; SAM: prettyalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:15 ; (c) 1992-1999 Regents of the University of California, Santa Cruz ; ; Sequence Alignment and Modeling Software System ; http://www.cse.ucsc.edu/research/compbio/sam.html ; ; ------ Citations (HMMs, SAM) ------ ; A. Krogh et al., Hidden Markov models in computational biology: ; ------------- 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: ; 1 gi|1723110|sp|P47380|Y134_MYCGE_1:99 ; 2 gi|2496313|sp|P75502|Y134_MYCPN_1:99 ; 3 gi|6899040|gb|AAF30493.1|AE002108_6_1:89 ; 4 gi|7190651|gb|AAF39443.1|_7:95 ; 5 gi|7468701|pir||B71528_7:95 ; 6 gi|7468586|pir||B72127_7:94 ; 7 gi|7269963|emb|CAB79780.1|_71:176 ; 8 gi|3738329|gb|AAC63670.1|_69:174 ; 9 gi|7444751|pir||S75165_11:113 ; 10 gi|7444750|pir||B71649_2:107 ; 11 gi|7226685|gb|AAF41804.1|_1:109 ; 12 gi|7380299|emb|CAB84885.1|_1:109 ; 13 gi|140249|sp|P17577|YBAB_ECOLI_1:109 ; 14 gi|43322|emb|CAA28176.1|_1:73 ; 15 T0091 ; 16 gi|1074405|pir||G64152_13:121 ; 17 gi|1175545|sp|P44711|YBAB_HAEIN_1:109 ; 18 gi|3150108|emb|CAA19160.1|_1:101 ; 19 gi|7477735|pir||E70795_1:102 ; 20 gi|7479647|pir||T35387_5:105 ; 21 gi|141372|sp|P24281|YAAK_BACSU_2:106 ; 22 gi|7007420|dbj|BAA90837.1|_1:102 ; 23 gi|3925824|dbj|BAA34649.1|_1:86 ; 24 gi|7471319|pir||A75548_1:91 ; 25 gi|7444752|pir||E72344_21:116 ; 26 gi|6969059|emb|CAB73630.1|_1:99 ; 27 gi|2644973|emb|CAA05823.1|_1:98 ; 28 gi|7463957|pir||C64524_1:94 ; 29 gi|7464580|pir||E71983_3:97 ; 30 gi|7463079|pir||E70157_14:105 10 20 30 40 50 60 | | | | | | 1 ----MSFKKIAEMMRQ.AERETKKKTLAFEQQAFEYNYKNGAIKITILGDLTLKSINIDPVLIDa 2 ----MSFKKITEMMRQ.AERQSKQKALDFEQKLFEYSYKNAAIKIIIFGNLTIKSITIDPALIDp 3 ----MDFQKLAQELKK.MQNTLSKKQKEFEEKVFDFDYK-GYVLVKIKGDLNIEAIEIKTEIVDp 4 --------KKKKEAKL.MERQFMEMEASLEQKRFSGEAGNGLVSVTINGKCNLVDVKIKPDCLDp 5 --------KKKKEAKL.MERQFMEMEASLEQKRFSGEAGNGLVSVTINGKCDLVDVRIKPDCLDp 6 --------KKKKEAKI.MEQQFLEMEASLLEKRYEGQAGNGLVSVVINGKCDLISVKVQPTCLDp 7 LGNMQNLYETVKKAQMvVQVEAVRVQKELAVAEFDGYCQGELVKVTLSGNQQPIRTDITDAAME. 8 FGNMQNMYETVKKAQMvVQVEAVRVQKELAAAEFDGYCAGELVKVTLSGNQQPIRTDITEAAME. 9 LGKIKELQEAFQKAQQ.VQEGAKVLQEELERMEIPGKSADGLVTVLMSGNQEPLSIEIDPSALE. 10 ----VNFNQFLKQAQS.MQKKMQEAQEQMANTRYTGKAGGMLVEIIITGKGEVEKISIDESLLKt 11 MFGKAGLGGLMKQAQQ.MQENMKKAQAKLAETEIEGEAGNGLVKITMTCAHEVRKIDISPDLIQe 12 MFGKAGLGGLMKQAQQ.MQENMKKAQAKLAETEIEGEAGNGLVKITMTCAHEVRKIDISPDLIQe 13 MFGKGGLGNLMKQAQQ.MQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE. 14 MFGKGGLGNLMKQAQQ.MQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE. 15 MFGKGGLGGLMKQAQQ.MQEKMQKMQEEIAQLEVTGESGAGLVKITINGAHNCRRIDIDPSLME. 16 MFGKGGLGGLMKQAQQ.MQEKMQKMQEEIAQLEVTGESGAGLVKITINGAHNCRRIDIDPSLME. 17 MFGKGGLGGLMKQAQQ.MQEKMQKMQEEIAQLEVTGESGAGLVKITINGAHNCRRIDIDPSLME. 18 MQPGGDMSALLAQAQQ.MQQKLLETQQQLANAQVHGQGGGGLVEVVVKGSGEVVSVAIDPKVVDp 19 MQPGGDMSALLAQAQQ.MQQKLLEAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDp 20 -GGQPNMQQLLQQAQK.MQQDLAKAQEELARTEVDGQAGGGLVKATVTGSGELRGLVIDPKAVDp 21 RGGMGNMQKMMKQMQK.MQKDMAKAQEELAEKVVEGTAGGGMVTVKANGQKEILDVIIKEEVVDp 22 ---MKNMGQMMKQMQK.MQKQMMKAQEELKEKTVEATAGGGMVTVVASGDKRILDVRISEDVVDp 23 ----MDMKKLMKQMQQ.AQVAAGKIQDELAAQSVEGTA-SGLVTVQMNGHGKVTSLKIKPEAVDg 24 ----MDMKKLMKQMQQ.AQVAAGKIQDELAAQSVEGTA-SGLVTVQMNGHGKVTSLKIKPEAVDg 25 ------LKDFARMQEE.LQKKIQELEESFSQIEVEASVGGGAVRIVATCDRRVKDIEIDEDLKE. 26 MFENMDFSKMGELLNQ.VQEKAKNIELELANREFSAKSGAGLVKVSANGKGEIIDVSIDDSLLE. 27 ---MFDPSKLSEMLTQ.FQDKAKEMEEKSHNTSFTAKSGGGLVSVSMSGAGELLDVSIDDSLLE. 28 ----MDFSQLGGLLDG.MKKEFSQLEEKNKDTIHTSKSGGGMVSVSFNGLGELVDLQIDDSLLE. 29 ---FSQLGGLSGLLDG.VKKEFSQLEEKNKDTIHTSKSGGGMVSVSFNGLGELVDLQIDDSLLE. 30 ----VNPLDFLKNMSS.VKNNIDNIKKEISKITVCGKAGSNIVTIEMDGEFNVKKVSINKEFFDd 70 80 90 100 | | | | 1 ..SDKVILEEMIIEATNEAVSDVKTKYDNLVEK---TMPKVPGL---- 2 ..EDKVTLEEMITEAVNEAVGDVKAKYDQLMEE---AMPQMPGL---- 3 ..EDKETLQDILRAAINEAISITCKERDAIMN---------------- 4 ..EDPEVVADLFRAAFKAA----KAALDSEMSAMHMGMP--------- 5 ..EDPEVVADLFRAAFKAA----KAALDSEMSAMQMGMP--------- 6 ..EDPEVIEDLFRAAFKLA----KEQMDQEMSLMRSTM---------- 7 ..LGSEKLSLLVTEAYKDAHSKSVLAMKERMSDLAQSLGMPPGL---- 8 ..LGSEKLSQLVTEAYKDAHAKSVVAMKERMSDLAQSLGMPPGL---- 9 ..KGAEGLSASVTEAMKAAYAESTETMRSKMEELTSGLNL-PG----- 10 ..EEKEMLEDLIKVAFNDAKQKCDEDSQNSLSGALNGMSLPPGFKIPF 11 aaDDKEMLEDLILAALKSARGKAEETANKTMGAFTQGL--PPGVGDF- 12 aaDDKEMLEDLILAALKSARDKAEETANKTMGAFTQGL--PPGVGDF- 13 ..DDKEMLEDLVAAAFNDAARRIEETQKEKMASVSSGMQLPPGFKMPF 14 ..DDKEMLEDLV------------------------------------ 15 ..DDKEMLEDLIAAAFNDAVRRAEELQKEKMASVTAGMPLPPGMKFPF 16 ..DDKEMLEDLIAAAFNDAVRRAEELQKEKMASVTAGMPLPPGMKFPF 17 ..DDKEMLEDLIAAAFNDAVRRAEELQKEKMASVTAGMPLPPGMKFPF 18 ..GDIETLQDLIVGAMADASKQVTKLAQERLGALTSAMR--------- 19 ..DDIETLQDLIVGAMRDASQQVTKMAQERLGALAGAMRP-------- 20 ..EDTETLADLVVAAVQAANENAQNLQQQKLGPLAQGMGG-------- 21 ..EDIDMLQDLVLAATNEALKKVDEITNETMGQFTKGMNM-PGL---- 22 ..DDVEMLQDLILAATNEALKKVDELVEQDMGKFTKGLNM-PGM---- 23 ..DDVEALEDLILAAINDAAEKAEGLQRE------------------- 24 ..DDVEALEDLILAAINDAAEKAEGLQREATAGL-------------- 25 ..-DFDTLKDLLIAGMNEVMEKIEKRREEEMSKITQQFGI-PG----- 26 ..-DKESLQILLISAINDVLAMVAQNRSSMANDVLGGFG--------- 27 ..-DKESLQILLISAINDVYKSVEENKKSMTLGMLGGMAPF------- 28 ..-DKEAMQIYLMSALNDGYKAVEENRKNLAFNMLGNF---------- 29 ..-DKEAMQIYLMSALNDGYKAVEENRKNLAFNMLGNF---------- 30 ..LDNDAFEQMIKSALNDAVSKVKEEIKLKTMGV--------------