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|81300343|ref|YP_400551.1|_15:315 hypothetical protein Synpcc7942_1534 [Synechococcus elongatus PCC 7942]
- gi|81169224|gb|ABB57564.1| conserved hypothetical protein [Synechococcus elongatus PCC 7942]
- gi|56752529|ref|YP_173230.1|_15:315 hypothetical protein syc2520_d [Synechococcus elongatus PCC 6301]
- gi|56687488|dbj|BAD80710.1| hypothetical protein [Synechococcus elongatus PCC 6301]
- gi|22298491|ref|NP_681738.1|_39:328 hypothetical protein tll0948 [Thermosynechococcus elongatus BP-1]
- gi|22294671|dbj|BAC08500.1| tll0948 [Thermosynechococcus elongatus BP-1]
- gi|86610170|ref|YP_478932.1|_13:319 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|86606806|ref|YP_475569.1|_15:309 Piwi domain protein [Synechococcus sp. JA-3-3Ab]
- gi|86555348|gb|ABD00306.1| Piwi domain protein [Synechococcus sp. JA-3-3Ab]
- gi|56478414|ref|YP_160003.1|_2:313 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|_2:179 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        60     
              |         |         |         |         |         |     
   1 NRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLE
   2 NRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLE
   3 NRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLE
   4 NRFYVKSLSQSDLTAYEYRCIFKKTPELGDEKRLLASICYKLGAIAVRIGSNIITKEAVRPEKL-
   5 NRFYVKSLSQSDLTAYEYRCIFKKTPELGDEKRLLASICYKLGAIAVRIGSNIITKEAVRPEKL-
   6 NRFFVKKLSRPDLTFHEYQCQFTQVPEQGSEQKAISSVCYKLGVTAVRLGSCIITREPIDPERM-
   7 NRFFVKELTQEELTFYEYSCRPNPLPDLGEEQRALSKICNQLGVMAVRLGNRIITREKVPASKL-
   8 NRFLVKELTQEDLTFYEYDCRPNPPPELGEEQRAIARVCNRLDVIAARLGSRIITQERVSPSQL-
   9 -------------PVYYYRLTFDDDHEDINPTQLTRRGARMLSGANGWCAVTDGEPLRVLSLRPL
  10 -----------------------------------------------------------------


         70        80        90       100       110                 120
         |         |         |         |         |                   |
   1 GTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERL.....R.....RLEGVWVEG
   2 GTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERL.....R.....RLEGVWVEG
   3 GTLARMGQNYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERL.....R.....RLEGVWVEG
   4 -------QGHDWQLVQMGTKQLDCRNDAHRCALETFERKFLERDLsa9vrK.....AAEGGLIWW
   5 -------QGHDWQLVQMGTKQLDCRNDAHRCALETFERKFLERDLsa9vrK.....AAEGGLIWW
   6 -------RTKDWQLQLIGCRELSCQNYRERQALETFERKILEEKL.....Ke10ekDYELGLIWW
   7 -------KTEEWELEELGSKALDCTDPTERQALETFERKKLDWSL.....Rs10erSTGGGLIWW
   8 -------KTPEWELEERGLRVLTCANAQERSALESFERKRIGLRL.....Ksq9veWIGGGLLWW
   9 KVLRHEWNGMCCTASDETAGTLKSANPSEREAIQRLLNQCLMQGA.....R.....KLAYSSDGG
  10 ---------------------------------------------.....-.....------ICW


                       130       140       150       160         170   
                        |         |         |         |           |   
   1 LAV.....YRREH.....ARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRIL..CEMSLEAWLA
   2 LAV.....YRREH.....ARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRIL..CEMSLEAWLA
   3 LAV.....YRREH.....ARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRIL..CEMSLEAWLA
   4 VVG.....AKGIE.....KSGNGWEVHRGRRIDVSLDAEGNLYLEIDIHHRFY..TPWTVHQWLE
   5 VVG.....AKGIE.....KSGNGWEVHRGRRIDVSLDAEGNLYLEIDIHHRFY..TPWTVHQWLE
   6 ISG.....EEGLE.....KTGHGWEVHRGRQIDLKIETDEKLYLEIDIHHRFY..TPFKLEWWLS
   7 VTG.....LEGVEr10kpLCGDGWEVHRGRELDVVIRQDKKLYLEIDIRYHFY..SPWTLHEWLE
   8 VTA.....QKGVE.....LSGEGWEIHRGRMIDVAVEPDGKLYLEVDIHYRFY..TPWTLHEWLE
   9 LEAe15qpSERVS.....AGGDYLDAFQSVTLIPDVLPDGTALVGFDVRHRLLprPHLTLDWVIR
  10 QKT.....EADIR.....SDVSGWEIYRGFKLDIFVSSQGNVFLEVDEHYKLF..SAWTLTQWLE


               180                  190       200             210      
                |                    |         |               |      
   1 QGHPLP.....KRV.....RNAY.DR.....RTWELLRLGEEDPKELP.....LP.GGLSLLDYH
   2 QGHPLP.....KRV.....RNAY.DR.....RTWELLRLGEEDPKELP.....LP.GGLSLLDYH
   3 QGHPLP.....KRV.....RNAY.DR.....RTWELLRLGEEDPKELP.....LP.GGLSLLDYH
   4 QYPEIPls6rnNYL.....DERH.GF.....INWQYGRFTQERPQDIL.....LDcLGMSLAEYH
   5 QYPEIPls6rnNYL.....DERH.GF.....INWQYGRFTQERPQDIL.....LDcLGMSLAEYH
   6 EYPNIQi....KYV.....RNTYkDK.....KKWILENFADKSPNEIQ.....IEaLGISLAEYH
   7 NYPDVS.....IEIvr8tkNNKY.PT.....WEYRGIISNQSPREVWL.....AE.LNTSLADYH
   8 SYPDVP.....IEI.....VRNT.YFda8ltWKYLGILSNQSPREIRL.....PE.QNISLAEYH
   9 KRPEWM.....EGI.....RRVR.HR.....YVSNGQYGTAELIGIATg10ptPK.GEVSLLGYH
  10 WYPDFSa....KIL.....RNTY.DG.....RTWKLQKITNEDPNNID.....SG.TGQTLATYH


       220              230            240       250       260        2
        |                |              |         |         |         
   1 ASKGRLQGR..E.....GGRVAWVA.....DPKDPRKPIPHLTGLLVPVLTLEDLHEE.EGSLAL
   2 ASKGRLQGR..E.....GGRVAWVA.....DPKDPRKPIPHLTGLLVPVLTLEDLHEE.EGSLAL
   3 AFKGRLQGR..E.....GGRVAWVA.....DPKDPRKPIPHLTGLLVPVLTLEDLHEE.EGSLAL
   4 LNKGATEEEvqQ.....SYVVYVKP.....ISWRKGKLTAHLSRRLSPSLTMEMLAKVaEDSTVC
   5 LNKGATEEEvqQ.....SYVVYVKP.....ISWRKGKLTAHLSRRLSPSLTMEMLAKVaEDSTVC
   6 RQEGATQQEidE.....SRVVIVKK.....ISDYKAKPVYHLSQRLSPILTMETLAQI.AEQGRE
   7 VQKYGATPE..E.....VDGSLVVQvv6erNFRQKAEPILHLSRRLSPVLTLEMLASI.EDQRWT
   8 LQKYNALVE..E.....VESS-WVV.....EVASKERRYPHLSRRLSPALTLEMLASL.EDNRSP
   9 ESKGNLPEG..Ere6aaSHVVQVRY.....GRDTRAKPMEHLAALLQPMFGFDTLSQI.DSRLLE
  10 KNHQKPATD..Qeins.SKVIYVKP.....YNSKKEESYPHLSSRVKPCLFLDTLSEL.ASQ---


      70       280       290     
      |         |         |     
   1 SLPWEERRRRTREIASWIGRRLGLGTP
   2 SLPWEERRRRTREIASWIGRRLGLGTP
   3 SLPWEERRRRTREIASWIGRRLGLGTP
   4 DREKREIRAVFKSIKQSINQRL-----
   5 DREKREIRAVFKSIKQSINQRL-----
   6 KKEIQGVFDY---IRKNI---------
   7 GKKVSSLVSEH--IR------------
   8 GGKVS--AAVIECIRKSLKER------
   9 RIARSLKWPVGERLKAAIRLVKGL---
  10 --GDRKVKEVFNLIKPSIEDRFSRATE