(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..ND.LAVYII.RCS.....GPG..TR.VV..EVGAGRFLYVSDYIRKH.SKVDLVL
   2 ...M...W..ND.LAVYII.RCS.....GPG..TR.VV..EVGAGRFLYVSDYIRKH.SKVDLVL
   3 ...MdtiF..KY.IDEHYR.NLK.....NKG..LK.VA..ELGIGFYFNNAKKLKEI.-GFDVIV
   4 ...M...L..Q-.IADYIA.ENY.....RG-..-K.VV..EVGIGRFTAVAELLARR.-GFEVFA
   5 ...MdtvF..KY.IDENYQ.NLK.....NNG..LK.IA..ELGIGFYFNNAKKLKD-.SGFDVIV
   6 ...MdtiF..KY.INENYG.HIK.....NKG..LK.VA..ELGIGFYFDNAKKLKD-.SGFEVIV
   7 ...MdtiC..KY.IDENYS.DIK.....NKE..LK.IA..ELGIGFYFDNAKKLKD-.SGFDVIV
   8 ...M...F..MLqIADYIA.ENY.....RG-..-K.VV..EVGIGRFTAVAELLARR.-GFEVFA
   9 ...MskvW..EN.FSEYII.NNY.....QDS..KK.II..EVGVGKITEPSDILKKHlPNTTINL
  10 ...Iig.Y..DD.LAEYIL.QHY.....PAG..SR.II..EVGIGRHPDTAELLSRY.--CDFTC
  11 ...M...W..DD.FAEFILtQAT.....ENP..TR.IV..EIAVGKFDGVYQYLKRN.ENIEIIK
  12 ...-...M..DY.IFEYLL.NNYshl..KNN..SK.IVvaEIGIGFYVEISKKMQK-.SGFNVIA
  13 ...Mn..V..KI.IVEFIK.KFA.....EENncKK.IA..EIGIGFKFDVARELSKY.--FDLIA
  14 cekMn..V..KI.IVEFIK.KFA.....EENncKK.IA..EIGIGFKFDVARELSKY.--FDLIA
  15 cekMn..V..KI.IVEFIK.KFA.....EENncKK.IA..EIGIGFKFDVARELSKY.--XDLIA
  16 ...M...I..E-.VAEIIA.REI.....RRG..-K.IV..EIGVGFYLEVAKRLRE-.SGIDILV
  17 ...-...M..DY.VCDYII.KNYy11knSES..FK.II..EIGVGYYFNIAKSLNNH.ENLNLIV
  18 ...M...I..E-.VAEFIA.REV.....KKG..-K.VI..EVGIGFYTRIAKRLKEL.-GFDVLA
  19 ykhI...E..HC.CGVYIA.QHY.....TNP..--.-V..EIGVGSNPDAAQCIHEA.-GIPVRA
  20 ...Mp..I..ED.FADFIA.SRV.....PKG..-K.VV..ELGIGFQFKVALRLKEL.-GYDVLA
  21 ...-...M..EA.LAELIK.RKV.....PNE..GL.II..EVGVGFYLKVAKKLKEY.-GFNVVV
  22 ...M...H..TD.SEGALV.DRL.....SSY..DA.LV..EVGVGNRPTVAAALDER.-GCRVTA
  23 ...M...RgaQE.IAEFIR.SHY.....TG-..-R.II..EIGVGQCGDVARLIP--.---DLIA
  24 ...Mcr.Y..KH.IERSIG.EYI.....AAR..YRrAV..EVGVGNNPEAAGLIAAA.-GALMLC
  25 ...M...T..QP.--PTVA.AVL.....AAH..SR.VV..EVGIGARPDVAAALAER.-GCAVTA
  26 ...Msg.Y..KY.IETAIA.RFI.....AGR..YRsVI..EVGAGTNLHTANLLFRT.-GILIRC
  27 kfkL...V..KP.LYNYIL.DNYlle..NPD..LQ.IL..ELGVGFYFEMALKLKQN.-NYNITV
  28 pysM...R..NG.IETAVG.RYI.....AAN..YRsAV..EVGFGGKTTAAEIVQNA.-GIPVLC
  29 ...M...H..SL.AQDALV.ERF.....SSY..TS.AV..EVGIGNRPAVAAALVSC.-GVDIVA


                      50               60             70        80     
                      |                |              |         |     
   1 TD.....I.....KP..SH...G.GI...VRDDITS.....PRMEIYRGAALIYSIRPPAEIHSS
   2 TD.....I.....KP..SH...G.GI...VRDDITS.....PRMEIYRGAALIYSIRPPAEIHSS
   3 ID.....Ink6vsDA..KE...T.GLna.FYDDLFK.....PNLEIYKNVGLIYSFRPPRDLQPF
   4 TD.....Vverr.AP..EG...C.RF...YVDDVTK.....PNLKIYEGASLIYSLRPPPELFSA
   5 ID.....Ink6vlDA..KD...N.GLna.FYDDLFE.....PNFEIYKNVGLIYSFRPPRDLQPF
   6 ID.....Ink6vlDA..KE...T.GLna.FYDDLFN.....PDLKIYKNVGLIYSFRPPRDLQPF
   7 ID.....Ink6vlDA..EK...N.GLna.FYDDLFN.....PNFEIYKNVGLIYSFRPPRDLQPF
   8 TD.....Vverr.AP..EG...C.RF...YVDDVTK.....PNLKIYEGASLIYSLRPPPELFSA
   9 VD.....I.....YP..CN...S.DV...IKDDITN.....PTDKIYEDADLIYSIRPPEELQPD
  10 TD.....V.....MP..EGpekL.NY...VRDDVFQ.....PDMRLYEGASLIYSIRPPVDLQDS
  11 TD.....I.....LP..ND...D.EV...IKDDITN.....PNLELYENADIIYSIRPPSELQPH
  12 IDsn6avI.....EA..FQ...H.GLns.KMDDIFK.....PDLKIYKNIKLIYSIRPPRDLQPY
  13 ID.....Ine6ieKA..KL...L.GLna.YKDDLFN.....PNISLYKNIDLIYSIRPPRDLQPY
  14 ID.....Ine6ieKA..KL...L.GLna.YKDDLFN.....PNISLYKNIDLIYSIRPPRDLQPY
  15 ID.....Ine6ieKA..KL...L.GLna.YKDDLFN.....PNISLYKNIDLIYSIRPPRDLQPY
  16 VD.....Ine6inYA..RK...Q.GIkg.VVDDIFN.....PTLGIYKDAKAIYSIRPAPEMMKP
  17 ID.....Ann6veKA..KK...E.GLna.FVDDIFN.....PKLDIYKDADLIYSIRPPRDLQPF
  18 ID.....Ink6vvNA..KN...S.GLna.EVDDIFN.....PNISLYMGAKAIYSIRPTPEMMNY
  19 RD.....Vracn.LP..TW...L.PF...ARDDIFE.....PDLSLYSGADVLYAIRPAEEMIPP
  20 VD.....Wnp6veKA..GE...L.GIna.VRDDLFS.....PNLELYRGVKALYSVRPTPEIVRS
  21 VD.....Inq6vkNA..IK...E.RIpg.FVDDVFN.....PNLKIYLKARAIYSIRPNPEIMMA
  22 TD.....Vdtca.VP..GT...V.RF...VRDDVTD.....PDVSVYSGAGAVYALNCPPELQRP
  23 TD.....I.....RP..VH...VdGVkt.VRDDIFN.....PSEELYRGASLLYSIRPPIEVQIA
  24 TD.....I.....RPgiRH...D.GLtv.VTDDVFE.....PDLRLYEGADLIYAVRPGVEMVPP
  25 TD.....Ieact.VP..ET...V.RF...VRDDVTD.....PERAVYEAADAVYALRCPPELQRA
  26 VD.....Iid...PP..LN...S.WIpy.VKDDVSD.....PEPGLYQGCDCIYAIRPVEEMIPP
  27 MD.....Fnq6vlNA..NY...L.GLda.FKDDLFN.....PNLKLYDSYDLMYSVRPPRDLQND
  28 TD.....V.....HA..YA...E.GPvpsVVDDCVE.....PTISLYQAAGVIYAIRPGTEIVPA
  29 TD.....Ivscp.VP..PT...V.TF...AYDDIVTts6raPD-SVY-DVELVYALNLPPELHRP


         90       100        110            120       130      
         |         |          |              |         |      
   1 LMRVADAVGARLIIKPLTGEDI.VTE..R...KMKLVNYGRTYFYEYIAEVRSR...
   2 LMRVADAVGARLIIKPLTGEDI.VTE..R...KMKLVNYGRTYFYEYIAEVRSR...
   3 ILEIAKKINCDLIIKALSGEEP.IEE..-...-LKLVNYKGKPIYVWKRD----...
   4 IVEVSRKVGADCLIKPLYGDYM.---..-...EARIVNYKGAQFYLIRRENYD-...
   5 ILKIAKKLNCDLIIKALSGEEP.IEE..-...-LKLVNYQGKPIYVWKRD----...
   6 ILEIAKKINCNLIVKALSGEEP.IEE..-...-LKLVNYKGKPIYVWKRD----...
   7 ILEIAKKINCDLIVKALSGEEP.IEK..-...-LKLVNYNGKPIYVWKRD----...
   8 IVEVSRKVGADCLIKPLYGDYM.---..-...EARIVNYKGAQFYLIRRENYD-...
   9 ILKLSDKYNSDVIIKPLFTEEI.NFNfqQ...RLKLVNYKRMAFYIMKRE----...
  10 IAAIANRVGADLLIRPFSSEKT.DLS..RhfsEFRCINYKRAVFFLYQNKR---...
  11 IERLSRKVDGTFIIKPLCNEDLnISS..H...KVKLKNYKKASFYIL-------...
  12 LLNLSKNINCDLVIKPLSGEEP.ISE..-...-LKLVNYFGKPLYIWKK-----...
  13 ILDLSKKVNANLIIRPLLNEMP.IKE..-...-LKLKNYKGEVFYIKEKQI---...
  14 ILDLSKKVNANLIIRPLLNEMP.IKE..-...-LKLKNYKGEVFYIKEKQI---...
  15 ILDLSKKVNANLIIRPLLNEMP.IKE..-...-LKLKNYKGEVFYIKEKQI---...
  16 LLDLARKLKIPLYIVPLTGDRT.--P..N...GMKLINYKGIPIYKWEP-----...
  17 ILNICKKYGISLLIKPLYGETP.IND..-...-LKLINYKGNALYCFNPY----...
  18 ILKISKAVKVPAYIVPLTGDPV.--P..Q...GMKLITYRGIPIYKWEP-----...
  19 LIDLAKKLDCDLVVYHLGFESY.--G..D...GGTIVDCGVKLHYYYRHRSEPVker
  20 ILELGKKLGVPVYILPLAGD--.VMP..K...TMRLINYRGLAIYVKDI-----...
  21 LLTLAKKVKVPLYIVPLSGDVP.--P..R...EMKLINYKGISVYVWEP-----...
  22 LVSLASRVDADCLFTTLGGDPT.LVD..A...TPETLPTQTLYHYP--------...
  23 MGDLALRIGADVLIRPLEDEIA.DLE..Gf..SREPICRGAARFYLYRNRRAMGeei
  24 LIALADRIDSDLLVYHLGCE--.IYG..D...GGEVVDCGPALLHRYRCRRL--...
  25 VVDVAGAVGAACYLTTLGGEPV.VVPv.S...ERRTVASG--ALFVARD-----...
  26 LIRLAHSVHADLVVYHLGFEGA.ARP..A...PLPGCEV-PLHIYVKN------...
  27 IARIAKLNDCNLIIQPLSNETA.LES..-...-LKPVCYNGKILCKL-------...
  28 LIELATRINADLIVYHLGFE-L.YEN..G...GERIVT-DGVMLHRYVKA----...
  29 FRDVADTVGADCRLTTLGYDAP.IVPc.H...PVSLP--GGETLYIVESESS--...