a2m2html output for file 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, 1999.
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:

- gi|1905972|gb|AAC49664.1| UV damage endonuclease UVDE [Schizosaccharomyces pombe] (Schizosaccharomyces pombe)
- gi|7491470|pir||T39815_1:599 hypothetical protein SPBC19C7.09c - fission yeast (Schizosaccharomyces pombe) (Schizosaccharomyces pombe)
- gi|7493593|pir||S71134 UV-endonuclease - fission yeast (Schizosaccharomyces pombe) (Schizosaccharomyces pombe)
- gi|1399001|dbj|BAA11415.1| (D78571) UV-endonuclease [Schizosaccharomyces pombe] (Schizosaccharomyces pombe)
- gi|1905972|gb|AAC49664.1| (U78487) UV damage endonuclease UVDE [Schizosaccharomyces pombe] (Schizosaccharomyces pombe)
- gi|3218413|emb|CAA19577.1| (AL023859) uv-endonuclease. [Schizosaccharomyces pombe] (Schizosaccharomyces pombe)
- gi|4210461|dbj|BAA74539.1|_28:591 (D11392) UV-endonuclease [Neurospora crassa] (Neurospora crassa)
- gi|1362529|pir||S55262_28:591 UV-endonuclease - Neurospora crassa (Neurospora crassa)
- gi|6759487|emb|CAB69813.1|_3:317 (AJ243712) putative UV-endonuclease [Bacillus cereus] (Bacillus cereus)
- gi|6759488|emb|CAB69814.1|_11:325 (AJ243712) putative UV-endonuclease [Bacillus cereus] (Bacillus cereus)
- gi|7473732|pir||C75350_2:326 probable UV damage endonuclease - Deinococcus radiodurans (strain R1) (Deinococcus radiodurans)
- gi|6459593|gb|AAF11370.1|AE002022_3 (AE002022) UV damage endonuclease, putative [Deinococcus radiodurans] (Deinococcus radiodurans)
- gi|1176954|sp|P45864|YWJD_BACSU_1:319 HYPOTHETICAL 36.9 KD PROTEIN IN ACDA 5'REGION (Bacillus subtilis)
- gi|1075938|pir||S55418 UV-endonuclease homolog ywjD - Bacillus subtilis (Bacillus subtilis)
- gi|853757|emb|CAA89865.1| (Z49782) Unknown [Bacillus subtilis] (Bacillus subtilis)
- gi|2636257|emb|CAB15748.1| (Z99123) similar to UV-endonuclease [Bacillus subtilis] (Bacillus subtilis)
- gi|6116766|dbj|BAA85759.1|_1:305 (AB033747) UV-endonuclease [Deinococcus radiodurans] (Deinococcus radiodurans)

                   10        20           30        40        50       
                   |         |            |         |         |       
   1 .....MLRLLKRNIQISKRIVFTILKQK...AFKGNHPCVPSVCTITYSRFHCLPDTLKSLLPMS
   2 .....MLRLLKRNIQISKRIVFTILKQK...AFKGNHPCVPSVCTITYSRFHCLPDTLKSLLPMS
   3 m27dsSAPSPARNLRRSGRNILQPSSEKdrdHEKRSGEELAGRMMGKDANGHCLR----------
   4 m27dsSAPSPARNLRRSGRNILQPSSEKdrdHEKRSGEELAGRMMGKDANGHCLR----------
   5 ml...-----------------------...-----------------IRFGYVS-HAMALWDCS
   6 m10ml-----------------------...-----------------IRFGYVS-HAMALWDCS
   7 m....GARLGQRALLLG-----------...ALPPGRNGMTSACEA-------------------
   8 .....-----------------------...-------------MI--FRFGFVS-NAMSLWDAS
   9 .....-----------------------...--------MTSACEA-------------------


       60        70        80        90       100       110       120  
       |         |         |         |         |         |         |  
   1 SKTTLSMLPQVNIGANSFSAETPVDLKKENETELANISGPHKKSTSTSTRKRARSSKKKATDSVS
   2 SKTTLSMLPQVNIGANSFSAETPVDLKKENETELANISGPHKKSTSTSTRKRARSSKKKATDSVS
   3 ------------------------EGKEQEEGVKMAIEGLARME-----RRLQRATKRQKKQLEE
   4 ------------------------EGKEQEEGVKMAIEGLARME-----RRLQRATKRQKKQLEE
   5 PAKTMTF----------------------------------------------------------
   6 PAKTMTF----------------------------------------------------------
   7 -------VPQLGLVCLTVGPEV-------------------RFRTVTLSRYRALSPA--------
   8 PAKTLTF---------------------------------------------ARYSKLSKT----
   9 -------VPQLGLVCLTVGPEV-------------------RFRTVTLSRYRALSPA--------


           130       140       150         160       170       180     
            |         |         |           |         |         |     
   1 DKIDESVASYDSSTHLRRSSRSKKPVNYNSSS..ESESEEQISKATKKVKQKEEEEYVEEVDEKS
   2 DKIDESVASYDSSTHLRRSSRSKKPVNYNSSS..ESESEEQISKATKKVKQKEEEEYVEEVDEKS
   3 DGIPVPSV---------VSRFPTAPYHHKSTNaeEREAKEPVLKTHSKDVEREAEIGVDDV----
   4 DGIPVPSV---------VSRFPTAPYHHKSTNaeEREAKEPVLKTHSKDVEREAEIGVDDV----
   5 --------------------------------..-------------------------------
   6 --------------------------------..-------------------------------
   7 --------------------------------..-------------------------EREAKL
   8 --------------------------------..--ERKEALLTVTK------------------
   9 --------------------------------..-------------------------EREAKL


        190       200           210       220       230       240      
         |         |             |         |         |         |      
   1 LKNESSSDEFEPVVPEQLETPIS....KRRRSRSSAKNLEKESTMNLDDHAPREMFDCLDKPIPW
   2 LKNESSSDEFEPVVPEQLETPIS....KRRRSRSSAKNLEKESTMNLDDHAPREMFDCLDKPIPW
   3 -------VKMEPAATNIIEPEDAqdaaERGAARPPAVNSS-------------------YLPLPW
   4 -------VKMEPAATNIIEPEDAqdaaERGAARPPAVNSS-------------------YLPLPW
   5 -----------------------....------TSFKKLSK-----------QEREDKLYHVIR-
   6 -----------------------....------TSFKKLSK-----------QEREDKLYHVIR-
   7 LDLYSSNIKT-------------....-------------------------------------L
   8 -----------------------....--------------------------------------
   9 LDLYSSNIKT-------------....-------------------------------------L


       250       260       270       280            290       300      
        |         |         |         |              |         |      
   1 RGRLGYACLNTILRSMKERVFCSRTCRITTIQRD.....GLESVKQLGTQNVLDLIKLVEWNHNF
   2 RGRLGYACLNTILRSMKERVFCSRTCRITTIQRD.....GLESVKQLGTQNVLDLIKLVEWNHNF
   3 KGRLGYACLNTYLRNAKPPIFSSRTCRMASIVDHr28elGHKFVQELGLANARDIVKMLCWNEKY
   4 KGRLGYACLNTYLRNSKPPIFSSRTCRMASIVDHr28elGHKFVQELGLANARDIVKMLCWNEKY
   5 ----------------------------------.....----------QNLEHTIRILHYNIAH
   6 ----------------------------------.....----------QNLEHTIRILHYNIAH
   7 RGAADYCA--------------------------.....------------------------AH
   8 ----------------------------------.....----------ANLRNTMRTLHYIIGH
   9 RGAADYCA--------------------------.....------------------------AH


       310       320          330        340       350       360       
        |         |            |          |         |         |       
   1 GIHFMRVSSDLFPFASHAKYGYT...LEFAQSH.LEEVGKLANKYNHRLTMHPGQYTQIASPREV
   2 GIHFMRVSSDLFPFASHAKYGYT...LEFAQSH.LEEVGKLANKYNHRLTMHPGQYTQIASPREV
   3 GIRFLRLSSEMFPFASHPVHGYK...LAPFASEvLAEAGRVAAELGHRLTTHPGQFTQLGSPRKE
   4 GIRFLRLSSEMFPFASHPVHGYK...LAPFASEvLAEAGRVAAELGHRLTTHPGQFTQLGSPRKE
   5 EIPLYRLSSSIVPLATHPEVEFDy..IGVFTPL.WRKIGALIKEHNLRISFHPNQFTLFTSDKPH
   6 EIPLYRLSSSIVPLATHPEVEFDy..IGVFTPL.WRKIGALIKEHNLRISFHPNQFTLFTSDKPH
   7 DIRLYRLSSSLFPMLDLAGDDTGaavLTHLAPQ.LLEAGHAFTDAGVRLLMHPEQFIVLNSDRPE
   8 GIPLYRFSSSIVPLATHPDVMWDf..VTPFQKE.FREIGELVKTHQLRTSFHPNQFTLFTSPKES
   9 DIRLYRLSSSLFPMLDLAGDDTGaavLTHLAPQ.LLEAGHAFTDAGVRLLMHPEQFIVLNSDRPE


      370       380       390       400       410       420       430  
       |         |         |         |         |         |         |  
   1 VVDSAIRDLAYHDEILSRMKLNEQLNKDAVLIIHLGGTFEGKKETLDRFRKNYQRLSDSVKARLV
   2 VVDSAIRDLAYHDEILSRMKLNEQLNKDAVLIIHLGGTFEGKKETLDRFRKNYQRLSDSVKARLV
   3 VVESAIRDLEYHDELLSLLKLPEQQNRDAVMIIHMGGQFGDKAATLERFKRNYARLSQSCKNRLV
   4 VVESAIRDLEYHDELLSLLKLPEQQNRDAVMIIHMGGQFGDKAATLERFKRNYARLSQSCKNRLV
   5 ITTNAITDMTYHYKILDAIGIADS----SYINIHVGGAYGNKEKAIERFHENIKKLPTHIKKQMT
   6 ITTNAITDMTYHYKILDAIGIADS----SYINIHVGGAYGNKEKAIERFHENIKKLPTHIKKQMT
   7 VRESSVRAMSAHARVMDGLGLA--RTPWNLLLLHGGKGGRGAELA-----ALIPDLPDPVRLRLG
   8 VTKNAVTDMAYHYRMLEAMGIADR----SVINIHIGGAYGNKDTATAQFHQNIKQLPQEIKERMT
   9 VRESSVRAMSAHARVMDGLGLA--RTPWNLLLLHGGKGGRGAELA-----ALIPDLPDPVRLRLG


           440       450       460         470         480       490   
            |         |         |           |           |         |   
   1 LENDDVSWSVQDLLPLCQELNIPLVLDWHHHNIV..PGTLREGSLDL..MPLIPTIRETWTRKGI
   2 LENDDVSWSVQDLLPLCQELNIPLVLDWHHHNIV..PGTLREGSLDL..MPLIPTIRETWTRKGI
   3 LENDDVGWTVHDLLPVCEELNIPMVLDYHHHNICfdPAHLREGTLDIsdPKLQERIANTWKRKGI
   4 LENDDVGWTVHDLLPVCEELNIPMVLDYHHHNICfdPAHLREGTLDIsdPKLQERIANTWKRKGI
   5 LENDDKTYTTAETLSICQKENIPFVFDYHHHMAN..---LCEEPL--..EELLPAIFETWSHTNI
   6 LENDDKTYTTAETLSICQKENIPFVFDYHHHMAN..---LCEEPL--..EELLPAIFETWSHTNI
   7 LENDERAYSPAELLPICEATGTPLVFDAHHHVVH..DKLPDQEDPSV..REWVLRARATWQPP-E
   8 LENDDKTYTTEETLQVCEQEDVPFVFDFHHFYAN..P----DDHADL..NVALPRMIKTWERIGL
   9 LENDERAYSPAELLPICEATGTPLVFDAHHHVVH..DKLPDQEDPSV..REWVLRARATWQPP-E


          500       510       520            530        540       550  
           |         |         |              |          |         |  
   1 TQKQHYSESADPTAISGMKRRAHSDRVF.....DFPPCDPTM.DLMIEAKEKEQAVFELCRRYEL
   2 TQKQHYSESADPTAISGMKRRAHSDRVF.....DFPPCDPTM.DLMIEAKEKEQAVFELCRRYEL
   3 KQKMHYSEPCDG-AVTPRDRRKHRPRVM.....TLPPCPPDM.DLMIEAKDKEQAVFELMRTFKL
   4 KQKMHYSEPCDG-AVTPRHRRKHRPRVM.....TLPPCPPDM.DLMIEAKDKEQAVFELMRTFKL
   5 SPKVHISSPRSE-----KEFRAHAEYIDle9lhIAKKHNHNF.DIMIESKQKDLALFQLIDELSA
   6 SPKVHISSPRSE-----KEFRAHAEYIDle9lhIAKKHNHNF.DIMIESKQKDLALFQLIDELSA
   7 WQVVHLSN-----GIEGPQDRRHSHLIA.....DFPSAYADVpWIEVEAKGKEEAIAAL------
   8 QPKVHLSSPKSEQAI-----RSHADYVDan9leRFRQWGTNI.DFMIEAKQKDKALLRLMDELSS
   9 WQVVHLSN-----GIEGPQDRRHSHLIA.....DFPSAYADVpWIEVEAKGKEEAIAAL------


           560       570          580       590            600
            |         |            |         |              |
   1 QNPPCPLEIMGPEYDQTRDGYYPPGA...EKRLTARKRRSRKEEVEEDEK......
   2 QNPPCPLEIMGPEYDQTRDGYYPPGA...EKRLTARKRRSRKEEVEEDEK......
   3 -PGFEKINDMVPYDRDDENRPAPPVKapkKKKGGKRKRTTDEEAAEPEEVd50kk.
   4 -PGFEKINDMVPYDRDDENRPAPPVKapkKKKGGKRKRTTDEEAAEPEEVd50kk.
   5 IRGI----------------------...-------KRISGAMLQW----......
   6 IRGI----------------------...-------KRISGAMLQW----......
   7 -------RLMAPFKKD----------...---------------------......
   8 IRGV----------------------...-KRIGGGALQWK---------s.....
   9 -------RLMAPFKKD----------...---------------------......