(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:

    • T0265 1wdo, hypothetical transcriptional regulator, Sulfolobus tokodaii
    • gi|27573726|pdb|1KU9|A_13:116 Chain A, X-Ray Structure Of A Methanococcus Jannaschii Dna-Binding Protein: Implications For Antibiotic Resistance In Staphylococcus Aureus [Taxonomy]
    • gi|27573727|pdb|1KU9|B Chain B, X-Ray Structure Of A Methanococcus Jannaschii Dna-Binding Protein: Implications For Antibiotic Resistance In Staphylococcus Aureus [Taxonomy]
    • gi|40889350|pdb|1Q1H|A_1:107 Chain A, An Extended Winged Helix Domain In General Transcription Factor EIIE ALPHA [Taxonomy]
                           10                      20          30      
                           |                       |           |      
   1 ....MMKEK..L.E.S....K.K.....DEI.....RCC.YK..I.TD.TD.VAVLLKM...V.E
   2 mpd.SMSEQ..L.R.Q....D.Mece..GLL.....ECF.HG..L.KE.LD.KECFQAL...V.E
   3 mpd.SMAEQ..L.R.H....D.Mtcd..GLL.....ECF.HG..L.KQ.LD.KGVFQAL...V.T
   4 skl.LLKTP..C.T.T....W.Tfd...SLM.....ACV.FG..I.KV.SD.VKVYFDI...L.K
   5 ihe.MIRAS..F.R.C....E.-.....DMV.....KCV.LG..L.KS.LD.IDAYKAL...L.-
   6 ....MMKEK..L.E.S....K.K.....DEI.....RCC.YK..I.TD.TD.VAVLLKM...V.E
   7 ire.MLRAN..C.Q.C....D.-.....DVA.....KCI.LG..L.KT.LD.MEAYKFL...L.A
   8 ihe.MIRAS..F.K.C....E.-.....DMV.....KCV.LG..L.KS.LD.IEAYKAL...L.-
   9 skl.VLNMP..C.N.T....F.Tl....ETI.....MCCvFG..L.KA.FD.VAVYFEI...L.K
  10 ....-MSEK..L.Y.D....A.K.....DVI.....RCC.YK..L.SD.TD.IDCLFKL...I.E
  11 mg..MIDFA..C.K.E....F.Rie...DVI.....KCA.LN..L.TK.AD.LNVMKHF...LnE
  12 ihe.MIRAS..F.R.C....E.-.....DMV.....KCV.LG..L.KS.LD.IEAYKIL...L.-
  13 ....MIDFA..C.K.E....F.Kve...DVI.....KCA.LN..L.TK.AD.LNVMKSF...LnE
  14 tgd.IMEAT..CsP.D....L.K.....CVL.....KCA.LN..I.SC.LE.MDVYLIL...L.K
  15 ....MIDFA..C.K.E....F.Kte...DVI.....KCA.LN..L.TK.AD.LKVMKYF...LnE
  16 ....-MSLK..L.S.E....S.K.....EVI.....RCC.YK..I.SD.TD.VECLFKL...V.E
  17 vpf.VTVRR..L.NvT....V.R.....DVL.....RCV.LG..L.RD.VE.VDTYFAL...L.E
  18 qve.NIRVR..L.P.S....G.KevglvDAL.....NFC.YD..I.SD.TD.FQVLKTL...L.N
  19 lse.GTRIK..L.P.S....G.KdaglvDIL.....SFC.YG..L.SE.TD.VTVLLAL...M.K
  20 qis.GTRIK..L.P.S....G.KdaglvDIL.....SFC.YG..L.SE.TD.VQVLIAL...A.K
  21 ....MKEFI..I.N.R....L.KkftieDLM.....RCI.LG..L.QE.IE.IRVYFDL...L.E
  22 m...SEKIS..L.P.D....G.RevdlhEFI.....AFM.YG..L.ST.SD.VEVLHLL...M.E
  23 ele.VTKIR..L.T.S....G.KevgiiEAL.....SFC.YD..I.SD.TD.FQVLKVL...L.N
  24 m...AEKVR..F.P.D....G.RevdihDFI.....AFM.YG..L.SK.SD.VEVLHIL...L.Q
  25 slkeMVST-..L.N.C....G.-.....NLL.....ECV.LG..L.TP.AD.VMVYEAL...L.R
  26 ....MIDFA..C.K.E....F.Kik...DVI.....KCA.LN..L.TR.AD.MKVLEYF...FeE
  27 mg..SFNQI..L.D.Enat.C.R.....DMF.....EYF.FD..L.SP.AD.VAVLYSL...-.D
  28 qle.TERIT..L.P.S....G.KeakliDAL.....TFC.YD..I.SD.TE.FKVLQTV...I.E
  29 elv.QGTAE..L.R.P....E.-.....RVL.....SCV.FG..I.KE.DE.AELYLKL...L.E
  30 ....-MSIE..I.T.EksviF.K.....RFL.....AVA.YG..L.SE.AE.IEAFLKI...M.E
  31 ....MEKME..I.P.K....E.L.....KPL.....TFI.YD..L.NE.RE.LEIFLYL...A.K
  32 ....-MSIE..I.S.EksflL.K.....RFL.....IVA.YG..L.SE.AD.VDAFIKI...V.S
  33 m...SERLK..F.P.D....G.RevdihEVL.....SFL.YG..L.GG.SE.IQVLHLL...L.T
  34 m...KQEEM..L.K.K....L.E.....DLL.....KAI.-G..L.KK.NE.IRIYRLL...V.E
  35 m...KQEEK..L.R.K....L.E.....SLL.....RTM.-G..L.KK.NE.IMIYNLL...V.E
  36 ....MGQHKs.I.E.R....L.E.....ELL.....KVI.-G..L.KK.NE.IRIYKLL...L.E
  37 ein.MPDGR..V.A.D....I.F.....NVI.....KFL.YG..L.SD.RD.IEILKLL...L.K
  38 hkg.GSSTM..I.D.P....L.Vq....RLL.....EQV.LD..-.TP.TK.LHMLLMF...H.E
  39 ....-MSNP..L.G.E....L.V.....KAL.....EK-.LS..F.KP.SD.VRIYSLL...L.E
  40 lkl.QLRII..LvE.P....L.L.....TEL.....ERL.FSa.L.SDrTR.LSITLLL...L.E
  41 mii.MEEAKklI.I.E....L.F.....SEL.....AKI.HG..L.NK.SV.GAVYAIL...Y.L
  42 lkg.LLSII..L.R.S....H.R.....VFI.....GRE.LGh.L.NL.TD.AQVACLLr..I.H
  43 sak.LMKRR..L.D.T....E.-.....--L.....KAG.FD..I.TS.SQ.WAVLK-L...L.S
  44 l...-----..I.I.E....L.F.....SEL.....AKI.HG..L.NK.SV.GAVYAIL...Y.L
  45 ....-----..M.E.P....L.T.....NEL.....ESL.FSa.LaDG.TR.LRIVLFL...L.D
  46 ....-----..-.-.-....-.-.....--L.....KAL.SD..-.-P.TR.IKILELL...-.-
  47 ....-----..-.-.-....-.-.....---.....---.-DarL.TH.KE.MAIYMVLcrhL.N
  48 lsk.LMNRK..L.N.A....K.M.....DG-.....K--.-K..I.SP.YP.MIILNQL...-.D
  49 ....MVNAE..-.D.L....F.I.....NLA.....KSL.LG..-.DD.V-.IDVLRIL...L.D
  50 ....MLEED..C.S.D....KnL.....EILfl7srKLV.QT..L.SN.TNsLKILK-L...L.E
  51 ....-MRKK..L.-.-....-.I.....KIL.....QDL.LD..I.SD.TE.LEIYSFI...L.N


                  40        50        60         70               80   
                  |         |         |          |                |   
   1 I..EK.P...ITSEELADIFKLSKTTVENSLKKLIELGLV.VRTK..TE..GKK...IGRPKY.Y
   2 A..EE.P...MTVDELAEAVDRERSTAYRAVQRLLQTGFI.EKEQ..VN..YEQ...GGY-YH.V
   3 T..ND.A...LTVDDIAERVDRERSTAYRAVQRLLSAGLI.QKEQ..IN..YDQ...GGY-YH.V
   4 -..NG.P...SKINDIAERINRDRSTVQRAVQNLMNAGLV.KRKQ..VN..IKD...GGY-YY.V
   5 M..HG.P...LTAEKLGEILNRERSTAYRSLQNLIACGIV.YRET..RS..IDS...GGY-YY.E
   6 I..EK.P...ITSEELADIFKLSKTTVENSLKKLIELGLV.VRTK..TE..GKK...IGRPKY.Y
   7 -..NG.P...MTAENLGEFLNRERSTAYRSLQNLISCGLV.YRET..KT..IDI...GGY-FY.E
   8 M..HG.P...QTAEKLGEILNRERSTAYRSLQNLIACGIV.YRET..RS..IES...GGY-YY.E
   9 C..K-.P...AKINEIAESLNRERSTIQRSAQSLMNAGLI.LRKQ..IN..IKE...GGY-YY.K
  10 L..NK.P...VTSDELSQMMKVSKTTVENSLKKLIDSGLV.IRSK..SE..DKK...IGRPKY.Y
  11 P..EK.W...VDTDTLSKSLNLDISTVQRSVKKLHEKGIL.QRSQ..QN..LDG...GGY-VF.I
  12 M..HG.P...LTTDGLGEILNRERSTAYRSLQNLITCGVV.YRET..RS..LES...GGY-YH.E
  13 P..DR.W...IDTDALSKSLKLDVSTVQRSVKKLHEKEIL.QRSQ..QN..LDG...GGY-VY.I
  14 -..NP.G...LDVETIAKELEKDESTVYKALRNLMERGLV.KREY..RI..LKG...GGY-KY.L
  15 K..EQ.W...VDTDSLSKVLKLDISTIQRSVKKLYEKDIL.QRSQ..QN..LDG...GGY-VF.K
  16 L..NR.P...ISAEELASIMKLSKTTVENSLKKLIEIGLI.VRNKdgEE..GKR...IGRPKY.L
  17 -..RG.E...ATVYDLAEELDRDRTTVQKALKSLVYAGLV.TRRK..ET..RPR...GGF-VY.V
  18 -..SG.P...KTEDELAEMLHLSKASINRSVNKLVSLGFV.DRVK..DS..SSK...GGRPRY.I
  19 G..DA.R...GT-EELESDLKLSKASINRSLNKLLEMGLV.MRIK..EP..GNK...AGRPRY.L
  20 S..EA.R...GT-EDLESDLKLSKASINRSLNKLLEMGLV.MRIK..EP..GNK...AGRPRY.L
  21 -..NG.E...GSVLEIAERVNRDRTTVQKALRSLMNCGLV.DRRK..VT..-EK...VGY-KY.I
  22 S..KE.K...LDADEIAEKLKVTKASVSKSLNNLLDKGLI.ERDK..AEeaEKK...KGRPSY.V
  23 S..EG.K...-NEDSLAEMLKLSKASINRSVNKLVSLGFV.ERVK..DS..SSK...GGRPRY.I
  24 -..NG.K...MTTDDLSQKLNVTKASISKALNNLLDKGLI.QREK..AP..AEKeerKGRPNY.I
  25 G..KE.-...-RVDEISECVGRGESAVYKSLQRLLLAGMA.YRVK..MP..LDG...GGY-YF.I
  26 P..DN.W...SKTERIATHMELDLSTVQRSVKKLHEKKIL.TRSQ..NN..LDG...GGY-SF.I
  27 N..ET.G...ATLDDVAVKVHKDRTTVFRSLQRLVGTGIV.TKKK..SI..LEK...GGY-YY.S
  28 -..KK.T...ITEDELVEMLKLSKASVNRSLNKLVSLGFI.EREK..VQ..SNK...GGRPKY.L
  29 NseEA.P...FTVEDVAEIINRSRSTAQKMLQSLVRVGMV.ERER..ET..LPG...GGR-RY.L
  30 S..KE.G...KNVDTISSELGISKSRASLILKKLSDAGLI.EKEK..SG..NNK...GGRPKF.M
  31 T..KE.Q...LNADELSEKLNISRSCIMGYIKKLENKGLI.LKKRd.VR..IVR...RGKPQY.V
  32 S..ET.G...KDVDAIAGELGISKSRASLILKKLADAGLV.EKEK..TS..VSR...GGRPKF.L
  33 -..EG.K...MRSDEIAEKLKVSKASINKAINTLLDKGLV.EREK..IT..EEKr..RGRPTF.I
  34 K..RR.G...MRIREIQRELGISERSVRTHVLNLYRRGLL.KRE-..--..LVQ...SGWLGY.I
  35 K..KR.G...MRIREIQRELGISERSVRAHVLSLYRKGLL.KRE-..--..LVQ...KGWLGY.I
  36 K..KK.N...MMIKEIQKELGISERSVRAHVLSLYKKGLL.KR--..-T..LVQ...RGWLGY.A
  37 S..QN.P...LTMEEISSKLNITKSVVNKSILNLEKKNII.IKEK..IE..TSK...KGRRAY.T
  38 H..PRcE...LTAAAIAERLFRDIWSVEQALEDLTAAGFL.SVAQ..VT..---...GGQPVY.R
  39 -..RG.G...MRVSEIARELDLSARFVRDRLKVLLKRGFV.RREI..VE..---...KGWVGY.I
  40 -..KG.E...LTVDEISKDLKKSQSLISHHLSCLRNCGIV.K---..--..VRK...DG--KYsL
  41 S..DK.P...LTISDIMEELKISKGNVSMSLKKLEELGFV.RKVW..IK..GER...K---NY.-
  42 R..EP.G...IKQDELATFFHVDKGTIARTLRRLEESGFI.EREQ..DP..ENR...R---RY.I
  43 C..EE.D...LSQAEISDKLNADRATCGAVIEKLMSKGFV.TK--..-T..LSK...DDRRSY.K
  44 S..DK.P...LTISDIXEELKISKGNVSXSLKKLEELGFV.RKVW..IK..GER...K---NY.-
  45 -..KG.Q...ATVDEISKSLGKSQSLISHHMACLRNCGIV.K---..--..VRK...DGKFSY.-
  46 R..EH.P...MSVSEIAERLGRDKSTVYRHIKALEDAGLV.EVVE..KI..GNEvv.YGRVAY.V
  47 Q..ET.GscfPSLSTIGKKVGMSKNTIIKSLNLLIECGYV.FKEK..RN..GED...GGHASN.V
  48 S..KK.P...TTLTDIREKLGIPNSTISTVLDKLLEKGLI.RKEK..DE..TDK...--RRTF.L
  49 K..GT.E...MTDEEIANQLNIKVNDVRKKLNLLEEQGFVsYRKT..RD..-KD...SGWFIY.Y
  50 T..KD.-...MSAGELAEKLSLGLSTLKYNLDSLLDAGMI.RVSE..VK..WSQ...RGRKIK.I
  51 -..NS.R...VTVKDIVNNLKISKKTAHEKLKKLISLGLI.DKK-..--..IDK...KG---Y.I


                         90           100                110
                         |             |                  |
   1 Y...SI..S...S...N..IL.EKIRN...DLLNCAK.R.MEL.....AAT...
   2 Y...SP..S...Dps.Q..IT.DDMQR...MLNDWYA.K.MGQliq..EFE...
   3 Y...EP..T...Dpa.E..IA.DDMQR...LLNDWYA.K.MGQliq..EFE...
   4 Y...EA..I...Pfe.E..TK.KIIKK...TMEEWCN.N.MKKwve..ELE...
   5 Y...VA..I...Epq.E..MK.QMVKK...NVDEWYS.Q.MNElie..KMD...
   6 Y...SI..S...S...N..IL.EKIRN...DLLNCAK.R.MEL.....AAT...
   7 Y...VA..V...Dpi.K..VK.EMIQE...NIDKWYE.K.VTVlva..NID...
   8 Y...VA..I...Epq.E..MK.RMVKK...NVDEWYN.Q.MNElie..KMD...
   9 Y...EA..I...Pfl.D..VK.EKIKK...TMSDWSR.D.VCKwvd..EIE...
  10 Y...SI..V...E...N..II.NKIRE...DLLNCSK.K.MQLsl...---...
  11 Y...KI..H...Srn.Q..IK.NVILK...IVNSWAD.R.LGQele..QWE...
  12 Y...VA..I...Epw.E..MK.QMVKK...NVDEWYC.Q.MNGlie..KMD...
  13 Y...KI..Y...Skn.Q..IR.NIIQK...IVQSWAD.R.LGQelk..EWE...
  14 Y...FP..K...Dfe.E..FK.KIAKD...AMEEWFR.H.FDSmik..DIE...
  15 Y...KI..N...Sra.K..IK.NIIMT...VVNSWAE.R.LGQele..KWE...
  16 Y...AV..I...H...N..AE.TKIKQ...DLTNCAS.K.ILSa....TSS...
  17 Y...KA..V...Pfe.E..AR.KIVLR...ALDEWYE.A.VKDale..RAD...
  18 Y...KP..I...Dad.R..IT.TKISN...DFKYCAD.L.FSSvi...PQEl..
  19 Y...KA..R...Dya.E..LK.GKMLS...DIKDCAD.K.MAQlvek.EF-...
  20 Y...KT..K...Dyn.E..LK.QKILS...DIKDCAE.K.MAQlv...DQEf..
  21 Y...NA..V...Dld.R..VS.DIIEE...LLDDWYQ.N.VKKwlt..YFR...
  22 Y...WVd.K...D...K..LI.YKLEK...DLEKLAS.S.MKEglek.HI-...
  23 Y...KA..I...Pte.R..LI.EKIVN...DFKRCAE.L.FGQlipk.EL-...
  24 Y...WVe.K...E...R..LY.RKLEA...DLEKLAG.T.VKEalq..KHT...
  25 Y...KP..A...Pre.K..VV.EEVEK...VLTALVE.R.VRKale..EFT...
  26 Y...KI..N...Nkk.E..IK.ELIMG...IVSKWAA.K.VEQele..DW-...
  27 Y...SR..I...Ska.K..IV.ELINN...REGEFHS.V.LQCllk..DME...
  28 Y...KA..L...Dke.E..LM.KKLTE...DFKKC-S.E.MFIntlp.SFI...
  29 Y...RP..A...Pwe.K..VK.ELGLE...NLRIVCE.E.IERwfr..EFT...
  30 Y...YVn.K...D...E..IR.TKLEK...KANELCD.Q.LKQlis..SLG...
  31 Y...YV..D...Nt..K..VR.EKITN...DIIELAV.E.VRKsfi..NYL...
  32 Y...RIn.K...E...E..LK.KKLIK...RSEETCK.D.LHTiis..SFL...
  33 Y...YVr.K...D...Y..MY.KKIEN...DTMNLIF.N.VKEnik..KLL...
  34 Y...TP..V...Spl.E..IL.QKIKE...HLMKSIE.E.LERdlk..NQT...
  35 Y...TA..V...Spl.E..IL.QRIRE...HIMKSIE.E.LEKefk..NQS...
  36 Y...TA..V...Sps.E..LL.KKIKE...TILRNIE.E.IEKelk..DDE...
  37 Y...KV..D...S...N..YLnKKLLV...DLDQLMK.D.LKVki6vi---...
  38 Y...TP..P...P...E..WH.EAIRR...LVRSYND.P.IERdmi..QRT...
  39 Y...SAekP...E...K..VL.KEFKS...SILGEIE.R.IEKm....FTD...
  40 Y...SI..A...S...D..NV.AELIK...VAMRIIK.D.YSEsil..GCE...
  41 Y...EA..V...DgfsS..IK.DIAKRkhdLIAKTYE.D.LKKlee..KCN...
  42 L...EV..TrrgE...E..II.PLILK...VEERWED.L.LFRdft..EDE...
  43 V...KI..S...P...K..AL.AILEK...MAQK-AD.E.VNDla6gl---...
  44 Y...EA..V...DgfsS..IK.DIAKRkhdLIAKTYE.D.LKKlee..KCN...
  45 Y...SIs.T...P...E..II.ELI-K...LSINHVK.K.YSQsil..SCD...
  46 F...LL..V...P...N..SN.KEIED...LRRAYLSrE.VEKliev.-LE...
  47 Y...YI..N...D...-..-I.STLVQ...PVNKVVQ.E.MNKggs..GDE...
  48 YlteKA..Y...E...E..ER.KIIKQ...HVEVFKE.V.LSKat...DEDl..
  49 W...KPn.I...D...Q..IN.EILLN...RKRLILD.K.LKTrl...EYEk..
  50 Y...EP..V...E...K..II.VLVPG...CRNSCKE.EiLGIfl...KNT...
  51 Y...EAk.A...D...KytIL.SLLKK...QLEKIYK.E.FEE.....EFSkl.