   9 G.S.KV.Tl...T..V.PKH.K.-..E.LKPG.LLRNLIKASGL....TIEEF...EV.Llk..
  10 G.S.KV.Tl...T..V.PKH.K.-..E.LKPG.LLRNLIKVSGL....TVEEF...EA.Llk..
  11 TkS.GR.V....T..V.PHP.K.R..D.LPLG.TLRSIERQADL....KLR--...--.-....
  12 D.G.RT.T....I..I.PVH.PtN..K.IGKG.MINKIIKDVKI....TRDEW...IE.Liks.
  13 G.S.KI.Tl...T..V.PKH.K.-..E.LKPS.LLRNLIKVSGL....TVEEF...ET.Llk..
  14 DfA.AV.I....T..V.PHP.K.K..D.VKPG.TLRQILKDANL....S----...--.-....
  15 K.P.GR.V....T..I.AGH.S.G..DdLAPG.TLNSILKQAQL....KIED-...--.-....
  16 D.G.RL.V....T..V.PVH.A.G..KtIGRG.WLSKILRDAEL....TREEF...IA.Lle..
  17 D.G.RV.T....T..V.PVH.P.G..EtLRPG.TLLAILKDVGW....SKETY...EQ.Krlg.
  18 D.G.RV.T....T..V.PVH.P.G..EtLRPG.TLLAILKDVGW....SKETY...EQ.Krlg.
  19 N.G.KY.T....T..I.PFH.A.K..EtCPSH.LIRKIIREAGI....SVEEFkkvLE.N....
  20 DkS.GI.V....V..V.PGKlS.N..D.IPIG.TLSAIWKQAKL....GDEK-...--.-....
  21 EtN.RY.T....T..I.PNH.S.G..D.MPEG.TLRAILKQTAI....EPEDF...LN.Rs...
  22 D.K.IL.V....Vi.V.PDH.P.-..E.IPSG.TLKSIIRQAGM....TDDEF...VKlL....
  23 EkS.QT.V....P..V.PHP.K.K..D.LPLG.TVKAIRKLAGL....A----...--.-....
  24 SkS.GL.V....T..I.PGKlS.D..D.IAIG.TLKNILKQAQL....NLDTN...--.-....
  25 N.G.HQ.T....I..V.PMH.N.K..D.LGKG.LEDTILKQAGL....K----...--.-....
  26 DkT.GT.V....T..VsGKP.S.V..D.VPIG.TLKNIWRQAQL....EED--...--.-....
  27 DkQ.GR.V....T..V.PHP.K.R..D.IPIG.TLRSIEKQSGL....KLR--...--.-....
  28 K.S.GK.V....T..V.PNH.K.G..D.IPIG.TVKAILKQAGL....K----...--.-....
  29 N.P.FLqV....V..V.PDH.Q.-..T.LPKG.TLRAIIRDADT....SVEDF...INlL....
  30 DrP.GH.I....S..V.PHP.K.K..D.LGIG.LLNSILKAAGL....K----...--.-....
  31 TkK.GI.V....T..V.QHP.E.K..D.LKKG.TEHSILKQAGL....K----...--.-....
  32 Q.G.NR.V....V..V.PIH.P.Gk.D.LKQG.TLMGMIKDIGL....EKEKF...FD.Llqk.
  33 DrP.GH.I....S..V.PHP.K.K..D.LGIG.LLNSILKAAGL....K----...--.-....
  34 K.K.GR.V....T..V.KHP.D.K..D.IPIA.TLKTIEKQSGI....RFK--...--.-....
  35 D.S.PR.R....T..V.PVPlH.D..E.LREG.TLKEIGEQAGMqdfqEFKAW...ID.R....
  36 TkP.GK.V....T..V.PHP.R.K..G.LPTA.TQRSILKQAGL....R----...--.-....
  37 TkK.GT.V....T..I.PHP.R.K..D.LG-H.LEKSIKKQAGL....-----...--.-....
  38 S.G.KI.I....V..I.PLH.K.-..R.IKTG.LLRAIIREVGV....SVKIF...IK.Lled.
  39 DkP.GL.V....T..V.PGKfS.D..D.LAPG.TLSSIWRQAQL....-----...--.-....
  40 E.T.ST.I....TfpI.PHP.R.Q..E.LNPL.TLKNILIQTNT....TLEDF...LNnL....
  41 G.S.IR.L....V..L.PNPhR.G..E.IGVD.LLKRILRQAGI....EEEEW...LE.-....
  42 S.Q.KI.R....-..I.PNP.H.GsqD.ISID.LVKEILKQADI....SNEDW...DN.A....
  43 S.G.KK.F....P..V.PHP.K.G..S.LPIG.TVRSIKKDAGI....-----...--.-....
  44 TkK.GT.V....T..I.PHP.R.K..D.LG-H.LEKSIKKQAGL....-----...--.-....
  45 DeN.KI.L....S..I.PVH.R.N..QnLKIG.TLKSIMKIANL....TDNDL...--.-....
  46 -.-.-I.K....T..L.PVK.R.H..RtIDRI.TANEICKQAGL....-LPNF...--.-....
  47 H.KaGL.V....T..VlGKP.S.D..E.LAPG.TLASILKQSSQ....AIRYY...FM.Kylv.
  48 GvR.KI.I....T..L.PYP.R.K..D.ISKG.LLRQAQKIAGI....KLS--...--.-....
  49 D.G.RT.V....T..I.PKP.KeK..D.YRPG.TLNNILKVLY-....-----...--.-....
  50 T.G.KT.F....P..V.PHP.K.K..D.LPLG.TVRSIKKMAGI....-----...--.-....
  51 D.G.RI.V....V..V.PFH.I.G..E.LPKG.TFKRILRDAGL....TEEEF...HN.L....
  52 D.K.IR.Q....V..L.PFH.S.G..EiLHPK.IVKEIMENA-L....K----...--.-....
  53 E.G.KI.IevgcV..I.PLQ.R.K..T.LAVG.TLKNILN----....-----...--.-....
  54 D.G.RV.V....T..V.PVH.-.-..-.IAI-.-----------....-----...--.-....
  55 D.K.IR.Q....V..L.PFH.S.G..EiLHPK.IVKEIMENI-L....-----...--.-....
  56 D.K.IR.Q....V..L.PFH.S.G..EiLHPK.IVKEIMENT-L....-----...--.-....
  57 Q.G.KT.I....T..V.PKT.G.G..Q.KVKGvYVQQIVELLNL....--EEW...ID.Edte.
  58 D.K.IR.Q....V..L.PFH.F.G..EtLHPK.IVKEIMENI-L....-----...--.-....
  59 R.T.G-.A....T..V.PVP.R.Ha.E.ISDA.LVRRICKEIGI....PPP--...--.-....
  60 G.E.RP.I....T..I.-LH.-.G..E.LNKY.TERGIRKQAGL....-----...--.-....
  61 D.G.KV.V....I..V.PHP.K.K..N.LPIG.TARSIAQQAG-....----W...FK.K....