(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:

    • T0471 TR8, Methanothermobacter thermautotrophicus, 133 residues
                      10                 20          30         40     
                      |                  |           |          |     
   1 ...M...W..NDLAVYII.RCS.....GPG..TR.VV..EVGAGRFLYVSDYIRKH.SKVDLVLT
   2 ...M...W..NDLAVYII.RCS.....GPG..TR.VV..EVGAGRFLYVSDYIRKH.SKVDLVLT
   3 ...-...M..DTIFKYID.EHYrnlk.NKG..LK.VA..ELGIGFYFNNAKKLKEI.-GFDVIVI
   4 ...M...L..Q-IADYIA.ENY.....RG-..-K.VV..EVGIGRFTAVAELLARR.-GFEVFAT
   5 ...Mf..M..LQIADYIA.ENY.....RG-..-K.VV..EVGIGRFTAVAELLARR.-GFEVFAT
   6 ...-...M..DTICKYID.ENYsdik.NKE..LK.IA..ELGIGFYFDNAKKLKD-.SGFDVIVI
   7 ...-...M..DTVFKYID.ENYqnlk.NNG..LK.IA..ELGIGFYFNNAKKLKD-.SGFDVIVI
   8 ...-...M..DTIFKYIN.ENYghik.NKG..LK.VA..ELGIGFYFDNAKKLKD-.SGFEVIVI
   9 ...Iig.Y..DDLAEYIL.QHY.....PAG..SR.II..EVGIGRHPDTAELLSRY.--CDFTCT
  10 ...MskvW..ENFSEYII.NNY.....QDS..KK.II..EVGVGKITEPSDILKKHlPNTTINLV
  11 ...M...W..DDFAEFILtQAT.....ENP..TR.IV..EIAVGKFDGVYQYLKRN.ENIEIIKT
  12 ...-...M..DYIFEYLL.NNYshl..KNN..SK.IVvaEIGIGFYVEISKKMQK-.SGFNVIAI
  13 ...Mn..V..KIIVEFIK.KFA.....EENncKK.IA..EIGIGFKFDVARELSKY.--FDLIAI
  14 cekMn..V..KIIVEFIK.KFA.....EENncKK.IA..EIGIGFKFDVARELSKY.--FDLIAI
  15 cekMn..V..KIIVEFIK.KFA.....EENncKK.IA..EIGIGFKFDVARELSKY.--XDLIAI
  16 ...M...I..E-VAEIIA.REI.....RRG..-K.IV..EIGVGFYLEVAKRLRE-.SGIDILVV
  17 ...-...M..DYVCDYII.KNYy11knSES..FK.II..EIGVGYYFNIAKSLNNH.ENLNLIVI
  18 ...M...I..E-VAEFIA.REV.....KKG..-K.VI..EVGIGFYTRIAKRLKEL.-GFDVLAI
  19 ykhI...E..HCCGVYIA.QHY.....TNP..--.-V..EIGVGSNPDAAQCIHEA.-GIPVRAR
  20 ...-...M..EALAELIK.RKV.....PNE..GL.II..EVGVGFYLKVAKKLKEY.-GFNVVVV
  21 ...Mp..I..EDFADFIA.SRV.....PKG..-K.VV..ELGIGFQFKVALRLKEL.-GYDVLAV
  22 ...M...H..TDSEGALV.DRL.....SSY..DA.LV..EVGVGNRPTVAAALDER.-GCRVTAT
  23 ...M...RgaQEIAEFIR.SHY.....TG-..-R.II..EIGVGQCGDVARLIP--.---DLIAT
  24 ykhI...E..RSIGEYIA.ARY.....R--..-R.AV..EVGVGNNPEAAGLIAAA.-GALMLCT
  25 ...Msg.Y..KYIETAIA.RFI.....AGR..YRsVI..EVGAGTNLHTANLLFRT.-GILIRCV
  26 ...M...T..QPPT--VA.AVL.....AAH..SR.VV..EVGIGARPDVAAALAER.-GCAVTAT
  27 kfkL...V..KPLYNYIL.DNYlle..NPD..LQ.IL..ELGVGFYFEMALKLKQN.-NYNITVM
  28 pysM...R..NGIETAVG.RYI.....AAN..YRsAV..EVGFGGKTTAAEIVQNA.-GIPVLCT
  29 ...M...H..SLAQDALV.ERF.....SSY..TS.AV..EVGIGNRPAVAAALVSC.-GVDIVAT
  30 ...-...M..EGLLT-IV.RRL.....RAR..-R.VV..EVGHGRNLRYLKGLLKA.-GIDAWGV


              50                   60               70        80       
              |                    |                |         |       
   1 DI.....KPS....H...GGI...V.RDDITS.....PRM..EIYRGAALIYSIRPPAEIHSSLM
   2 DI.....KPS....H...GGI...V.RDDITS.....PRM..EIYRGAALIYSIRPPAEIHSSLM
   3 DInk8daKET....G...LNA...F.YDDLFK.....PNL..EIYKNVGLIYSFRPPRDLQPFIL
   4 DVverr.APE....G...CRF...Y.VDDVTK.....PNL..KIYEGASLIYSLRPPPELFSAIV
   5 DVverr.APE....G...CRF...Y.VDDVTK.....PNL..KIYEGASLIYSLRPPPELFSAIV
   6 DInk8daEKN....G...LNA...F.YDDLFN.....PNF..EIYKNVGLIYSFRPPRDLQPFIL
   7 DInk8daKDN....G...LNA...F.YDDLFE.....PNF..EIYKNVGLIYSFRPPRDLQPFIL
   8 DInk8daKET....G...LNA...F.YDDLFN.....PDL..KIYKNVGLIYSFRPPRDLQPFIL
   9 DV.....MPE....GpekLNY...V.RDDVFQ.....PDM..RLYEGASLIYSIRPPVDLQDSIA
  10 DI.....YPC....N...SDV...I.KDDITN.....PTD..KIYEDADLIYSIRPPEELQPDIL
  11 DI.....LPN....D...DEV...I.KDDITN.....PNL..ELYENADIIYSIRPPSELQPHIE
  12 DSne8eaFQH....G...LNS...K.MDDIFK.....PDL..KIYKNIKLIYSIRPPRDLQPYLL
  13 DIne8kaKLL....G...LNA...Y.KDDLFN.....PNI..SLYKNIDLIYSIRPPRDLQPYIL
  14 DIne8kaKLL....G...LNA...Y.KDDLFN.....PNI..SLYKNIDLIYSIRPPRDLQPYIL
  15 DIne8kaKLL....G...LNA...Y.KDDLFN.....PNI..SLYKNIDLIYSIRPPRDLQPYIL
  16 DIne8yaRKQ....G...IKG...V.VDDIFN.....PTL..GIYKDAKAIYSIRPAPEMMKPLL
  17 DAnn8kaKKE....G...LNA...F.VDDIFN.....PKL..DIYKDADLIYSIRPPRDLQPFIL
  18 DInk8naKNS....G...LNA...E.VDDIFN.....PNI..SLYMGAKAIYSIRPTPEMMNYIL
  19 DVracn.LPT....W...LPF...A.RDDIFE.....PDL..SLYSGADVLYAIRPAEEMIPPLI
  20 DInq8naIKE....R...IPG...F.VDDVFN.....PNL..KIYLKARAIYSIRPNPEIMMALL
  21 DWnp8kaGEL....G...INA...V.RDDLFS.....PNL..ELYRGVKALYSVRPTPEIVRSIL
  22 DVdtca.VPG....T...VRF...V.RDDVTD.....PDV..SVYSGAGAVYALNCPPELQRPLV
  23 DI.....RPV....H...VDGvktV.RDDIFN.....PSE..ELYRGASLLYSIRPPIEVQIAMG
  24 DI.....RPGirhdG...LTV...V.TDDVFE.....PDL..RLYEGADLIYAVRPGVEMVPPLI
  25 DIidpp.LNS....W...IPY...V.KDDVSD.....PEP..GLYQGCDCIYAIRPVEEMIPPLI
  26 DIeact.VPE....T...VRF...V.RDDVTD.....PER..AVYEAADAVYALRCPPELQRAVV
  27 DFnq8naNYL....G...LDA...F.KDDLFN.....PNL..KLYDSYDLMYSVRPPRDLQNDIA
  28 DVhay..AEG....P...VPS...V.VDDCVE.....PTI..SLYQAAGVIYAIRPGTEIVPALI
  29 DIvscp.VPP....T...VTF...A.YDDIVTts6raPD-..SVY-DVELVYALNLPPELHRPFR
  30 EIdv8raLEE....E...VPS...VnVDAVEK.....SRWvrRVLRP-DLVYAVRPPVELAVGLI


       90       100        110           120       130      
       |         |          |             |         |      
   1 RVADAVGARLIIKPLTGEDI.VTE...R.KMKLVNYGRTYFYEYIAEVRSR...
   2 RVADAVGARLIIKPLTGEDI.VTE...R.KMKLVNYGRTYFYEYIAEVRSR...
   3 EIAKKINCDLIIKALSGEEP.I--...E.ELKLVNYKGKPIYVWKRD----...
   4 EVSRKVGADCLIKPLYGDYM.---...-.EARIVNYKGAQFYLIRRENYD-...
   5 EVSRKVGADCLIKPLYGDYM.---...-.EARIVNYKGAQFYLIRRENYD-...
   6 EIAKKINCDLIVKALSGEEP.I--...E.KLKLVNYNGKPIYVWKRD----...
   7 KIAKKLNCDLIIKALSGEEP.I--...E.ELKLVNYQGKPIYVWKRD----...
   8 EIAKKINCNLIVKALSGEEP.I--...E.ELKLVNYKGKPIYVWKRD----...
   9 AIANRVGADLLIRPFSSEKT.DLSrhfS.EFRCINYKRAVFFLYQNKR---...
  10 KLSDKYNSDVIIKPLFTEEI.NFNfq.Q.RLKLVNYKRMAFYIMKRE----...
  11 RLSRKVDGTFIIKPLCNEDLnISS...H.KVKLKNYKKASFYIL-------...
  12 NLSKNINCDLVIKPLSGEEP.I--...S.ELKLVNYFGKPLYIWKK-----...
  13 DLSKKVNANLIIRPLLNEMP.I--...K.ELKLKNYKGEVFYIKEKQI---...
  14 DLSKKVNANLIIRPLLNEMP.I--...K.ELKLKNYKGEVFYIKEKQI---...
  15 DLSKKVNANLIIRPLLNEMP.I--...K.ELKLKNYKGEVFYIKEKQI---...
  16 DLARKLKIPLYIVPLTGDRT.--P...N.GMKLINYKGIPIYKWEP-----...
  17 NICKKYGISLLIKPLYGETP.I--...N.DLKLINYKGNALYCFNPY----...
  18 KISKAVKVPAYIVPLTGDPV.--P...Q.GMKLITYRGIPIYKWEP-----...
  19 DLAKKLDCDLVVYHLGFESY.--G...D.GGTIVDCGVKLHYYYRHRSEPVker
  20 TLAKKVKVPLYIVPLSGDVP.--P...R.EMKLINYKGISVYVWEP-----...
  21 ELGKKLGVPVYILPLAGD--.VMP...K.TMRLINYRGLAIYVKDI-----...
  22 SLASRVDADCLFTTLGGDPT.LVD...A.TPETLPTQTLYHYP--------...
  23 DLALRIGADVLIRPLEDEIA.DLE...GfSREPICRGAARFYLYRNRRAMGeei
  24 ALADRIDSDLLVYHLGCE--.IYG...D.GGEVVDCGPALLHRYRCRRL--...
  25 RLAHSVHADLVVYHLGFEGA.ARP...A.PLPGCEV-PLHIYVKN------...
  26 DVAGAVGAACYLTTLGGEPV.VVPv..S.ERRTVASG--ALFVARD-----...
  27 RIAKLNDCNLIIQPLSNETA.L--...E.SLKPVCYNGKILCKL-------...
  28 ELATRINADLIVYHLGFELY.ENG...G.E-RIVT-DGVMLHRYVKA----...
  29 DVADTVGADCRLTTLGYDAP.IVPc..H.PVSLP--GGETLYIVESESS--...
  30 E---RYP-------------.---...-.----------------------...