(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:

    • T0248 1260B, Mycoplasma pneumoniae M129
    • gi|45534794|ref|ZP_00185350.1|_2:142 hypothetical protein Mflo110601 [Mesoplasma florum L1]
                 10        20        30          40        50        60
                 |         |         |           |         |         |
   1 ...MINKPNQFVNHLSALKKHFASYKELREAFNDYHKHN..GDELTTFFLHQFDKVMELVKQKDF
   2 ...MINKPNQFVNHLSALKKHFASYKELREAFNDYHKHN..GDELTTFFLHQFDKVMELVKQKDF
   3 ...MINKPNQFLNHLDGLKQHFSDYDSLQKSFKKYLSEN..QTELNNFFFNQFEKIIVLVKKKEF
   4 ilwLVGIMKKWSNLIKTMMTKNKTFHTINEIINDLSNSElaNDQNTQFYLSLLMMIKTDLDNKDF
   5 ...---------------------MSKKEASKKKQTEKP..KDQLTIYYENILSKVDALVKDKKI
   6 ...-----------------MVCIILKIKKGMLKIMNNN..KSYIKKYFDDILIQAKQVLKKHDY
   7 ...--------------------------PDSNEQRSSN..SP--KNYYDVIVEKIKTKILENS-
   8 ...------------------------------------..---MANYYDQILKKIKQLVEKNNL
   9 ...------------------------------------..----MNFYDELIIELKELVLKNDF
  10 ...------------------------------------..----MNFYDELIIELKELVLKNDF
  11 ...------------------------------------..------------------------


              70        80        90           100        110        12
              |         |         |             |          |          
   1 KTAQSRCEEELAAPYLPKPLVSFFQSLLQL.V..NHDL.LEQQNAALASLPAA.KIIE.LVLQDY
   2 KTAQSRCEEELAAPYLPKPLVSFFQSLLQL.V..NHDL.LEQQNAALASLPAA.KIIE.LVLQDY
   3 KTAQERCEEELATPYFSKPLVGFFQSLLQL.I..NHDL.IEQKNQQLANMSCE.KIVE.MVLSDY
   4 KKALTSIQEELDTDYLPLALIDYFKQ-AHL.V..TKRLmYENEFDWLEKLDKK.ELIN.KTIINF
   5 NEALEMVNDELDSPYIPSEFEEAFMTISYN.L..SAEInYLNESVKYESLNRE.ELFN.SILNGK
   6 AYAYDLISNEFNNPLIDLKTLQEFEAFAIE.IkkSAELnFIDENE--AKLAKT.DFYC.K-IHDP
   7 KEALFLVEKELNAPYIPKEYENIFRELLLKaI..QN--.YENNRAQI-KLSPS.ECLE.-ILISK
   8 TKALDIINQELELSYIPSDFE---KSL-YK.I..KKEI.KEKQ---YSQLNKTySILEiKTLLNS
   9 ETALLKINQELSMPYVPSDIEEQLLEFKTQ.I..FEQI.SKKANSN-NNLNAE.YILQ.L-LKSS
  10 ETALLKINQELSMPYVPSDIEEQLLEFKTQ.I..FEQI.SKKANSN-NNLNAE.YILQ.L-LKSS
  11 ------------------------------.-..----.--------------.----.------


      0         130        140           150        160       170      
     |           |          |             |          |         |      
   1 PNKL.NMIHY.LLPKTKAFVK.PHL.L.Q..RLQFVLTDSELLELK.RFSFFQALNQIPGFQGEQ
   2 PNKL.NMIHY.LLPKTKAFVK.PHL.L.Q..RLQFVLTDSELLELK.RFSFFQALNQIPGFQGEQ
   3 PNKL.NLIHY.LLAKEASFVN.PNL.L.Q..RMTFVLTDLELLELK.RFSFFKALNQIPAFKNHK
   4 PENL.WYFDY.LATKEENFWN.IDD.F.E..FFRHIFITKTYDNSD.KLVAAQLLQKIEPFINLS
   5 TINS.VALSI.FLERYKDNIE.VSE.L.K..IFDSFLSSKKIFDID.KQNLIIALKPLN--LDYE
   6 KTTY.VSLAY.LETFLMRFINeMDE.L.DitFLNSLLTNKLINGST.KLDILDLLATNN--IDQN
   7 NRRL.KPLA-.LAE--LRNYA.LRP.FiN..EINQLFQKEEI-EIQiKASIYEFLCE----QDIN
   8 KNNLdQIIGI.---KNLININ.IRLvL.D..EIKKYLININNAYEN.KSLLLISLSDQQ--IDQD
   9 DREQ.QAFGInFLNK----IN.LRDkL.N..DVSELLTLEKIDNSI.KTLILFTLKEQE--INKS
  10 DREQ.QAFGInFLNK----IN.LRDkL.N..DVSELLTLEKIDNSI.KTLILFTLKEQE--INKS
  11 ----.-----.----------.---.-.-..---------------.------------------


       180       190       200          210       220        230       
        |         |         |            |         |          |       
   1 VEYFNSKLKQKFTLTLGEFEIAQQPDAKAYFE...QLITQIQQLFLKE.PVNAEFANEI.IDAFL
   2 VEYFNSKLKQKFTLTLGEFEIAQQPDAKAYFE...QLITQIQQLFLKE.PVNAEFANEI.IDAFL
   3 VTYFNSKLKQKFVITLGEFAFPQTDKTKQFFQ...QLIKKVSQLFLKE.PVSCEFAYEI.IDALL
   4 FEVYNNKLKQTFTVTLKKDDIWAK-NTQAYFN...DVLDQIESSFYKD.PSKEQLATEI.VNNIM
   5 FDYYNSFADQIFKINIKSVNVLLSSP---YFV...ELNKLVEEFTYKE.PSLQEFCYLI.IFDLY
   6 FNFYNKYLKQ--TKNVNPVNF--NNHYQE-ID...QIQNYLNKYLAKN.PSLLHLANKL.LMMYI
   7 FEF---KIGKE---SLNPVKNKSLVNNSFYLL...N-RNKINEKTFKD.VSITNVALEI.LNSYC
   8 FEVFKDK-KTSFLINPKSLNIKEIYNI--YYQiesQILEVIDQ---KD.IFLIQTCKQV.LFSYF
   9 FDVLYSGVQQSW----NPIEIDFENNFK-FIT...EIDEVISKSIENEnPGIAHDAKMLnINFYL
  10 FDVLYSGVQQSW--------------------...-------------.----------.-----
  11 --------------------------------...--------LFLKE.PVSCEFAYEI.IDALL


       240        250       260        270              280       290  
        |          |         |          |                |         |  
   1 VSYFPLHPP.VPLAQLAAKIYEYVSQIVLN.EAVNLK..DELI.KL..I..VHTLYEQLDRPVGD
   2 VSYFPLHPP.VPLAQLAAKIYEYVSQIVLN.EAVNLK..DELI.KL..I..VHTLYEQLDRPVGD
   3 VSFFPLHPN.LEVNHLAKKIHQYVSKIVIN.EVVDLK..DPTT.KL..I..VDTLYEQLDRAIGE
   4 QDYYPSYPDfVSVKELASGIIQYVKNCFDN.KKPNTKi.NSIVyDV..I..INCIDQ--------
   5 VYYFPNHPD.YQISDLAYAIFQYMLNSLQG.NIKEYK..NP--.EI..IkdIEKIVGIFLRAAEN
   6 TYYFPFKFA.HNHNLIAKTIIDYVKNAMEN.HVCQYS..EEQ-.KA..I..VACINKILE---EE
   7 ATVFPEAIL.IGEKDYSTEFI-YIAKKLLGiEKDEEK..TPLC.DI..I..YSRIFSN-------
   8 LYIFPYVEL.LKTNDVIVAII-YLSFQLNN.LKFDIKklNKNI.EFnqVn.VDKI--IIDI---K
   9 NNL------.--------------------.------..----.--..-..--------------
  10 ---------.--------------------.------..----.--..-..--------------
  11 VSFFPLHPN.LEVNHLAKKIHQYVSKIVIN.EVVDLK..DPTT.KL..I..VDTLYEQLDRAIGE


            
           
   1 EN....
   2 EN....
   3 EN....
   4 --....
   5 NNlks.
   6 QV....
   7 --....
   8 KS....
   9 --....
  10 --....
  11 EN....