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