(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:

    • T0473 CmR9, Clostridium thermocellum, 68 residues
    • gi|191160896|ref|ZP_03022779.1|_3:62 conserved hypothetical protein [Geobacter sp. M21]
    • gi|190997627|gb|EDV73072.1| conserved hypothetical protein [Geobacter sp. M21]
    • gi|191160909|ref|ZP_03022792.1|_2:56 conserved hypothetical protein [Geobacter sp. M21]
    • gi|190997640|gb|EDV73085.1| conserved hypothetical protein [Geobacter sp. M21]
              10             20                   30        40         
              |              |                    |         |         
   1 MKITKDMIIADVLQMD....RG.TAPIF....IN.N.GMH.....CLGCPSSMGESIEDACAVHG
   2 MKITKDMIIADVLQMD....RG.TAPIF....IN.N.GMH.....CLGCPSSMGESIEDACAVHG
   3 MQITKDMTIGEIVRNF....PN.SIEIL....MS.F.GMG.....CVGCPSAQGESLEQAAMVHG
   4 MQITKDMTIGEIVRNF....PS.SIEIL....MS.F.GMG.....CVGCPSAQGESLEQAAMVHG
   5 MTITKEMTITEVVTKY....PK.TIPIF....YK.H.GMG.....CLGCAAAQFENIEQGARAHG
   6 -KVTKDMTISEVLKKN....PK.TAEVF....MK.H.GMQ.....CLGCPSAAGETVEQAAMVHG
   7 MKITETMGIGECVAKF....PN.TVPVF....MS.F.GMS.....CLGCSAARFENIGQGARAHG
   8 MTITRDMLIGDLLRMK....PE.AASIL....MG.F.GMG.....CLGCPSSQMESLEQAAAVHG
   9 --ITKDWTITDIVEKY....PK.TTEIL....MN.H.GMH.....CFGCMAARFENIEQGAMAHG
  10 MQITKDMGIMDIVNKY....PQ.AVSVF....QA.Y.GMG.....CIGCMAARFETLEEGANAHG
  11 --ITKDMTIGEILRVK....PE.SAQVL....MD.M.GMG.....CLGCPSAQFETLEQACEVHG
  12 -QITKDTIIGDILDIA....PE.TAPLF....LS.I.GMH.....CLGCPSSRGETVEQACMVHG
  13 --ITTDTIIADVLRID....RG.TIPIF....LN.N.GLH.....CLGCPSAQGESIEEACALHG
  14 MKITKDMTIGEIVRNH....EG.AAEVL....MS.F.GMG.....CVGCPSAQSETLAEAAMVHG
  15 -KVTKDMIISDVLNMD....KG.TVPIF....LE.S.GMH.....CLGCPSSSGESIEDACAIHG
  16 MKITKDMLIGDIIQIH....PD.AVEIL....FN.F.GLS.....CVGCPASQMETLEEATMVHG
  17 --ITKDMTIGEVIRKM....PT.AAEVL....MS.F.GMG.....CVGCPSAQAETLEEAAIVHG
  18 -KVTKDMLIGQLITLD....PN.IAPIL....MR.A.GMH.....CLGCPSSQMESLEEAAMVHG
  19 MKINRDMTIMDVMQLD....RE.VATIF....MK.Y.GLH.....CLGXPGATMESISDAGNVHG
  20 --ITKEMSITEVVSKY....PQ.TVPVF....ME.H.GMG.....CLGCAAARFENIEQGALAHG
  21 --VTRDTIIGDILDMD....QT.TAPYF....ME.I.GMH.....CLGCPASRGETIEEACEVHG
  22 -EITKDTVIGDILKIN....PE.SASTL....ME.A.GMH.....CLGCPASQMETLEEACSVHG
  23 --ITKDMVIQEIVTKY....PQ.TLPVF....GQ.F.NMG.....CLGCSGALFETLEQGALAHG
  24 MKIKKEMLIGQILSEK....PE.SIGTL....MS.F.GMG.....CIMCPSSQMETLEEAAMVHG
  25 --ITKDMTIGEVVKND....SS.KAEVL....MS.F.GMG.....CVGCPSAQAETIEEAAMVHG
  26 --ITKDMVIGDLLAID....EN.FAAIL....MA.S.GMH.....CVGCPSSQGETLEEAAFVHG
  27 --ITKDMIIADIVSED....AE.NTKIL....ME.F.GMH.....CIGCPSSQMETLEDACAVHG
  28 --FTKNTTIGELLSVY....PE.CAPIL....ME.I.GMH.....CLGCPSAQMETLGEAAMVHG
  29 --ITKDMTVGQVLRSY....PQ.TVQTF....LE.L.GMH.....CLGCPSSTMESIEGAALTHG
  30 --FSKDTKIGELIDQF....PE.SAPIL....ME.I.GMH.....CLGCPASQMETLEEAAMVHG
  31 --ITKDMTVGQVLRSY....PQ.TVQTF....LE.L.GMH.....CLGCPSSTMESIEGAALTHG
  32 --VTKDTIIGDILDMD....RT.TAPFF....LE.M.GMH.....CLGCPASRGESLEQACLVHN
  33 -KITKDTLIGNALKIN....PN.SASIL....MS.F.GMG.....CLGCPSSQMETIEQAAAVHG
  34 -KITKDMKFSEILNYG....QP.VVQVF....MK.Y.QMG.....CLGCAVAKFETLEQGANAHG
  35 MPIRHDSVVDDLMRTQ....PA.TIRTF....LD.F.RMG.....CCGCPIATFHTVDDACREHD
  36 -AISKDMIIADLIALD....PN.YAAIL....MA.S.GMG.....CVGCPSSQGESIEQAAYVHG
  37 -KITKDMIIKDIININ....MG.CIPIL....LN.E.GMH.....CVGCPASQGETLEEACIVHG
  38 ---TKDMTIGEVIQKN....PG.AAEIL....MS.F.GMG.....CVCCPSALGETIEEAAMVHG
  39 MKITKDMIIADIIAID....QN.LIPIL....LD.T.GMH.....CIGCPSAQGESLEEACMVHG
  40 -KVTEDMTIAEVLKMD....RE.VAGIF....MK.Y.GLH.....CLGCPGATMESISDAGNVHG
  41 -QITKDLSIMDVLRAY....PQ.VRPVF....IR.H.GMG.....CLECMGAMDETIASGARMHG
  42 --ITKDMTIGEVVSAD....QS.KAQVL....MS.F.GMG.....CVGCPSAQAETIAEAATVHG
  43 --ITKDLTIGEIIRIK....EN.APQIL....MS.F.GMG.....CVGCPSAQAETIEDAVKVHG
  44 --ITKDMIIGDIIRKH....PR.TLTVF....VK.Y.GLD.....CNECQIADYEELEHGAGVHK
  45 -KITRDMTMGYIVKEF....PQ.TVEVF....QR.Y.GMG.....CLSCPTAQLESLEKGAMLHG
  46 --ITKDMTVGEIIRIK....EN.AAEIL....MS.F.GMG.....CIGCPSAQSESLEDAANVHG
  47 MKYTKDSLVGEVLDND....ES.LARYF....LE.M.GMH.....CLGCPSSRGETIEQACEVHG
  48 -QISKTMTISEILSVD....KV.VIPVL....MN.S.GMH.....CLGCPSAQGETLEEACMHHG
  49 -KITKDMTFFAVMQAY....PQ.SLDVL....RK.H.RLG.....CVGCMGAQNESLEQGANAHG
  50 -KITKDSIIGQVIRDN....PR.TIAVF....RA.H.GMG.....CLGCPSASGESVEKAAGIHG
  51 --VSRDTTIGEALSMN....PG.IAPIL....QE.I.GMH.....CLGCPASQGESLAEAAMVHG
  52 MTITKDSIIGDILDAY....GEvTAPFF....LE.M.GMH.....CLGCPASRGETVAQACDVHG
  53 --ITKDMIIGDIIRQH....PA.TVQVF....AR.H.GLE.....CYECQIADLETLEHGAGHHK
  54 --FHRDMLVGSIIGMD....PQ.AAQIL....SD.S.GMG.....CLGCPASQSETLADACLVHG
  55 -KVTKDMNIMEAVEKY....PI.IAQVL....MR.Y.GLG.....CVGCIISSAETLGEGIAVHG
  56 --ISKEMTIGEIIRRY....PQ.TLPVF....EK.Y.GLD.....CHDCQIADFEAVEHGASVHK
  57 -------KITDVVEKY....PQ.SVEVF....QK.Y.GMH.....CFGCMAARFENVEQGAMAHG
  58 --ITKEMTMGELLSID....RG.VAVVL....MN.A.GMH.....CIGCPSSIGESLEEACMVHG
  59 --VTKEMTMGELLQTYyeqcPE.IVDVL....TG.L.GMH.....CIGCPSSIGESLADAAYVHG
  60 -KISKDMLINDILAVD....AG.NAAIL....MA.A.GMH.....CIGCLAAAGETLEEAAAVHG
  61 -KINKDTTVGEVIRMN....PA.NAQKL....MN.F.GMG.....CVGCPSAQSETLREASLVHG
  62 MPISFDELVDDVMRRR....PE.TIRVF....LA.F.QMR.....CVGCPIACFHNVADACREHG
  63 --ITRDMIIADIIRKY....PE.TLPVF....KK.H.RLE.....CYECQISDLETLEHGAEVHR
  64 --ITKTMRIGDIIRTY....PQ.SLKIF....EK.Y.GLD.....CYECQVADYEELEHGAGVHK
  65 MKISKDMTIGEVVRNH....PE.CVEVL....FN.F.GLG.....CVGCPSAQAETIEEACSVHG
  66 --LHDDMTMDAIMREW....PA.TIRVV....LD.H.GLL.....CVGCPIAPFHTIIDAAREHD
  67 -PFGSDDLVDDIMRTA....PH.TIRVF....LA.F.RLA.....CVGCPIATFHTVEDACREHG
  68 -TIRDDLPVDEVMRSW....PA.TIRTF....LD.F.RMQ.....CCGCPIAAFHTMKDACREHG
  69 --VTKDMTFAAVMRMH....PD.VVKVL....AK.Y.NLG.....CIGCMGAQNESLEQGCAAHG
  70 -QITKDMTFGELLSKYystcPK.LVDDL....ME.A.GMG.....CIGCPHSQMESIEEGAMGHG
  71 -KISKDMLINDILAID....AG.NAAIL....MA.A.GMH.....CIGCLAAAGESLEEAAAVHG
  72 -KFTKDMTFAQALQTH....PG.VAGVL....RS.Y.NLG.....CIGCMGAQNESLEQGANAHG
  73 -HLDPDMTLEEIMRAW....PP.AISVI....LR.H.HML.....CVGCPITAFHTVNDACREHM
  74 -SIDRTLVVEDVMSRW....PA.TIRVF....LD.F.KLA.....CVGCPIATFHTIEDSCHEHG
  75 -KITKDMTFLEMLRTY....PE.TAKVL....KK.Y.NLA.....CAGCMGAQSEPIDLGAINHG
  76 ---TGDMNIMEAVEKY....PV.IVEVL....QR.N.GLG.....CVGCMIASGETLAEGIEAHG
  77 ---TGDMNIMEAVEKY....PI.IVEVL....QR.N.GLG.....CVGCMIASGETLAEGIEAHG
  78 ---TGDMNIMEAVEKY....PV.IVEVL....QR.N.GLG.....CVGCMIASGETLAEGIEAHG
  79 MKLDSKMTVGELVTRH....PS.VMEVF....IK.R.RMP.....CVGCPTERFHTIEDIARING
  80 --IDAATLVDDLMRQR....PQ.TIGVF....LR.R.RLY.....CVGCPVGHFHTIEEAAREHG
  81 -QVTKDMTFAAVMRMH....PD.VVKVL....AK.Y.NLG.....CIGCMGAQNESLEQGCAAHG
  82 --LTADSTIAELLREK....PE.SAQVL....FR.F.GMG.....CLGCAIANNETIREAAQAHG
  83 --LTADSTIYDLLQAK....PE.ATEAL....FK.F.GMG.....CVGCAIARGETIREAAEAHG
  84 -AITLDSTIADLLREK....PE.SAATL....QS.F.GMG.....CLGCAIANNETIREAAMVHG
  85 ---DPDIPLIELMALW....PQ.TIPVF....VR.H.RML.....CVGCLVSPFHTVTDACAEYD
  86 -------TISEILRRY....PE.TLPVF....ER.H.HLD.....CYDCQLADFEQLEHGATVHK
  87 MKFTLEMKLKDIMAAN....PK.TVEAM....QE.L.GLH.....CLGCPFSVNETLLNAAQMHK
  88 -------TISEILRRY....PE.TLPVF....ER.H.HLD.....CYDCQLADFEQLEHGATVHK
  89 --LSKDSTILEVLQEK....PD.AGAIF....AR.F.GMG.....CVGCAISRGETVAEAAAAHG
  90 MKFTLEMKLKDIMAAN....PK.TVEAM....QE.L.GLH.....CLGCPFSVNETLLNAAQMHK
  91 -QFTKDMTFAQALQAN....PE.VAKVL....RK.Y.NLG.....CIGCMGAQNESLEQGCSAHG
  92 ------VTVGEWLRRW....PE.TVRVF....LN.Y.KMN.....CPACPIAPFMTIDEAASEYR
  93 ---DPDLPLSRLFDRW....PA.TAAVF....LT.R.RML.....CPGCPIAPFHTVVEACAEYG
  94 -QVTKDMTFAQVMRMH....QD.AVKVL....AK.Y.NLG.....CVGCMGAQNESLEQGCGAHG
  95 ---DPDLPLARLLQTW....PA.SAGVF....LE.R.RML.....CPGCPIAPFHTVIEACAEYG
  96 ----PDLPLDVLMTTW....PE.TVRVF....MD.H.DML.....CVGCMVSPFHSVSEACAEYH
  97 ---DPDLPLARLFQTW....PA.SAGVF....LE.R.RML.....CPGCPIAPFHTVIEACAEYG
  98 ----PDLPLDVLMTTW....PE.TVRVF....MD.H.DML.....CVGCMVSPFHSVSEACAEYH
  99 --------------RK....PE.TIRVF....LA.F.QMR.....CVGCPIACFHNVADACREHG
 100 ----PDLPLSTLFGEW....PD.MVEVF....LA.K.QML.....CPGCPVAPFHAITDACEEYE
 101 -KITKKTSIGDVIQNY....PE.TESVV....KKyF.GAG.....CYTCPGSKTEDIAFGATMHN
 102 --ITKKMSTGEVTKKY....PA.TKEVF....AK.YfGKG.....CFDCPSFGTEDINLACMMHN
 103 MEINKNTVIKDLIEAH....PE.TLAVF....KK.Y.NLV.....IAGGVRGPNEPIAFFAKAHE
 104 --ISRSMTIEDILGMF....PY.KAQKLsqeiTN.A.GLH.....CVGCHAAVWETLEAGMMTHG
 105 ----------HLLKQR....PG.CAQVF....WQ.R.GML.....CPGCPFVTFCDLDDVCREYD
 106 ---DKTTKMAAVLKGH....PK.AKEVL....ES.F.GLQ.....CSTCSGAKHESIELGATNHG
 107 --ITKDMIINDVIQKY....SK.TIGIF....KD.F.GVDs....CCG----GGFSIEKTAAMSG
 108 --VDKDTKVFDIVDQY....PE.TLQIF....LD.Y.GFSqm6pv-IRNTMGRVATIDMAAKMHN


        50        60        
        |         |        
   1 ...IDADKLVKELNEYFEKKEV
   2 ...IDADKLVKELNEYFEKK--
   3 ...MDIEKLLEALNK-------
   4 ...MDIEKLLEALNK-------
   5 ...INIDELIADLNKVVAE---
   6 ...ADADKLLEELNKVFE----
   7 ...IDVDKLIEELNKVVGKDD-
   8 ...INIEQLLEKLN--------
   9 ...INVDELMKELNDAI-----
  10 ...INVDDLVDDLN--------
  11 ...QDVEDILAKLN--------
  12 ...VDVDALLAELNKM------
  13 ...IDAQKLVDELNEYLKS---
  14 ...MELDALLEALN--------
  15 ...IDADQLIDNLNKYL-----
  16 ...LNLDLLLDVLN--------
  17 ...INLDDLIEAIN--------
  18 ...MDADVLVQQINDFL-----
  19 ...IDVDKLVDDLNKFFEEK--
  20 ...IDVDGLIADLNKV------
  21 ...VNCDELLEKLNTHL-----
  22 ...IDVEELLNKLN--------
  23 ...IDVDAMLKALNDLI-----
  24 ...IDPNTIVAALNEDHK----
  25 ...INLDELIEALN--------
  26 ...MNVNELLGRLNEYME----
  27 ...LNVEELIKKLN--------
  28 ...IDADLLVEKIN--------
  29 ...KKPDELVEKLNKV------
  30 ...IDCGLLVEKINA-------
  31 ...KKPDELVEKLNKV------
  32 ...VDPDELVEKLNEH------
  33 ...IDAEALLEKLN--------
  34 ...VDVDALLKDLNAAI-----
  35 ...VDRDVFLVALRDAMADQ--
  36 ...MDLDELLGRLNEYAQ----
  37 ...LDADVLAKKLNDF------
  38 ...IDADEIIKSLNY-------
  39 ...IDVDELVAKLNA-------
  40 ...IDVSLLIADLNKHF-----
  41 ...LDLDQLLKDLNEAIKNR--
  42 ...LNLDDLLEALN--------
  43 ...INLEELLEQLN--------
  44 ...VNIEQLLSELNEHIGS---
  45 ...LDVQELLEELNK-------
  46 ...LNLDDLLKAL---------
  47 ...ADCARLLEQLN--------
  48 ...LNADELETQINDA------
  49 ...IDVNALLKDLND-------
  50 ...IDLEELLSELN--------
  51 ...IDAELLVEKINAF------
  52 ...VDADELVKKLNEA------
  53 ...LDIEALLEELNR-------
  54 ...LDVEEILKQLN--------
  55 ...LNPDIIIEEVNMILEKQE-
  56 ...VDIGRLMEDLNRI------
  57 ...IDVPSLIKDLNKAIG----
  58 ...IEVDELLKNINEYF-----
  59 ...IDSDLLVEKLNATI-----
  60 ...LDAAELEVEINDYLAKKE-
  61 ...IDLDRLIKAL---------
  62 ...VDADTFLSAL---------
  63 ...VGIDGLLEELNR-------
  64 ...TDLEKLLKELNEL------
  65 ...MDVNELVEALN--------
  66 ...LDPASLARDLKRAVAEE--
  67 ...IDRDKFLAALC--------
  68 ...VDRDSFVAALE--------
  69 ...ISVDEIVADINK-------
  70 ...IDPDLLVAKLNATL-----
  71 ...LDAVELEQEINDYLAKK--
  72 ...LNVEDILRDLN--------
  73 ...IDEGAFLEELRAAI-----
  74 ...IAEAPFLAALRKAVAKS--
  75 ...LDPEQLLADLNA-------
  76 ...LDTKAILAEINSLI-----
  77 ...LDAKAILDEINSLI-----
  78 ...LDTKAILDEINSLI-----
  79 ...IVLEHLLKDLLDAIGV---
  80 ...LEPKALLAELR--------
  81 ...INVDEIVADINK-------
  82 ...IPLEEMLSAL---------
  83 ...IPLAELLNAL---------
  84 ...IPLEELAKKL---------
  85 ...LDEGEFLAELKM-------
  86 ...IDVESLLCELNCS------
  87 ...LDPEKLLEAVNS-------
  88 ...IDVESLLCELNCN------
  89 ...IPLEELMSAL---------
  90 ...LDPEKLLEAVNS-------
  91 ...LDVNEVLKDLN--------
  92 ...VDANLLKRDLMQMLKE---
  93 ...LDEDEFRRAL---------
  94 ...LNVDDVVRDLN--------
  95 ...LDEGEVRRAL---------
  96 ...LDEEVFRAALAEA------
  97 ...LDEGEVRRAL---------
  98 ...LDEVVFRAALADA------
  99 ...VDPDLFLSAL---------
 100 ...LDEEVFRAELR--------
 101 ...VDPEVIIKELNEIIEK---
 102 ...TDVDKFVQELNE-------
 103 ...VDYDTLVRELNEAIEK---
 104 ktdAQIDELVRRLNALLQ----
 105 ...QDRDELTQAMR--------
 106 ...LDVNELLTHLNALFDE---
 107 ...GDMEKLLEKLNKAI-----
 108 ...VDREKFIQSLNDRI-----