(c) 1992-2000 Regents of the University of California, Santa Cruz
Sequence Alignment and Modeling Software System
http://www.soe.ucsc.edu/research/compbio/sam.html

Citations (SAM, SAM-T99, HMMs)

Sequence numbers correspond to the following labels:

    • T0370 FG7419A, STREPTOMYCES AVERMITILIS, 154 res
              10        20        30          40          50           
              |         |         |           |           |           
   1 MTTPPARTAKQRIQDTLNRLELDVDAWVSTAGADGG..APYLVPLSYL..WDGETFL..VA....
   2 MTTPPARTAKQRIQDTLNRLELDVDAWVSTAGADGG..APYLVPLSYL..WDGETFL..VA....
   3 ------PRSRARRRRDTERRLAHDVDVWVATASAGG..VPYLVPLSFD..WDGEALL..LS....
   4 ---PAEPRTRARRRRDTEHRLAHDVDVWVASAAPDG..TPYLVPLSFS..WDGAAVW..VA....
   5 --GYVERARELLPWSHVEQRLTHAINYWLCTVRPDG..RPHAVPKWAV..WVDGKLY..FD....
   6 -------PRDVRLADTRHHLESDIDLWVATAHPDGG..APGLVPLSFD..WDGRDLL..LA....
   7 MKDQRRGRKIAMSPAEVDAFLAEERTCRVATTSADG..-PHLTPLWFV..WDGQALW..LN....
   8 MKEQRRGRKIAMSRDEIDAFLTEERTCRVATSSPSG..-PHLTPLWFV..WDGAALW..LN....
   9 MFREMRRKRQLLPQEESVAILEKMTNGTLALHGDNG..YPYAVPLSYV..YADGKIY..FH....
  10 MFREMRRKRQLLPQEESVAILEKMTNGTLALHGDNG..YPYAVPLSYV..YADGKIY..FH....
  11 ------------SPDVARALFATRPVAYLASCSGAG..VPHIVPIVFV..VNGNTIV..TAvd6p
  12 ----------AVVPEDREDILTKRSFAHVATIGPHG..EPQSNPVWFE..WDGEYIK..FS....
  13 -----RGRRITMTPGELEAFLTTRRTCRVATVSADG..APHVSTLWFV..WDGASMW..LY....
  14 ------------------DFLTERHLATLTTLRADG..SPHVVPVGFT..WDNEAVVvrVI....
  15 ----------MTDEEWRAFVSDGTRTGKLSTVRADG..SPHIAPIWFL..LDGDDLV..FN....
  16 -------------EPWVERRLREEKILWLTTVRADG..QPQPVPVWFL..WGTEGFL..IY....
  17 ---------KMTEEEWRAFVSHGTRTGKLSTVRADG..RPHVAPIWFL..LDGDDLV..FN....
  18 -ACSYSGPMTLSFDDSVRTLLDGKNFAGVATLGPDG..APQNSVVWIK..REGDTVL..FS....
  19 ------------------AFVAERHLATLTTLRADG..TPHVVAVGFT..WDPEAGIarII....
  20 --------APEVSASVEAFLTQTPHIGVLTTIRPDG..SPHVAPVRFT..WDAEAGLarVM....
  21 ----------MSPEERRGFLLAGTRTAKLSTVRPDG..RPHVAPVWFL..LDGEAVV..FT....
  22 -----------EFGAKVAERLEREQVVWLTTVGPTG..TPQPNPVWFQ..WRDGEFL..LF....
  23 ------------SEDEIWEFVGAAHTGVLTTLRADG..APVSLPTWFV..VVDRTVC..LS....
  24 -----------------------RHTCWLTTINPDG..APHVTGIGAL..FVDGCFW..FE....
  25 -------------------------NFISRIAFNGD..YPYIAPFLYV..FDGEHLY..FL....
  26 --RPGAADVTATEWAEARRRLEAAEIFWVTTVRPGG..GPHVTPVIAA..WHDGVLY..FS....
  27 -----------------------KELVFVATADEEG..TPNVVPIGFArpLDERTIL..IA....
  28 --------------------LLARDLTRLAYVAKDG..TPRTIPIAFA..WHGSTVV..MC....
  29 -------------------LLASTSAAHLAYTAKDG..TPRVIPVGYF..WTGAEFV..IA....
  30 -----------LSDELKTYIDEAKVFATVATNGPGG..QPHLTVVWLA..RDGDDLL..FS....
  31 --------------EERRNFVGAHRTAILGYARRHD..GPALSAVYYV..TDGDEIL..VS....
  32 -----RRSREISDRAEIDAILASDKVLHLALARDN-..VPFLVPVFYG..FDGKALY..VH....
  33 ----------------IDEFLRSHNTCTLATCH-GG..QPRATPLEYI..YDGDSLL..II....
  34 -----------LPDDEVEALLRRANTGTLSLA-DGG..DTYAVPQSFG..YDGETLYfqLA....
  35 --------------QECWQRLGTHGIGRISYVAGPGkeAPVVVPVNFL..VDGRSVV..YR....
  36 -----------LPVEECWQLLTTAPVGRIAWSTTGG..-PVVVPVNFV..VDGRTIK..IR....


          60        70             80                  90              
          |         |              |                   |              
   1 .TPAASPTGRNLSETG..RVRLGIGP...TRD.....L.....VLVEGTALP.....LEPAG...
   2 .TPAASPTGRNLSETG..RVRLGIGP...TRD.....L.....VLVEGTALP.....LEPAG...
   3 .TPADSPTGRNLAATR..TARLALGH...TRD.....V.....AVIDGDVEV.....LEIDA...
   4 .TPAGSPTGRNLAATG..AARLALGP...TRD.....V.....TLIDGGVEV.....FELDA...
   5 .GSPATRHARNIATNP..HVVIHLES...GED.....V.....VIVEGIARA.....IDTPApe6
   6 .TGRSTPAGRNMRASG..LVRLSLGE...LRD.....V.....IMVDATVVE.....VPLSS...
   7 .SVVKSQRWTDLERDP..RVAIVVDT...GHE.....FtelrgVEIRGRAESvg8vgTPDPG...
   8 .SVVKSQRWTDIARDP..RVAVLIDG...GHA.....FnelhgVELRGKLESvg8tgTPDPD...
   9 .CAKIGHKVDAIMQNN..KVSFCVVE...QDN.....Ik11rsVIVFGKAYI.....LTDET...
  10 .CAKIGHKVDAIMQNN..KVSFCVVE...QDN.....Ik11rsVIVFGKAYI.....LTDET...
  11 kSGRVLRRIRNIRENP..SVAVLADR...YTDdw6lwW.....IRADGRARL.....MDGAD...
  12 .QTTTRQKYRNLKRDS..RIALSVHD...PDEphr..Y.....IEIRGRAEK.....IEPDP...
  13 .SVVRSRRWADLRRDP..RVAIVVDT...GEE.....YdelrgVELSGRVAF.....VGEAPrt8
  14 .TNDVSQKAINAGRSG..TAAVCQVE...GRR.....W.....LSLEGRSRV.....LDDAD...
  15 .TGKDTVKGRNLLRDG..RIALCVDD...DRPpfh..F.....VVLQGRARI.....SEDLG...
  16 .SRPNAQKLRNIRSNP..RVGLNLNC...DERggs..V.....VRAEGTAEI.....VEDAA...
  17 .TARDSVKGRNLARDG..RAALCVDE...DRPpfa..F.....VVFQGQAEL.....SEDLD...
  18 .STAGRQKVRNLRRDP..RISLSVFD...LANp....-yts..VEIRGTAEI.....LPDEN...
  19 .TNDGSVKVRNVRRSG..YAAVSQVD...GAR.....W.....LTLEGPATV.....LDDPD...
  20 .TVSSSRKARNLIAAPgsRVAICQVA...GFA.....W.....VTLEGSAVV.....ADDPV...
  21 .THESTVKARNMRRNP..RVSLCVDD...ERPpys..F.....VLVEGTARL.....SAGDP...
  22 .SQPDTPKIRNIRRNP..RVSVHFNStvhGGD.....V.....VVFTGTARI.....AEDRP...
  23 .TPTGARKLGRVRRDP..RAAFLVES...GQA.....WaelraVHLSGRVGT.....VEDAT...
  24 .TGERTRKARNLARDP..RCALSVAT...AEF.....D.....VVLEGRASR.....VTDPV...
  25 .STRYGRKIELLKRNP..YVAVEIEH...YSDdl6yrF.....VTLQGQIVE.....ENDPS...
  26 .TGPGEQKARNLAHDA..HCALITGG...NSLte...-gfd..LVVEGEAEP.....VGDRA...
  27 .DNYMKKTIRNLHENP..RIALIPQN...ARE.....Cp....YQFKGTVEI.....FKSGK...
  28 .TTKNAPKIHALRANP..MVALTIDT...EVHppk..I.....LLIRGRAEL.....DFTDG...
  29 .TAATSPKVAALSACA..DVALSIDG...GDTpet..-ara..LSIRGRARV.....QIVDG...
  30 .TTVDRQQGKNLAADP..RVTVLINP...PEKpyv..Y.....AEIRGTATL.....TPDPDrt.
  31 .TPGARAKTRAIARNP..KVSLCVLD...EKYpps..Y.....VTLFCDAVV.....DEDFD...
  32 .SASAGTKIEILKTNN..RVCFEVTT...ENG.....Vv15rtVIGFGRASF.....VDDVA...
  33 .S-EGGEKFAGLPENE..RVSVAVYE...DYTsm...-sdlagMQITGAASI.....LHGKD...
  34 .YDDDSRKMEYIETTD..TATFTVYE...ERPa....-qs...VIVQGPFEP.....VPEG-...
  35 .TDPAGV--AGIRAGE..PVAFEADH...VDEmtgl.-gws..VLLAGTAEH.....----P...
  36 .TAAYSAMVQK-ADVE..RVAFQVDR...IDEathtg-ws...VLARGRAEV.....RYGE-...


         100            110           120        130       140       15
          |              |             |          |         |         
   1 ..LPDGVGDTFAEKT.....GF...DPRRLT.TSYLY.FRISPRRVQAWREANELSGRELMRDGE
   2 ..LPDGVGDTFAEKT.....GF...DPRRLT.TSYLY.FRISPRRVQAWREANELSGRELMRDGE
   3 ..LPRERGDRFAART.....GF...DPRALS.TPYRW.FCIFPRRIQAWREENELAGRELMRDGR
   4 ..LPQEHGDRFAARA.....GF...DPRGAA.GPYRW.FRITPRRILAWREVNELKGRELMRDGR
   5 tlVAQAYTTKYATMG.....YA...PDPHQW.DNGGL.FAITPHTVIAWTAFTEDPTKF------
   6 ..VPSARWEAYAART.....GW...DPREAG.PDHAA.YVVTPVTIQAWREYPELVDRMLMREGR
   7 ..LATPELLYARKYA.....GR...DEMHYD.GRHAW.LRVTPEKITSW----------------
   8 ..LETPEKLFAQKYT.....GR...DEMHYD.GRHAW.LRLTPEKITSW----------------
   9 ..EKRMALTLLMNKY.....SF...GEPGLS.DEI--.---------------------------
  10 ..EKRMALTLLVNKY.....SF...GEPGLS.DEI--.---------------------------
  11 ..PSAQRAWGALTAR.....YP...QYAEHP.PAGMV.IAIDVHRWSGWAASDAAIARATSAEPT
  12 ..NRSFINKMSKKYL.....GQ...ETYPPE.SPGEE.RVVVY----------------------
  13 aeLDFPETLFARKNF.....GL...QEMPHD.GRHAW.LRLTPEEVVSWD---------------
  14 ..SVLDAETRYAARY.....RP...PRINPT.RVVIE.IAV------------------------
  15 ..ELRHWAGRIGARY.....MG...EE----.-----.---------------------------
  16 ..PASEIPEYVQKYRed6rlGY...EPAGFAlDYAVA.VRVTPRRWQSW----------------
  17 ..EVRLWATRLGARY.....MG...EE----.-----.---------------------------
  18 ..KRLPYELSHKYLG.....ID...PPAEKD.DEVRViIRVVPQKIV------------------
  19 ..SVADAEHRYAGRY.....RV...PRENPT.RVVIA.IRV------------------------
  20 ..RVTEGARRYTRRY.....RS...GPPNPP.GRVV-.---------------------------
  21 ..ELLDWTTRIGGRY.....MG...QE----.-----.---------------------------
  22 ..TEQEIAAFTAKY-.....--...------.-----.---------------------------
  23 ..TRDRVRSLLDEKY.....--...------.---AA.FRVSPQR--------------------
  24 ..TVVAMAERWAAEG.....WP...ARVDES.G----.---------------------------
  25 ..TKRRVKEMFADLI.....--...------.-----.---------------------------
  26 ..VLEEVIAAYEAKY.....GA...HITSAD.GTF--.---------------------------
  27 ..YFDMVVEWAQNVM.....--...------.-----.---------------------------
  28 ..IPDEYLEAN----.....--...------.-----.---------------------------
  29 ..VVPEYLAAARKSM.....--...------.-----.---------------------------
  30 ..LPDQLSLKYTGQR.....YAefnPASAQD.GDRIV.VRVTPRK--------------------
  31 ..LAVDVAFRVAQRI.....IG...------.-----.---------------------------
  32 ..EKTRALDLIVSRF.....T-...------.-----.---------------------------
  33 ..AEHVYKLRGLNPD.....AV...KDLNID.-----.---------------------------
  34 ..-------------.....--...------.-----.---------------------------
  35 ..VEREALEALARRR.....GA...VPWAGG.RRDLW.VRVLPHQV-------------------
  36 ..-------------.....--...------.-----.---------------------------


      0    
     |    
   1 WLVTD
   2 WLVTD
   3 WL---
   4 WL---
   5 -----
   6 WL---
   7 -----
   8 -----
   9 -----
  10 -----
  11 WPEDG
  12 -----
  13 -----
  14 -----
  15 -----
  16 -----
  17 -----
  18 -----
  19 -----
  20 -----
  21 -----
  22 -----
  23 -----
  24 -----
  25 -----
  26 -----
  27 -----
  28 -----
  29 -----
  30 -----
  31 -----
  32 -----
  33 -----
  34 -----
  35 -----
  36 -----