(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:

    • T0245 AF2059, Archaeoglobus fulgidus 
              10             20         30         40        50        
              |              |          |          |         |        
   1 MMWEQFKKEKLRGY.....LEAKNQRKVDFDIVE.LLDLIN.SFDDFVTLSSCSGRIAVVDLEKP
   2 -EFRKWKAQCLSK-.....ADLSRKGSVDEDVVE.LVQFLN.MRDQFFTTSSCAGRILLLDRGIN
   3 -EFRKWKAQCLSK-.....ADLSRKGSVDEDVVE.LVQFLN.MRDQFFTTSSCAGRILLLDRGIN
   4 -EFGRWKAQSLSK-.....ADLSRKGSVDEDAVE.VVELLN.SREEFFTTSSCAGRILLLDGSTE
   5 -EFGRWKAQSLSK-.....ADLSRKGSVDEDAVE.VVELLN.SREEFFTTSSCAGRILLLDGSTE
   6 MMWEQFKKEKLRGY.....LEAKNQRKVDFDIVE.LLDLIN.SFDDFVTLSSCSGRIAVVDLEKP
   7 -SFQQWKNQCLNK-.....CDFSKKGSVDEDISH.VVSFIN.SQDRYFTTSSCSGRIILFDAVSD
   8 -NFERAKKEALISL.....EIALRRGEVDEDIIP.LLKKIN.EKPNYFTTSSCSGRISIMEMPDF
   9 -----AKREALISL.....FTAIKEGKVDEDIID.LLMLIN.SIKGVYTTSSCSGRIGIIEEPSL
  10 -NFERAKKEALMSL.....EIALRKGEVDEDIIP.LLKKIN.SIENYFTTSSCSGRISVMEMPHF
  11 -NFERAKKEALMSL.....EIALRKGEVDEDIIP.LLKKIN.SIENYFTTSSCSGRISVMEMPHF
  12 -NFERAKKEALISL.....EIALRKGEVDEDIIP.LLKKIN.SLDNYFTTSSCSGRISVMEMPHF
  13 -NFERAKKEALISL.....EIALRKGEVDEDIIP.LLKKIN.SLDNYFTTSSCSGRISVMEMPHF
  14 ----KAKREALLSL.....FQAIKENKVDEDIVE.LLLLIN.SIKGVYTTSSCSGRIGIIEEPSL
  15 -----AKREALLSL.....FQAIKENKVDEDIVE.LLLLIN.SIKGVYTTSSCSGRIGIIEEPSL
  16 MDFEKRKAATLASIrssv.TDKSPKGFLDEPIIP.LLETIN.HHPSYFTTSSCSGRISILSQPKP
  17 MDFEKRKAATLASIrssv.TDKSPKGFLDEPIIP.LLETIN.HHPSYFTTSSCSGRISILSQPKP
  18 -SFDQKKQSILSEIss7dnLDASPKGTIDEYCLP.IIDTIN.SHRDMVTTSSCSGRVSIFLEGVK
  19 -PFDQKKKSILAEIga7itPDASPKGTIDEFCIP.IIHLIN.SNKDMVTTSSCSGRVSVFLEGMK
  20 -GFDQKKKSILSGInseg.PDLSPKGDIDSLCIP.IIELIN.SHKDMVTTSSCSGRVSVFVEGRK
  21 -GFLEDKKRTLMNL.....ELAIREGLVDEEIIP.ILNKIN.EIDNYYTTSSCIGRVGIMEIPKD
  22 MEFDRRKAAALAALaspa.PDKSPKGGVDAPIAP.LLDALN.SHPDLFTTSSCSGRVSVLAQPPP
  23 -----AKREALISL.....FHAIKEEKVDSDIID.LLLLIN.SIKGIYTTSSCSGRIGILEEPSL
  24 -AFEQKKRAILNEIdstq.PDLSPKGTIDELCLP.IIDLIN.ASADMVTTSSCSGRVSVFLEGTK
  25 -HWEGEKRRRLKEL.....ERAIERGEVDEAAIP.VLETLN.SFEEYCTTSSCSGRVVVLHEPEV
  26 -AFDQKKLAILQEInsdq.LDLSPKGTIDVLCLP.IIDLIN.SSPDMVTTSSCSGRISVFIEGQK
  27 -SFDAQKKEILEGLkssv.PDASPKGHPDSPIFP.LLDVIN.SHPDWVTTSSCSGRISVYVQGAN
  28 -EFGRWKQRCLEK-.....LDVSRKGSVDEAISH.VVALVN.SREQFFTTSSCSGRSVLIDRVGG
  29 -SFAQKKAYILEQIsl7dnPDDSPKGTIDEFLKP.LIATIN.GLDDFVTTSSCSGRVSVFLEGEK
  30 --FNDDKEFTLKKL.....QEALDNDFVDLEVMY.LVDKIN.EFKDYYTTSSCIGRCGIIEFPKD
  31 --FDELKKQFLERL.....EREKQLGYVDKPIIP.LLDLIN.SFDNYFTLSSCSGRISLFVEG--
  32 -NWFTYKQRAWERV.....IRDKEIGYLDPDIFD.TLEVFF.KRRDTFTQSSCSGRITIIDAEMP
  33 -VWEELREKALNKI.....YHDKEIGYLDPDILGfLLAFYR.NRNDVYTQSSCSGRITIVDAEMP
  34 ------KKNVYNDI.....DDKSIKKSIDLLIYP.CVYEIN.KNEFYYTTSCCSGRIVIFKEVHI
  35 -PFLEKKAKIIAQLat7tyTDASPKGSVDVGIRE.LIAEIN.CQAGLVTTSSCAGRVSVFLEGKK
  36 -AFVERKKKILDQLai7eyTDASPKGSVDEGIRD.LIDEIN.QQSGFVTTSSCAGRVSVFLEGRR
  37 -VFVSRKNKILAELsa7eySDLSPKGSVDEGIRD.LIEDIN.TLPGLVTTSSCAGRISVFLEGRK
  38 -VFEARKRAFVERL.....EREALQERVDGDILP.LLRLLN.RHPHIYTTSSCSGRIMVAEAVRP
  39 --------------.....-EERLIGYLDPGAEK.VLARIN.RPSKIVSTSSCTGRITLIEGEAH
  40 -SFLTRKSKILSQLsv7eyTDASPKGSVDVAIRE.LIDEINhGYEGLVTTSSCAGRVSVYLEGVK
  41 -EFATHKAHILTNLqtna.CDLSPKGSLDAKCLP.VMGVLN.THKDYVTTSSCSGRIALFHSIKH


           60        70                 80                   90       1
           |         |                  |                    |        
   1 .....GDKASSLFLGKWH.....EG...V.EVSEVAEAALR.....SR.KV.....AWLIQYPPI
   2 gfe..VQKQNCCWLLVTH.....KL...C.VKDDVIVALKK.....AN.GD.....ATLKFEPFV
   3 gfe..VQKQNCCWLLVTH.....KL...C.VKDDVIVALKK.....AN.GD.....ATLKFEPFV
   4 gsg..VQKQHCCWLLVTH.....KP...C.ARDDVMAALKG.....AT.SE.....AVLKFEPFI
   5 gsg..VQKQHCCWLLVTH.....KP...C.ARDDVMAALKG.....AT.SE.....AVLKFEPFI
   6 .....GDKASSLFLGKWH.....EG...V.EVSEVAEAALR.....SR.KV.....AWLIQYPPI
   7 cpd..VQKQNCSWLFVTH.....QK...C.QMEDVVRGLEK.....SV.GD.....ATFKFEPFV
   8 .....GDKVNAKWLGKWH.....RE...V.SLDEVLEAIRKh....RE.GQ.....LWLLVRSPI
   9 .....GAKPLSRWLIKVH.....RP...M.EFEEAIDALKKa....NK.GI.....IFLKSQPPI
  10 .....GDKVNAKWLGKWH.....RE...V.SLYEVLEAIKK.....HRsGQ.....LWFLVRSPI
  11 .....GDKVNAKWLGKWH.....RE...V.SLYEVLEAIKK.....HRsGQ.....LWFLVRSPI
  12 .....GDKVNAKWLGKWH.....RE...V.SLDEVLGAIKK.....HRsGQ.....LWFLVRSPI
  13 .....GDKVNAKWLGKWH.....RE...V.SLDEVLGAIKK.....HRsGQ.....LWFLVRSPI
  14 .....GAKPLSRWLIKVH.....RP...I.KFEEAKKALKNa....QK.GL.....IFLKSQPPI
  15 .....GAKPLSRWLIKVH.....RP...I.KFEEAKKALKNa....QK.GL.....IFLKSQPPI
  16 ks7tkKKARGGSWLYITH.....DP...A.DSDLVISLLFP.....SK.SNq10seLVFRFEPLI
  17 ks7tkKKARGGSWLYITH.....DP...A.DSDLVISLLFP.....SK.SNq10seLVFRFEPLI
  18 tn8vvAKGHEGRWLFVTH.....EP...K.DLNNWYDSIDF.....NY.DTs11rsILYKFEPLI
  19 n10igAKGNYGRWIFVTH.....DP...K.DLPDWSSSVNF.....KY.ITd14ryILYKFEPLI
  20 ag6pgGKGEGGRWLFVSH.....DK...E.LVRGWRAAHDL.....DW.DAa12rfMLYKFEPFI
  21 k....NPKLYSRWLGKWH.....HY...A.SYDELFNALKNk....KE.GY.....IVFVMNSPI
  22 p12tkKKARGGGWVYISH.....DP...A.DPEALVEVLFGvk7ggGD.DE.....LVFRFEPMI
  23 .....GAKPLSRWLIKVH.....RP...M.SFEEARDALKRa....RE.GL.....IFLKSQPPI
  24 sy9igGKGQGGKWLYVTH.....DR...E.KVIGWLDELKS.....KS.EFs20ryILYKYEPFI
  25 .....GDKIGSEFVAKWH.....EP...P.EPEEVREAVLKap...EE.GI.....TWVKAQPPL
  26 ai9vgGKGDGGVWLFVSH.....EF...K.DIDNWFDRTTA.....SK.NLn20smILYKYEPFI
  27 .....SRKGGGYWLFVSHq12edEK...V.EYGKVPSSPVE.....GN.RE.....IQYAFEPMI
  28 q11sdIQKQDCVWLFVSH.....QS...C.KPEDLVSALER.....SS.AD.....AVFKFEPFV
  29 gv8kvTGKGGGKWLFVSH.....DP...K.EIEGWEKKVFG.....QD.DKm15slILFKYEAMI
  30 k....NPKINSRWLGKWH.....HY...A.NYDEIDEALLKkse..NF.EK.....ISFVLNSPI
  31 .....GKKYNSYPLFKSH.....YP...V.KAEELYEYYINyk...GE.KP.....LIFKFEPFI
  32 .....WERKNSSVVFKNH.....LG...I.TVTDLLETINKg....KV.WN.....LWLVVQGPI
  33 .....WDRKNSTIIFKNH.....LR...I.TEQDLEDVLSKn....QV.RR.....LWLIVQGPI
  34 nnk..NDNQKKIFKNSTT.....SQ...E.KKEENISHHLS.....NI.NLl179nIFIKFEPFI
  35 a19vgGKGGGGRWLYVSH.....EPfgdV.GGRSWEEVLFG.....AD.GPg16rlVHFKFEPMI
  36 v15vgGKGAGGAWLFVSH.....DP...IpDKGDGVTDWSS.....QF.GLe18rlVHFKFEAMI
  37 a20psGGKGAGRWLYVSH.....DP...L.EIKENQSFLKL.....FG.MVp18rlVRFHFEPMI
  38 sy...SKGRGFRPVAKWH.....YP...I.D-SDIVKEVLE.....GV.DN.....AWLMVRGAI
  39 .....WLRNGARVAYKTH.....HP...I.SRSEVERVLRR.....GF.TN.....LWLKVTGPI
  40 r45ssGGKGGGEWLFVSH.....DP...L.ETVDAKTGREY.....DG.DHw32rlIHFKFEPMI
  41 s19krGENAALGWVFVKHgml..RP...M.EMAQVVGFLCG.....AP.TTp68gtVSLKMEPFV


      00       110        120            130            140            
      |         |          |              |              |            
   1 IHVACRNIGAAKLLMNAAN.TAGFRRSGVISL.....S...NYVVEIAS..LERIELPVAE....
   2 LHVQCRQLQDAQILHSMAI.DSGFRNSGITVG.....Krg.KTMLAVRS..THGLEVPLSH....
   3 LHVQCRQLQDAQILHSMAI.DSGFRNSGITVG.....Krg.KTMLVVRS..THGLEVPLSH....
   4 LHVQCRTLQDAQTLHSVAI.DSGFRNSGITVG.....Krg.KTMLAVRG..THGLEVPLTH....
   5 LHVQCRTLQDAQTLHSVAI.DSGFRNSGITVG.....Krg.KTMLAVRG..THGLEVPLTH....
   6 IHVACRNIGAAKLLMNAAN.TAGFRRSGVISL.....S...NYVVEIAS..LERIELPVAE....
   7 LHVQCKQLEDAQLLHTVAI.NSGFRNSGITVG.....Kkg.KIIMAVRS..THCLEVPLSH....
   8 LHVGARTLEDGIKLLNLGV.SCGFKYSNIKSI.....Sdr.KLIVEIRS..TERLDALLGE....
   9 LHVVAENLEMAKLLHQIGL.SSGFKYTTFKVI.....Sn..RYLVEING..TEYLTVPLGR....
  10 LHVGAKTLEDAVKLVNLAV.SCGFKYSNIKSI.....Snk.KLIVEIRS..TERMDVLLGE....
  11 LHVGAKTLEDAVKLVNLAV.SCGFKYSNIKSI.....Snk.KLIVEIRS..TERMDVLLGE....
  12 LHVGAKTLEDAIRLVNLAV.SCGFKYSNIKSI.....Snk.KLIVEIRS..TERMDVLLGE....
  13 LHVGAKTLEDAIRLVNLAV.SCGFKYSNIKSI.....Snk.KLIVEIRS..TERMDVLLGE....
  14 FHVVTESLELARKIHEIGL.SSGFKYTTYKVI.....Sr..RYLVEING..TEYLTVPLGK....
  15 FHVVTESLELARKIHEIGL.SSGFKYTTYKVI.....Sr..RYLVEING..TEYLTVPLGK....
  16 IAVECKDLGSAQFLVALAI.SAGFRESGITSC.....GdgkRVIIAIRC..SIRMEVPIGD....
  17 IAVECKDLGSAQFLVALAI.SAGFRESGITSC.....GdgkRVIIAIRC..SIRMEVPIGD....
  18 LHVKCRNESMAQKLYVLAM.NNGFRESGI--G.....N...NFNVAIRI..NIKLDIPIGFqn6e
  19 LHVKCRDLEMANNLYSVAM.SCGFRESGI--G.....T...NNIVGIRI..SIKLDVPIGFln6n
  20 LHVKCRDFAAAARLLRVAM.ACGFRESGI--G.....S...NNLVGIRI..SIKLDVPIGRld6t
  21 LHIACKDIESAKKMLELAI.HSGLKASSIKSI.....Sdk.RVIVEILT..TYKVDTPIGE....
  22 VAVECRDAAAAAALVAAAV.GAGFRESGITSL.....Qk..RVMVALRC..SIRMEVPLGQ....
  23 FHVVAETIENAKLVHEIGL.ASGFKYTTFKAI.....Ss..RFLVEING..TEYLTVPLGK....
  24 LHVKCRDFQAASKLYNTAM.SCGFRESGI--G.....S...NNLVAIRI..NIKLDVPLGYld6s
  25 FHVMCRDLEAAVRLRNIAS.EAGFKASSIRSV.....Kss.KVIVEILG..GERMDVPAKV....
  26 LHVKCRDFESASKLYNTAM.ACGFRESGI--G.....S...NFIVAIRI..NIKLDVPIGYvken
  27 LHVQTRSLANAQHLQRVAA.SCGFRETGIQGS.....Eq..KFIVAIRT..SLRMDIPIGCltas
  28 LHVQCRQLQDGQLMHSVAI.NAGFRNSGLTVG.....Ksg.KIMMAVRS..THVLEVPLSR....
  29 LHVQCRSLLAAQALYSTAM.GCGFRESGI--G.....S...NNNVAIRI..SLNIGCPIGYgegd
  30 LHVASRNADTSKKLLELAY.HNGLKASSIKSI.....Ssk.RYIVEIMT..TAKMDAPIAY....
  31 IHIQARTLYDGLKLLSIAQ.KLGLKYSALFNIk20gfE...RVILYIMG..HDRIETIVY-....
  32 FHVYTRTNEEAWNILKLAR.SVGFKHSGVLTV.....Nek.GVLVELRT..GVKMVHLLKD....
  33 IHIYAKNIETGWDILKIAR.EAGFKHSGILAT.....Nqk.GVLVELRT..GIRMVHLLRE....
  34 IHVKCTTFLSALKLLKIAQ.YAGLKQSGILNF.....Nk..HVTVAIRG..SMRLEHLLG-....
  35 LHILTASSEHAQSVIRCGL.EAGFRESGAINLlg8qq-a..TPMVAIRSm.GLGLESIIGTlaag
  36 LHVLTASPEHAQILLRCGL.QAGFRESGALNIvp7da-t..TPMVAIRTm.GLAFESLIGQqvdg
  37 LHIMTATLHHAQPVLSAAS.SSGFRESGLQGLrc9kg-p..SPIVAVRSa.GLALESVIGYye6s
  38 LHISAADAKTAYRLVELGR.ETGHKHSGIIAM.....Nkg.GIFVEILG..EERLDIPLKS....
  39 LHLRVEGWQCAKSLLEAAR.RNGFKHSGVISI.....AedsRLVIEIMS..SQSMSVPLVM....
  40 LHILTTSPYHAHLAIQSGM.TSGFRETGAVSIl49vtP...NPIVAIRSm.GLSFESLIGVqrgs
  41 MHVQCRTMEAAKLLLSAVVsDSGFRNSGVVPP.....Gk..KIMCGIRSaaGLGLEVPVVV....


      150         160       170       180       190      
       |           |         |         |         |      
   1 .KGLMLV..DDAYLSYVVRWANEKLLKGKEKLGRLQEALESLQRENAYCSD
   2 .KGKLMV..TEEYIDFLLNVANQKMEENKKRIERFYNCLQHALERE-----
   3 .KGKLMV..TEEYIDFLLNVANQKMEENKKRIERFYNCLQHALERE-----
   4 .KGKLMV..TEEYIEFLLTIANQKMEENKRRIGRFYNYLQHALKR------
   5 .KGKLMV..TEEYIEFLLTIANQKMEENKRRIGRFYNYLQHALKR------
   6 .KGLMLV..DDAYLSYVVRWANEKLLKGKEKLGRLQEALESLQRENAYCS-
   7 .RSHVLV..THQYLDFLVGVANQKMEENLKRIQRFSECLQAAL--------
   8 .NGEILV..SDDYMRKLVEIANAQVRRFKRKLKRFEERIE-----------
   9 .DGKVLV..SEEYLKFAVEIGNEMLRRGKSRLPRLYKNFQELKEK------
  10 .NGEIFV..GEEYLNKIVEIANDQMRRFKEKLKRLESKIN-----------
  11 .NGEIFV..GEEYLNKIVEIANDQMRRFKEKLKRLESKIN-----------
  12 .NGRILV..GEEYLRKIVEIANAQVRRFKEKLKRLESNID-----------
  13 .NGRILV..GEEYLRKIVEIANAQVRRFKEKLKRLESNID-----------
  14 .DGKVFV..TDEYLEFVIEIGNQMLMRGKSRLPRLREKFEELKE-------
  15 .DGKVFV..TDEYLEFVIEIGNQMLMRGKSRLPRLREKFEELKE-------
  16 .TEKLMV..SPEYVKFLVDIANEKMDANRKRTDGFSVALA-----------
  17 .TEKLMV..SPEYVKFLVDIANEKMDANRKRTDGFSVALA-----------
  18 eDLNCFV..TKEYLKYITDISHERFNENFKKLEQLHRAIERMIEDE-----
  19 qELTSFV..SEDYLRIITKLSEDRFKENFKKLDALYKAIESLNTLK-----
  20 dRLRMFV..SPEYVDLLDELAVGKFMENERKMQELYEAIDE----------
  21 .DGEIFV..DNNYLKFLLDYSNSKLKRAREILMRWANRLDEL---------
  22 .TKELVV..SPDYIRYLVRIANSKMEANKKRMGGFLDLLQ-----------
  23 .DGRIIA..SDEYLKFAISIGNKMLERGKSKLPRLRDNFEKIKK-------
  24 gTLKFFV..TPEYVSVLDSLSLSKFDENTRKMQALYDRIE-----------
  25 .NGKLTL..REKAWDSVVALCNDILRSGHERLSRLVEALKG----------
  26 gHLALIV..DPSYITVLDRITKAKFIENEKKMTVLFAKIK-----------
  27 eKLQFYI..TREYMCFLFKRSVEYFTENGNRMARLKEQLERQVEK------
  28 .NGRVLV..DEEYIHFLSQLANQKMEENVRR--------------------
  29 .NLHLLV..PTSYLQLLTQQSRTLFTENFRRMDMLHRAIEGLQIKKETV--
  30 .DGKMVV..NREYLDILLDEGNLKLKHARKSLKRFYEKLNEL---------
  31 .KNKHLV..SEEYIKVLVEEANRKLLKNWALIESLYNEIKNLKE-------
  32 .NY----..DEKEANELVVIANKVLQKGKEKLRKLKEVVEN----------
  33 .SNTERV..DKDKIKTLVNVCNEVLARGKQKMNLLKDLLS-----------
  34 .DIHPTL..QQTNLMEIIHICNNKLSKNLSQLVHFYKCFKQFKEHEHTY--
  35 .GLQCLV..TPQYLAMLVRISNERFRQNAERIERFRLALQE----------
  36 .QRQRIV..SPEYLQTLVDIANERFDENKKRIERFQNAFRE----------
  37 dVIRSLV..SEEYLQMLVTMSNERFSVNTERKKRFRIAL------------
  38 .RGRVLT..D---VEVAVEAANKTLILAKLRLFWLAARIE-----------
  39 .EGARIV..GDDALDMLIEKANTILVESRIGLDTFSREVEEL---------
  40 .QRQSLV..SPEYLSLLVKIANERFEENKKRIARFQEAL------------
  41 .DGVNHVasQRAYVWALLGLANEKMEANEKKIKLLE---------------