(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:

    • T0214 Hypothetical protein, Pyrococcus furiosus
    • T0213 Hypothetical protein, E. coli
    • T0227 TTHB84orF1350600, T. thermophilus
                           10         20         30         40         
                           |          |          |          |         
   1 ...M...E..W.EMGL..Q.E.E.FLELIKLRKKKIEGRLYD.EKRRQIKPG.DVI.S...F...
   2 ...M...K..W.EMGL..Q.E.E.YIELIKAGKKKIEGRLYD.EKRRQIKPG.DII.I...F...
   3 ...M...E..W.EMGL..Q.E.E.FLELIKLRKKKIEGRLYD.EKRRQIKPG.DVI.S...F...
   4 ...M...E..W.EMGL..Q.E.E.YIELIKRGLKKIEGRLYD.EKRRKIKPG.DII.V...F...
   5 ...M...Q..PnDITF..Y.Q.R.FEADILAGRKTITIR--D.KSESYFKAG.DIL.RvgrF...
   6 ...M...Rv.Y.RLYL..R.D.E.YLEMVKSGKKKIEVRVAY.PQLRGIKKG.DKI.I...F...
   7 ...M...Q..PnDITF..F.Q.R.FQNDILAGRKTITIR--D.ASESHFKAG.DVL.RvgrF...
   8 ...M...R..Y.EMGL..YnK.P.FQS-IQSGKKVYEVRLYD.KKRQLINKG.DEI.V...F...
   9 ...M...R..Y.EMGL..YnK.P.FQS-IKLGKKVYEVRLYD.KKRQLIKQG.DHI.I...F...
  10 ...M...Q..PnDITF..Y.Q.R.FEADILAGHKTISIR--D.DSESHFKAG.DIL.RvgrF...
  11 ...M...R..Y.EMGL..YnK.P.FQS-IQSGKKVYEVRLYD.KKRQLINKG.DEI.V...F...
  12 ...M...Q..PnDITF..F.Q.R.FQNDILAGRKTITIR--D.ASESHFKAG.DAL.RvgrF...
  13 ...M...Kv.Y.RLYL..K.D.E.YLEMVKSGKKRIEVRVAY.PQLKDIKRG.DKI.I...F...
  14 m..M...Kv.Y.RLYL..R.D.E.YLEMVKSGKKRIEVRVAY.PQLKGMKRG.DKI.I...F...
  15 ...M...Q..PnDITF..F.Q.R.FQDDILAGRKTITIR--D.ESESHFKTG.DVL.RvgrF...
  16 ...M...Q..PnDITF..F.Q.R.FQDDILAGRKTITIR--D.ESESHFKTG.DVL.RvgrF...
  17 ...M...Q..PnDITF..F.Q.R.FQDDILAGRKTITIR--D.ESESHFKTG.DVL.RvgrF...
  18 ...Mta.P..T.KMTF..F.S.R.FEADILAGKKTITIR--D.ESEKDYQPG.TTV.EvstL...
  19 ...Mta.P..T.KMTF..F.S.R.FEADILAGKKTITIR--D.ESEKDYQPG.TTV.EvstL...
  20 ...M...R..Y.EMGL..YnK.P.FQS-IRSGKKVYEVRLYD.KKRQLINKD.DEI.V...F...
  21 gkrL...Rv.H.HMGL..E.E.E.YLNLIKEGKKTVEGRVKD.DKRARIKPG.DKI.L...F...
  22 ...M...D..SnKITF..F.T.R.FEQDILAGRKTITIR--D.KSESSFQPN.QIL.A...Vytn
  23 lkeV...N..F.ELHV..Q.E.P.YFTQLKDGLKTVEGRCAV.GDYMRISSG.DFL.L...F...
  24 evvMta.P..T.KMTF..F.S.R.FEADILAGKKTITIR--D.ESEKDYQPG.TTV.EvstL...
  25 evvMta.P..T.KMTF..F.S.R.FEADILAGKKTITIR--D.ESEKDYQPG.TTV.EvstL...
  26 lkeV...N..F.ELHV..Q.E.P.YFTQLKDGLKTVEGRCAV.GDYMRISSG.AFL.L...F...
  27 ...M...K..H.AMGL..F.KvP.FES-IKAGRKTVEVRLND.AKRRQVAVG.DTI.E...Ftkl
  28 ...M...N..-.NITF..F.S.R.FEADILAGKKNITIR--D.KSEAYFQPQ.QELkV...F...
  29 ...M...N..-.KITF..F.S.R.FEADILGGKKTITIR--D.KSESYFQPQ.QQL.NvftH...
  30 ...M...L..T.EITF..F.E.R.FEHDILMGKKTITLR--N.EAESHVIPG.QIL.PvstF...
  31 ...M...N..R.EITF..F.G.R.FEADILADRKTITIR--D.SSESDFRSG.EVL.R...Vcrn
  32 ...M...T..T.-MQL..I.H.PqWL-LIKSGLKTIEIRLND.AKRQALQVG.DIV.N...F...
  33 ...-...-..-.-MGLn.H.S.Q.FL-LMQQGDKSVEIRLND.RKRSFLKEG.SLI.T...F...
  34 ...M...N..-.DITF..Y.Q.R.FEADILAGRKTITIR--D.KSESHFKAG.DIL.RvgrF...
  35 tttI...P..T.EMTF..F.A.R.FEHDILSSKKTITIR--D.ESERYYVPG.TTV.KvstL...
  36 ...M...Y..S.CITF..F.Q.R.LERSILSGNKTATIR--D.KSDSHYLVG.QML.DactH...
  37 ...M...K..-.NLKF..D.G.R.YKDDIISGKKRATIRLGR.K--INLKPGeEVL.V...H...
  38 kviM...L..-.-MGLn.H.D.Q.FV-LVQRGTKTIEIGLYD.EKRAQLKIG.HKI.L...F...
  39 ...M...K..-.NLKF..D.G.R.YKDDIISGKKKATIRLGR.K--VNLKPGeEVL.I...H...
  40 rskM...N..R.EITF..F.G.R.FEADILADRKTITIR--D.SSESDFRSG.EVL.R...Vcrn
  41 ...M...Er.P.KLGLivR.E.P.YASLIVDGRKVWEIR--R.RKTRHRGPL.GIV.SggrL...
  42 ...M...Er.P.KLGLivR.E.P.YASLIVDGRKVWEIR--R.RKTRHRGPL.GIV.SggrL...
  43 ...M...-..I.EIMT..R.E.E.FFDLITEGLKTAEIRPSDhRSFRYLEPG.DTL.V...F...
  44 ...MsshP..T.KITF..F.E.F.LTPLITSGQKTITIR--D.ESESHYVPN.TEV.EvftL...
  45 gkeV...K..-.NLKF..D.G.R.YKDDIISGKKKATIRLGR.K--VNLKPGeEVL.I...H...
  46 ...M...-..-.-LLA..P.K.P.FE-MMKSGQKTIELRLYD.EKRKHIQIG.DRI.R...Fyct
  47 ...M...SisT.QITF..F.E.F.LTPLVASGQKTITIR--D.KSESHYVPG.TRV.EvftL...


                  50        60         70                 80           
                  |         |          |                  |           
   1 ..EG....GKLKVRVKAIRVYNSFREML.EKEGLENVLP..GV.K..S..I..EEGIQVY.....
   2 ..EG....GKLKVKVKGIRVYSSFKEML.EKEGIENVLP..GV.K..S..I..EEGVKVY.....
   3 ..EG....GKLKVRVKAIRVYNSFREML.EKEGLENVLP..GV.K..S..I..EEGIQVY.....
   4 ..EG....GKLKVRVKALRVYKSFKEML.EKEGIENVLP..GV.N..S..V..EEGVKIY.....
   5 ..ED....NQYFCTIEVLSVSPITLDELtEQHAKQENMG..LA.E..-..-..------L.....
   6 ..-N....DMIPAEVIDVKRYETFRQVL.REEPIEKIFP..DE.P..S..F..ERALRRF.....
   7 ..ED....DGYFCTIEVTGTSTVTLDTLnEKHAQQENM-..--.-..S..L..DE----L.....
   8 ..TNlttkEMMAVKVTEIKRYENFQAMY.EQ--IDKKLL..DC.E..NdrL..EEMLEST.....
   9 ..TNlttaATMAVKVTEIKRYENFQAMY.EQ--IDKKLL..DC.EndS..L..EEMLEST.....
  10 ..ED....NQYFCNIEVLSVSPITLDELtQPHAKQENM-..--.-..G..L..DE----L.....
  11 ..TNlttkEMMAVKVTEIKRYESFKVMY.EQ--IDKKLM..DC.EndS..L..EEMLEST.....
  12 ..ED....DGYFCTIEVTGTSTVTLDTLnEKHAQQENM-..--.-..S..L..DE----L.....
  13 ..-N....DLIPAEVVEVKKYETFRQVL.REEPIDKIFP..DK.P..S..F..EKALKRF.....
  14 ..-N....DEVPAEVIEVKHYETFRQVL.REEPIDKIFP..DE.P..S..F..ERALRRF.....
  15 ..ED....DGYFCTIEVTATSTVTLDTLtEKHAEQENMT..LT.E..-..-..------L.....
  16 ..ED....DGYFCTIEVTATSTVTLDTLtEKHAEQENMT..LT.E..-..-..------L.....
  17 ..ED....DGYFCTIEVTATSTVTLDTLtEKHAEQENMT..LT.E..-..-..------L.....
  18 ..EE....GRVFCQLKILSVEPIAFSELnEFHAEQENMT..LA.T..-..-..------L.....
  19 ..EE....GRVFCQLKILSVEPIAFSALnEFHAEQENMT..--.-..-..-..---LETL.....
  20 ..TNlkttEMMTVKVTEIKRYESFKAIY.EQ--IDKKLL..DC.EndS..L..EEMLEST.....
  21 ..-N....RRLLVKVIDVREYDSFEEML.REEGLENVLP..NV.D..S..I..EEGVEIY.....
  22 ..ET....DRFFANIKVLSVTPIHFEALsEAHAQQENMT..LP.E..-..-..------L.....
  23 ..-N....KCLLLEVQDVHRYTSFSEML.KVEGLAKVLP..GV.E..S..I..EEGVQVY.....
  24 ..EE....GRVFCQLKILSVEPIAFSELnEFHAEQENMT..LA.T..-..-..------L.....
  25 ..EE....GRVFCQLKILSVEPIAFSALnEFHAEQENMT..--.-..-..-..---LETL.....
  26 ..-N....KCLLLEVQDVHRYTSFSEML.KVEGLSKVLP..GV.E..S..I..EEGVQVY.....
  27 peKE....ETLKVVVTKLRSYDTFEAMY.-KEIPFEAF-..DC.E..G..WtmDEMLDGT.....
  28 ..TNet..NLFFADIRVISVTPIRFEQLnEQHAKQENMS..LA.E..-..-..------L.....
  29 ..ET....DRLFAQIRVLSVVAIDFDDLnEQHAQQENMS..LA.E..-..-..------L.....
  30 ..ET....HRWFCDIQVLEVTPITLSGLtTLHAQQENMT..LA.E..-..-..------L.....
  31 ..ED....GVFFCHIKVKSVTPVTLDGLsERHAEQENM-..--.-..S..L..DE----L.....
  32 ..IDlttgQQLTTQLIDITRFASFESLLsEYTAVQVGSA..PG.T..P..V..TQMVQEM.....
  33 ..IDlktdKKIEVIVKKIYKFKTFCELY.KSFTSTEVGS..ATnD..S..L..EKMVNDT.....
  34 ..ED....NQYFCTIEILSVSPITLDELtELHAKEENMR..WR.-..-..-..-------.....
  35 ..EE....GREFCNLEIVSVEPILFDELtQYHADQENMT..--.-..-..-..---LPVL.....
  36 ..ED....NRKMCQIEILSIEYVTFSELnRAHANAEGLP..--.-..-..-..--FLFML.....
  37 ..AG....GYVLGKARIIRVETKKVEEL.TDEDARKD--..GF.R..N..K..EELIKAL.....
  38 ..TDlennNQIMVSVKQLYKFTTFADLYaQFNGAKVGSN..ST.D..N..I..EKIVNDT.....
  39 ..AG....GYVLGKARITRVTTKKVSEL.TDEDARKD--..GF.K..S..R..EELLEAL.....
  40 ..ED....GVFFCHIKVKSVTPVTLDGLsERHAEQENM-..--.-..S..L..DE----L.....
  41 ..IG....QADLVGVEGPFSVEELLAHQ.EKHLAEEAFL..RA.Y..A..K..DEPLYAWvl9ye
  42 ..IG....QADLVGVEGPFSVEELLAHQ.EKHLAEEAFL..RA.Y..A..K..DEPLYAWvl9ye
  43 ..KNfka.GTMRC-IETV-VRNVEKDLD.PKEAAERFYQeaGF.E..S..P..EECLEGL.....
  44 ..ET....DRKVCDIKILSVEPLNFDEInEFHAEQEAIE..LP.K..-..-..------L.....
  45 ..AG....GYVLGKARITRVTTKKVSEL.TDEDARKD--..GF.K..S..R..EELLEAL.....
  46 ..EN....QTQTIEVQVLDLH--IFDNF.AQLYKELDLL..SC.G..Y..T..QSSIRGA.....
  47 ..ET....QRKVCEIDILAVEPLKFDEInEFHAEQEAIE..LP.K..-..-..------L.....


             90       100              110    
             |         |                |    
   1 RR.....FYDEEKEKKYGVVAIEI...EP...LE.Y....
   2 RQ.....FYDEEREKKYGVVAIEI...EP...IE.-....
   3 RR.....FYDEEKEKKYGVVAIEI...EP...LE.Y....
   4 RK.....FYDEEREKKYGVVAIEI...EP...IEeG....
   5 RE.....VIKTIYPNESEFWVIEI...RL...VN.-....
   6 HN.....MYPKWKEYRYGVIAIKF...RI...LG.Rerk.
   7 KR.....VIAEIYPNQTQFYVIDF...KC...L-.-....
   8 YK.....IYTKEQEKKWGTVAIGI...EV...IK.-....
   9 YK.....IYTKEQEKKWGTVAIGI...KV...IK.-....
  10 KE.....VIRGIYPNEIIFWVIQFslkEY...FN.E....
  11 YK.....IYTKEQEKEWGTVAIGI...EV...IK.-....
  12 KR.....VIAEIYPNQTQFYVIDF...KC...L-.-....
  13 HN.....MYPKWKEYRYGVLAIKF...RV...LG.Rdke.
  14 HN.....LYPKWKENRYGVIAIKF...KL...LG.Rerk.
  15 KK.....VIADIYPGQTQFYVIEF...KC...L-.-....
  16 KK.....VIADIYPGQTQFYVIEF...KC...L-.-....
  17 KK.....VIADIYPDQTQFYVIEF...KC...L-.-....
  18 KE.....VIQEIYPGIEQLYVIQY...QR...V-.-....
  19 KE.....VIQEIYPGIEQLYVIQY...QR...V-.-....
  20 YK.....IYTKEQEKEWGTVAIRI...EV...IK.-....
  21 RR.....FYSSGKEKMFGVLAIEI...EP...IM.Dlwe.
  22 RQ.....VIKEIYPQEDCFWVIAF...EL...VD.-....
  23 RN.....FYSEEKERMNGVVAIRV...AK...PA.Nqps.
  24 KE.....VIQEIYPGIEQLYVIQY...QR...V-.-....
  25 KE.....VIQEIYPGIEQLYVIQY...QR...V-.-....
  26 RN.....FYSEEKERMNGVVAIRV...AK...PA.Nqps.
  27 YE.....IYTSEQENEWGALPIYV...ER...M-.-....
  28 KQ.....VIREIYPNDNDFFVIEF...EL...IE.-....
  29 RQ.....VIREIYPNEQKFFVIKF...AL...IE.-....
  30 RL.....VIAEIYPDLEQLYMIRF...KV...LT.K....
  31 KK.....VIKAIYPGLDRFYVIEF...TR...C-.-....
  32 LT.....LYSPVQVAQSGVVALQV...RPl..IG.Q....
  33 YK.....IYSPAQERNFGVLAIRI...RL...IH.-....
  34 --.....-----------------...--...--.-....
  35 KD.....VIQDIYPGITQLYVVSY...KL...VA.-....
  36 KW.....IVRKIYPTSNDLFFISF...RV...VT.Idil.
  37 KE.....HYKFVRPDSPATIV-EF...EM...IK.Lldk.
  38 YE.....IYTPEQERHYGVLAIEM...-L...LG.D....
  39 RE.....HYKFVKPDSPATIV-EF...EM...LS.Vldk.
  40 KK.....VIKAIYPGLDRFYVIEF...TR...C-.-....
  41 KP.....LHVPRRPGRVMFVDLSE...VR...W-.-....
  42 KP.....LHVPRRPGRVMFVDLSE...VR...W-.-....
  43 KE.....MYDGL-PEKVDVA--EF...EPvreWE.E....
  44 KQ.....LIREIYPNIDKLFVIEY...EL...IK.K....
  45 RE.....HYKFVKPDSPATIV-EF...EM...LS.Vldk.
  46 KPedmedYYSREQLEQYGAVGIEL...RV...IDsI....
  47 KA.....LIQEIYPNIDELYVITY...QL...AK.-....