a2m2html output for tmp.a2m

Citations (SAM, SAM-T99, HMMs)

R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting remote protein homologies, Bioinformatics 14(10):846-856, 1998.
A. Krogh et al., Hidden Markov models in computational biology: Applications to protein modeling, JMB 235:1501-1531, Feb 1994.

Sequence numbers correspond to the following labels:

- T0487
- gi|46255097|ref|YP_006009.1|_12:306 hypothetical protein TT_P0026 [Thermus thermophilus HB27]
- gi|46197946|gb|AAS82356.1| hypothetical protein TT_P0026 [Thermus thermophilus HB27]
- gi|55978251|ref|YP_145307.1|_12:306 hypothetical protein TTHB068 [Thermus thermophilus HB8]
- gi|55773424|dbj|BAD71864.1| conserved hypothetical protein [Thermus thermophilus HB8]
- gi|56752529|ref|YP_173230.1|_15:320 hypothetical protein syc2520_d [Synechococcus elongatus PCC 6301]
- gi|56687488|dbj|BAD80710.1| hypothetical protein [Synechococcus elongatus PCC 6301]
- gi|81300343|ref|YP_400551.1|_15:320 hypothetical protein Synpcc7942_1534 [Synechococcus elongatus PCC 7942]
- gi|81169224|gb|ABB57564.1| conserved hypothetical protein [Synechococcus elongatus PCC 7942]
- gi|22298491|ref|NP_681738.1|_39:337 hypothetical protein tll0948 [Thermosynechococcus elongatus BP-1]
- gi|22294671|dbj|BAC08500.1| tll0948 [Thermosynechococcus elongatus BP-1]
- gi|86606806|ref|YP_475569.1|_15:315 Piwi domain protein [Synechococcus sp. JA-3-3Ab]
- gi|86555348|gb|ABD00306.1| Piwi domain protein [Synechococcus sp. JA-3-3Ab]
- gi|86610170|ref|YP_478932.1|_13:331 Piwi domain protein [Synechococcus sp. JA-2-3B'a(2-13)]
- gi|86558712|gb|ABD03669.1| Piwi domain protein [Synechococcus sp. JA-2-3B'a(2-13)]
- gi|56478414|ref|YP_160003.1|_1:314 hypothetical protein containing the PIWI domain [Azoarcus sp. EbN1]
- gi|56314457|emb|CAI09102.1| hypothetical protein containing the PIWI domain [Azoarcus sp. EbN1]
- gi|170077638|ref|YP_001734276.1|_10:179 conserved hypothetical protein containing Piwi domain [Synechococcus sp. PCC 7002]
- gi|169885307|gb|ACA99020.1| conserved hypothetical protein containing Piwi domain [Synechococcus sp. PCC 7002]

                 10        20        30        40            50        
                 |         |         |         |             |        
   1 ...NRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRA....GGVTVRMGDGL..ASW
   2 vflNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRA....GGVTVRMGDGL..ASW
   3 vflNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRA....GGVTVRMGDGL..ASW
   4 ivlNRFYVKSLSQSDLTAYEYRCIFKKTPELGDEKRLLASICYKL....GAIAVRIGSNI..IT-
   5 ivlNRFYVKSLSQSDLTAYEYRCIFKKTPELGDEKRLLASICYKL....GAIAVRIGSNI..IT-
   6 vilNRFFVKKLSRPDLTFHEYQCQFTQVPEQGSEQKAISSVCYKL....GVTAVRLGSCI..ITR
   7 vilNRFLVKELTQEDLTFYEYDCRPNPPPELGEEQRAIARVCNRL....DVIAARLGSRI..ITQ
   8 vtlNRFFVKELTQEELTFYEYSCRPNPLPDLGEEQRALSKICNQL....GVMAVRLGNRI..IT-
   9 ...------------MPVYYYRLTFDDDHEDINPTQLTRRGARMLsganGWCAVTDGEPLrvLSL
  10 ...------------------------------------------....-----------..---


        60        70        80        90       100       110           
        |         |         |         |         |         |           
   1 SPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERL.....RR.L..
   2 SPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERL.....RR.L..
   3 SPPEVLVLEGTLARMGQNYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERL.....RR.L..
   4 --KEAVRPEK-----LQGHDWQLVQMGTKQLDCRNDAHRCALETFERKFLERDLsa9vrKA.A..
   5 --KEAVRPEK-----LQGHDWQLVQMGTKQLDCRNDAHRCALETFERKFLERDLsa9vrKA.A..
   6 EP---IDPE----RM-RTKDWQLQLIGCRELSCQNYRERQALETFERKILEEKL.....KEtF..
   7 ER----VSPSQL----KTPEWELEERGLRVLTCANAQERSALESFERKRIGLRLksqy.KK.T..
   8 -------REKVPASKLKTEEWELEELGSKALDCTDPTERQALETFERKKLDWSLr10ieRS.T..
   9 RPLKVLRHEWNGMCCTASDE----TAGT--LKSANPSEREAIQRLLNQCLMQGA.....RK.Lay
  10 ------------------------------------------------------.....--.-..


                     120                130        140            150  
                      |                  |          |              |  
   1 ...EG...VWVE.....GLAVY....RREH.....ARGPGWRV.LGGAVLDLW.....VSDSGAF
   2 ...EG...VWVE.....GLAVY....RREH.....ARGPGWRV.LGGAVLDLW.....VSDSGAF
   3 ...EG...VWVE.....GLAVY....RREH.....ARGPGWRV.LGGAVLDLW.....VSDSGAF
   4 ...EGgliWWVV.....GAKGI....EKS-.....--GNGWEV.HRGRRIDVS.....LDAEGNL
   5 ...EGgliWWVV.....GAKGI....EKS-.....--GNGWEV.HRGRRIDVS.....LDAEGNL
   6 ...KK...TIIEkdyelGLIWWisgeEGLE.....KTGHGWEV.HRGRQIDLK.....IETDEKL
   7 ...EV...EWIGg....GLLWWvtaqKGVE.....LSGEGWEI.HRGRMIDVA.....VEPDGKL
   8 ...GGgliWWVT.....GLEGV....ERIEds7kpLCGDGWEV.HRGRELDVV.....IRQDKKL
   9 ssdGG...LEAEq....GAGNL....VRLT.....ACQPSERVsAGGDYLDAFqs8pdVLPDGTA
  10 ...--...----.....---TE....ADIR.....SDVSGWEI.YRGFKLDIF.....VSSQGNV


           160         170        180                  190         200 
            |           |          |                    |           | 
   1 LLEVDPAYRILC.E.MSLEAWLAQGHPLP.K...RVRNAY...DRR.....TWELLRL..GEEDP
   2 LLEVDPAYRILC.E.MSLEAWLAQGHPLP.K...RVRNAY...DRR.....TWELLRL..GEEDP
   3 LLEVDPAYRILC.E.MSLEAWLAQGHPLP.K...RVRNAY...DRR.....TWELLRL..GEEDP
   4 YLEIDIHHRFYT.P.WTVHQWLEQYPEIPlS...YVRNNYl..DERhgfi.NWQYGRF..TQERP
   5 YLEIDIHHRFYT.P.WTVHQWLEQYPEIPlS...YVRNNYl..DERhgfi.NWQYGRF..TQERP
   6 YLEIDIHHRFYT.P.FKLEWWLSEYPNIQiK...YVRNTYk..DKK.....KWILENF..ADKSP
   7 YLEVDIHYRFYT.P.WTLHEWLESYPDVPiE...IVRNTYfdaNGKrl...TWKYLGIl.SNQSP
   8 YLEIDIRYHFYS.P.WTLHEWLENYPDVSiE...IVRNTY...RTKnnkypTWEYRGIi.SNQSP
   9 LVGFDVRHRLLPrPhLTLDWVIRKRPEWM.EgirRVRHRYvs.NGQyg...TAELIGIatGRTAL
  10 FLEVDEHYKLFS.A.WTLTQWLEWYPDFSaK...ILRNTY...DGR.....TWKLQKI..TNEDP


              210          220             230        240            25
               |            |               |          |              
   1 KELPLPG.G.LSLLDYH..ASK.GRLQGR.EG.....GRVA.WVADPKDPR...KP..IPHLTGL
   2 KELPLPG.G.LSLLDYH..ASK.GRLQGR.EG.....GRVA.WVADPKDPR...KP..IPHLTGL
   3 KELPLPG.G.LSLLDYH..AFK.GRLQGR.EG.....GRVA.WVADPKDPR...KP..IPHLTGL
   4 QDILLDClG.MSLAEYH..LNK.GATEEEvQQ.....SYVV.YV-KPISWR...KGklTAHLSRR
   5 QDILLDClG.MSLAEYH..LNK.GATEEEvQQ.....SYVV.YV-KPISWR...KGklTAHLSRR
   6 NEIQIEAlG.ISLAEYH..RQE.GATQQEiDE.....SRVV.IVKKISDYKa..KP..VYHLSQR
   7 REIRLPEqN.ISLAEYH..LQK.YNALVE.E-.....VESS.WVVEVASKE...RR..YPHLSRR
   8 REVWLAElN.TSLADYH..VQKyGATPEEvDG.....SLVVqVVSRERNFRqkaEP..ILHLSRR
   9 STFPTPK.GeVSLLGYH..ESK.GNLPEG.EReavaaSHVV.QVRYGRDTRa..KP..MEHLAAL
  10 NNIDSGT.G.QTLATYHknHQK.PATDQEiNS.....SKVI.YVKPYNSKK...EEs.YPHLSSR


      0       260        270        280       290        
     |         |          |          |         |        
   1 LVPVLTLEDLHE.EEGSLALSLPWEERRR.RTREIASWIGRRLGLGTP...
   2 LVPVLTLEDLHE.EEGSLALSLPWEERRR.RTREIASWIGRRLGLGTPeav
   3 LVPVLTLEDLHE.EEGSLALSLPWEERRR.RTREIASWIGRRLGLGTPeav
   4 LSPSLTMEMLAKvAEDSTVCDREKREIRA.VFKSIKQSINQRLQEAQKtas
   5 LSPSLTMEMLAKvAEDSTVCDREKREIRA.VFKSIKQSINQRLQEAQKtas
   6 LSPILTMETLAQ.IAEQ---GREKKEIQG.VFDYIRKNIGTRLQESQKiaq
   7 LSPALTLEMLAS.LEDNR--SPGGKVSAA.VIECIRKSLKERFEESEEtar
   8 LSPVLTLEMLAS.IEDQRW--TGKKVSSL.VSEHIRKSLEERLKESKEtak
   9 LQPMFGFDTLSQ.I-DSRLLERIARSLKWpVGERLKAAI--RLVKGLKvse
  10 VKPCLFLDTL--.---SELASQGDRKVKE.VFNLIKPSIEDRFSRATEiak