(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:

    • T0352 NESG:ER225, E.Coli, 117 res
              10        20        30            40        50        60 
              |         |         |             |         |         | 
   1 MTTHDRVRLQLQALEALLREHQHWRNDEPQ....PHQFNSTQPFFMDTMEPLEWLQWVLIPRMHD
   2 MTTHDRVRLQLQTLEALLREHQHWRNDEPQ....PHQFNSTQPFFMDTMEPLEWLQWVLIPRMHD
   3 MTTHDRVRLQLQALEALLREHQHWRNDEPQ....PHQFNSTQPFFMDTMEPLEWLQWVLIPRMHD
   4 MTTHDRVRLQLQALEALLREHQHWRNDEPQ....PHQFNSTQPFFMDTMEPLEWLQWVLIPRMHD
   5 MTTHDRVRLQLQTLEALLREHQHWRNDEPQ....PHQFNSTQPFFMDTMEPLEWLQWVLIPRMHD
   6 MTTHDRVRLQLQALEALLREHQHWRNDEPL....PHQFNSTQPFFMDTMEPLEWLQWVLIPRMHD
   7 MTTHDRVRLQLQALEALLREHQHWRNDEPQ....PHQFNSTQPFFMDTMEPLEWLQWVLIPRMHD
   8 MTTHDRVRLQLQALEALLREHQHWRNDEPL....PHQFNSTQPFFMDTMEPLEWLQWVLIPRMHD
   9 MTTHDRVRLQLQALEALLREHQHWRNDEPL....PHQFASTQPFFMDTMEPLEWLQWVLIPRMHD
  10 MTTHDRVRLQLQALEALLREHQHWRNDEPQ....PHQFNSTQPFFMDTMEPLEWLQWGLIPRMHD
  11 MTTHDRVRQQLHTLETLLREHRHWRQDAPQ....AHLFTSTQPFFMDTMEPLEWLQWVLIPRMHT
  12 MTTHDRVRQQLHTLETLLREHRHWRQDAPQ....AHLFTSTQPFFMDTMEPLEWLQWVLIPRMHT
  13 MTTHDRVRQQLHALETLLREHRHWRLDAPQ....AHLFTSTQPFFMDTMEPLEWLQWVLIPRMHT
  14 ---LPEVAEQLLLIERELRTLGWWDATPPS....EQALASQEPFSVDTLEFAQWLQWIFLPRMKI
  15 MSTENKVRQSLQDIEFAMRETDLWQTVPPE....AEAFESNEPFSIDTMAAEQWLQWVFLPRMYA
  16 MSTENKVRQSLQDIEFAMRETDLWQTVPPE....AEAFESNEPFSIDTMAAEQWLQWVFLPRMYA
  17 ---LPEVAEQLLLIERELRALGWWDATPPS....EQALASQEPFSVDTLEFAQWLQWIFLPRMKV
  18 -NTENQVRQSLQDIELAMRAIDLWQIVPPQ....AEAFESNEPFSIDTMDAEQWLQWVLIPRMYA
  19 ---LPEVAEQLLLIERELRVLGWWDTTPPS....EQALASQEPFSVDTLEFAQWLQWIFLPRMKV
  20 -NIENKVRQSLQDIELAMRAIDLWQTVPPQ....AEAFESNEPFSIDTMDAEQWLQWVLIPRMYA
  21 -EQYQKAARLLDRIERELNSLGLWQSHQPP....VEALDSQQPFAMDTLEFHQWLQFIMIPRMWS
  22 -----DIADHLLLIERELQVQGWWDDEPPS....DEALASTVPFAVDTLSFEQWLQWIFLPRMKI
  23 ---VYALADQLLLIERELRALGWWSESSPA....PEALASPEPFCVDTLALEQWLQWIFLPRMKL
  24 -----DIADHLLLIERELQVQGWWDDEPPS....DEALASTVPFAVDTLSFEQWLQWIFLPRMKI
  25 ---VYALADQLLLIERELRALGWWSESRPA....PEALASPEPFCVDTLALEQWLQWIFLPRMKL
  26 -EQYQKAARLLDRIERELNSLGLWQSHHPP....VQALESQQPFAVDTLEFHQWLQFIMLPRMWA
  27 -STENKVRQSLQDIEFAMRETDLWQTVPPE....AEAFESNEPFSIDTMAAEQWLQWVFLPRMYA
  28 ---VYALADQLLLIERELRALHWWSESSPA....AEALASPEPFCVDTLALEEWLQWIFLPRMKL
  29 ---VYALADQLLLIERELRALGWWSESSPA....PEALASPEPFCVDTLALEQWLQWIFLPRMKL
  30 -STENQVRQNLRDIELAMRAIDLWQIVPPP....ATAFESNEPFSIDTMDAEQWLQWVLIPRMYA
  31 ---VYALADQLLLIERELRALGWWSESSPA....PEALASPEPFCVDTLALEQWLQWIFLPRMKL
  32 --TNTQLVDLLHQLEAQLREHNLWQYTMPS....EQALQSTEPFAIDTLHPHEWLQWIFIARMHS
  33 -----QTKQHLEQLQITMQQLNLWQTMPPA....AEAFLSEEPFSIDTMSAEEWLQWVFIPRMQA
  34 --TNTQLVDLLHQLETQLKEHKLWQHTRPS....EQALQSVEPFAIDTLHPHEWLQWIFIDRMHV
  35 -----QTKQHLEQLQITMQQLNLWQTMPPA....AEAFLSEEPFSIDTMSAEEWLQWVFIPRMQA
  36 MTTSTKLVELLYQLEAQLQKHELWQQTMPS....PEALQSVEPFAIDTLDPHEWLQWIFIARMHA
  37 -----ALAEQMLLIEQELRALGMWASSLPS....DEALSSEQPFCIDTLVFEEWLQWIFLPRMKV
  38 --IRQKTRQNLTALQAIMHELALWQSVPPA....EEAFLSEQPFAIDTMSATEWLQWIFIPRMHA
  39 -----QTKQHLEQLQITMQQLNLWQTMPPA....AEAFLSEEPFSIDTMSAEEWLQWVFIPRMQA
  40 -HMHQQTKMHLQQLQLNMQSLGLWQMTPPP....ESAFLSEQPFALDTMSPTEWLQWIFIPRMYA
  41 ---FPRIAEQLLLIERELRVQGLWDDAVPS....AEALASTQPFAVDTLEFEQWLQWIFLPRMKM
  42 -----QTKQHLEQLQITMQQLNLWQTMPPA....AEAFLSEEPFSIDTMSAEEWLQWVFIPRMQA
  43 -DKYHHSQRLLEELELVLRQHSHWQLTPPD....EQLLTSTEPFAIDTLDCHQWLQWIFIPKFGQ
  44 -NTENQVRQSLQNIELAMREIDLWQTVPPQ....AEAFESNEPFSIDTMDAEQWLQWVLIPRMYA
  45 -STAKQILHKLQLIEEAMREIDLWQSHPPK....PEAFESVEPFSIDRMLAEEWLQWVLIPRMYA
  46 ------VMHLLDNLEHNLKKHQLWQQELPS....LDALNSSAPFCCDTLAFEQWLQFIFIPKMRQ
  47 --RFSKVADQLLLIERELRAQGWWDDVQPS....VEALSSVEPFSVDTLDFEQWLQWIFLPRMKI
  48 ---YSQTQTKLAQIAHELQSAGLWSTSAPS....DEAMASTAPFACDLMSLEQWLQFIFIPRMQA
  49 ---YSQTQTKLAQIAHELQSAGLWSTRAPS....DEAMASTAPFACDLMSLAQWLQFIFIPRMQA
  50 -----DIADHLLLIERELKVQGWWSDAAPS....PEALASVVPFAVDSMAFEQWLQWIFLPRMKL
  51 -SRENLVRQSLFDIERALRESPFWQVVPPE....DGAFNSTEPFCLDTMRPEEWLQWVFLPRMHA
  52 ---YSQTQTKLAQIAHELQSAGLWSTSAPS....DEAMASMAPFACDLMSLEQWLQFIFIPRMQA
  53 --LYRYTQTKLAQIASELKQTGLWSATAPS....VEAMASTAPFACDLMPFEQWLQFIFIPRMQA
  54 -DKYHHSQRLLEELELVLRQHSHWQLTPPD....EQLLTSTEPFAIDTLDCHQWLQWIFIPKFGQ
  55 MSRENQVRQSLFDIERALRESPFWQVVPPE....EEAFNSTEPFSLDTMKPEEWLQWVFLPRMHA
  56 ---YAELADVLLGLESELRRMGLWREDQPH....EDALASVTPFCADTLEFHEWLQFIFIERMKV
  57 ------ISTLLADLAFELKSLNLWQIPQPS....AAELSSNAPFCCDTLAFGQWLQFIFIPKITM
  58 ----SQLALLLTSLECELKALDLWEASKPS....EHLLNSELPFCIDTLSFPQWLQFVFIEKMKI
  59 -----KVRQHLTDLEIALRTHKQWDAVAPS....LEDLANDQPFCIGTLSPTQWLQWVFIPRMHA
  60 -------HNYLIKLEQLLKEFQLWSDTSPP....VSALTSTAPFSCDVMAFEQWLQFIFIPKMTE
  61 ----SRCKTHLVRLEALLKQQNLWSDSEPS....PAALASTAPFSCDTMAFEEWLQFIFIPKLGA
  62 -TTSLELSTLLEQLALQLEHHGHWQRTSPS....IADLSSTEPFAIDTLSASEWLQWIFIPKMNY
  63 ----SQTQAKLEQIAQCLQQFGLWSQRSPS....DEAMASTAPFACDLMPLEHWLQFIFIPRMQA
  64 -------LPLLTALEDELRNKGLWQEIKPD....QQALDSREPFAIDSLSFVQWLQFIFLDKMAK
  65 MTIHLQTKKHLQQLQFAMQSLDLWQTVPPA....EEAFLSTEPFAIDRMTATEWLQWIFIPRMYA
  66 ---YSQTQAKLAQIAQALQAAELWSEQTPS....AVAMASTAPFACDLMPLEQWLQFILLPRMQT
  67 MTLHQQVRQRLFDIEQAMHDAEIWQPQPPV....RAAFDSVEPFCIDTMEAQQWLQWVLLQRMHA
  68 ----DQVTDGLLQIEIELRQLGVWQTESLP....PEAFQSTQPFCLDTMDFTQWLQFVFLEKMKA
  69 -TRHNELGNLLFELEKELREAQLWGKQSPA....PEALLSTEPFSIDLLTFTEWLQFIFLPRMYA
  70 ----TKVRQHLNDLELALRLHKQWQVTAPS....LDQLANDQPFCLGSLTATEWLQWIFIPRMHA
  71 --NTSTLTGLLRQLELELKRLGWWDEIPPE....PALLQSEMPFAVDTLAPQQWLQWIFIARIQQ
  72 ---HHKLADLLLNLEKVMRQVNVWDMPIPS....EEALTSKEPFCIDTMNFDQWLRYVMLEKFKP
  73 -----KLISLLDELEQALKAALLWRDEMPT....AQALASQAPFGCDLLAFEEWLQFIFLPRFRV
  74 -DKYRHSMLLLEMLEAALRNAERWESAPPS....NTALASAEPFAVDTLSCSQWLQWIFIPRMTQ
  75 -----QVEKLLSQLAEALKTAEQWTYSPPS....QWAMQSELPFACDRMGFAQWLQFIFIPKMNE
  76 -----QTQAYLVQLRALLKKHQLWQNEPIA....AEALQSNVPFCHDTMAFEQWLQFVFIEKVEQ
  77 -----VLVKLLDELEVRLRAAQLWQATPPS....SQALVSQEPFAVDTLLPHEWLQWIFLPKMQQ
  78 -----VLVKLLDELEVRLRAAQLWQATPPS....SQALVSQEPFAVDTLLPHEWLQWIFLPKMQQ
  79 --AATKLPPLLQQLEQQMRQCSLWSELPPS....NEALASVEPFAIDSLQPEEWLQWIFIVKINA
  80 MTSHEALMEALERLVATLRSVDMWRVEEPP....AAAFDSQQPFCVDTMELPQWLRYVFVARLET
  81 ----NQLLSLLMDLEMHLRSASLWQAQLPS....QAALASTQPFCVDTLEFQQWLQFVFIPRLRV
  82 ------VCHLLDQCQALMERQNQWQTIAPL....PRKLMSTAPFMVDTLSFLEWFQWVYIARLRA
  83 -------KTHLQALQKIMQDLELWQSFPPD....EQAFSSTAPFSMDTMSANEWLQWVFIPRMYA
  84 ---ATKLPLLLQQLEQQMRQCSLWSDVSPS....DEALASVEPFAIDSLQPEEWLQWIFIVKINA
  85 -------KTHLKALQKIMQDLELWQSFPPD....EQAFSSTAPFSMDTMSANEWLQWVFIPRMYA
  86 ---------QLRLIEAELKRLQLWQDQPPS....AEAMADPTPFACESMTFEQWLQFIFLPKMGE
  87 -DKYRHSMLLLEKLETALRDADLWENVPPS....DVALASTEPFAVDTLSCSQWLQWILIPRMTQ
  88 ------LSEALDNLEVIMQEEGIWPDAKPTrkalDSALQSTVPFAVDSLPFESWLAFIFIPKMRI
  89 ----EECAEAVDKIEAEMKRIGYWQEAPLR....EEQYGFQQAFAMDTMTYAQWLQFAFLPRVRE


             70         80        90       100       110       
             |          |         |         |         |       
   1 LLDNKQPLPG.AFAVAPYYEMALATDHPQRALILAELEKLDALFADDASLEHHHHHH
   2 LLDNKQPLPG.AFAVAPYYEMALATDHPQRALILAELEKLDALFAD-----------
   3 LLNNNQPLPG.AFAVAPYYEMALATDHPQRALILAELEKLDALFAD-----------
   4 LLDNKQPLPG.AFAVAPYYEMALATDHPQRALILAELEKLDALFAD-----------
   5 LLNNNQPLPG.AFAVAPYYEMALATDHPQRALILAELEKLDALFAD-----------
   6 LLDNNQPLPG.AFAVAPYYEMALATDHPQRALILAELEKLDALFAD-----------
   7 LLNNNQPLPG.AFAVAPYYEMALATDHPQHALILAELEKLDALFAD-----------
   8 LLDNNQPLPG.AFAVAPYYEMALATDYPQRALILAELEKLDALFAD-----------
   9 LLDNNQPLPG.AFAVAPYYEMALATDHPQRALILAELEKLDALFAD-----------
  10 LLNNNQPLPG.AFAVAPYYEMALATDHPQRALILAELEKLDALFAD-----------
  11 LLDNAQPLPE.AFAVAPYYEMALAADHPQRETILAVLQDLDALFAR-----------
  12 LLDNAQPLPE.AFAVAPYYEMALAADHPQREAILAVLQDLDALFAR-----------
  13 LLDNAQPLPE.AFAVAPYYEMALAADHPQREAILAVLQDLDALFV------------
  14 ILENDLPLPN.ASGILEMAEMVYAGRQSEARLLQQHLARFDQL--------------
  15 LLELNGPFPT.RFAITPYFEEALSGDGRPD---------------------------
  16 LLELNGPFPT.RFAITPYFEEALSGDGRPD---------------------------
  17 ILERDLPLPN.ASGILEMAEMVYAGRLSETRLLQQHLARFDQL--------------
  18 LLESNGPLPT.RFAITPYFEEALSGDDRPDCTV------------------------
  19 ILERDLPLPN.ASGILEMAEMVYAGCMSETRQLQAHLARFDQL--------------
  20 LLESNGPLPT.RFAITPYFEEALSGDDRPDCTT------------------------
  21 LIDAKQPLPD.SIAVSPMAAHSYRNAIEQHEQLIELIREFDVLLSGSD---------
  22 IIELGHPLPN.ASSILVMAETVFTDRPEQSRELRRLLAAFDQLI-------------
  23 ILESDSALPQ.ASGILAMAEVAYAQRGEEVAGLLAALGEFDRLIG------------
  24 IIELGHPLPN.ASSILVMAETVFTDRPEQSRELRRLLAAFDQLI-------------
  25 ILESDSALPQ.ASGILAMAEVAYAQRGEEVAGLLAALGEFDRLIG------------
  26 LVDSKRPLPE.GIAVSPMAAHIYRSELEQYEQLIALIREFDVLLSGTD---------
  27 LLELNGPFPT.RFAITPYFEEALSGDGRPD---------------------------
  28 ILESDSALPQ.ASGILAMAEVVYAQRGEKVAGLLAALGEFDRLIG------------
  29 ILESDSALPQ.ASGILAIAEVAYAQRGEEVAGLLAALGEFDRLIG------------
  30 LLESNSPLPA.RFAITPYFEEALSGDGRPDCT-------------------------
  31 TLESDSALPQ.ASGILAIAEVAYAQRGEEVAGLLAALGEFDRLIGG-----------
  32 LVKNNQPLPR.GFSLEPYFSEAWKQEPQFAELLV-----------------------
  33 LLESGSALPN.KIAISPYIEEAMKEFNELQQLLIPL---------------------
  34 LVENNQPLPR.GFSLEPYFSEAWKQEPQFAELLV-----------------------
  35 LLESGSALPH.KIAISPYIEEAMKEFDELQQLLTPL---------------------
  36 LVESSQPLPR.GFSIEPYFAEVWKQEPQYAELL------------------------
  37 IVEENRTLPA.SSGILPMAELAYRERLAEVARLLGAIGEVDRLISGG----------
  38 LLDSEHPLPT.QIAVVPYIEEALKEQERLAELLRPI---------------------
  39 LLESGSALPN.KIAISPYIEEAMKEFDELQKLLAP----------------------
  40 LIESEAGLPN.KISITPYLEEALKEMDGLADLLS-----------------------
  41 ILEQDLPLPN.ASGIQEMAEMVFSTRPMQG---------------------------
  42 LLESGSALPN.KIAISPYIEEAMKEFNELQQLLTP----------------------
  43 LIDLQLPLPT.QFEISPYIEEAMKEKVGVNDIL------------------------
  44 LLESNGALPT.RFAITPYFEEALSGEDRPDCT-------------------------
  45 LLEQGLALPT.AFAIAPYFEESYKEDTTGR---------------------------
  46 LIALNIPLPA.SMTLLPMAEQSWQAKLSQYQDLLEIISGFDQL--------------
  47 ILEQNLPLPN.ASGIQEMAEMVFAQRNLQ----------------------------
  48 LIDAGQPLPS.KIAIAPMAEHVWSEQAALAPLI-GVLNE------------------
  49 LIDAGQPLPS.KIAIAPMAEHVWSEQAALTPLI-GVLN-------------------
  50 ILEHGHPLPN.ASGILVMAETVFVDRPEQSRELRRLLAEFDQLI-------------
  51 VLDSDLSLPA.ELALLPYFEEALEGTPEQTAAVLLRLGLLDELFRSD----------
  52 LIDAGQPLPS.KIAIAPMAEHVWSEQAALAPLI-GVLNE------------------
  53 LIDAGQALPS.QIAIAPMAEHLWSEQAALAPLIS-----------------------
  54 LIALQLPLPT.QFEISPYIEEAMKEKVGVNDIL------------------------
  55 LLDSELALPR.SWFYCLILKKRWKGRQKRPRR-------------------------
  56 IVEYRAPMPPmRSGIEPAAEMAYQGRLGQVAGLLASLRQVDEAINNARDALS-----
  57 MIHQQQSLPT.KISLTPMAEEAFTHLSTSAKPLIDVIQKIDKALAE-----------
  58 ILNMAMPLPQ.TISVAPMATEYFTLQQLPSSPLIILLEQIDTLITE-----------
  59 LLDAGADLPR.NFSITPYLEEALKDESYL----------------------------
  60 LVVQRQPLPT.NMALAPMAEHVWQGMHYGDVLI------------------------
  61 IVDAKQPLPS.QMHLAPMASQVWQANPVYQPIIEQLIA-------------------
  62 LIENNKPTPK.GVSIAPYIEEALKDIEGYNEI-------------------------
  63 LIDAGQPLPT.SIAIAPMAQHVWQEITKLQPLI-GLLN-------------------
  64 LVRLPQPLPS.GMQVLPMAQEYFKSLPVNSAEITDIIGRIDLL--------------
  65 LLESGTELPA.QIAISPYIEEALKETDNLSLLLSPI---------------------
  66 LIETGAPLPT.QIAIAPMAEHVWQDMPQRQALI-GVLNEL-----------------
  67 LLDRDAPLPE.RFALTPYFEEALPEAFAL----LTQLRQ------------------
  68 LVEAGHALPE.ASGIAPMAEEHFRGREQSGRELISALEEMDRLLS------------
  69 TIEAAEELPE.TCSIAPMAEQFFSAEEASLKTSPKTSVESP----------------
  70 LLDADADLPR.NFSITPYLEEALKQEA------------------------------
  71 MMAQGASLPK.GFLLTPYFEEAWKEQRDTQTL-------------------------
  72 MLASGQSLPS.SSCIAPMAQEFYRTQDELA---------------------------
  73 LLETRQPLPA.AMSILPMALHVWGTHADKDALLIILANLD-----------------
  74 LIALKQPLPQ.HFELSPYVEEAMKHDSGVNIILG-----------------------
  75 LLQEEKPLPT.RMALMPMAQEWAKEYTTGQPTR------------------------
  76 LIIDKQPLPR.NFAIAPMAQMTLASKKGSGEIIT-----------------------
  77 AIGQN-AVPR.GFALEPYFSEVWQGEARYQAVL------------------------
  78 AIAQN-AVPR.GFALEPYFSEVWQGEARYQAVL------------------------
  79 MMDAQMSLPK.GFAIHPYFGEVWKNEADKAELLV-----------------------
  80 LAETEAPLPA.TCSVAPAIDTWLKEASPSVR--------------------------
  81 LAETGQPLPL.LCNVAPMVSD------------------------------------
  82 LIEAGQPLPQ.GALVAPYAEESLKADGAENPELIALIRQLDE---------------
  83 LLESQQSLPY.KMAITPYIEEALKDLDGLNDLLQP----------------------
  84 MMDAQMSLPR.GFAIHPYFGEVWKNEAEKAELLV-----------------------
  85 LLESQQSLPY.KMAITPYIEEALKDLDGLNDLLQP----------------------
  86 IIAVNGALPS.QIALTPMAEHVWQGRAEMRVLITIINQ-------------------
  87 LIALKQPLPQ.HFELSPYVEEAMKHDSGINIILG-VIR-------------------
  88 IIAQKQTLP-.AMQITPAAQVYLNGIGHRTIAQL-----------------------
  89 AITSQQ-FPK.SSDVGTQAIREF----------------------------------