(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:

    • T0401 YP_211376.1, Bacteroides fragilis, 143 residues 
              10        20         30        40                 50     
              |         |          |         |                  |     
   1 MEVIESKWYKKDGASSASIDDVEKLL.NTTLPKQYKSFLLWSNGGEGKL.....G....D..NYI
   2 ---NIPDLIEKSAASDIEIQAVENRM.NVTLPNVYKELLRCTNGFSI--.....-....G..SGL
   3 ---NIPDLIEKSAASDIEIQAVENRM.NVTLPNVYKELLRCTNGFSI--.....-....G..SGL
   4 ---NIPDLIEKSAASDIEIQAVENRM.NVTLPNVYKELLRCTNGFSI--.....-....G..SGL
   5 ---NIPDLIEKSAASDIEIQAVENRM.NVTLPNVYKELLRCTNGFSI--.....-....G..SGL
   6 --VIESKWYKKDGASSASIDDVEKLL.NTTLPKQYKSFLLWSNGGEGKL.....G....D..NYI
   7 ----DKFEYPENPASTEEIQALEKWL.GTDLPSEYKKFLLETNGAETPI.....GvqepD..DSV
   8 ----DKFEYPENPASTEEIQALEKWL.GTDLPSEHKKFLLETNGAETPI.....GvqepD..DSV
   9 ----DKFEYPENPASTEEIQALEKWL.GTDLPSEHKKFLLETNGAETPI.....GvqepD..DSV
  10 ---FKNVWTIQPGTNLNTIQKIESIF.KVTFPEDYKQILLWSNGGEGKV.....G....N..RYL
  11 -HKYIEDMDLEQPTSLENITVIESQL.NISFPTDYISFMLESNGAEGAI.....Ge...N..GYL
  12 ---NVSGLIKNKPANDIEIQEIEDVM.KVELPNVHKDLLKYTNGFSI--.....-....G..GGL
  13 ---FKNVWTIQPGTNLNTIQKIESIF.KVTFPEDYKQILLWSNGGEGKV.....G....N..RYL
  14 ---LHNIFTANPPASEHEILLIEQTM.AIHLPQEYKNVLKESNGFSF--.....-....T..NGV
  15 ---VYRIDAKKSPSKEEEIKALQDFS.TIDVPTEYIEIIQLASDIEINV.....Nd...Q..IYI
  16 ---FSQNPYNPKPASDKQIKKAESQL.NMVLPHAHKTLLKQTNGCSV--.....-....G..GDV
  17 -HKYIEDMDLEQPTSLENITIIESQL.NISFPTDYISFMLGSNGAEGAI.....Ge...N..GYL
  18 ----YTVDTKEPPSKEKEIKALQHFS.VIDVPTEYIEMIQLASNVEINV.....Nd...Q..MYI
  19 ---RDKFEYPESPATPEDVELLEKWL.GNNLPSEYKIFLLETNGAETPI.....GvqepD..DSI
  20 ----FEKRLFDNLQKSKALPFELKEE.KYKLPAVYKEFICKYDGLSL--.....-....E..NGC
  21 ---VSYLFGHRRAQGVQSLEEVETWL.GRPLPEPYRSFLA-GTAVSFLA.....A....N..GRT
  22 ---VSYLFGHRRAQGVQSLEEVETWL.GRPLPEPYRSFLA-GTAVSFLA.....A....N..GRT
  23 ----FTLEAYESPTSKEAIQKLQKFS.SIDVPLDYLEVIQQCTNAEINVk....N....E..IYI
  24 ---LHNIVTGNPPASEHDILLIEQTM.AIHLPQEYKNVLKEANGFAL--.....-....T..NGV
  25 --YVADLWHREPPADERAIARVESEL.DVVFPVDYREFLLWSNGGQAQV.....G....S..AYF
  26 ---VSCPFGHRRAQGVQSLEEVETWL.GRPLPEPYRSFLA-GTAVSFLA.....A....N..GRT
  27 ---VSCSFGHRRAQGVQSLEEVETWL.GRPLPEPYRSFLA-GTAVSFLA.....A....N..GRT
  28 -------AYKPASTVDDIIALHNYFS.GIDIPQEYIDFITQLTEAEILIl....D....E..SYV
  29 ----FTLEAYESPTSKEAIQKLQKFS.SIDVPLDYLEVIQQCTNAEINVk....N....E..IYI
  30 --ENFKLEVKNAGSSDEEINTIRTIFsGKEIPEEYLCFISQVSEAEILVq....G....K..SYI
  31 --EILKKMDKETPATKIMIEKVEKEW.NISLPCEYKQLILFSNGIEGPI.....G....Ka.NYL
  32 -------FHRNAPSTPAAIASLETSL.CASLPPNYKDLLLWSDGGEGEV.....G....D..LYL
  33 IHSISSNLSLKNPATKDELTDIQKCL.HVELPNDLYQLLQETNGIEGEY.....G....D..FIW
  34 ------------------LEEVETWL.GRPLPEPYRSFLA-GTAVSFLA.....A....N..GRT
  35 ------NVELYPAVNSVEIDRIESEM.GLKLPKVFKELLYLSNGFVT--.....-....D..DGI
  36 IHSISSNLSLKNPATKDELTDIQKCL.HVELPNDLYQLLQETNGIEGEY.....G....D..FIW
  37 IHSISPNLSLKQPAMTDELTDIQNCL.HVELPNDLHQLLQETNGVEGEY.....G....D..FIW
  38 IHSISPNLSLKQPAMTDELTDIQNCL.HVELPNDLHQLLQETNGVEGEY.....G....D..FIW
  39 IHSISSNLSLKNPATKEELIEIQKCL.LVELPNDLSQLLQETNGIAGEY.....G....D..FIW
  40 ------------GASLSEIEACEASI.SIILPEDYKAFLRISNGFNDEV.....G....Q..GYL
  41 -----------------KLNSIEKEL.NIKLPNFYRKFLSEKIQNEPYIeitgkD....Q..ENI
  42 -------FHLPKPVRSETLDAFEAEF.KQPLPSEYQTFLELHDGAKLFMl....G....D..EGL
  43 ----------------EEVAKAEKKL.GVTLPDTYKKLILEQNGGYIVH.....N....A..FPT
  44 -----------PPATDEQVSSLEKKL.SITLPDDYKDFLKISNGFGGTW.....N....GyhLDN
  45 -----------------DIQRLEKTY.CISLPEDYKTFLLLNNGFVVKS.....P....D..YCN
  46 ----------DPAALADAVAELETAL.GTALPEPYRSFLLTYGGGAP--.....-....-..-YP
  47 -------TILHPPAPESSISATEKRL.NTSLPADYKSYLLLSNGNDAAF.....G....GiiNEA
  48 --------------TEEKILEFEKEK.EITLPSKYKEWMLFSDGGELFL.....-....P..AGV
  49 --------------SERDIQKAEKKL.GVKLPEEYKALILEQNGGYINF.....Nafp.S..ERP
  50 ------DFQPDDAPDQDSLARAERLL.EVRLPQEYKNFLLQYGGGYFAF.....G....Nv.FSL
  51 ----------KGPADELSIVNIEKKL.GITFPNDYREFLKKYNGGYPEP.....D....G..FYF
  52 ---------LRQGCSSADIAALEKRL.EISLPEEYKEFLAVTNGLEAI-.....-....-..---
  53 ------------GATDLEIESFEKKI.KVSLPEDYKTFLKLHNGARI--.....-....-..FDL
  54 ---------CYPGANEEEISATEARL.GVTLPPSYREFLKVSNGLHS-T.....S....K..CDI


                60              70              80        90           
                |               |               |         |           
   1 YIWAIE.....DVIA....YN..HDYGIQKYLQ.....KEYW.AFGMDGDIGYILHL.....SD.
   2 LIYGTE.....HIAE....RN..EVWEVDEYAR.....GYVS.IGDDGGGNVFLMAQha...EE.
   3 LIYGTE.....HIAE....RN..EVWEVDEYAR.....GYVS.IGDDGGGNVFLMAQha...EE.
   4 LIYGTE.....HIAE....RN..EVWEVDEYAR.....GYVS.IGDDGGGNVFLMAQha...EE.
   5 LIYGTE.....HIAE....RN..EVWEVDEYAR.....GYVS.IGDDGGGNVFLMAQha...EE.
   6 YIWAIE.....DVIA....YN..HDYGIQKYLQ.....KEYW.AFGMDGDIGYILHL.....SD.
   7 VLWSAK.....EISE....LT..EAYCYEQYLP.....GLVA.IGSDGGGESIVFDTth6ssED.
   8 VLWSAK.....EISE....LT..EAYCYEQYLP.....GLVA.IGSDGGGESIVFDTth6ssED.
   9 VLWSAK.....EISE....LT..EAYCYEQYLP.....GLVA.IGSDGGGESIVFDTth6ssED.
  10 SLWKIE.....ELVQ....FN..EDYQIKKYIP.....EIVS.IGTDGGEFCYAFDY.....RNn
  11 QLWSID.....VLIQ....HN..EGYEVKEFAP.....GVTL.FGSDGGNVAYGFFEkg...GE.
  12 IIYGTD.....DIIE....RN..ETWEVIEYAN.....GYVA.IGDDGSGNVFLMSQ.....GAd
  13 SLWKIE.....ELVQ....LN..EDYQIKKYIP.....EIVS.IGTDGGEFCYAFDY.....RNn
  14 FIYGTE.....EIME....RN..ETWEVKEYAK.....GYVA.IGDDGGGMVFLMALek...EA.
  15 RIWGAS.....GCIE....MN..EAYEVQKYLP.....NSLA.IGDDEGGGALIYLLgk...DG.
  16 LIYGTE.....DIAE....RN..ATWEVHHYAN.....GYVA.IGDDGGGQVFLMRQte...EE.
  17 QLWSID.....VLTQ....HN..EGYEVKEFAP.....GVSL.FGSDGGNVAYGFFEks...GE.
  18 RIWGAS.....DCIE....MN..EAYKVQNYLL.....HSLA.IGDDEGGGALIYLQgk...DG.
  19 VLWSAR.....EVSE....LT..EAYCYEQYLP.....GLIA.IGSDGGGESIVFDTth6ssEE.
  20 TFYSLE.....ELDA....MN..KDLQVNIYQP.....DIVA.VGDDGGDLVFLMKQek...EA.
  21 LVYGRT.....AVME....RN..DTHESRAYCP.....GHLM.IGDNSGGVALVLSL.....AD.
  22 LVYGRT.....AVME....RN..DTHESRAYCP.....GHLM.IGDNSGGVALVLSL.....AD.
  23 RIWGPI.....DCIE....MN..EAHDIQKYIP.....NSLA.IGDDEGGMALLYIDgk...EG.
  24 LIYGTE.....EIME....RN..ETWEVSEYAK.....GYVA.IGDDGGGMVFLMALek...EA.
  25 SFWRVW.....DIVD....RN..ISASIKKYMS.....PLFVgIGTNGGGECYALDYsddi.SS.
  26 LVYGRT.....AVME....RN..DTHESRAYCP.....GHLM.IGDNSGGVALVLSL.....AD.
  27 LVYGRT.....AVME....RN..DTHESRAYCP.....GHLM.IGDNSGGVALVLSL.....AD.
  28 RIWSAI.....GCIE....MN..SAYNIQKYIP.....GSIA.IGDDEGGKVVFYANgk...EG.
  29 RILGPI.....DCIE....MN..EAHDIQKYIP.....NSLA.IGDDEGGMALLYIDgk...EG.
  30 RIWGAE.....GCIE....MN..ESYHIQKYIP.....NAIA.IGDDEGGQVIFYATgd...DG.
  31 SIWPIN.....ELIE....LN..QEYAVDEFLP.....GIKY.FGSDGGDMAYGFEFdh...DR.
  32 ALWTVE.....QIVE....LN..ALYSITKRVGh....GFVG.IGTDGGDYCFALDLr....GG.
  33 SASKIKte6smRNIV....DF..KDLYMPFDCL.....LFFA.DGGNGDLFGYSILN.....GK.
  34 LVYGRN.....AVME....RN..DTYESRAYCP.....GHLM.IGDNSGGAALVLSL.....AD.
  35 AIFGTD.....IIAE....RN..LTYEVPEYAE.....GYIA.VGSNGGGKFLLMLAne...ES.
  36 SASKIKte6smRNIV....DF..KDLYMPFDCL.....LFFA.DGGNGDLFGYSILN.....GK.
  37 SASKIKte6nmRNIV....DF..KDLYMPFDCL.....LFFA.DGGNGDLFGYSILN.....GI.
  38 SASKIKte6nmRNIV....DF..KDLYMPFDCL.....LFFA.DGGNGDLFGYSILN.....GI.
  39 SVSKIKte6nmRNIV....DF..KDLYMPFDCL.....LFFT.DGGNGDLFGYSILN.....GI.
  40 VLWSVA.....ELAK....AD..-GYELFEFQV.....DRFL.IGSNGGPTAYGIIG.....GS.
  41 YVYNCE.....YVIK....RN..KTYNIQEAKP.....NYFL.IGQDGDLGYFIYVE.....KD.
  42 VLYPLE.....EVIEktieAK..EDGLIDEDYD.....HYWI.IGEVNEGYLLIHTNhakt.ED.
  43 AHSNSWa11llGIAEdegiMD..SAYLIKEWELpe...GLVL.INGDG-HTWVAMDYr....KT.
  44 PLYGVD.....DVSW....AR..ESFEVP----.....----.--------------.....--.
  45 LAYGGVd21cd--IE....YNneELFSELDFID.....SKLI.IGDDPGGNYYLMLN.....GE.
  46 LIFDYApd8erFLDR....LN..RPARVQELANg10pqGFAP.IGEDPGGLIVLLSL.....HP.
  47 PLWKCE.....DI--....--..----------.....----.--------------.....--.
  48 QLYGIEhk...PLID....VN..DNSRP---SD.....DYIV.IGAFASGDP-ILCK.....KA.
  49 TSWAKDh14kaGILE....--..SKYIIKEWELpd...NLIL.IHG-DGHTWIALDYr....ET.
  50 EAGSEW.....NLID....IN..AE--FAHLRA.....GRVL.ISENSNGDFFGFDV.....--.
  51 IDSKDGs14ksDSIA....AC..YDLYKKRIPQ.....GFVP.IATDPGGNLLLLCGtke..-Ns
  52 ------.....----....--..----------.....----.--------------.....--.
  53 LFYG--.....----....--..----------.....----.--------------.....--.
  54 RFYSV-.....----....--..----------.....----.--------------.....--.


            100       110       120       130       140   
             |         |         |         |         |   
   1 ....NSIYRVDLGDLDITSIKYIAPSFDDFLGKAIYLNFNKLQNVANNNLTT
   2 ....KEVVVIDSGDMNPNHATVITADFKKWVNSGCVSEIEQKAIHKSSDICN
   3 ....KEVVVIDSGDMNPSHATVITADFKKWVNSGCVSEIEQKAIHKSSDICN
   4 ....KEVVVIDSGDMNPSHATVITADFKKWVNSGCVSEIEQKAIHKSSDICN
   5 ....KEVVVIDSGDMNPSHATVITADFKKWVNSGCVSEIEQKAIHKSSDICN
   6 ....NSIYRVDLGDLDITSIKYIAPSFDDFLGKAIYLNFNKLQNVANNNLT-
   7 ....WPVYRVPFGDLTKESMVLLAANFNEWVSSGYS----------------
   8 ....WPVYRVPFGDLTKESMVLLAANFNEWVSSGYS----------------
   9 ....WPVYRVPFGDLTKESMVLLAANFNEWVSSGYS----------------
  10 sni.PNFIEVPLGDLDSNSIVTLGDKMTLVLQTWI-----------------
  11 ....TQIIEIPLMGMDLDEMAVISNTFVDFLDCL------------------
  12 v...REVRAVDSGDMNPNHATVVTLDFIEWVNTGCLNQKIQKIKEEIPDTCN
  13 sni.PNFIEVPLGDLDSNSIVTLGDKMTLVLQTWI-----------------
  14 ....CQVFVVDVGDMNPQHAILVSSHLNKWLQEG------------------
  15 ....FGIYYNRFADLDIEEAVKIAPSLTELLENNVGV---------------
  16 ....KRVWIVDAGVMDPQHAELVTENLLEWVSGGCI----------------
  17 ....TQIIEIPLMGMDLDEMAVISNTFVDFLD--------------------
  18 ....FGIYYNSFGNLDMEDAVKIAPSLTELLVNNVGVN--------------
  19 ....WPLYRVPFADLTKEAMVLLAVSFKDWVTNGYT----------------
  20 ....KTVYLVDAGDYDLESPYQIIPDFNKWMEKGFEIEDIDGEDVRGVDYGD
  21 ....GQVHSVGMGAMTPDCFEPVAQSFAAW----------------------
  22 ....GQVHSVGMGAMTPDCFEPVAQSFAAW----------------------
  23 ....FGLYTVGFGNLDIEETIKIAPSLKVLLIDCVGV---------------
  24 ....CQVFVVDVGDMNPQHAILVSSQLNRWLQ--------------------
  25 ....PNFVIVPLGDLDHASKFVIASSLAGVFEKSLNGDFSDADYN-------
  26 ....GQVHSVGMGAMTPDCFEPVAQSFAAW----------------------
  27 ....GQVHSVGMGAMTPDCFEPVAQSFAAW----------------------
  28 ....FGLYKVGFGDLDINAAEWISPSLVSFLIDGIG----------------
  29 ....FGLYTVGFGNLDIEETIKIAPSLKVLLIDCVGV---------------
  30 ....YGLYKVGFGNLDIEDAVFISNSLYDLLMKGN-----------------
  31 ....TTIIEIPFDSINKEEVKKYGESFFEFLI--------------------
  32 ....ERFVVVPLGALTEDEIKPLARDLVDGLTSIRDGGI-------------
  33 ....VQRDDIYVWNHENDSRTWVAPSLKTFMEWW------------------
  34 ....GQVHSVGMGAMTPDCFEPVAQSFTAW----------------------
  35 ....TQLLQVDCGVMNPEYATLVTTDFSEWINEG------------------
  36 ....VQRDDIYVWNHENDSRTWVAPSLKTFMEWW------------------
  37 ....VQRDDIYVWNHENDSRTWVAPSLKIFMVWW------------------
  38 ....VQRDDIYVWNHENDSRTWVAPSLKIFMVWW------------------
  39 ....VQRDDIYVWNHENDSRTWVAPSLEIFMEWW------------------
  40 ....YISIPFVFAGAWSDEVRVLGRTFDEF----------------------
  41 ....KESDIIYSLDLGALGSVEMDKEADKEANDIYS----------------
  42 ....TPYMYWKYHEGSTEDTDAIGQNFGTFLER-------------------
  43 ....KENPAIHYFDVEMEEDFKLANSFDEFIQGLYTAE--------------
  44 ....------------------------------------------------
  45 ....RQQ---------------------------------------------
  46 ....GDFGAIYAWSATA-----------------------------------
  47 ....------------------------------------------------
  48 ....EETISIYNQKIGEIDEELVYPDFVAFLNDL------------------
  49 ....KENPPVHYFDSEFEENYKLADSFGEFLSKLYTDNPMD-----------
  50 ....------------------------------------------------
  51 g7wdHEEEVADGEQPDMRNMHYISPTFNDFIDS-------------------
  52 ....------------------------------------------------
  53 ....------------------------------------------------
  54 ....------------------------------------------------