; SAM: prettyalign v3.2 (June, 2000) compiled 07/10/00_09:40:44 ; (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 (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|7496507|pir||T19469_26:136 ; 2 gi|3914549|sp|O05964|RBFA_RICPR_6:119 ; 3 gi|7465357|pir||G64650_3:109 ; 4 gi|7465302|pir||F71940_3:109 ; 5 gi|1723113|sp|P47389|RBFA_MYCGE_2:110 ; 6 gi|2496316|sp|P75589|RBFA_MYCPN_2:114 ; 7 gi|7444622|pir||H72324_1:123 ; 8 gi|7473662|pir||A75463_23:112 ; 9 gi|6225917|sp|Q9Z5I8|RBFA_MYCLE_1:119 ; 10 gi|3914556|sp|P71614|RBFA_MYCTU_1:119 ; 11 gi|6225918|sp|Q9Z527|RBFA_STRCO_1:119 ; 12 gi|3914553|sp|O34272|RBFA_YEREN_3:127 ; 13 gi|140742|sp|P09170|RBFA_ECOLI_3:129 ; 14 gi|1172847|sp|P45141|RBFA_HAEIN_2:127 ; 15 T0110 ; 16 gi|3914555|sp|O65693|RBFA_ARATH_18:146 ; 17 gi|3914560|sp|Q55625|RBFA_SYNY3_1:127 ; 18 gi|3914548|sp|O05340|RBFA_STIAU_1:115 ; 19 gi|418464|sp|P32731|RBFA_BACSU_3:114 ; 20 gi|4583984|emb|CAB40558.1|_1:110 ; 21 gi|3947715|emb|CAA05920.1|_5:120 ; 22 gi|7226619|gb|AAF41747.1|_5:119 ; 23 gi|7380227|emb|CAB84813.1|_5:119 ; 24 gi|6093904|sp|O83860|RBFA_TREPA_3:118 ; 25 gi|3914554|sp|O51742|RBFA_BORBU_7:122 ; 26 gi|6899298|gb|AAF30730.1|AE002129_6_1:113 ; 27 gi|4586219|emb|CAB40971.1|_1:110 ; 28 gi|8163433|gb|AAF73669.1|_21:138 ; 29 gi|6685851|sp|Q9Z8M0|RBFA_CHLPN_1:117 ; 30 gi|8163212|gb|AAF73551.1|_1:126 ; 31 gi|6685836|sp|O84097|RBFA_CHLTR_1:119 10 20 30 40 | | | | 1 -RLDDKKVVQLSRILEERIAEVV.A---........TDEMLGrlQLQITRVRVDRAFT....... 2 -KTNSHRQQKLASIINEVLIEILkRGKM........LDKRLFdcPLTITKIIVTADLK....... 3 -----AHKERLESNLLELLQEAL.A-SL........NDSELN..SLSVTKVECSKGKH....... 4 -----AHKERLESNLLELLQEAL.A-SL........NDSELN..SLSVTKVECSKGKH....... 5 ---ASYRKQRIENDIIRLINRTI.INEI........YDPVVK..LGHVSHVKLSADFF....... 6 ---ASYKKERLENDIIRLINRTV.IHEI........YNETVK..TGHVTHVKLSDDLL....... 7 -MNPAYRKAMLESEIQKLLMEAL.Q-QL........RDPRLKkdFVTFSRVELSKDKR....... 8 --GPLMKPEQVQAQMSRVLSSAI.A-EL........RDPRVPl.IVTVERVHVTPDYG....... 9 -MADQARARRLAKRICTIVASAI.EFEI........KDPGLD..GVTIVDVKVTADLH....... 10 -MADAARARRLAKRIAAIVASAI.EYEI........KDPGLA..GVTITDAKVTADLH....... 11 -MADNARAKRLADLIREVVAQKL.QRGI........KDPRLGs.HVTITDTRVTGDLR....... 12 -----SRSQRVSQEMQKEIALIL.QREI........KDPRVG..MATVSGIELSRDLA....... 13 --KEFGRPQRVAQEMQKEIALIL.QREI........KDPRLGm.MTTVSGVEMSRDLA....... 14 -AREFKRSDRVAQEIQKEIAVIL.QREV........KDPRIG..MVTVSDVEVSSDLS....... 15 MAREFKRSDRVAQEIQKEIAVIL.QREV........KDPRIG..MVTVSDVEVSSDLS....... 16 CMANPRRVKMVAKQIMRELSDML.LTDTvlq13algADRYLSs.LTTISDVEVSNDLQvmr12lc 17 -MATSRRVSRVSSLIKREVSQML.LHEI........KDDRVGtgMVSVTEVEVSGDLQ....... 18 -MTTHSRPERVGQEIQAAIGQLLtRGEL........RDPRIG..FITITGVKVSPDLR....... 19 -----MRANRVGEQMKKELGDII.SRKL........KDPRIG..FLTVTDVRVSGDLQ....... 20 -MGNSFRSDRVAVEIQREINDIL.RNKV........RDPRVQ..DVNITDVQLTGDLS....... 21 LIMANHRIDRVGMEIKREVNEIL.RLRV........NDPRVQ..DVTITDVQMLGDLS....... 22 -QRGYARQDRVKEQIMRELAELV.RTGL........KDPRAG..FITVNEVEVTRDYS....... 23 -QRGYARQDRVKEQIMRELAELV.RTGL........KDPRAG..FITVNEVEVTRDYS....... 24 -QVSQLRVRKLGEHIRAEIAQLImLGKI........KDPRVSp.FLSVNWVDVSGGMV....... 25 FMYKNIKKFKLESFIAQEIGNLIvSGGI........KDPRIHs.FLTVVKVEFSKDLI....... 26 -MANEVRVARLESLIKDVINNAL.ANEI........NDKIAK..LARVTAVRLSNDLS....... 27 --MDNKRLSKIERLLQKELSEIF.LRDA........KSLPGV..IVSVTNVRVSPDLS....... 28 CMTENRRIKRVNALLQEAIAKVI.LKDV........KHPKISnlWITVTRVSLSKDLH....... 29 -MTENRRIKRVNALLQEAIAKVI.LKDV........KHPKISnlWITVTRVSLSKDLH....... 30 -MTENRRMKKVNAMLRESIAKVI.LKDV........KHPKISnrWITITRVSLSRDLQ....... 31 -MAENRRMKKVNAMLREAIAKVI.LKDV........KHPKISnrWITITRVSLSRDLQ....... 50 60 70 80 90 100 | | | | | | 1 .QVSVYWMCRG....D..GDS----EIVDFLEESKHQIRRRVEESIG..I-TCPEVKFIGDKALL 2 .IANCYFFPFN....T..--KLTFDEIMDALNNSKHAIRNFITNRIN..MKFSPEIRFYYDYGFD 3 .HAYVFVLSSD....H..-------KILSKLKKAEGLIRQFVLQASG..WFKCPKLSFVSDNSLE 4 .HALVFVLSSD....H..-------KILSKLKKAEGLIRQFVLQASG..WFKCPKLSFVLDDSLE 5 .HAVVYLDCYD....R..---SQIQTVVNAFKKAQGVFSQMLAQNLY..LAKSVKLHFVKDDAID 6 .HVTVYLDCYN....R..---EQIDRVVGAFNQAKGVFSRVLAHNLY..LAKAVQIHFVKDKAID 7 .YADVYVSFLG....T..--PEERKETVEILNRAKGFFRTFIAKNLR..LYVAPEIRFYEDKGIE 8 .QARVYVSAIG....A..----DMPELLDALTHARGRLQRELSAHVR..MRRTPTLEF------- 9 .DATVFYTVMG....RtlEDAPDYTAATAALNRAKGTLRSKVGAGTG..VRFTPTLTFIRDTTSD 10 .DATVYYTVMG....RtlHDEPNCAGAAAALERAKGVLRTKVGAGTG..VRFTPTLTFTLDTISD 11 .EATVFYTVYG....D..--DEERKAATAGLESAKGILRSEVGKAAG..VKFTPTLTFVMDALPD 12 .YAKVFVTFLNvltdN..ADPDTAKNGIKALQDASGYIRTLLGKAMR..LRIVPELTFAYDNSLI 13 .YAKVYVTFLN....D..KDEDAVKAGIKALQEASGFIRSLLGKAMR..LRIVPELTFFYDNSLV 14 .YAKIFVTFLF....D..HDEMAIEQGMKGLEKASPYIRSLLGKAMR..LRIVPEIRFIYDQSLV 15 .YAKIFVTFLF....D..HDEMAIEQGMKGLEKASPYIRSLLGKAMR..LRIVPEIRFIYDQSLV 16 nVVKVYVSVFG....D..--DRGKDVAIAGLKSKAKYVRSELGKRMK..LRLTPEVRFIEDEAME 17 .HAKIFVSIYG....S..--PEAKASTMAGLHSAAPFVRRELGQRMR..LRRTPEVSFLEDRSLE 18 .VAQVFYSMMG....T..--AQERAETQKGLDAAKGFVRREVTAAVN..LRVSPEVFFTFDESVG 19 .IAKVYISVLG....D..--EKKREEALKGLAKAKGFIRSEIGSRIR..LRKTPEIEFEFDESID 20 .QATVYYSLLS....N..-LASDNEKAATALKKATGLFKSELAKRMT..IFKIPDLTFAKDESVE 21 .MAKVFYTIHS....T..-LASDNQKAQIGLEKATGTIKRELGKNLT..MYKIPDLQFVKDESIE 22 .HATVFYTILN....Q..---DAREITEEVLEHARGHLRSELAKRIK..LFKTPELHFKYDESLE 23 .HATVFYTVLN....Q..---DAREITEEVLEHARGHLRSELAKRIK..LFKIPELHFKYDESLE 24 .CARVYVSSFM....G..--KYKTKQGVQGLESAAGFIRSVLAKKLR..LRQCPRLSFVYDESVR 25 .NAKVFMGSIK....E..--GASLDNAVKALNNAKGFIQSQIIKRIK..VRSTPKLLFVKDDSLS 26 .VAKIFLDAHK....R..---ESMLKVLENVNKVSGLLRSKLAAEWT..SYKVPELRFVIDETID 27 .IARIHLSIFP....S..---EKSSEILESIKHNTKTIRYDLGQQVRtqLRKIPDLTFYIDDSLD 28 .SARVYVSVMP....H..--ENTKEEALEALKVSAGFIAHRASKNVV..LKYFPELHFYLDDIFS 29 .SARVYVSVMP....H..--ENTKEEALEALKVSAGFIAHRASKNVV..LKYFPELHFYLDDIFS 30 .SARVYVSIMP....H..--ENSQEETLAALKASAGFIACQASKDVV..LKYFPDLNFYMEDIFS 31 .SACVYVSIMP....H..--ENSQEETLAALKASAGFIAFQASKDLV..LKYFPDLNFYVEDIFS 110 120 | | 1 MEQEMDKLFREADYG---------- 2 NAIKIEELLKN-------------- 3 KQLRLDAIFNEIAKGKD-------- 4 KQLRLDAIFNEIAKGKD-------- 5 NALKIEQIINSL------------- 6 NAMRIESIINSLKKSK--------- 7 ASVKVHQLLVQLGYDPLKDKEK--- 8 ------------------------- 9 SVARMEELLARARAA---------- 10 SVHRMDELLARARAA---------- 11 TARNIEDLLDKARQSDEK------- 12 EGMRMSNLVTNVIKNDVERQVNP-- 13 EGMRMSNLVTSVVKHDEERRVNPDD 14 EGMRMSNLVTNVVREDEKKHVEES- 15 EGMRMSNLVTNVVREDEKKHVEESN 16 RG----------------------- 17 RGDKILNLLNNLPQAIATEDLEDDD 18 EGDKIDRLLREVKQ----------- 19 YGNRIETLIHELHSEK--------- 20 YGSKIDEIL---------------- 21 YGNKIDEMLRNLDK----------- 22 RGLNLSALIDQVAAEK--------- 23 RGLNLSALIDQVAAEK--------- 24 DGFSLSRKIDRLES----------- 25 KSFYVNKLIEGLN------------ 26 YANHIDELFKKIKQ----------- 27 YLENIDRLLN--------------- 28 PQDYIENLLWQIQEK---------- 29 PQDYIENLLWQIQEK---------- 30 PQDHIESLLLKIAEQDKKLTHNNN- 31 PQDHIESLLLKIAEQDK--------